From 35947b9e0b6ae1be74f17d15cd6a65ceadc6d310 Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Wed, 3 Aug 2011 17:06:32 +0000 Subject: [PATCH] Wrapper for Clustal Omega. git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4458 e3abac25-378b-4346-85de-24260fe3988d --- ExecutionStatistic/log/log.ctrl | Bin 48 -> 48 bytes ExecutionStatistic/log/log10.dat | Bin 1048576 -> 1048576 bytes ExecutionStatistic/log/logmirror.ctrl | Bin 48 -> 48 bytes ExecutionStatistic/seg0/c470.dat | Bin 1183744 -> 1183744 bytes ExecutionStatistic/seg0/c481.dat | Bin 495616 -> 495616 bytes ExecutionStatistic/seg0/c90.dat | Bin 28672 -> 28672 bytes binaries/src/clustalo/AUTHORS | 20 + binaries/src/clustalo/COPYING | 339 + binaries/src/clustalo/ChangeLog | 15 + binaries/src/clustalo/Doxyfile | 1510 ++ binaries/src/clustalo/Doxyfile.in | 1510 ++ binaries/src/clustalo/INSTALL | 400 + binaries/src/clustalo/Makefile.am | 25 + binaries/src/clustalo/Makefile.in | 706 + binaries/src/clustalo/README | 619 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Germany +Michael Remmert Gene Center Munich, Germany + +* Clustal 2 +Mark Larkin UCD Dublin, Ireland + +* Clustal 1.X +Toby Gibson EMBL Heidelberg, Germany +Des Higgins UCC Cork, Ireland +Julie Thompson IGBMC Strasbourg, France + +* Contributors: +Chenna Ramu EMBL Heidelberg, Germany +Nigel Brown EMBL Heidelberg, Germany + + diff --git a/binaries/src/clustalo/COPYING b/binaries/src/clustalo/COPYING new file mode 100644 index 0000000..d159169 --- /dev/null +++ b/binaries/src/clustalo/COPYING @@ -0,0 +1,339 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. 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It is safest +to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may +consider it more useful to permit linking proprietary applications with the +library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. diff --git a/binaries/src/clustalo/ChangeLog b/binaries/src/clustalo/ChangeLog new file mode 100644 index 0000000..a44aa31 --- /dev/null +++ b/binaries/src/clustalo/ChangeLog @@ -0,0 +1,15 @@ +2010-06-17 Release 0.0.1 (Dubliniensis) + + First "release" as program has been able for a while to perform + all basic tasks without problems. + + Non-standard features already built-in include: + HMM-iteration (using HMMER for building an HMM) and guide-tree + iteration. On top of that HMM input works fine and + background-frequencies are added to the HHalign process. + + Known issues: RNA/DNA alignment is considered buggy. Aligned + sequences have to be dealigned for HHalign to work properly. + + The HMMER version message can be ignored if no HMM-iteration + was used. diff --git a/binaries/src/clustalo/Doxyfile b/binaries/src/clustalo/Doxyfile new file mode 100644 index 0000000..41b2865 --- /dev/null +++ b/binaries/src/clustalo/Doxyfile @@ -0,0 +1,1510 @@ +# Doxyfile 1.5.8 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded +# by quotes) that should identify the project. + +PROJECT_NAME = "Clustal Omega" + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = 1.0.2 + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = ./doc/doxygen/ + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + +CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Farsi, Finnish, French, German, Greek, +# Hungarian, Italian, Japanese, Japanese-en (Japanese with English messages), +# Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, Polish, +# Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, Slovene, +# Spanish, Swedish, and Ukrainian. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + +FULL_PATH_NAMES = YES + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful is your file systems +# doesn't support long names like on DOS, Mac, or CD-ROM. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + +OPTIMIZE_OUTPUT_FOR_C = YES + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it parses. +# With this tag you can assign which parser to use for a given extension. +# Doxygen has a built-in mapping, but you can override or extend it using this tag. +# The format is ext=language, where ext is a file extension, and language is one of +# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP, +# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat +# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C + +EXTENSION_MAPPING = + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate getter +# and setter methods for a property. Setting this option to YES (the default) +# will make doxygen to replace the get and set methods by a property in the +# documentation. This will only work if the methods are indeed getting or +# setting a simple type. If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to +# determine which symbols to keep in memory and which to flush to disk. +# When the cache is full, less often used symbols will be written to disk. +# For small to medium size projects (<1000 input files) the default value is +# probably good enough. For larger projects a too small cache size can cause +# doxygen to be busy swapping symbols to and from disk most of the time +# causing a significant performance penality. +# If the system has enough physical memory increasing the cache will improve the +# performance by keeping more symbols in memory. Note that the value works on +# a logarithmic scale so increasing the size by one will rougly double the +# memory usage. The cache size is given by this formula: +# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols + +SYMBOL_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespace are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + +SORT_BRIEF_DOCS = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + +SORT_BY_SCOPE_NAME = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or define consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and defines in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + +SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + +SHOW_DIRECTORIES = NO + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. +# This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by +# doxygen. The layout file controls the global structure of the generated output files +# in an output format independent way. The create the layout file that represents +# doxygen's defaults, run doxygen with the -l option. You can optionally specify a +# file name after the option, if omitted DoxygenLayout.xml will be used as the name +# of the layout file. + +LAYOUT_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + +QUIET = YES + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + +WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + +WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be abled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + +WARN_NO_PARAMDOC = YES + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = ./src/clustal ./src/clustal-omega.h ./src/clustal-omega.c + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx +# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +FILE_PATTERNS = *.h *.c + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + +RECURSIVE = NO + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. + +EXCLUDE = ./src/config.h + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix filesystem feature) are excluded +# from the input. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = ./src/ + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. +# If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. +# Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. +# The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER +# is applied to all files. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + +FILTER_SOURCE_FILES = NO + +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. +# Otherwise they will link to the documentation. + +REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + +ALPHABETICAL_INDEX = NO + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + +HTML_ALIGN_MEMBERS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + +GENERATE_HTMLHELP = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + +GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER +# are set, an additional index file will be generated that can be used as input for +# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated +# HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add. +# For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's +# filter section matches. +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + +DISABLE_INDEX = NO + +# This tag can be used to set the number of enum values (range [1..20]) +# that doxygen will group on one line in the generated HTML documentation. + +ENUM_VALUES_PER_LINE = 4 + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to FRAME, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, +# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are +# probably better off using the HTML help feature. Other possible values +# for this tag are: HIERARCHIES, which will generate the Groups, Directories, +# and Class Hierarchy pages using a tree view instead of an ordered list; +# ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which +# disables this behavior completely. For backwards compatibility with previous +# releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE +# respectively. + +GENERATE_TREEVIEW = NONE + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + +TREEVIEW_WIDTH = 250 + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + +GENERATE_LATEX = YES + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, a4wide, letter, legal and +# executive. If left blank a4wide will be used. + +PAPER_TYPE = a4wide + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + +LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + +MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + +XML_OUTPUT = xml + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. +# This is useful +# if you want to understand what is going on. +# On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + +MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# in the INCLUDE_PATH (see below) will be search if a #include is found. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all function-like macros that are alone +# on a line, have an all uppercase name, and do not end with a semicolon. Such +# function macros are typically used for boiler-plate code, and will confuse +# the parser if not removed. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option is superseded by the HAVE_DOT option below. This is only a +# fallback. It is recommended to install and use dot, since it yields more +# powerful graphs. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + +HAVE_DOT = YES + +# By default doxygen will write a font called FreeSans.ttf to the output +# directory and reference it in all dot files that doxygen generates. This +# font does not include all possible unicode characters however, so when you need +# these (or just want a differently looking font) you can specify the font name +# using DOT_FONTNAME. You need need to make sure dot is able to find the font, +# which can be done by putting it in a standard location or by setting the +# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory +# containing the font. + +DOT_FONTNAME = FreeSans + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the output directory to look for the +# FreeSans.ttf font (which doxygen will put there itself). If you specify a +# different font using DOT_FONTNAME you can set the path where dot +# can find it using this tag. + +DOT_FONTPATH = + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# the CLASS_DIAGRAMS tag to NO. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for groups, showing the direct groups dependencies + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + +UML_LOOK = NO + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + +TEMPLATE_RELATIONS = NO + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + +INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH and HAVE_DOT options are set to YES then +# doxygen will generate a call dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable call graphs +# for selected functions only using the \callgraph command. + +CALL_GRAPH = NO + +# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then +# doxygen will generate a caller dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable caller +# graphs for selected functions only using the \callergraph command. + +CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will graphical hierarchy of all classes instead of a textual one. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. The dependency relations are determined by the #include +# relations between the files in the directories. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are png, jpg, or gif +# If left blank png will be used. + +DOT_IMAGE_FORMAT = png + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) +# support this, this feature is disabled by default. + +DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + +DOT_CLEANUP = YES + +#--------------------------------------------------------------------------- +# Options related to the search engine +#--------------------------------------------------------------------------- + +# The SEARCHENGINE tag specifies whether or not a search engine should be +# used. If set to NO the values of all tags below this one will be ignored. + +SEARCHENGINE = NO diff --git a/binaries/src/clustalo/Doxyfile.in b/binaries/src/clustalo/Doxyfile.in new file mode 100644 index 0000000..2ae5566 --- /dev/null +++ b/binaries/src/clustalo/Doxyfile.in @@ -0,0 +1,1510 @@ +# Doxyfile 1.5.8 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded +# by quotes) that should identify the project. + +PROJECT_NAME = "@PACKAGE_NAME@" + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = @PACKAGE_VERSION@ + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = ./doc/doxygen/ + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + +CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Farsi, Finnish, French, German, Greek, +# Hungarian, Italian, Japanese, Japanese-en (Japanese with English messages), +# Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, Polish, +# Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, Slovene, +# Spanish, Swedish, and Ukrainian. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + +FULL_PATH_NAMES = YES + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful is your file systems +# doesn't support long names like on DOS, Mac, or CD-ROM. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + +OPTIMIZE_OUTPUT_FOR_C = YES + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it parses. +# With this tag you can assign which parser to use for a given extension. +# Doxygen has a built-in mapping, but you can override or extend it using this tag. +# The format is ext=language, where ext is a file extension, and language is one of +# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP, +# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat +# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C + +EXTENSION_MAPPING = + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate getter +# and setter methods for a property. Setting this option to YES (the default) +# will make doxygen to replace the get and set methods by a property in the +# documentation. This will only work if the methods are indeed getting or +# setting a simple type. If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to +# determine which symbols to keep in memory and which to flush to disk. +# When the cache is full, less often used symbols will be written to disk. +# For small to medium size projects (<1000 input files) the default value is +# probably good enough. For larger projects a too small cache size can cause +# doxygen to be busy swapping symbols to and from disk most of the time +# causing a significant performance penality. +# If the system has enough physical memory increasing the cache will improve the +# performance by keeping more symbols in memory. Note that the value works on +# a logarithmic scale so increasing the size by one will rougly double the +# memory usage. The cache size is given by this formula: +# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols + +SYMBOL_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespace are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + +SORT_BRIEF_DOCS = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + +SORT_BY_SCOPE_NAME = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or define consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and defines in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + +SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + +SHOW_DIRECTORIES = NO + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. +# This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by +# doxygen. The layout file controls the global structure of the generated output files +# in an output format independent way. The create the layout file that represents +# doxygen's defaults, run doxygen with the -l option. You can optionally specify a +# file name after the option, if omitted DoxygenLayout.xml will be used as the name +# of the layout file. + +LAYOUT_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + +QUIET = YES + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + +WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + +WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be abled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + +WARN_NO_PARAMDOC = YES + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = ./src/clustal ./src/clustal-omega.h ./src/clustal-omega.c + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx +# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +FILE_PATTERNS = *.h *.c + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + +RECURSIVE = NO + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. + +EXCLUDE = ./src/config.h + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix filesystem feature) are excluded +# from the input. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = ./src/ + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. +# If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. +# Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. +# The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER +# is applied to all files. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + +FILTER_SOURCE_FILES = NO + +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. +# Otherwise they will link to the documentation. + +REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + +ALPHABETICAL_INDEX = NO + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + +HTML_ALIGN_MEMBERS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + +GENERATE_HTMLHELP = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + +GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER +# are set, an additional index file will be generated that can be used as input for +# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated +# HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add. +# For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's +# filter section matches. +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + +DISABLE_INDEX = NO + +# This tag can be used to set the number of enum values (range [1..20]) +# that doxygen will group on one line in the generated HTML documentation. + +ENUM_VALUES_PER_LINE = 4 + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to FRAME, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, +# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are +# probably better off using the HTML help feature. Other possible values +# for this tag are: HIERARCHIES, which will generate the Groups, Directories, +# and Class Hierarchy pages using a tree view instead of an ordered list; +# ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which +# disables this behavior completely. For backwards compatibility with previous +# releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE +# respectively. + +GENERATE_TREEVIEW = NONE + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + +TREEVIEW_WIDTH = 250 + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + +GENERATE_LATEX = YES + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, a4wide, letter, legal and +# executive. If left blank a4wide will be used. + +PAPER_TYPE = a4wide + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + +LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + +MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + +XML_OUTPUT = xml + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. +# This is useful +# if you want to understand what is going on. +# On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + +MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# in the INCLUDE_PATH (see below) will be search if a #include is found. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all function-like macros that are alone +# on a line, have an all uppercase name, and do not end with a semicolon. Such +# function macros are typically used for boiler-plate code, and will confuse +# the parser if not removed. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option is superseded by the HAVE_DOT option below. This is only a +# fallback. It is recommended to install and use dot, since it yields more +# powerful graphs. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + +HAVE_DOT = YES + +# By default doxygen will write a font called FreeSans.ttf to the output +# directory and reference it in all dot files that doxygen generates. This +# font does not include all possible unicode characters however, so when you need +# these (or just want a differently looking font) you can specify the font name +# using DOT_FONTNAME. You need need to make sure dot is able to find the font, +# which can be done by putting it in a standard location or by setting the +# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory +# containing the font. + +DOT_FONTNAME = FreeSans + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the output directory to look for the +# FreeSans.ttf font (which doxygen will put there itself). If you specify a +# different font using DOT_FONTNAME you can set the path where dot +# can find it using this tag. + +DOT_FONTPATH = + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# the CLASS_DIAGRAMS tag to NO. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for groups, showing the direct groups dependencies + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + +UML_LOOK = NO + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + +TEMPLATE_RELATIONS = NO + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + +INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH and HAVE_DOT options are set to YES then +# doxygen will generate a call dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable call graphs +# for selected functions only using the \callgraph command. + +CALL_GRAPH = NO + +# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then +# doxygen will generate a caller dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable caller +# graphs for selected functions only using the \callergraph command. + +CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will graphical hierarchy of all classes instead of a textual one. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. The dependency relations are determined by the #include +# relations between the files in the directories. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are png, jpg, or gif +# If left blank png will be used. + +DOT_IMAGE_FORMAT = png + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) +# support this, this feature is disabled by default. + +DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + +DOT_CLEANUP = YES + +#--------------------------------------------------------------------------- +# Options related to the search engine +#--------------------------------------------------------------------------- + +# The SEARCHENGINE tag specifies whether or not a search engine should be +# used. If set to NO the values of all tags below this one will be ignored. + +SEARCHENGINE = NO diff --git a/binaries/src/clustalo/INSTALL b/binaries/src/clustalo/INSTALL new file mode 100644 index 0000000..ede75b5 --- /dev/null +++ b/binaries/src/clustalo/INSTALL @@ -0,0 +1,400 @@ +The impatient can try: + +$ ./configure +$ make +$ make install + + +Clustal-Omega needs argtable2 (http://argtable.sourceforge.net/). If +argtable2 is installed in a non-standard directory you might have to +point configure to its installation directory. For example, if you are +on a Mac and have argtable installed via MacPorts then you should use +the following command line: + +$ ./configure CFLAGS='-I/opt/local/include' LDFLAGS='-L/opt/local/lib' + +ClustalO will automatically support multi-threading if your compiler +supports OpenMP. For some reason automake's OpenMP detection for +Apple's gcc is broken. You can force OpenMP detection by calling configure +like so: + +$ ./configure OPENMP_CFLAGS='-fopenmp' CFLAGS='-DHAVE_OPENMP' + +You could use a non-Apple gcc installed via MacPorts, adding + +CC=/opt/local/bin/gcc-mp-4.5 + +to the configure call (you will have to change the exact string to match +your gcc version). + +See below for generic installation instructions: + +---------------------------------------------------------------------- + + + +Installation Instructions +************************* + +Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005, +2006, 2007, 2008, 2009 Free Software Foundation, Inc. + + Copying and distribution of this file, with or without modification, +are permitted in any medium without royalty provided the copyright +notice and this notice are preserved. This file is offered as-is, +without warranty of any kind. + +Basic Installation +================== + + Briefly, the shell commands `./configure; make; make install' should +configure, build, and install this package. The following +more-detailed instructions are generic; see the `README' file for +instructions specific to this package. Some packages provide this +`INSTALL' file but do not implement all of the features documented +below. The lack of an optional feature in a given package is not +necessarily a bug. More recommendations for GNU packages can be found +in *note Makefile Conventions: (standards)Makefile Conventions. + + The `configure' shell script attempts to guess correct values for +various system-dependent variables used during compilation. It uses +those values to create a `Makefile' in each directory of the package. +It may also create one or more `.h' files containing system-dependent +definitions. Finally, it creates a shell script `config.status' that +you can run in the future to recreate the current configuration, and a +file `config.log' containing compiler output (useful mainly for +debugging `configure'). + + It can also use an optional file (typically called `config.cache' +and enabled with `--cache-file=config.cache' or simply `-C') that saves +the results of its tests to speed up reconfiguring. Caching is +disabled by default to prevent problems with accidental use of stale +cache files. + + If you need to do unusual things to compile the package, please try +to figure out how `configure' could check whether to do them, and mail +diffs or instructions to the address given in the `README' so they can +be considered for the next release. If you are using the cache, and at +some point `config.cache' contains results you don't want to keep, you +may remove or edit it. + + The file `configure.ac' (or `configure.in') is used to create +`configure' by a program called `autoconf'. You need `configure.ac' if +you want to change it or regenerate `configure' using a newer version +of `autoconf'. + + The simplest way to compile this package is: + + 1. `cd' to the directory containing the package's source code and type + `./configure' to configure the package for your system. + + Running `configure' might take a while. While running, it prints + some messages telling which features it is checking for. + + 2. Type `make' to compile the package. + + 3. Optionally, type `make check' to run any self-tests that come with + the package, generally using the just-built uninstalled binaries. + + 4. Type `make install' to install the programs and any data files and + documentation. When installing into a prefix owned by root, it is + recommended that the package be configured and built as a regular + user, and only the `make install' phase executed with root + privileges. + + 5. Optionally, type `make installcheck' to repeat any self-tests, but + this time using the binaries in their final installed location. + This target does not install anything. Running this target as a + regular user, particularly if the prior `make install' required + root privileges, verifies that the installation completed + correctly. + + 6. You can remove the program binaries and object files from the + source code directory by typing `make clean'. To also remove the + files that `configure' created (so you can compile the package for + a different kind of computer), type `make distclean'. There is + also a `make maintainer-clean' target, but that is intended mainly + for the package's developers. If you use it, you may have to get + all sorts of other programs in order to regenerate files that came + with the distribution. + + 7. Often, you can also type `make uninstall' to remove the installed + files again. In practice, not all packages have tested that + uninstallation works correctly, even though it is required by the + GNU Coding Standards. + + 8. Some packages, particularly those that use Automake, provide `make + distcheck', which can by used by developers to test that all other + targets like `make install' and `make uninstall' work correctly. + This target is generally not run by end users. + +Compilers and Options +===================== + + Some systems require unusual options for compilation or linking that +the `configure' script does not know about. Run `./configure --help' +for details on some of the pertinent environment variables. + + You can give `configure' initial values for configuration parameters +by setting variables in the command line or in the environment. Here +is an example: + + ./configure CC=c99 CFLAGS=-g LIBS=-lposix + + *Note Defining Variables::, for more details. + +Compiling For Multiple Architectures +==================================== + + You can compile the package for more than one kind of computer at the +same time, by placing the object files for each architecture in their +own directory. To do this, you can use GNU `make'. `cd' to the +directory where you want the object files and executables to go and run +the `configure' script. `configure' automatically checks for the +source code in the directory that `configure' is in and in `..'. This +is known as a "VPATH" build. + + With a non-GNU `make', it is safer to compile the package for one +architecture at a time in the source code directory. After you have +installed the package for one architecture, use `make distclean' before +reconfiguring for another architecture. + + On MacOS X 10.5 and later systems, you can create libraries and +executables that work on multiple system types--known as "fat" or +"universal" binaries--by specifying multiple `-arch' options to the +compiler but only a single `-arch' option to the preprocessor. Like +this: + + ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \ + CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \ + CPP="gcc -E" CXXCPP="g++ -E" + + This is not guaranteed to produce working output in all cases, you +may have to build one architecture at a time and combine the results +using the `lipo' tool if you have problems. + +Installation Names +================== + + By default, `make install' installs the package's commands under +`/usr/local/bin', include files under `/usr/local/include', etc. You +can specify an installation prefix other than `/usr/local' by giving +`configure' the option `--prefix=PREFIX', where PREFIX must be an +absolute file name. + + You can specify separate installation prefixes for +architecture-specific files and architecture-independent files. If you +pass the option `--exec-prefix=PREFIX' to `configure', the package uses +PREFIX as the prefix for installing programs and libraries. +Documentation and other data files still use the regular prefix. + + In addition, if you use an unusual directory layout you can give +options like `--bindir=DIR' to specify different values for particular +kinds of files. Run `configure --help' for a list of the directories +you can set and what kinds of files go in them. In general, the +default for these options is expressed in terms of `${prefix}', so that +specifying just `--prefix' will affect all of the other directory +specifications that were not explicitly provided. + + The most portable way to affect installation locations is to pass the +correct locations to `configure'; however, many packages provide one or +both of the following shortcuts of passing variable assignments to the +`make install' command line to change installation locations without +having to reconfigure or recompile. + + The first method involves providing an override variable for each +affected directory. For example, `make install +prefix=/alternate/directory' will choose an alternate location for all +directory configuration variables that were expressed in terms of +`${prefix}'. Any directories that were specified during `configure', +but not in terms of `${prefix}', must each be overridden at install +time for the entire installation to be relocated. The approach of +makefile variable overrides for each directory variable is required by +the GNU Coding Standards, and ideally causes no recompilation. +However, some platforms have known limitations with the semantics of +shared libraries that end up requiring recompilation when using this +method, particularly noticeable in packages that use GNU Libtool. + + The second method involves providing the `DESTDIR' variable. For +example, `make install DESTDIR=/alternate/directory' will prepend +`/alternate/directory' before all installation names. The approach of +`DESTDIR' overrides is not required by the GNU Coding Standards, and +does not work on platforms that have drive letters. On the other hand, +it does better at avoiding recompilation issues, and works well even +when some directory options were not specified in terms of `${prefix}' +at `configure' time. + +Optional Features +================= + + If the package supports it, you can cause programs to be installed +with an extra prefix or suffix on their names by giving `configure' the +option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'. + + Some packages pay attention to `--enable-FEATURE' options to +`configure', where FEATURE indicates an optional part of the package. +They may also pay attention to `--with-PACKAGE' options, where PACKAGE +is something like `gnu-as' or `x' (for the X Window System). The +`README' should mention any `--enable-' and `--with-' options that the +package recognizes. + + For packages that use the X Window System, `configure' can usually +find the X include and library files automatically, but if it doesn't, +you can use the `configure' options `--x-includes=DIR' and +`--x-libraries=DIR' to specify their locations. + + Some packages offer the ability to configure how verbose the +execution of `make' will be. For these packages, running `./configure +--enable-silent-rules' sets the default to minimal output, which can be +overridden with `make V=1'; while running `./configure +--disable-silent-rules' sets the default to verbose, which can be +overridden with `make V=0'. + +Particular systems +================== + + On HP-UX, the default C compiler is not ANSI C compatible. If GNU +CC is not installed, it is recommended to use the following options in +order to use an ANSI C compiler: + + ./configure CC="cc -Ae -D_XOPEN_SOURCE=500" + +and if that doesn't work, install pre-built binaries of GCC for HP-UX. + + On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot +parse its `' header file. The option `-nodtk' can be used as +a workaround. If GNU CC is not installed, it is therefore recommended +to try + + ./configure CC="cc" + +and if that doesn't work, try + + ./configure CC="cc -nodtk" + + On Solaris, don't put `/usr/ucb' early in your `PATH'. This +directory contains several dysfunctional programs; working variants of +these programs are available in `/usr/bin'. So, if you need `/usr/ucb' +in your `PATH', put it _after_ `/usr/bin'. + + On Haiku, software installed for all users goes in `/boot/common', +not `/usr/local'. It is recommended to use the following options: + + ./configure --prefix=/boot/common + +Specifying the System Type +========================== + + There may be some features `configure' cannot figure out +automatically, but needs to determine by the type of machine the package +will run on. Usually, assuming the package is built to be run on the +_same_ architectures, `configure' can figure that out, but if it prints +a message saying it cannot guess the machine type, give it the +`--build=TYPE' option. TYPE can either be a short name for the system +type, such as `sun4', or a canonical name which has the form: + + CPU-COMPANY-SYSTEM + +where SYSTEM can have one of these forms: + + OS + KERNEL-OS + + See the file `config.sub' for the possible values of each field. If +`config.sub' isn't included in this package, then this package doesn't +need to know the machine type. + + If you are _building_ compiler tools for cross-compiling, you should +use the option `--target=TYPE' to select the type of system they will +produce code for. + + If you want to _use_ a cross compiler, that generates code for a +platform different from the build platform, you should specify the +"host" platform (i.e., that on which the generated programs will +eventually be run) with `--host=TYPE'. + +Sharing Defaults +================ + + If you want to set default values for `configure' scripts to share, +you can create a site shell script called `config.site' that gives +default values for variables like `CC', `cache_file', and `prefix'. +`configure' looks for `PREFIX/share/config.site' if it exists, then +`PREFIX/etc/config.site' if it exists. Or, you can set the +`CONFIG_SITE' environment variable to the location of the site script. +A warning: not all `configure' scripts look for a site script. + +Defining Variables +================== + + Variables not defined in a site shell script can be set in the +environment passed to `configure'. However, some packages may run +configure again during the build, and the customized values of these +variables may be lost. In order to avoid this problem, you should set +them in the `configure' command line, using `VAR=value'. For example: + + ./configure CC=/usr/local2/bin/gcc + +causes the specified `gcc' to be used as the C compiler (unless it is +overridden in the site shell script). + +Unfortunately, this technique does not work for `CONFIG_SHELL' due to +an Autoconf bug. Until the bug is fixed you can use this workaround: + + CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash + +`configure' Invocation +====================== + + `configure' recognizes the following options to control how it +operates. + +`--help' +`-h' + Print a summary of all of the options to `configure', and exit. + +`--help=short' +`--help=recursive' + Print a summary of the options unique to this package's + `configure', and exit. The `short' variant lists options used + only in the top level, while the `recursive' variant lists options + also present in any nested packages. + +`--version' +`-V' + Print the version of Autoconf used to generate the `configure' + script, and exit. + +`--cache-file=FILE' + Enable the cache: use and save the results of the tests in FILE, + traditionally `config.cache'. FILE defaults to `/dev/null' to + disable caching. + +`--config-cache' +`-C' + Alias for `--cache-file=config.cache'. + +`--quiet' +`--silent' +`-q' + Do not print messages saying which checks are being made. To + suppress all normal output, redirect it to `/dev/null' (any error + messages will still be shown). + +`--srcdir=DIR' + Look for the package's source code in directory DIR. Usually + `configure' can determine that directory automatically. + +`--prefix=DIR' + Use DIR as the installation prefix. *note Installation Names:: + for more details, including other options available for fine-tuning + the installation locations. + +`--no-create' +`-n' + Run the configure checks, but stop before creating any output + files. + +`configure' also accepts some other, not widely useful, options. 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+ +#dist-hook: +# svnversion . > $(distdir)/src/svnversion.h 2>/dev/null +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/binaries/src/clustalo/NEWS b/binaries/src/clustalo/NEWS new file mode 100644 index 0000000..e69de29 diff --git a/binaries/src/clustalo/README b/binaries/src/clustalo/README new file mode 100644 index 0000000..109f65e --- /dev/null +++ b/binaries/src/clustalo/README @@ -0,0 +1,619 @@ + + +CLUSTAL-OMEGA is a general purpose multiple sequence alignment program +for proteins. + + + +INTRODUCTION + +Clustal-Omega is a general purpose multiple sequence alignment (MSA) +program for proteins. It produces high quality MSAs and is capable of +handling data-sets of hundreds of thousands of sequences in reasonable +time. + +In default mode, users give a file of sequences to be aligned and +these are clustered to produce a guide tree and this is used to guide +a "progressive alignment" of the sequences. There are also facilities +for aligning existing alignments to each other, aligning a sequence to +an alignment and for using a hidden Markov model (HMM) to help guide +an alignment of new sequences that are homologous to the sequences +used to make the HMM. This latter procedure is referred to as +"external profile alignment" or EPA. + +Clustal-Omega uses HMMs for the alignment engine, based on the HHalign +package from Johannes Soeding [1]. Guide trees are made using an +enhanced version of mBed [2] which can cluster very large numbers of +sequences in O(N*log(N)) time. Multiple alignment then proceeds by +aligning larger and larger alignments using HHalign, following the +clustering given by the guide tree. + +In its current form Clustal-Omega can only align protein sequences but +not DNA/RNA sequences. It is envisioned that DNA/RNA will become +available in a future version. + + + +SEQUENCE INPUT: + +-i, --in, --infile={,-} + Multiple sequence input file (- for stdin) + +--hmm-in= + HMM input files + +--dealign + Dealign input sequences + +--profile1, --p1= + Pre-aligned multiple sequence file (aligned columns will be kept fixed) + +--profile2, --p2= + Pre-aligned multiple sequence file (aligned columns will be kept fixed) + + +For sequence and profile input Clustal-Omega uses the Squid library +from Sean Eddy [3]. + + +Clustal-Omega accepts 3 types of sequence input: (i) a sequence file +with un-aligned or aligned sequences, (ii) profiles (a multiple +alignment in a file) of aligned sequences, (iii) a HMM. Valid +combinations of the above are: + +(a) one file with un-aligned or aligned sequences (i); the sequences + will be aligned, and the alignment will be written out. For this + mode use the -i flag. If the sequences are aligned (all sequences + have the same length and at least one sequence has at least one + gap), then the alignment is turned into a HMM, the sequences are + de-aligned and the now un-aligned sequences are aligned using the + HMM as an External Profile for External Profile Alignment (EPA). + If no EPA is desired use the --dealign flag. + + Use the above option to make a multiple alignment from a set of + sequences. A sequence file must contain more than one sequence (at + least two sequences). + +(b) two profiles (ii)+(ii); the columns in each profile will be kept + fixed and the alignment of the two profiles will be written + out. Use the --p1 and --p2 flags for this mode. + + Use this option to align two alignments (profiles) together. + +(c) one file with un/aligned sequences (i) and one profile (ii); the + profile is converted into a HMM and the un-aligned sequences will + be multiply aligned (using the HMM background information) to form + a profile; this constructed profile is aligned with the input + profile; the columns in each profile (the original one and the one + created from the un-aligned sequences) will be kept fixed and the + alignment of the two profiles will be written out. Use the -i flag + in conjunction with the --p1 flag for this mode. + The un/aligned sequences file (i) must contain at least two + sequences. If a single sequence has to be aligned with a profile + the profile-profile option (b) has to be used. + + Use the above option to add new sequences to an existing + alignment. + +(d) one file with un-aligned sequences (i) and one HMM (iii); the + un-aligned sequences will be aligned to form a profile, using the + HMM as an External Profile. So far only one HMM can be input and + only HMMer2 and HMMer3 formats are allowed. The alignment will be + written out; the HMM information is discarded. As, at the moment, + only one HMM can be used, no HMM is produced if the sequences are + already aligned. Use the -i flag in conjunction with the --hmm-in + flag for this mode. Multiple HMMs can be inputted, however, in the + current version all but the first HMM will be ignored. + + Use this option to make a new multiple alignment of sequences from + the input file and use the HMM as a guide (EPA). + + +Invalid combinations of the above are: + +(v) an un/aligned sequence file containing just one sequence (i) + +(w) an un/aligned sequence file containing just one sequence and a profile + (i)+(ii) + +(x) an un/aligned sequence file containing just one sequence and a HMM + (i)+(iii) + +(y) two or more HMMs (iii)+(iii)+... cannot be aligned to one another. + +(z) one profile (ii) cannot be aligned with a HMM (iii) + + +The following MSA file formats are allowed: + + a2m=fasta, (vienna) + clustal, + msf, + phylip, + selex, + stockholm + + +Prior to MSA, Clustal-Omega de-aligns all sequence input (i). However, +alignment information is automatically converted into a HMM and used +during MSA, unless the --dealign flag is specifically set. Profiles +(ii) are not de-aligned. + +The Clustal-Omega alignment engine can at the moment not process +DNA/RNA. If a sequence input file (i) or a profile (ii) is interpreted +as DNA/RNA the program will terminate during the file input stage. + + + +CLUSTERING: + + --distmat-in= + Pairwise distance matrix input file (skips distance computation) + + --distmat-out= + Pairwise distance matrix output file + + --guidetree-in= + Guide tree input file + (skips distance computation and guide tree clustering step) + + --guidetree-out= + Guide tree output file + + --full + Use full distance matrix for guide-tree calculation (slow; mBed is default) + + --full-iter + Use full distance matrix for guide-tree calculation during iteration (mBed is default) + + +In order to produce a multiple alignment Clustal-Omega requires a +guide tree which defines the order in which sequences/profiles are +aligned. A guide tree in turn is constructed, based on a distance +matrix. Conventionally, this distance matrix is comprised of all the +pair-wise distances of the sequences. The distance measure +Clustal-Omega uses for pair-wise distances of un-aligned sequences is +the k-tuple measure [4], which was also implemented in Clustal 1.83 +and ClustalW2 [5,6]. If the sequences inputted via -i are aligned +Clustal-Omega uses the Kimura-corrected pairwise aligned identities +[7]. The computational effort (time/memory) to calculate and store a +full distance matrix grows quadratically with the number of sequences. +Clustal-Omega can improve this scalability to N*log(N) by employing a +fast clustering algorithm called mBed [2]; this option is +automatically invoked (default). If a full distance matrix evaluation +is desired, then the --full flag has to be set. The mBed mode +calculates a reduced set of pair-wise distances. These distances are +used in a k-means algorithm, that clusters at most 100 sequences. For +each cluster a full distance matrix is calculated. No full distance +matrix (of all input sequences) is calculated in mBed mode. If there +are less than 100 sequences in the input, then in effect a full +distance matrix is calculated in mBed mode, however, no distance +matrix can be outputted (see below). + + +Clustal-Omega uses Muscle's [8] fast UPGMA implementation to construct +its guide trees from the distance matrix. By default, the distance +matrix is used internally to construct the guide tree and is then +discarded. By specifying --distmat-out the internal distance matrix +can be written to file. This is only possible in --full mode. The +guide trees by default are used internally to guide the multiple +alignment and are then discarded. By specifying the --guidetree-out +option these internal guide trees can be written out to +file. Conversely, the distance calculation and/or guide tree building +stage can be skipped, by reading in a pre-calculated distance matrix +and/or pre-calculated guide tree. These options are invoked by +specifying the --distmat-in and/or --guidetree-in flags, +respectively. However, distance matrix reading is disabled in the +current version. By default, distance matrix and guide tree files are +not over-written, if a file with the specified name already exists. In +this case Clustal-Omega aborts during the command-line processing +stage. To force over-writing of already existing files use the --force +flag (see MISCELLANEOUS). In mBed mode a full distance matrix cannot +be outputted, distance matrix output is only possible in --full mode. +mBed or --full distance mode do not affect the ability to write out +guide-trees. + +Guide trees can be iterated to refine the alignment (see section +ITERATION). Clustal-Omega takes the alignment, that was produced +initially and constructs a new distance matrix from this alignment. +The distance measure used at this stage is the Kimura distance [7]. By +default, Clustal-Omega constructs a reduced distance matrix at this +stage using the mBed algorithm, which will then be used to create an +improved (iterated) new guide tree. To turn off mBed-like clustering +at this stage the --full-iter flag has to be set. While Kimura +distances in general are much faster to calculate than k-tuple +distances, time and memory requirements still scale quadratically with +the number of sequences and --full-iter clustering should only be +considered for smaller cases (<< 10,000 sequences). + + + +ALIGNMENT OUTPUT: + + -o, --out, --outfile={file,-} Multiple sequence alignment output file (default: stdout) + + --outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} MSA output file format (default: fasta) + + +By default Clustal-Omega writes its results (alignments) to stdout. An +output file can be specified with the -o flag. Output to stdout is not +possible in verbose mode (-v, see MISCELLANEOUS) as verbose/debugging +messages would interfere with the alignment output. By default, +alignment files are not over-written, if a file with the specified +name already exists. In this case Clustal-Omega aborts during the +command-line processing stage. To force over-writing of already +existing files use the --force flag (see MISCELLANEOUS). + +Clustal-Omega can output alignments in various formats by setting the +--outfmt flag: + + * for Fasta format set: --outfmt=a2m or --outfmt=fa or --outfmt=fasta + + * for Clustal format set: --outfmt=clu or --outfmt=clustal + + * for Msf format: set --outfmt= msf + + * for Phylip format set: --outfmt=phy or --outfmt=phylip + + * for Selex format set: --outfmt=selex + + * for Stockholm format set: --outfmt=st or --outfmt=stockholm + + * for Vienna format set: --outfmt=vie or --outfmt=vienna + + +ITERATION: + + --iterations, --iter= Number of (combined guide tree/HMM) iterations + + --max-guidetree-iterations= Maximum guide tree iterations + + --max-hmm-iterations= Maximum number of HMM iterations + + +By default, Clustal-Omega calculates (or reads in) a guide tree and +performs a multiple alignment in the order specified by this guide +tree. This alignment is then outputted. Clustal-Omega can 'iterate' +its guide tree. The hope is that the (Kimura) distances, that can be +derived from the initial alignment, will give rise to a better guide +tree, and by extension, to a better alignment. + +A similar rationale applies to HMM-iteration. MSAs in general are very +'vulnerable' at their early stages. Sequences that are aligned at an +early stage remain fixed for the rest of the MSA. Another way of +putting this is: 'once a gap, always a gap'. This behaviour can be +mitigated by HMM iteration. An initial alignment is created and turned +into a HMM. This HMM can help in a new round of MSA to 'anticipate' +where residues should align. This is using the HMM as an External +Profile and carrying out iterative EPA. In practice, individual +sequences and profiles are aligned to the External HMM, derived after +the initial alignment. Pseudo-count information is then transferred to +the (internal) HMM, corresponding to the individual +sequence/profile. The now somewhat 'softened' sequences/profiles are +then in turn aligned in the order specified by the guide +tree. Pseudo-count transfer is reduced with the size of the +profile. Individual sequences attain the greatest pseudo-count +transfer, larger profiles less so. Pseudo-count transfer to profiles +larger than, say, 10 is negligible. The effect of HMM iteration is +more pronounced in larger test sets (that is, with more sequences). + +Both, HMM- and guide tree-iteration come at a cost of increasing the +run-time. One round of guide tree iteration adds on (roughly) the time +it took to construct the initial alignment. If, for example, the +initial alignment took 1min, then it will take (roughly) 2min to +iterate the guide tree once, 3min to iterate the guide tree twice, and +so on. HMM-iteration is more costly, as each round of iteration adds +three times the time required for the alignment stage. For example, if +the initial alignment took 1min, then each additional round of HMM +iteration will add on 3min; so 4 iterations will take 13min +(=1min+4*3min). The factor of 3 stems from the fact that at every +stage both intermediate profiles have to be aligned with the +background HMM, and finally the (softened) HMMs have to be aligned as +well. All times are quoted for single processors. + +By default, guide tree iteration and HMM-iteration are coupled. This +means, at each iteration step both, guide tree and HMM, are +re-calculated. This is invoked by setting the --iter flag. For +example, if --iter=1, then first an initial alignment is produced +(without external HMM background information and using k-tuple +distances to calculate the guide tree). This initial alignment is then +used to re-calculate a new guide tree (using Kimura distances) and to +create a HMM. The new guide tree and the HMM are then used to produce +a new MSA. + +Iteration of guide tree and HMM can be de-coupled. This means that the +number of guide tree iterations and HMM iterations can be +different. This can be done by combining the --iter flag with the +--max-guidetree-iterations and/or the --max-hmm-iterations flag. The +number of guide tree iterations is the minimum of --iter and +--max-guidetree-iterations, while the number of HMM iterations is the +minimum of --iter and --max-hmm-iterations. If, for example, HMM +iteration should be performed 5 times but guide tree iteration should +be performed only 3 times, then one should set --iter=5 and +--max-guidetree-iterations=3. All three flags can be specified at the +same time (however, this makes no sense). It is not sufficient just to +specify --max-guidetree-iterations and --max-hmm-iterations but not +--iter. If any iteration is desired --iter has to be set. + + +LIMITS (will exit early, if exceeded): + + --maxnumseq= Maximum allowed number of sequences + + --maxseqlen= Maximum allowed sequence length + +Limits can be imposed on the number of sequences in the input file +and/or the lengths of the sequences. This cap can be set with the +--maxnumseq and --maxseqlen flags, respectively. Clustal-Omega will +exit early, if these limits are exceeded. + + +MISCELLANEOUS: + + --auto Set options automatically (might overwrite some of your options) + + --threads= Number of processors to use + + -l, --log= Log all non-essential output to this file + + -h, --help Print help and exit + + -v, --verbose Verbose output (increases if given multiple times) + + --version Print version information and exit + + --long-version Print long version information and exit + + --force Force file overwriting + + +Users may feel unsure which options are appropriate in certain +situations even though using ClustalO without any special options +should give you the desired results. The --auto flag tries to +alleviate this problem and selects accuracy/speed flags according to +the number of sequences. For all cases will use mBed and thereby +possibly overwrite the --full option. For more than 1,000 sequences +the iteration is turned off as the effect of iteration is more +noticeable for 'larger' problems. Otherwise iterations are set to 1 if +not already set to a higher value by the user. Expert users may want +to avoid this flag and exercise more fine tuned control by selecting +the appropriate options manually. + +Certain parts of the MSA calculation have been parallelised. Most +noticeably, the distance matrix calculation, and certain aspects of +the HMM building stage. Clustal-Omega uses OpenMP. By default, +Clustal-Omega will attempt to use as many threads as possible. For +example, on a 4-core machine Clustal-Omega will attempt to use 4 +threads. The number of threads can be limited by setting the --threads +flag. This may be desirable, for example, in the case of +benchmarking/timing. + +Usually, non-essential (verbose) output is written to screen. This +output can be written to file by specifying the --log flag. + +Help is available by specifying the -h flag. + +By default Clustal-Omega does not print any information to stdout +(other than the final alignment, if no output file is +specified). Information concerning the progress of the alignment can +be obtained by specifying one verbosity flag (-v). This may be +desirable, to verify what Clustal-Omega is actually doing at the +moment. If two verbosity flags (-v -v) are specified, command-line +flags (explicitly and implicitly set) are printed in addition to the +progress report. Triple verbose level (-v -v -v) is the most verbose +level. In addition to single- and double-verbose information much more +information is displayed: input sequences and names, details of the +tree construction and intermediate alignments. Tree construction +information includes pairwise distances. The number of pairwise +distances scales with the square of the number of sequences, and +double verbose mode is probably only useful for a small number of +sequences. + +The current version number of Clustal-Omega can be displayed by +setting the --version flag. + +The current version number of Clustal-Omega as well as the code-name +and the build date can be displayed by setting the --long-version +flag. + +By default, Clustal-Omega does not over-write files. These can be (i) +alignment output, (ii) distance matrix and (iii) guide +tree. Overwriting can be forced by setting the --force flag. + + +EXAMPLES: + +./clustalo -i globin.fa + +Clustal-Omega reads the sequence file globin.fa, aligns the sequences +and prints the result to screen in fasta/a2m format. + + +./clustalo -i globin.fa -o globin.sto --outfmt=st + +If the file globin.sto does not exist, then Clustal-Omega reads the +sequence file globin.fa, aligns the sequences and prints the result to +globin.sto in Stockholm format. If the file globin.sto does exist +already, then Clustal-Omega terminates the alignment process before +reading globin.fa. + + +./clustalo -i globin.fa -o globin.aln --outfmt=clu --force + +Clustal-Omega reads the sequence file globin.fa, aligns the sequences +and prints the result to globin.aln in Clustal format, overwriting the +file globin.aln, if it already exists. + + +./clustalo -i globin.fa --distmat-out=globin.mat --guidetree-out=globin.dnd --force + +Clustal-Omega reads the sequence file globin.fa, aligns the sequences, +prints the result to screen in fasta/a2m format (default), the guide +tree to globin.dnd and the distance matrix to globin.mat, overwriting +those files if they already exist. + + +./clustalo -i globin.fa --guidetree-in=globin.dnd + +Clustal-Omega reads the files globin.fa and globin.dnd, skipping +distance calculation and guide tree creation, using instead the guide +tree specified in globin.dnd. + + +./clustalo -i globin.fa --hmm-in=PF00042.hmm + +Clustal-Omega reads the sequence file globin.fa and the HMM file +PF00042.hmm (in HMMer2 or HMMer3 format). It then performs the +alignment, transferring pseudo-count information contained in +PF00042.hmm to the sequences/profiles during the MSA. + + +./clustalo -i globin.sto + +Clustal-Omega reads the file globin.sto (of aligned sequences in +Stockholm format). It converts the alignment into a HMM, de-aligns the +sequences and re-aligns them, transferring pseudo-count information to +the sequences/profiles during the MSA. The guide tree is constructed +using a full distance matrix of Kimura distances. + + +./clustalo -i globin.sto --dealign + +Clustal-Omega reads the file globin.sto (of aligned sequences in +Stockholm format). It de-aligns the sequences and then re-aligns +them. No HMM is produced in the process, no pseudo-count information +is transferred. Consequently, the output must be the same as for +unaligned output (like in the first example ./clustalo -i globin.fa) + + +./clustalo -i globin.fa --iter=2 + +Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree +built from k-tuple distances, and performs an initial alignment. This +initial alignment is converted into a HMM and a new guide tree is +built from the Kimura distances of the initial alignment. The +un-aligned sequences are then aligned (for the second time but this +time) using pseudo-count information from the HMM created after the +initial alignment (and using the new guide tree). This second +alignment is then again converted into a HMM and a new guide tree is +constructed. The un-aligned sequences are then aligned (for a third +time), again using pseudo-count information of the HMM from the +previous step and the most recent guide tree. The final alignment is +written to screen. + + +./clustalo -i globin.fa --iter=5 --max-guidetree-iterations=1 + +Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree +built from k-tuple distances, and performs an initial alignment. This +initial alignment is converted into a HMM and a new guide tree is +built from the Kimura distances of the initial alignment. The +un-aligned sequences are then aligned (for the second time but this +time) using pseudo-count information from the HMM created after the +initial alignment (and using the new guide tree). For the last 4 +iterations the guide tree is left unchanged and only HMM iteration is +performed. This means that intermediate alignments are converted to +HMMs, and these intermediate HMMs are used to guide the MSA during +subsequent iteration stages. + + +./clustalo -i globin.fa -o globin.a2m -v + +In case the file globin.a2m does not exist, Clustal-Omega reads the +file globin.fa, prints a progress report to screen and writes the +alignment in (default) Fasta format to globin.a2m. The progress report +consists of the number of threads used, the number of sequences read, +the current progress in the k-tuple distance calculation, completion +of the guide tree computation and current progress of the MSA stage. +If the file globin.a2m already exists Clustal-Omega aborts before +reading the file globin.fa. Note that in verbose mode an output file +has to be specified, because progress/debugging information, which is +printed to screen, would interfere with the alignment being printed to +screen. + + +./clustalo -i PF00042_full.fa --dealign --full --outfmt=vie -o PF00042_full.vie --force + +Clustal-Omega reads the file PF00042_full.fa. This file contains +several thousand aligned sequences. --dealign tells Clustal-Omega to +erase all alignment information and re-align the sequences from +scratch. As there are several thousand sequences calculating a full +distance matrix may be slow. Setting the --full flag specifically +selects the full distance mode over the default mBed mode. The +alignment is then written out in Vienna format (fasta format all on +one line, no line breaks per sequence) to file PF00042_full.vie. + + +./clustalo -i PF00042_full.fa --dealign --outfmt=vie -o PF00042_full.vie --force + +Clustal-Omega reads the file PF00042_full.fa. This file contains +several thousand aligned sequences. --dealign tells Clustal-Omega to +erase all alignment information and re-align the sequences from +scratch. Calculating the distance matrix will be done by mBed +(default). Clustal-Omega will calculate pairwise distances to a +small number of reference sequences only. This will give a significant +speed-up. The speed-up is greater for larger families (more +sequences). The alignment is then written out in Vienna format (fasta +format all on one line, no line breaks per sequence) to file +PF00042_full.vie. + + +./clustalo --p1=globin.sto --p2=PF00042_full.vie -o globin+pf00042.fa + +Clustal-Omega reads files globin.sto and PF00042_full.vie of aligned +sequences (profiles). Both profiles are then aligned. The relative +positions of residues in both profiles are not changed during this +alignment, however, columns of gaps may be inserted into the profiles, +respectively. The final alignment is written to file globin+pf00042.fa +in fasta format. + + +./clustalo -i globin.fa --p1=PF00042_full.vie -o pf00042+globin.fa + +Clustal-Omega reads file globin.fa of un-aligned sequences and the +profile (of aligned sequences) in file PF00042_full.vie. A HMM is +created from the profile. This HMM is used to guide the alignment of +the un-aligned sequences in globin.fa. The profile that was generated +during this alignment of un-aligned globin.fa sequences is then +aligned to the input profile PF00042_full.vie. The relative positions +of residues in profile PF00042_full.vie is not changed during this +alignment, however, columns of gaps may be inserted into the +profile. The final alignment is output to file pf00042+globin.fa in +fasta format. The alignment in this example may be slightly different +from the alignment in the previous example, because no HMM guidance +was used generate the profile globin.sto. In this example HMM guidance +was used to align the sequences in globin.fa; the hope being that this +intermediate alignment will have profited from the bigger profile. + + + +LITERATURE: + +[1] Johannes Soding (2005) Protein homology detection by HMM-HMM + comparison. Bioinformatics 21 (7): 951–960. + +[2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence + embedding for fast construction of guide trees for multiple + sequence alignment. Algorithms Mol Biol. 2010 May 14;5:21. + +[3] http://www.genetics.wustl.edu/eddy/software/#squid + +[4] Wilbur and Lipman, 1983; PMID 6572363 + +[5] Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving + the sensitivity of progressive multiple sequence alignment through + sequence weighting, position-specific gap penalties and weight + matrix choice. Nucleic Acids Res., 22, 4673-4680. + +[6] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, + McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, + Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version + 2.0. Bioinformatics, 23, 2947-2948. + +[7] Kimura M (1980). "A simple method for estimating evolutionary + rates of base substitutions through comparative studies of + nucleotide sequences". Journal of Molecular Evolution 16: 111–120. + +[8] Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high + accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797. + diff --git a/binaries/src/clustalo/TODO b/binaries/src/clustalo/TODO new file mode 100644 index 0000000..9df01b3 --- /dev/null +++ b/binaries/src/clustalo/TODO @@ -0,0 +1,45 @@ +IMPORTANT +--------- + +- consensus output (sto,aln) and compatibilety with bioperl/biopython + +- Split Homfam refs in two. Use one part as background HMM, the other parts + for benchmarking + +- Implement meta flags: + accurate: --iterations 3 + default: --mbed --iterations 1 + fast: --mbed + and for more than 10k sequences: --mbed --mbed-iter + +- SSE instructions for hhalign (little use in ClustalO frontend; DD) + / + Patch new code which already contains SSE instructions + + also fix automake/configure then + +- Multi-HMMs; also for Pfam+iteration (FS) + +- Show degradation of alignment quality when using x reference sequences + added to y random/false sequences + (Lio Pachter) + +- Seed pre-alignment with M-Coffee, MSAProbs, ... + +- GUI/API: + Will have to catch/override exits from source. + find . -name \*.c -or -name \*.cpp -or -name \*.h | xargs grep 'exit(' + Also best to allow for user override of + void Fatal(char *msg, ...); + void Error(char *msg, ...); + void Warn(char *msg, ...); + void Info(int level, char *msg, ...); + + +- Soeding: DNA/RNA alignment incl. reading of nucleotide HMMs + +- Automatic HMM-selection/search/download for input + +- Structure input: Psipred predictions are apparently part of their + hhms and should therefore be ready to use (part automatic + HMM-selection) diff --git a/binaries/src/clustalo/aclocal.m4 b/binaries/src/clustalo/aclocal.m4 new file mode 100644 index 0000000..7a8bfaa --- /dev/null +++ b/binaries/src/clustalo/aclocal.m4 @@ -0,0 +1,925 @@ +# generated automatically by aclocal 1.10.2 -*- Autoconf -*- + +# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, +# 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +# This file is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + +m4_ifndef([AC_AUTOCONF_VERSION], + [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl +m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.63],, +[m4_warning([this file was generated for autoconf 2.63. +You have another version of autoconf. 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See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA +# 02110-1301, USA. +# +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that program. + + +# Originally written by Per Bothner . +# Please send patches to . Submit a context +# diff and a properly formatted ChangeLog entry. +# +# This script attempts to guess a canonical system name similar to +# config.sub. If it succeeds, it prints the system name on stdout, and +# exits with 0. Otherwise, it exits with 1. +# +# The plan is that this can be called by configure scripts if you +# don't specify an explicit build system type. + +me=`echo "$0" | sed -e 's,.*/,,'` + +usage="\ +Usage: $0 [OPTION] + +Output the configuration name of the system \`$me' is run on. + +Operation modes: + -h, --help print this help, then exit + -t, --time-stamp print date of last modification, then exit + -v, --version print version number, then exit + +Report bugs and patches to ." + +version="\ +GNU config.guess ($timestamp) + +Originally written by Per Bothner. +Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, +2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. + +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." + +help=" +Try \`$me --help' for more information." + +# Parse command line +while test $# -gt 0 ; do + case $1 in + --time-stamp | --time* | -t ) + echo "$timestamp" ; exit ;; + --version | -v ) + echo "$version" ; exit ;; + --help | --h* | -h ) + echo "$usage"; exit ;; + -- ) # Stop option processing + shift; break ;; + - ) # Use stdin as input. + break ;; + -* ) + echo "$me: invalid option $1$help" >&2 + exit 1 ;; + * ) + break ;; + esac +done + +if test $# != 0; then + echo "$me: too many arguments$help" >&2 + exit 1 +fi + +trap 'exit 1' 1 2 15 + +# CC_FOR_BUILD -- compiler used by this script. Note that the use of a +# compiler to aid in system detection is discouraged as it requires +# temporary files to be created and, as you can see below, it is a +# headache to deal with in a portable fashion. + +# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still +# use `HOST_CC' if defined, but it is deprecated. + +# Portable tmp directory creation inspired by the Autoconf team. + +set_cc_for_build=' +trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ; +trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ; +: ${TMPDIR=/tmp} ; + { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } || + { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } || + { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } || + { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ; +dummy=$tmp/dummy ; +tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ; +case $CC_FOR_BUILD,$HOST_CC,$CC in + ,,) echo "int x;" > $dummy.c ; + for c in cc gcc c89 c99 ; do + if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then + CC_FOR_BUILD="$c"; break ; + fi ; + done ; + if test x"$CC_FOR_BUILD" = x ; then + CC_FOR_BUILD=no_compiler_found ; + fi + ;; + ,,*) CC_FOR_BUILD=$CC ;; + ,*,*) CC_FOR_BUILD=$HOST_CC ;; +esac ; set_cc_for_build= ;' + +# This is needed to find uname on a Pyramid OSx when run in the BSD universe. +# (ghazi@noc.rutgers.edu 1994-08-24) +if (test -f /.attbin/uname) >/dev/null 2>&1 ; then + PATH=$PATH:/.attbin ; export PATH +fi + +UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown +UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown +UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown +UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown + +# Note: order is significant - the case branches are not exclusive. + +case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in + *:NetBSD:*:*) + # NetBSD (nbsd) targets should (where applicable) match one or + # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*, + # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently + # switched to ELF, *-*-netbsd* would select the old + # object file format. This provides both forward + # compatibility and a consistent mechanism for selecting the + # object file format. + # + # Note: NetBSD doesn't particularly care about the vendor + # portion of the name. We always set it to "unknown". + sysctl="sysctl -n hw.machine_arch" + UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \ + /usr/sbin/$sysctl 2>/dev/null || echo unknown)` + case "${UNAME_MACHINE_ARCH}" in + armeb) machine=armeb-unknown ;; + arm*) machine=arm-unknown ;; + sh3el) machine=shl-unknown ;; + sh3eb) machine=sh-unknown ;; + sh5el) machine=sh5le-unknown ;; + *) machine=${UNAME_MACHINE_ARCH}-unknown ;; + esac + # The Operating System including object format, if it has switched + # to ELF recently, or will in the future. + case "${UNAME_MACHINE_ARCH}" in + arm*|i386|m68k|ns32k|sh3*|sparc|vax) + eval $set_cc_for_build + if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep __ELF__ >/dev/null + then + # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). + # Return netbsd for either. FIX? + os=netbsd + else + os=netbsdelf + fi + ;; + *) + os=netbsd + ;; + esac + # The OS release + # Debian GNU/NetBSD machines have a different userland, and + # thus, need a distinct triplet. However, they do not need + # kernel version information, so it can be replaced with a + # suitable tag, in the style of linux-gnu. + case "${UNAME_VERSION}" in + Debian*) + release='-gnu' + ;; + *) + release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'` + ;; + esac + # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM: + # contains redundant information, the shorter form: + # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used. + echo "${machine}-${os}${release}" + exit ;; + *:OpenBSD:*:*) + UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'` + echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE} + exit ;; + *:ekkoBSD:*:*) + echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE} + exit ;; + *:SolidBSD:*:*) + echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE} + exit ;; + macppc:MirBSD:*:*) + echo powerpc-unknown-mirbsd${UNAME_RELEASE} + exit ;; + *:MirBSD:*:*) + echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE} + exit ;; + alpha:OSF1:*:*) + case $UNAME_RELEASE in + *4.0) + UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'` + ;; + *5.*) + UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'` + ;; + esac + # According to Compaq, /usr/sbin/psrinfo has been available on + # OSF/1 and Tru64 systems produced since 1995. I hope that + # covers most systems running today. This code pipes the CPU + # types through head -n 1, so we only detect the type of CPU 0. + ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1` + case "$ALPHA_CPU_TYPE" in + "EV4 (21064)") + UNAME_MACHINE="alpha" ;; + "EV4.5 (21064)") + UNAME_MACHINE="alpha" ;; + "LCA4 (21066/21068)") + UNAME_MACHINE="alpha" ;; + "EV5 (21164)") + UNAME_MACHINE="alphaev5" ;; + "EV5.6 (21164A)") + UNAME_MACHINE="alphaev56" ;; + "EV5.6 (21164PC)") + UNAME_MACHINE="alphapca56" ;; + "EV5.7 (21164PC)") + UNAME_MACHINE="alphapca57" ;; + "EV6 (21264)") + UNAME_MACHINE="alphaev6" ;; + "EV6.7 (21264A)") + UNAME_MACHINE="alphaev67" ;; + "EV6.8CB (21264C)") + UNAME_MACHINE="alphaev68" ;; + "EV6.8AL (21264B)") + UNAME_MACHINE="alphaev68" ;; + "EV6.8CX (21264D)") + UNAME_MACHINE="alphaev68" ;; + "EV6.9A (21264/EV69A)") + UNAME_MACHINE="alphaev69" ;; + "EV7 (21364)") + UNAME_MACHINE="alphaev7" ;; + "EV7.9 (21364A)") + UNAME_MACHINE="alphaev79" ;; + esac + # A Pn.n version is a patched version. + # A Vn.n version is a released version. + # A Tn.n version is a released field test version. + # A Xn.n version is an unreleased experimental baselevel. + # 1.2 uses "1.2" for uname -r. + echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` + exit ;; + Alpha\ *:Windows_NT*:*) + # How do we know it's Interix rather than the generic POSIX subsystem? + # Should we change UNAME_MACHINE based on the output of uname instead + # of the specific Alpha model? + echo alpha-pc-interix + exit ;; + 21064:Windows_NT:50:3) + echo alpha-dec-winnt3.5 + exit ;; + Amiga*:UNIX_System_V:4.0:*) + echo m68k-unknown-sysv4 + exit ;; + *:[Aa]miga[Oo][Ss]:*:*) + echo ${UNAME_MACHINE}-unknown-amigaos + exit ;; + *:[Mm]orph[Oo][Ss]:*:*) + echo ${UNAME_MACHINE}-unknown-morphos + exit ;; + *:OS/390:*:*) + echo i370-ibm-openedition + exit ;; + *:z/VM:*:*) + echo s390-ibm-zvmoe + exit ;; + *:OS400:*:*) + echo powerpc-ibm-os400 + exit ;; + arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) + echo arm-acorn-riscix${UNAME_RELEASE} + exit ;; + arm:riscos:*:*|arm:RISCOS:*:*) + echo arm-unknown-riscos + exit ;; + SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) + echo hppa1.1-hitachi-hiuxmpp + exit ;; + Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*) + # akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE. + if test "`(/bin/universe) 2>/dev/null`" = att ; then + echo pyramid-pyramid-sysv3 + else + echo pyramid-pyramid-bsd + fi + exit ;; + NILE*:*:*:dcosx) + echo pyramid-pyramid-svr4 + exit ;; + DRS?6000:unix:4.0:6*) + echo sparc-icl-nx6 + exit ;; + DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*) + case `/usr/bin/uname -p` in + sparc) echo sparc-icl-nx7; exit ;; + esac ;; + sun4H:SunOS:5.*:*) + echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; + sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) + echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; + i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) + echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; + sun4*:SunOS:6*:*) + # According to config.sub, this is the proper way to canonicalize + # SunOS6. Hard to guess exactly what SunOS6 will be like, but + # it's likely to be more like Solaris than SunOS4. + echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; + sun4*:SunOS:*:*) + case "`/usr/bin/arch -k`" in + Series*|S4*) + UNAME_RELEASE=`uname -v` + ;; + esac + # Japanese Language versions have a version number like `4.1.3-JL'. + echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'` + exit ;; + sun3*:SunOS:*:*) + echo m68k-sun-sunos${UNAME_RELEASE} + exit ;; + sun*:*:4.2BSD:*) + UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null` + test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3 + case "`/bin/arch`" in + sun3) + echo m68k-sun-sunos${UNAME_RELEASE} + ;; + sun4) + echo sparc-sun-sunos${UNAME_RELEASE} + ;; + esac + exit ;; + aushp:SunOS:*:*) + echo sparc-auspex-sunos${UNAME_RELEASE} + exit ;; + # The situation for MiNT is a little confusing. The machine name + # can be virtually everything (everything which is not + # "atarist" or "atariste" at least should have a processor + # > m68000). The system name ranges from "MiNT" over "FreeMiNT" + # to the lowercase version "mint" (or "freemint"). Finally + # the system name "TOS" denotes a system which is actually not + # MiNT. But MiNT is downward compatible to TOS, so this should + # be no problem. + atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint${UNAME_RELEASE} + exit ;; + atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint${UNAME_RELEASE} + exit ;; + *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) + echo m68k-atari-mint${UNAME_RELEASE} + exit ;; + milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) + echo m68k-milan-mint${UNAME_RELEASE} + exit ;; + hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) + echo m68k-hades-mint${UNAME_RELEASE} + exit ;; + *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) + echo m68k-unknown-mint${UNAME_RELEASE} + exit ;; + m68k:machten:*:*) + echo m68k-apple-machten${UNAME_RELEASE} + exit ;; + powerpc:machten:*:*) + echo powerpc-apple-machten${UNAME_RELEASE} + exit ;; + RISC*:Mach:*:*) + echo mips-dec-mach_bsd4.3 + exit ;; + RISC*:ULTRIX:*:*) + echo mips-dec-ultrix${UNAME_RELEASE} + exit ;; + VAX*:ULTRIX*:*:*) + echo vax-dec-ultrix${UNAME_RELEASE} + exit ;; + 2020:CLIX:*:* | 2430:CLIX:*:*) + echo clipper-intergraph-clix${UNAME_RELEASE} + exit ;; + mips:*:*:UMIPS | mips:*:*:RISCos) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c +#ifdef __cplusplus +#include /* for printf() prototype */ + int main (int argc, char *argv[]) { +#else + int main (argc, argv) int argc; char *argv[]; { +#endif + #if defined (host_mips) && defined (MIPSEB) + #if defined (SYSTYPE_SYSV) + printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_SVR4) + printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) + printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); + #endif + #endif + exit (-1); + } +EOF + $CC_FOR_BUILD -o $dummy $dummy.c && + dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` && + SYSTEM_NAME=`$dummy $dummyarg` && + { echo "$SYSTEM_NAME"; exit; } + echo mips-mips-riscos${UNAME_RELEASE} + exit ;; + Motorola:PowerMAX_OS:*:*) + echo powerpc-motorola-powermax + exit ;; + Motorola:*:4.3:PL8-*) + echo powerpc-harris-powermax + exit ;; + Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) + echo powerpc-harris-powermax + exit ;; + Night_Hawk:Power_UNIX:*:*) + echo powerpc-harris-powerunix + exit ;; + m88k:CX/UX:7*:*) + echo m88k-harris-cxux7 + exit ;; + m88k:*:4*:R4*) + echo m88k-motorola-sysv4 + exit ;; + m88k:*:3*:R3*) + echo m88k-motorola-sysv3 + exit ;; + AViiON:dgux:*:*) + # DG/UX returns AViiON for all architectures + UNAME_PROCESSOR=`/usr/bin/uname -p` + if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] + then + if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ + [ ${TARGET_BINARY_INTERFACE}x = x ] + then + echo m88k-dg-dgux${UNAME_RELEASE} + else + echo m88k-dg-dguxbcs${UNAME_RELEASE} + fi + else + echo i586-dg-dgux${UNAME_RELEASE} + fi + exit ;; + M88*:DolphinOS:*:*) # DolphinOS (SVR3) + echo m88k-dolphin-sysv3 + exit ;; + M88*:*:R3*:*) + # Delta 88k system running SVR3 + echo m88k-motorola-sysv3 + exit ;; + XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) + echo m88k-tektronix-sysv3 + exit ;; + Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) + echo m68k-tektronix-bsd + exit ;; + *:IRIX*:*:*) + echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` + exit ;; + ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. + echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id + exit ;; # Note that: echo "'`uname -s`'" gives 'AIX ' + i*86:AIX:*:*) + echo i386-ibm-aix + exit ;; + ia64:AIX:*:*) + if [ -x /usr/bin/oslevel ] ; then + IBM_REV=`/usr/bin/oslevel` + else + IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} + fi + echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} + exit ;; + *:AIX:2:3) + if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #include + + main() + { + if (!__power_pc()) + exit(1); + puts("powerpc-ibm-aix3.2.5"); + exit(0); + } +EOF + if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` + then + echo "$SYSTEM_NAME" + else + echo rs6000-ibm-aix3.2.5 + fi + elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then + echo rs6000-ibm-aix3.2.4 + else + echo rs6000-ibm-aix3.2 + fi + exit ;; + *:AIX:*:[456]) + IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` + if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then + IBM_ARCH=rs6000 + else + IBM_ARCH=powerpc + fi + if [ -x /usr/bin/oslevel ] ; then + IBM_REV=`/usr/bin/oslevel` + else + IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} + fi + echo ${IBM_ARCH}-ibm-aix${IBM_REV} + exit ;; + *:AIX:*:*) + echo rs6000-ibm-aix + exit ;; + ibmrt:4.4BSD:*|romp-ibm:BSD:*) + echo romp-ibm-bsd4.4 + exit ;; + ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and + echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to + exit ;; # report: romp-ibm BSD 4.3 + *:BOSX:*:*) + echo rs6000-bull-bosx + exit ;; + DPX/2?00:B.O.S.:*:*) + echo m68k-bull-sysv3 + exit ;; + 9000/[34]??:4.3bsd:1.*:*) + echo m68k-hp-bsd + exit ;; + hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) + echo m68k-hp-bsd4.4 + exit ;; + 9000/[34678]??:HP-UX:*:*) + HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` + case "${UNAME_MACHINE}" in + 9000/31? ) HP_ARCH=m68000 ;; + 9000/[34]?? ) HP_ARCH=m68k ;; + 9000/[678][0-9][0-9]) + if [ -x /usr/bin/getconf ]; then + sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` + sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` + case "${sc_cpu_version}" in + 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 + 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 + 532) # CPU_PA_RISC2_0 + case "${sc_kernel_bits}" in + 32) HP_ARCH="hppa2.0n" ;; + 64) HP_ARCH="hppa2.0w" ;; + '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 + esac ;; + esac + fi + if [ "${HP_ARCH}" = "" ]; then + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + + #define _HPUX_SOURCE + #include + #include + + int main () + { + #if defined(_SC_KERNEL_BITS) + long bits = sysconf(_SC_KERNEL_BITS); + #endif + long cpu = sysconf (_SC_CPU_VERSION); + + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1"); break; + case CPU_PA_RISC2_0: + #if defined(_SC_KERNEL_BITS) + switch (bits) + { + case 64: puts ("hppa2.0w"); break; + case 32: puts ("hppa2.0n"); break; + default: puts ("hppa2.0"); break; + } break; + #else /* !defined(_SC_KERNEL_BITS) */ + puts ("hppa2.0"); break; + #endif + default: puts ("hppa1.0"); break; + } + exit (0); + } +EOF + (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` + test -z "$HP_ARCH" && HP_ARCH=hppa + fi ;; + esac + if [ ${HP_ARCH} = "hppa2.0w" ] + then + eval $set_cc_for_build + + # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating + # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler + # generating 64-bit code. GNU and HP use different nomenclature: + # + # $ CC_FOR_BUILD=cc ./config.guess + # => hppa2.0w-hp-hpux11.23 + # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess + # => hppa64-hp-hpux11.23 + + if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | + grep __LP64__ >/dev/null + then + HP_ARCH="hppa2.0w" + else + HP_ARCH="hppa64" + fi + fi + echo ${HP_ARCH}-hp-hpux${HPUX_REV} + exit ;; + ia64:HP-UX:*:*) + HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` + echo ia64-hp-hpux${HPUX_REV} + exit ;; + 3050*:HI-UX:*:*) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #include + int + main () + { + long cpu = sysconf (_SC_CPU_VERSION); + /* The order matters, because CPU_IS_HP_MC68K erroneously returns + true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct + results, however. */ + if (CPU_IS_PA_RISC (cpu)) + { + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; + case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; + default: puts ("hppa-hitachi-hiuxwe2"); break; + } + } + else if (CPU_IS_HP_MC68K (cpu)) + puts ("m68k-hitachi-hiuxwe2"); + else puts ("unknown-hitachi-hiuxwe2"); + exit (0); + } +EOF + $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` && + { echo "$SYSTEM_NAME"; exit; } + echo unknown-hitachi-hiuxwe2 + exit ;; + 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) + echo hppa1.1-hp-bsd + exit ;; + 9000/8??:4.3bsd:*:*) + echo hppa1.0-hp-bsd + exit ;; + *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) + echo hppa1.0-hp-mpeix + exit ;; + hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) + echo hppa1.1-hp-osf + exit ;; + hp8??:OSF1:*:*) + echo hppa1.0-hp-osf + exit ;; + i*86:OSF1:*:*) + if [ -x /usr/sbin/sysversion ] ; then + echo ${UNAME_MACHINE}-unknown-osf1mk + else + echo ${UNAME_MACHINE}-unknown-osf1 + fi + exit ;; + parisc*:Lites*:*:*) + echo hppa1.1-hp-lites + exit ;; + C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) + echo c1-convex-bsd + exit ;; + C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) + if getsysinfo -f scalar_acc + then echo c32-convex-bsd + else echo c2-convex-bsd + fi + exit ;; + C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) + echo c34-convex-bsd + exit ;; + C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) + echo c38-convex-bsd + exit ;; + C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) + echo c4-convex-bsd + exit ;; + CRAY*Y-MP:*:*:*) + echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*[A-Z]90:*:*:*) + echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ + | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ + -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ + -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*TS:*:*:*) + echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*T3E:*:*:*) + echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*SV1:*:*:*) + echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit ;; + *:UNICOS/mp:*:*) + echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit ;; + F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) + FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` + FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` + FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` + echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit ;; + 5000:UNIX_System_V:4.*:*) + FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` + FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` + echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit ;; + i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) + echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} + exit ;; + sparc*:BSD/OS:*:*) + echo sparc-unknown-bsdi${UNAME_RELEASE} + exit ;; + *:BSD/OS:*:*) + echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} + exit ;; + *:FreeBSD:*:*) + case ${UNAME_MACHINE} in + pc98) + echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; + amd64) + echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; + *) + echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; + esac + exit ;; + i*:CYGWIN*:*) + echo ${UNAME_MACHINE}-pc-cygwin + exit ;; + *:MINGW*:*) + echo ${UNAME_MACHINE}-pc-mingw32 + exit ;; + i*:windows32*:*) + # uname -m includes "-pc" on this system. + echo ${UNAME_MACHINE}-mingw32 + exit ;; + i*:PW*:*) + echo ${UNAME_MACHINE}-pc-pw32 + exit ;; + *:Interix*:[3456]*) + case ${UNAME_MACHINE} in + x86) + echo i586-pc-interix${UNAME_RELEASE} + exit ;; + EM64T | authenticamd) + echo x86_64-unknown-interix${UNAME_RELEASE} + exit ;; + IA64) + echo ia64-unknown-interix${UNAME_RELEASE} + exit ;; + esac ;; + [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) + echo i${UNAME_MACHINE}-pc-mks + exit ;; + i*:Windows_NT*:* | Pentium*:Windows_NT*:*) + # How do we know it's Interix rather than the generic POSIX subsystem? + # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we + # UNAME_MACHINE based on the output of uname instead of i386? + echo i586-pc-interix + exit ;; + i*:UWIN*:*) + echo ${UNAME_MACHINE}-pc-uwin + exit ;; + amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) + echo x86_64-unknown-cygwin + exit ;; + p*:CYGWIN*:*) + echo powerpcle-unknown-cygwin + exit ;; + prep*:SunOS:5.*:*) + echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; + *:GNU:*:*) + # the GNU system + echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` + exit ;; + *:GNU/*:*:*) + # other systems with GNU libc and userland + echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu + exit ;; + i*86:Minix:*:*) + echo ${UNAME_MACHINE}-pc-minix + exit ;; + arm*:Linux:*:*) + eval $set_cc_for_build + if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ARM_EABI__ + then + echo ${UNAME_MACHINE}-unknown-linux-gnu + else + echo ${UNAME_MACHINE}-unknown-linux-gnueabi + fi + exit ;; + avr32*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + cris:Linux:*:*) + echo cris-axis-linux-gnu + exit ;; + crisv32:Linux:*:*) + echo crisv32-axis-linux-gnu + exit ;; + frv:Linux:*:*) + echo frv-unknown-linux-gnu + exit ;; + ia64:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + m32r*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + m68*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + mips:Linux:*:*) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #undef CPU + #undef mips + #undef mipsel + #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) + CPU=mipsel + #else + #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) + CPU=mips + #else + CPU= + #endif + #endif +EOF + eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' + /^CPU/{ + s: ::g + p + }'`" + test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } + ;; + mips64:Linux:*:*) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #undef CPU + #undef mips64 + #undef mips64el + #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) + CPU=mips64el + #else + #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) + CPU=mips64 + #else + CPU= + #endif + #endif +EOF + eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' + /^CPU/{ + s: ::g + p + }'`" + test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } + ;; + or32:Linux:*:*) + echo or32-unknown-linux-gnu + exit ;; + ppc:Linux:*:*) + echo powerpc-unknown-linux-gnu + exit ;; + ppc64:Linux:*:*) + echo powerpc64-unknown-linux-gnu + exit ;; + alpha:Linux:*:*) + case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in + EV5) UNAME_MACHINE=alphaev5 ;; + EV56) UNAME_MACHINE=alphaev56 ;; + PCA56) UNAME_MACHINE=alphapca56 ;; + PCA57) UNAME_MACHINE=alphapca56 ;; + EV6) UNAME_MACHINE=alphaev6 ;; + EV67) UNAME_MACHINE=alphaev67 ;; + EV68*) UNAME_MACHINE=alphaev68 ;; + esac + objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null + if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi + echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} + exit ;; + parisc:Linux:*:* | hppa:Linux:*:*) + # Look for CPU level + case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in + PA7*) echo hppa1.1-unknown-linux-gnu ;; + PA8*) echo hppa2.0-unknown-linux-gnu ;; + *) echo hppa-unknown-linux-gnu ;; + esac + exit ;; + parisc64:Linux:*:* | hppa64:Linux:*:*) + echo hppa64-unknown-linux-gnu + exit ;; + s390:Linux:*:* | s390x:Linux:*:*) + echo ${UNAME_MACHINE}-ibm-linux + exit ;; + sh64*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + sh*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + sparc:Linux:*:* | sparc64:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + vax:Linux:*:*) + echo ${UNAME_MACHINE}-dec-linux-gnu + exit ;; + x86_64:Linux:*:*) + echo x86_64-unknown-linux-gnu + exit ;; + xtensa*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + i*86:Linux:*:*) + # The BFD linker knows what the default object file format is, so + # first see if it will tell us. cd to the root directory to prevent + # problems with other programs or directories called `ld' in the path. + # Set LC_ALL=C to ensure ld outputs messages in English. + ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \ + | sed -ne '/supported targets:/!d + s/[ ][ ]*/ /g + s/.*supported targets: *// + s/ .*// + p'` + case "$ld_supported_targets" in + elf32-i386) + TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu" + ;; + a.out-i386-linux) + echo "${UNAME_MACHINE}-pc-linux-gnuaout" + exit ;; + coff-i386) + echo "${UNAME_MACHINE}-pc-linux-gnucoff" + exit ;; + "") + # Either a pre-BFD a.out linker (linux-gnuoldld) or + # one that does not give us useful --help. + echo "${UNAME_MACHINE}-pc-linux-gnuoldld" + exit ;; + esac + # Determine whether the default compiler is a.out or elf + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #include + #ifdef __ELF__ + # ifdef __GLIBC__ + # if __GLIBC__ >= 2 + LIBC=gnu + # else + LIBC=gnulibc1 + # endif + # else + LIBC=gnulibc1 + # endif + #else + #if defined(__INTEL_COMPILER) || defined(__PGI) || defined(__SUNPRO_C) || defined(__SUNPRO_CC) + LIBC=gnu + #else + LIBC=gnuaout + #endif + #endif + #ifdef __dietlibc__ + LIBC=dietlibc + #endif +EOF + eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' + /^LIBC/{ + s: ::g + p + }'`" + test x"${LIBC}" != x && { + echo "${UNAME_MACHINE}-pc-linux-${LIBC}" + exit + } + test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; } + ;; + i*86:DYNIX/ptx:4*:*) + # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. + # earlier versions are messed up and put the nodename in both + # sysname and nodename. + echo i386-sequent-sysv4 + exit ;; + i*86:UNIX_SV:4.2MP:2.*) + # Unixware is an offshoot of SVR4, but it has its own version + # number series starting with 2... + # I am not positive that other SVR4 systems won't match this, + # I just have to hope. -- rms. + # Use sysv4.2uw... so that sysv4* matches it. + echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION} + exit ;; + i*86:OS/2:*:*) + # If we were able to find `uname', then EMX Unix compatibility + # is probably installed. + echo ${UNAME_MACHINE}-pc-os2-emx + exit ;; + i*86:XTS-300:*:STOP) + echo ${UNAME_MACHINE}-unknown-stop + exit ;; + i*86:atheos:*:*) + echo ${UNAME_MACHINE}-unknown-atheos + exit ;; + i*86:syllable:*:*) + echo ${UNAME_MACHINE}-pc-syllable + exit ;; + i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*) + echo i386-unknown-lynxos${UNAME_RELEASE} + exit ;; + i*86:*DOS:*:*) + echo ${UNAME_MACHINE}-pc-msdosdjgpp + exit ;; + i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*) + UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'` + if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then + echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL} + else + echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL} + fi + exit ;; + i*86:*:5:[678]*) + # UnixWare 7.x, OpenUNIX and OpenServer 6. + case `/bin/uname -X | grep "^Machine"` in + *486*) UNAME_MACHINE=i486 ;; + *Pentium) UNAME_MACHINE=i586 ;; + *Pent*|*Celeron) UNAME_MACHINE=i686 ;; + esac + echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} + exit ;; + i*86:*:3.2:*) + if test -f /usr/options/cb.name; then + UNAME_REL=`sed -n 's/.*Version //p' /dev/null >/dev/null ; then + UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')` + (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 + (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ + && UNAME_MACHINE=i586 + (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ + && UNAME_MACHINE=i686 + (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ + && UNAME_MACHINE=i686 + echo ${UNAME_MACHINE}-pc-sco$UNAME_REL + else + echo ${UNAME_MACHINE}-pc-sysv32 + fi + exit ;; + pc:*:*:*) + # Left here for compatibility: + # uname -m prints for DJGPP always 'pc', but it prints nothing about + # the processor, so we play safe by assuming i386. + echo i386-pc-msdosdjgpp + exit ;; + Intel:Mach:3*:*) + echo i386-pc-mach3 + exit ;; + paragon:*:*:*) + echo i860-intel-osf1 + exit ;; + i860:*:4.*:*) # i860-SVR4 + if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then + echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4 + else # Add other i860-SVR4 vendors below as they are discovered. + echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4 + fi + exit ;; + mini*:CTIX:SYS*5:*) + # "miniframe" + echo m68010-convergent-sysv + exit ;; + mc68k:UNIX:SYSTEM5:3.51m) + echo m68k-convergent-sysv + exit ;; + M680?0:D-NIX:5.3:*) + echo m68k-diab-dnix + exit ;; + M68*:*:R3V[5678]*:*) + test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;; + 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0) + OS_REL='' + test -r /etc/.relid \ + && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4.3${OS_REL}; exit; } + /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ + && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; + 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4; exit; } ;; + m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) + echo m68k-unknown-lynxos${UNAME_RELEASE} + exit ;; + mc68030:UNIX_System_V:4.*:*) + echo m68k-atari-sysv4 + exit ;; + TSUNAMI:LynxOS:2.*:*) + echo sparc-unknown-lynxos${UNAME_RELEASE} + exit ;; + rs6000:LynxOS:2.*:*) + echo rs6000-unknown-lynxos${UNAME_RELEASE} + exit ;; + PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) + echo powerpc-unknown-lynxos${UNAME_RELEASE} + exit ;; + SM[BE]S:UNIX_SV:*:*) + echo mips-dde-sysv${UNAME_RELEASE} + exit ;; + RM*:ReliantUNIX-*:*:*) + echo mips-sni-sysv4 + exit ;; + RM*:SINIX-*:*:*) + echo mips-sni-sysv4 + exit ;; + *:SINIX-*:*:*) + if uname -p 2>/dev/null >/dev/null ; then + UNAME_MACHINE=`(uname -p) 2>/dev/null` + echo ${UNAME_MACHINE}-sni-sysv4 + else + echo ns32k-sni-sysv + fi + exit ;; + PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort + # says + echo i586-unisys-sysv4 + exit ;; + *:UNIX_System_V:4*:FTX*) + # From Gerald Hewes . + # How about differentiating between stratus architectures? -djm + echo hppa1.1-stratus-sysv4 + exit ;; + *:*:*:FTX*) + # From seanf@swdc.stratus.com. + echo i860-stratus-sysv4 + exit ;; + i*86:VOS:*:*) + # From Paul.Green@stratus.com. + echo ${UNAME_MACHINE}-stratus-vos + exit ;; + *:VOS:*:*) + # From Paul.Green@stratus.com. + echo hppa1.1-stratus-vos + exit ;; + mc68*:A/UX:*:*) + echo m68k-apple-aux${UNAME_RELEASE} + exit ;; + news*:NEWS-OS:6*:*) + echo mips-sony-newsos6 + exit ;; + R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) + if [ -d /usr/nec ]; then + echo mips-nec-sysv${UNAME_RELEASE} + else + echo mips-unknown-sysv${UNAME_RELEASE} + fi + exit ;; + BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. + echo powerpc-be-beos + exit ;; + BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. + echo powerpc-apple-beos + exit ;; + BePC:BeOS:*:*) # BeOS running on Intel PC compatible. + echo i586-pc-beos + exit ;; + SX-4:SUPER-UX:*:*) + echo sx4-nec-superux${UNAME_RELEASE} + exit ;; + SX-5:SUPER-UX:*:*) + echo sx5-nec-superux${UNAME_RELEASE} + exit ;; + SX-6:SUPER-UX:*:*) + echo sx6-nec-superux${UNAME_RELEASE} + exit ;; + SX-7:SUPER-UX:*:*) + echo sx7-nec-superux${UNAME_RELEASE} + exit ;; + SX-8:SUPER-UX:*:*) + echo sx8-nec-superux${UNAME_RELEASE} + exit ;; + SX-8R:SUPER-UX:*:*) + echo sx8r-nec-superux${UNAME_RELEASE} + exit ;; + Power*:Rhapsody:*:*) + echo powerpc-apple-rhapsody${UNAME_RELEASE} + exit ;; + *:Rhapsody:*:*) + echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE} + exit ;; + *:Darwin:*:*) + UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown + case $UNAME_PROCESSOR in + unknown) UNAME_PROCESSOR=powerpc ;; + esac + echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} + exit ;; + *:procnto*:*:* | *:QNX:[0123456789]*:*) + UNAME_PROCESSOR=`uname -p` + if test "$UNAME_PROCESSOR" = "x86"; then + UNAME_PROCESSOR=i386 + UNAME_MACHINE=pc + fi + echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE} + exit ;; + *:QNX:*:4*) + echo i386-pc-qnx + exit ;; + NSE-?:NONSTOP_KERNEL:*:*) + echo nse-tandem-nsk${UNAME_RELEASE} + exit ;; + NSR-?:NONSTOP_KERNEL:*:*) + echo nsr-tandem-nsk${UNAME_RELEASE} + exit ;; + *:NonStop-UX:*:*) + echo mips-compaq-nonstopux + exit ;; + BS2000:POSIX*:*:*) + echo bs2000-siemens-sysv + exit ;; + DS/*:UNIX_System_V:*:*) + echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE} + exit ;; + *:Plan9:*:*) + # "uname -m" is not consistent, so use $cputype instead. 386 + # is converted to i386 for consistency with other x86 + # operating systems. + if test "$cputype" = "386"; then + UNAME_MACHINE=i386 + else + UNAME_MACHINE="$cputype" + fi + echo ${UNAME_MACHINE}-unknown-plan9 + exit ;; + *:TOPS-10:*:*) + echo pdp10-unknown-tops10 + exit ;; + *:TENEX:*:*) + echo pdp10-unknown-tenex + exit ;; + KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) + echo pdp10-dec-tops20 + exit ;; + XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) + echo pdp10-xkl-tops20 + exit ;; + *:TOPS-20:*:*) + echo pdp10-unknown-tops20 + exit ;; + *:ITS:*:*) + echo pdp10-unknown-its + exit ;; + SEI:*:*:SEIUX) + echo mips-sei-seiux${UNAME_RELEASE} + exit ;; + *:DragonFly:*:*) + echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` + exit ;; + *:*VMS:*:*) + UNAME_MACHINE=`(uname -p) 2>/dev/null` + case "${UNAME_MACHINE}" in + A*) echo alpha-dec-vms ; exit ;; + I*) echo ia64-dec-vms ; exit ;; + V*) echo vax-dec-vms ; exit ;; + esac ;; + *:XENIX:*:SysV) + echo i386-pc-xenix + exit ;; + i*86:skyos:*:*) + echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//' + exit ;; + i*86:rdos:*:*) + echo ${UNAME_MACHINE}-pc-rdos + exit ;; +esac + +#echo '(No uname command or uname output not recognized.)' 1>&2 +#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2 + +eval $set_cc_for_build +cat >$dummy.c < +# include +#endif +main () +{ +#if defined (sony) +#if defined (MIPSEB) + /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, + I don't know.... */ + printf ("mips-sony-bsd\n"); exit (0); +#else +#include + printf ("m68k-sony-newsos%s\n", +#ifdef NEWSOS4 + "4" +#else + "" +#endif + ); exit (0); +#endif +#endif + +#if defined (__arm) && defined (__acorn) && defined (__unix) + printf ("arm-acorn-riscix\n"); exit (0); +#endif + +#if defined (hp300) && !defined (hpux) + printf ("m68k-hp-bsd\n"); exit (0); +#endif + +#if defined (NeXT) +#if !defined (__ARCHITECTURE__) +#define __ARCHITECTURE__ "m68k" +#endif + int version; + version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`; + if (version < 4) + printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); + else + printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); + exit (0); +#endif + +#if defined (MULTIMAX) || defined (n16) +#if defined (UMAXV) + printf ("ns32k-encore-sysv\n"); exit (0); +#else +#if defined (CMU) + printf ("ns32k-encore-mach\n"); exit (0); +#else + printf ("ns32k-encore-bsd\n"); exit (0); +#endif +#endif +#endif + +#if defined (__386BSD__) + printf ("i386-pc-bsd\n"); exit (0); +#endif + +#if defined (sequent) +#if defined (i386) + printf ("i386-sequent-dynix\n"); exit (0); +#endif +#if defined (ns32000) + printf ("ns32k-sequent-dynix\n"); exit (0); +#endif +#endif + +#if defined (_SEQUENT_) + struct utsname un; + + uname(&un); + + if (strncmp(un.version, "V2", 2) == 0) { + printf ("i386-sequent-ptx2\n"); exit (0); + } + if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ + printf ("i386-sequent-ptx1\n"); exit (0); + } + printf ("i386-sequent-ptx\n"); exit (0); + +#endif + +#if defined (vax) +# if !defined (ultrix) +# include +# if defined (BSD) +# if BSD == 43 + printf ("vax-dec-bsd4.3\n"); exit (0); +# else +# if BSD == 199006 + printf ("vax-dec-bsd4.3reno\n"); exit (0); +# else + printf ("vax-dec-bsd\n"); exit (0); +# endif +# endif +# else + printf ("vax-dec-bsd\n"); exit (0); +# endif +# else + printf ("vax-dec-ultrix\n"); exit (0); +# endif +#endif + +#if defined (alliant) && defined (i860) + printf ("i860-alliant-bsd\n"); exit (0); +#endif + + exit (1); +} +EOF + +$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` && + { echo "$SYSTEM_NAME"; exit; } + +# Apollos put the system type in the environment. + +test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; } + +# Convex versions that predate uname can use getsysinfo(1) + +if [ -x /usr/convex/getsysinfo ] +then + case `getsysinfo -f cpu_type` in + c1*) + echo c1-convex-bsd + exit ;; + c2*) + if getsysinfo -f scalar_acc + then echo c32-convex-bsd + else echo c2-convex-bsd + fi + exit ;; + c34*) + echo c34-convex-bsd + exit ;; + c38*) + echo c38-convex-bsd + exit ;; + c4*) + echo c4-convex-bsd + exit ;; + esac +fi + +cat >&2 < in order to provide the needed +information to handle your system. + +config.guess timestamp = $timestamp + +uname -m = `(uname -m) 2>/dev/null || echo unknown` +uname -r = `(uname -r) 2>/dev/null || echo unknown` +uname -s = `(uname -s) 2>/dev/null || echo unknown` +uname -v = `(uname -v) 2>/dev/null || echo unknown` + +/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null` +/bin/uname -X = `(/bin/uname -X) 2>/dev/null` + +hostinfo = `(hostinfo) 2>/dev/null` +/bin/universe = `(/bin/universe) 2>/dev/null` +/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null` +/bin/arch = `(/bin/arch) 2>/dev/null` +/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` +/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` + +UNAME_MACHINE = ${UNAME_MACHINE} +UNAME_RELEASE = ${UNAME_RELEASE} +UNAME_SYSTEM = ${UNAME_SYSTEM} +UNAME_VERSION = ${UNAME_VERSION} +EOF + +exit 1 + +# Local variables: +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "timestamp='" +# time-stamp-format: "%:y-%02m-%02d" +# time-stamp-end: "'" +# End: diff --git a/binaries/src/clustalo/config.sub b/binaries/src/clustalo/config.sub new file mode 100644 index 0000000..6759825 --- /dev/null +++ b/binaries/src/clustalo/config.sub @@ -0,0 +1,1658 @@ +#! /bin/sh +# Configuration validation subroutine script. +# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, +# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 +# Free Software Foundation, Inc. + +timestamp='2008-01-16' + +# This file is (in principle) common to ALL GNU software. +# The presence of a machine in this file suggests that SOME GNU software +# can handle that machine. It does not imply ALL GNU software can. +# +# This file is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA +# 02110-1301, USA. +# +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that program. + + +# Please send patches to . Submit a context +# diff and a properly formatted ChangeLog entry. +# +# Configuration subroutine to validate and canonicalize a configuration type. +# Supply the specified configuration type as an argument. +# If it is invalid, we print an error message on stderr and exit with code 1. +# Otherwise, we print the canonical config type on stdout and succeed. + +# This file is supposed to be the same for all GNU packages +# and recognize all the CPU types, system types and aliases +# that are meaningful with *any* GNU software. +# Each package is responsible for reporting which valid configurations +# it does not support. The user should be able to distinguish +# a failure to support a valid configuration from a meaningless +# configuration. + +# The goal of this file is to map all the various variations of a given +# machine specification into a single specification in the form: +# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM +# or in some cases, the newer four-part form: +# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM +# It is wrong to echo any other type of specification. + +me=`echo "$0" | sed -e 's,.*/,,'` + +usage="\ +Usage: $0 [OPTION] CPU-MFR-OPSYS + $0 [OPTION] ALIAS + +Canonicalize a configuration name. + +Operation modes: + -h, --help print this help, then exit + -t, --time-stamp print date of last modification, then exit + -v, --version print version number, then exit + +Report bugs and patches to ." + +version="\ +GNU config.sub ($timestamp) + +Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, +2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. + +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." + +help=" +Try \`$me --help' for more information." + +# Parse command line +while test $# -gt 0 ; do + case $1 in + --time-stamp | --time* | -t ) + echo "$timestamp" ; exit ;; + --version | -v ) + echo "$version" ; exit ;; + --help | --h* | -h ) + echo "$usage"; exit ;; + -- ) # Stop option processing + shift; break ;; + - ) # Use stdin as input. + break ;; + -* ) + echo "$me: invalid option $1$help" + exit 1 ;; + + *local*) + # First pass through any local machine types. + echo $1 + exit ;; + + * ) + break ;; + esac +done + +case $# in + 0) echo "$me: missing argument$help" >&2 + exit 1;; + 1) ;; + *) echo "$me: too many arguments$help" >&2 + exit 1;; +esac + +# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). +# Here we must recognize all the valid KERNEL-OS combinations. +maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` +case $maybe_os in + nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \ + uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \ + storm-chaos* | os2-emx* | rtmk-nova*) + os=-$maybe_os + basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` + ;; + *) + basic_machine=`echo $1 | sed 's/-[^-]*$//'` + if [ $basic_machine != $1 ] + then os=`echo $1 | sed 's/.*-/-/'` + else os=; fi + ;; +esac + +### Let's recognize common machines as not being operating systems so +### that things like config.sub decstation-3100 work. We also +### recognize some manufacturers as not being operating systems, so we +### can provide default operating systems below. +case $os in + -sun*os*) + # Prevent following clause from handling this invalid input. + ;; + -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \ + -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \ + -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \ + -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ + -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ + -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ + -apple | -axis | -knuth | -cray) + os= + basic_machine=$1 + ;; + -sim | -cisco | -oki | -wec | -winbond) + os= + basic_machine=$1 + ;; + -scout) + ;; + -wrs) + os=-vxworks + basic_machine=$1 + ;; + -chorusos*) + os=-chorusos + basic_machine=$1 + ;; + -chorusrdb) + os=-chorusrdb + basic_machine=$1 + ;; + -hiux*) + os=-hiuxwe2 + ;; + -sco6) + os=-sco5v6 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco5) + os=-sco3.2v5 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco4) + os=-sco3.2v4 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco3.2.[4-9]*) + os=`echo $os | sed -e 's/sco3.2./sco3.2v/'` + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco3.2v[4-9]*) + # Don't forget version if it is 3.2v4 or newer. + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco5v6*) + # Don't forget version if it is 3.2v4 or newer. + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco*) + os=-sco3.2v2 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -udk*) + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -isc) + os=-isc2.2 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -clix*) + basic_machine=clipper-intergraph + ;; + -isc*) + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -lynx*) + os=-lynxos + ;; + -ptx*) + basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'` + ;; + -windowsnt*) + os=`echo $os | sed -e 's/windowsnt/winnt/'` + ;; + -psos*) + os=-psos + ;; + -mint | -mint[0-9]*) + basic_machine=m68k-atari + os=-mint + ;; +esac + +# Decode aliases for certain CPU-COMPANY combinations. +case $basic_machine in + # Recognize the basic CPU types without company name. + # Some are omitted here because they have special meanings below. + 1750a | 580 \ + | a29k \ + | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ + | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ + | am33_2.0 \ + | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \ + | bfin \ + | c4x | clipper \ + | d10v | d30v | dlx | dsp16xx \ + | fido | fr30 | frv \ + | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ + | i370 | i860 | i960 | ia64 \ + | ip2k | iq2000 \ + | m32c | m32r | m32rle | m68000 | m68k | m88k \ + | maxq | mb | microblaze | mcore | mep \ + | mips | mipsbe | mipseb | mipsel | mipsle \ + | mips16 \ + | mips64 | mips64el \ + | mips64vr | mips64vrel \ + | mips64orion | mips64orionel \ + | mips64vr4100 | mips64vr4100el \ + | mips64vr4300 | mips64vr4300el \ + | mips64vr5000 | mips64vr5000el \ + | mips64vr5900 | mips64vr5900el \ + | mipsisa32 | mipsisa32el \ + | mipsisa32r2 | mipsisa32r2el \ + | mipsisa64 | mipsisa64el \ + | mipsisa64r2 | mipsisa64r2el \ + | mipsisa64sb1 | mipsisa64sb1el \ + | mipsisa64sr71k | mipsisa64sr71kel \ + | mipstx39 | mipstx39el \ + | mn10200 | mn10300 \ + | mt \ + | msp430 \ + | nios | nios2 \ + | ns16k | ns32k \ + | or32 \ + | pdp10 | pdp11 | pj | pjl \ + | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ + | pyramid \ + | score \ + | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ + | sh64 | sh64le \ + | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ + | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ + | spu | strongarm \ + | tahoe | thumb | tic4x | tic80 | tron \ + | v850 | v850e \ + | we32k \ + | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \ + | z8k) + basic_machine=$basic_machine-unknown + ;; + m6811 | m68hc11 | m6812 | m68hc12) + # Motorola 68HC11/12. + basic_machine=$basic_machine-unknown + os=-none + ;; + m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) + ;; + ms1) + basic_machine=mt-unknown + ;; + + # We use `pc' rather than `unknown' + # because (1) that's what they normally are, and + # (2) the word "unknown" tends to confuse beginning users. + i*86 | x86_64) + basic_machine=$basic_machine-pc + ;; + # Object if more than one company name word. + *-*-*) + echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 + exit 1 + ;; + # Recognize the basic CPU types with company name. + 580-* \ + | a29k-* \ + | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \ + | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \ + | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \ + | arm-* | armbe-* | armle-* | armeb-* | armv*-* \ + | avr-* | avr32-* \ + | bfin-* | bs2000-* \ + | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \ + | clipper-* | craynv-* | cydra-* \ + | d10v-* | d30v-* | dlx-* \ + | elxsi-* \ + | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \ + | h8300-* | h8500-* \ + | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ + | i*86-* | i860-* | i960-* | ia64-* \ + | ip2k-* | iq2000-* \ + | m32c-* | m32r-* | m32rle-* \ + | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ + | m88110-* | m88k-* | maxq-* | mcore-* \ + | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ + | mips16-* \ + | mips64-* | mips64el-* \ + | mips64vr-* | mips64vrel-* \ + | mips64orion-* | mips64orionel-* \ + | mips64vr4100-* | mips64vr4100el-* \ + | mips64vr4300-* | mips64vr4300el-* \ + | mips64vr5000-* | mips64vr5000el-* \ + | mips64vr5900-* | mips64vr5900el-* \ + | mipsisa32-* | mipsisa32el-* \ + | mipsisa32r2-* | mipsisa32r2el-* \ + | mipsisa64-* | mipsisa64el-* \ + | mipsisa64r2-* | mipsisa64r2el-* \ + | mipsisa64sb1-* | mipsisa64sb1el-* \ + | mipsisa64sr71k-* | mipsisa64sr71kel-* \ + | mipstx39-* | mipstx39el-* \ + | mmix-* \ + | mt-* \ + | msp430-* \ + | nios-* | nios2-* \ + | none-* | np1-* | ns16k-* | ns32k-* \ + | orion-* \ + | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ + | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ + | pyramid-* \ + | romp-* | rs6000-* \ + | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ + | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ + | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ + | sparclite-* \ + | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \ + | tahoe-* | thumb-* \ + | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ + | tron-* \ + | v850-* | v850e-* | vax-* \ + | we32k-* \ + | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \ + | xstormy16-* | xtensa*-* \ + | ymp-* \ + | z8k-*) + ;; + # Recognize the basic CPU types without company name, with glob match. + xtensa*) + basic_machine=$basic_machine-unknown + ;; + # Recognize the various machine names and aliases which stand + # for a CPU type and a company and sometimes even an OS. + 386bsd) + basic_machine=i386-unknown + os=-bsd + ;; + 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) + basic_machine=m68000-att + ;; + 3b*) + basic_machine=we32k-att + ;; + a29khif) + basic_machine=a29k-amd + os=-udi + ;; + abacus) + basic_machine=abacus-unknown + ;; + adobe68k) + basic_machine=m68010-adobe + os=-scout + ;; + alliant | fx80) + basic_machine=fx80-alliant + ;; + altos | altos3068) + basic_machine=m68k-altos + ;; + am29k) + basic_machine=a29k-none + os=-bsd + ;; + amd64) + basic_machine=x86_64-pc + ;; + amd64-*) + basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + amdahl) + basic_machine=580-amdahl + os=-sysv + ;; + amiga | amiga-*) + basic_machine=m68k-unknown + ;; + amigaos | amigados) + basic_machine=m68k-unknown + os=-amigaos + ;; + amigaunix | amix) + basic_machine=m68k-unknown + os=-sysv4 + ;; + apollo68) + basic_machine=m68k-apollo + os=-sysv + ;; + apollo68bsd) + basic_machine=m68k-apollo + os=-bsd + ;; + aux) + basic_machine=m68k-apple + os=-aux + ;; + balance) + basic_machine=ns32k-sequent + os=-dynix + ;; + blackfin) + basic_machine=bfin-unknown + os=-linux + ;; + blackfin-*) + basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` + os=-linux + ;; + c90) + basic_machine=c90-cray + os=-unicos + ;; + convex-c1) + basic_machine=c1-convex + os=-bsd + ;; + convex-c2) + basic_machine=c2-convex + os=-bsd + ;; + convex-c32) + basic_machine=c32-convex + os=-bsd + ;; + convex-c34) + basic_machine=c34-convex + os=-bsd + ;; + convex-c38) + basic_machine=c38-convex + os=-bsd + ;; + cray | j90) + basic_machine=j90-cray + os=-unicos + ;; + craynv) + basic_machine=craynv-cray + os=-unicosmp + ;; + cr16) + basic_machine=cr16-unknown + os=-elf + ;; + crds | unos) + basic_machine=m68k-crds + ;; + crisv32 | crisv32-* | etraxfs*) + basic_machine=crisv32-axis + ;; + cris | cris-* | etrax*) + basic_machine=cris-axis + ;; + crx) + basic_machine=crx-unknown + os=-elf + ;; + da30 | da30-*) + basic_machine=m68k-da30 + ;; + decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) + basic_machine=mips-dec + ;; + decsystem10* | dec10*) + basic_machine=pdp10-dec + os=-tops10 + ;; + decsystem20* | dec20*) + basic_machine=pdp10-dec + os=-tops20 + ;; + delta | 3300 | motorola-3300 | motorola-delta \ + | 3300-motorola | delta-motorola) + basic_machine=m68k-motorola + ;; + delta88) + basic_machine=m88k-motorola + os=-sysv3 + ;; + djgpp) + basic_machine=i586-pc + os=-msdosdjgpp + ;; + dpx20 | dpx20-*) + basic_machine=rs6000-bull + os=-bosx + ;; + dpx2* | dpx2*-bull) + basic_machine=m68k-bull + os=-sysv3 + ;; + ebmon29k) + basic_machine=a29k-amd + os=-ebmon + ;; + elxsi) + basic_machine=elxsi-elxsi + os=-bsd + ;; + encore | umax | mmax) + basic_machine=ns32k-encore + ;; + es1800 | OSE68k | ose68k | ose | OSE) + basic_machine=m68k-ericsson + os=-ose + ;; + fx2800) + basic_machine=i860-alliant + ;; + genix) + basic_machine=ns32k-ns + ;; + gmicro) + basic_machine=tron-gmicro + os=-sysv + ;; + go32) + basic_machine=i386-pc + os=-go32 + ;; + h3050r* | hiux*) + basic_machine=hppa1.1-hitachi + os=-hiuxwe2 + ;; + h8300hms) + basic_machine=h8300-hitachi + os=-hms + ;; + h8300xray) + basic_machine=h8300-hitachi + os=-xray + ;; + h8500hms) + basic_machine=h8500-hitachi + os=-hms + ;; + harris) + basic_machine=m88k-harris + os=-sysv3 + ;; + hp300-*) + basic_machine=m68k-hp + ;; + hp300bsd) + basic_machine=m68k-hp + os=-bsd + ;; + hp300hpux) + basic_machine=m68k-hp + os=-hpux + ;; + hp3k9[0-9][0-9] | hp9[0-9][0-9]) + basic_machine=hppa1.0-hp + ;; + hp9k2[0-9][0-9] | hp9k31[0-9]) + basic_machine=m68000-hp + ;; + hp9k3[2-9][0-9]) + basic_machine=m68k-hp + ;; + hp9k6[0-9][0-9] | hp6[0-9][0-9]) + basic_machine=hppa1.0-hp + ;; + hp9k7[0-79][0-9] | hp7[0-79][0-9]) + basic_machine=hppa1.1-hp + ;; + hp9k78[0-9] | hp78[0-9]) + # FIXME: really hppa2.0-hp + basic_machine=hppa1.1-hp + ;; + hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) + # FIXME: really hppa2.0-hp + basic_machine=hppa1.1-hp + ;; + hp9k8[0-9][13679] | hp8[0-9][13679]) + basic_machine=hppa1.1-hp + ;; + hp9k8[0-9][0-9] | hp8[0-9][0-9]) + basic_machine=hppa1.0-hp + ;; + hppa-next) + os=-nextstep3 + ;; + hppaosf) + basic_machine=hppa1.1-hp + os=-osf + ;; + hppro) + basic_machine=hppa1.1-hp + os=-proelf + ;; + i370-ibm* | ibm*) + basic_machine=i370-ibm + ;; +# I'm not sure what "Sysv32" means. Should this be sysv3.2? + i*86v32) + basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` + os=-sysv32 + ;; + i*86v4*) + basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` + os=-sysv4 + ;; + i*86v) + basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` + os=-sysv + ;; + i*86sol2) + basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` + os=-solaris2 + ;; + i386mach) + basic_machine=i386-mach + os=-mach + ;; + i386-vsta | vsta) + basic_machine=i386-unknown + os=-vsta + ;; + iris | iris4d) + basic_machine=mips-sgi + case $os in + -irix*) + ;; + *) + os=-irix4 + ;; + esac + ;; + isi68 | isi) + basic_machine=m68k-isi + os=-sysv + ;; + m68knommu) + basic_machine=m68k-unknown + os=-linux + ;; + m68knommu-*) + basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'` + os=-linux + ;; + m88k-omron*) + basic_machine=m88k-omron + ;; + magnum | m3230) + basic_machine=mips-mips + os=-sysv + ;; + merlin) + basic_machine=ns32k-utek + os=-sysv + ;; + mingw32) + basic_machine=i386-pc + os=-mingw32 + ;; + mingw32ce) + basic_machine=arm-unknown + os=-mingw32ce + ;; + miniframe) + basic_machine=m68000-convergent + ;; + *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*) + basic_machine=m68k-atari + os=-mint + ;; + mips3*-*) + basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'` + ;; + mips3*) + basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown + ;; + monitor) + basic_machine=m68k-rom68k + os=-coff + ;; + morphos) + basic_machine=powerpc-unknown + os=-morphos + ;; + msdos) + basic_machine=i386-pc + os=-msdos + ;; + ms1-*) + basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'` + ;; + mvs) + basic_machine=i370-ibm + os=-mvs + ;; + ncr3000) + basic_machine=i486-ncr + os=-sysv4 + ;; + netbsd386) + basic_machine=i386-unknown + os=-netbsd + ;; + netwinder) + basic_machine=armv4l-rebel + os=-linux + ;; + news | news700 | news800 | news900) + basic_machine=m68k-sony + os=-newsos + ;; + news1000) + basic_machine=m68030-sony + os=-newsos + ;; + news-3600 | risc-news) + basic_machine=mips-sony + os=-newsos + ;; + necv70) + basic_machine=v70-nec + os=-sysv + ;; + next | m*-next ) + basic_machine=m68k-next + case $os in + -nextstep* ) + ;; + -ns2*) + os=-nextstep2 + ;; + *) + os=-nextstep3 + ;; + esac + ;; + nh3000) + basic_machine=m68k-harris + os=-cxux + ;; + nh[45]000) + basic_machine=m88k-harris + os=-cxux + ;; + nindy960) + basic_machine=i960-intel + os=-nindy + ;; + mon960) + basic_machine=i960-intel + os=-mon960 + ;; + nonstopux) + basic_machine=mips-compaq + os=-nonstopux + ;; + np1) + basic_machine=np1-gould + ;; + nsr-tandem) + basic_machine=nsr-tandem + ;; + op50n-* | op60c-*) + basic_machine=hppa1.1-oki + os=-proelf + ;; + openrisc | openrisc-*) + basic_machine=or32-unknown + ;; + os400) + basic_machine=powerpc-ibm + os=-os400 + ;; + OSE68000 | ose68000) + basic_machine=m68000-ericsson + os=-ose + ;; + os68k) + basic_machine=m68k-none + os=-os68k + ;; + pa-hitachi) + basic_machine=hppa1.1-hitachi + os=-hiuxwe2 + ;; + paragon) + basic_machine=i860-intel + os=-osf + ;; + parisc) + basic_machine=hppa-unknown + os=-linux + ;; + parisc-*) + basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'` + os=-linux + ;; + pbd) + basic_machine=sparc-tti + ;; + pbb) + basic_machine=m68k-tti + ;; + pc532 | pc532-*) + basic_machine=ns32k-pc532 + ;; + pc98) + basic_machine=i386-pc + ;; + pc98-*) + basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pentium | p5 | k5 | k6 | nexgen | viac3) + basic_machine=i586-pc + ;; + pentiumpro | p6 | 6x86 | athlon | athlon_*) + basic_machine=i686-pc + ;; + pentiumii | pentium2 | pentiumiii | pentium3) + basic_machine=i686-pc + ;; + pentium4) + basic_machine=i786-pc + ;; + pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*) + basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pentiumpro-* | p6-* | 6x86-* | athlon-*) + basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*) + basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pentium4-*) + basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pn) + basic_machine=pn-gould + ;; + power) basic_machine=power-ibm + ;; + ppc) basic_machine=powerpc-unknown + ;; + ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + ppcle | powerpclittle | ppc-le | powerpc-little) + basic_machine=powerpcle-unknown + ;; + ppcle-* | powerpclittle-*) + basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + ppc64) basic_machine=powerpc64-unknown + ;; + ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + ppc64le | powerpc64little | ppc64-le | powerpc64-little) + basic_machine=powerpc64le-unknown + ;; + ppc64le-* | powerpc64little-*) + basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + ps2) + basic_machine=i386-ibm + ;; + pw32) + basic_machine=i586-unknown + os=-pw32 + ;; + rdos) + basic_machine=i386-pc + os=-rdos + ;; + rom68k) + basic_machine=m68k-rom68k + os=-coff + ;; + rm[46]00) + basic_machine=mips-siemens + ;; + rtpc | rtpc-*) + basic_machine=romp-ibm + ;; + s390 | s390-*) + basic_machine=s390-ibm + ;; + s390x | s390x-*) + basic_machine=s390x-ibm + ;; + sa29200) + basic_machine=a29k-amd + os=-udi + ;; + sb1) + basic_machine=mipsisa64sb1-unknown + ;; + sb1el) + basic_machine=mipsisa64sb1el-unknown + ;; + sde) + basic_machine=mipsisa32-sde + os=-elf + ;; + sei) + basic_machine=mips-sei + os=-seiux + ;; + sequent) + basic_machine=i386-sequent + ;; + sh) + basic_machine=sh-hitachi + os=-hms + ;; + sh5el) + basic_machine=sh5le-unknown + ;; + sh64) + basic_machine=sh64-unknown + ;; + sparclite-wrs | simso-wrs) + basic_machine=sparclite-wrs + os=-vxworks + ;; + sps7) + basic_machine=m68k-bull + os=-sysv2 + ;; + spur) + basic_machine=spur-unknown + ;; + st2000) + basic_machine=m68k-tandem + ;; + stratus) + basic_machine=i860-stratus + os=-sysv4 + ;; + sun2) + basic_machine=m68000-sun + ;; + sun2os3) + basic_machine=m68000-sun + os=-sunos3 + ;; + sun2os4) + basic_machine=m68000-sun + os=-sunos4 + ;; + sun3os3) + basic_machine=m68k-sun + os=-sunos3 + ;; + sun3os4) + basic_machine=m68k-sun + os=-sunos4 + ;; + sun4os3) + basic_machine=sparc-sun + os=-sunos3 + ;; + sun4os4) + basic_machine=sparc-sun + os=-sunos4 + ;; + sun4sol2) + basic_machine=sparc-sun + os=-solaris2 + ;; + sun3 | sun3-*) + basic_machine=m68k-sun + ;; + sun4) + basic_machine=sparc-sun + ;; + sun386 | sun386i | roadrunner) + basic_machine=i386-sun + ;; + sv1) + basic_machine=sv1-cray + os=-unicos + ;; + symmetry) + basic_machine=i386-sequent + os=-dynix + ;; + t3e) + basic_machine=alphaev5-cray + os=-unicos + ;; + t90) + basic_machine=t90-cray + os=-unicos + ;; + tic54x | c54x*) + basic_machine=tic54x-unknown + os=-coff + ;; + tic55x | c55x*) + basic_machine=tic55x-unknown + os=-coff + ;; + tic6x | c6x*) + basic_machine=tic6x-unknown + os=-coff + ;; + tile*) + basic_machine=tile-unknown + os=-linux-gnu + ;; + tx39) + basic_machine=mipstx39-unknown + ;; + tx39el) + basic_machine=mipstx39el-unknown + ;; + toad1) + basic_machine=pdp10-xkl + os=-tops20 + ;; + tower | tower-32) + basic_machine=m68k-ncr + ;; + tpf) + basic_machine=s390x-ibm + os=-tpf + ;; + udi29k) + basic_machine=a29k-amd + os=-udi + ;; + ultra3) + basic_machine=a29k-nyu + os=-sym1 + ;; + v810 | necv810) + basic_machine=v810-nec + os=-none + ;; + vaxv) + basic_machine=vax-dec + os=-sysv + ;; + vms) + basic_machine=vax-dec + os=-vms + ;; + vpp*|vx|vx-*) + basic_machine=f301-fujitsu + ;; + vxworks960) + basic_machine=i960-wrs + os=-vxworks + ;; + vxworks68) + basic_machine=m68k-wrs + os=-vxworks + ;; + vxworks29k) + basic_machine=a29k-wrs + os=-vxworks + ;; + w65*) + basic_machine=w65-wdc + os=-none + ;; + w89k-*) + basic_machine=hppa1.1-winbond + os=-proelf + ;; + xbox) + basic_machine=i686-pc + os=-mingw32 + ;; + xps | xps100) + basic_machine=xps100-honeywell + ;; + ymp) + basic_machine=ymp-cray + os=-unicos + ;; + z8k-*-coff) + basic_machine=z8k-unknown + os=-sim + ;; + none) + basic_machine=none-none + os=-none + ;; + +# Here we handle the default manufacturer of certain CPU types. It is in +# some cases the only manufacturer, in others, it is the most popular. + w89k) + basic_machine=hppa1.1-winbond + ;; + op50n) + basic_machine=hppa1.1-oki + ;; + op60c) + basic_machine=hppa1.1-oki + ;; + romp) + basic_machine=romp-ibm + ;; + mmix) + basic_machine=mmix-knuth + ;; + rs6000) + basic_machine=rs6000-ibm + ;; + vax) + basic_machine=vax-dec + ;; + pdp10) + # there are many clones, so DEC is not a safe bet + basic_machine=pdp10-unknown + ;; + pdp11) + basic_machine=pdp11-dec + ;; + we32k) + basic_machine=we32k-att + ;; + sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele) + basic_machine=sh-unknown + ;; + sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v) + basic_machine=sparc-sun + ;; + cydra) + basic_machine=cydra-cydrome + ;; + orion) + basic_machine=orion-highlevel + ;; + orion105) + basic_machine=clipper-highlevel + ;; + mac | mpw | mac-mpw) + basic_machine=m68k-apple + ;; + pmac | pmac-mpw) + basic_machine=powerpc-apple + ;; + *-unknown) + # Make sure to match an already-canonicalized machine name. + ;; + *) + echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 + exit 1 + ;; +esac + +# Here we canonicalize certain aliases for manufacturers. +case $basic_machine in + *-digital*) + basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'` + ;; + *-commodore*) + basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'` + ;; + *) + ;; +esac + +# Decode manufacturer-specific aliases for certain operating systems. + +if [ x"$os" != x"" ] +then +case $os in + # First match some system type aliases + # that might get confused with valid system types. + # -solaris* is a basic system type, with this one exception. + -solaris1 | -solaris1.*) + os=`echo $os | sed -e 's|solaris1|sunos4|'` + ;; + -solaris) + os=-solaris2 + ;; + -svr4*) + os=-sysv4 + ;; + -unixware*) + os=-sysv4.2uw + ;; + -gnu/linux*) + os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'` + ;; + # First accept the basic system types. + # The portable systems comes first. + # Each alternative MUST END IN A *, to match a version number. + # -sysv* is not here because it comes later, after sysvr4. + -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \ + | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\ + | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \ + | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \ + | -aos* \ + | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \ + | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \ + | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \ + | -openbsd* | -solidbsd* \ + | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \ + | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \ + | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \ + | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \ + | -chorusos* | -chorusrdb* \ + | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \ + | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \ + | -uxpv* | -beos* | -mpeix* | -udk* \ + | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \ + | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \ + | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \ + | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \ + | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \ + | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \ + | -skyos* | -haiku* | -rdos* | -toppers* | -drops*) + # Remember, each alternative MUST END IN *, to match a version number. + ;; + -qnx*) + case $basic_machine in + x86-* | i*86-*) + ;; + *) + os=-nto$os + ;; + esac + ;; + -nto-qnx*) + ;; + -nto*) + os=`echo $os | sed -e 's|nto|nto-qnx|'` + ;; + -sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \ + | -windows* | -osx | -abug | -netware* | -os9* | -beos* | -haiku* \ + | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*) + ;; + -mac*) + os=`echo $os | sed -e 's|mac|macos|'` + ;; + -linux-dietlibc) + os=-linux-dietlibc + ;; + -linux*) + os=`echo $os | sed -e 's|linux|linux-gnu|'` + ;; + -sunos5*) + os=`echo $os | sed -e 's|sunos5|solaris2|'` + ;; + -sunos6*) + os=`echo $os | sed -e 's|sunos6|solaris3|'` + ;; + -opened*) + os=-openedition + ;; + -os400*) + os=-os400 + ;; + -wince*) + os=-wince + ;; + -osfrose*) + os=-osfrose + ;; + -osf*) + os=-osf + ;; + -utek*) + os=-bsd + ;; + -dynix*) + os=-bsd + ;; + -acis*) + os=-aos + ;; + -atheos*) + os=-atheos + ;; + -syllable*) + os=-syllable + ;; + -386bsd) + os=-bsd + ;; + -ctix* | -uts*) + os=-sysv + ;; + -nova*) + os=-rtmk-nova + ;; + -ns2 ) + os=-nextstep2 + ;; + -nsk*) + os=-nsk + ;; + # Preserve the version number of sinix5. + -sinix5.*) + os=`echo $os | sed -e 's|sinix|sysv|'` + ;; + -sinix*) + os=-sysv4 + ;; + -tpf*) + os=-tpf + ;; + -triton*) + os=-sysv3 + ;; + -oss*) + os=-sysv3 + ;; + -svr4) + os=-sysv4 + ;; + -svr3) + os=-sysv3 + ;; + -sysvr4) + os=-sysv4 + ;; + # This must come after -sysvr4. + -sysv*) + ;; + -ose*) + os=-ose + ;; + -es1800*) + os=-ose + ;; + -xenix) + os=-xenix + ;; + -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*) + os=-mint + ;; + -aros*) + os=-aros + ;; + -kaos*) + os=-kaos + ;; + -zvmoe) + os=-zvmoe + ;; + -none) + ;; + *) + # Get rid of the `-' at the beginning of $os. + os=`echo $os | sed 's/[^-]*-//'` + echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2 + exit 1 + ;; +esac +else + +# Here we handle the default operating systems that come with various machines. +# The value should be what the vendor currently ships out the door with their +# machine or put another way, the most popular os provided with the machine. + +# Note that if you're going to try to match "-MANUFACTURER" here (say, +# "-sun"), then you have to tell the case statement up towards the top +# that MANUFACTURER isn't an operating system. 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Disable this feature. + alias -g '${1+"$@"}'='"$@"' + setopt NO_GLOB_SUBST +else + case `(set -o) 2>/dev/null` in + *posix*) set -o posix ;; +esac + +fi + + + + +# PATH needs CR +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + +as_nl=' +' +export as_nl +# Printing a long string crashes Solaris 7 /usr/bin/printf. +as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo +as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo +if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='printf %s\n' + as_echo_n='printf %s' +else + if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then + as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"' + as_echo_n='/usr/ucb/echo -n' + else + as_echo_body='eval expr "X$1" : "X\\(.*\\)"' + as_echo_n_body='eval + arg=$1; + case $arg in + *"$as_nl"*) + expr "X$arg" : "X\\(.*\\)$as_nl"; + arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; + esac; + expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl" + ' + export as_echo_n_body + as_echo_n='sh -c $as_echo_n_body as_echo' + fi + export as_echo_body + as_echo='sh -c $as_echo_body as_echo' +fi + +# The user is always right. +if test "${PATH_SEPARATOR+set}" != set; then + PATH_SEPARATOR=: + (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && { + (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 || + PATH_SEPARATOR=';' + } +fi + +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + + +# IFS +# We need space, tab and new line, in precisely that order. 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This makes it impossible to quote backslashes using + # echo "$something" | sed 's/\\/\\\\/g' + # + # So, first we look for a working echo in the user's PATH. + + lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR + for dir in $PATH /usr/ucb; do + IFS="$lt_save_ifs" + if (test -f $dir/echo || test -f $dir/echo$ac_exeext) && + test "X`($dir/echo '\t') 2>/dev/null`" = 'X\t' && + echo_testing_string=`($dir/echo "$echo_test_string") 2>/dev/null` && + test "X$echo_testing_string" = "X$echo_test_string"; then + ECHO="$dir/echo" + break + fi + done + IFS="$lt_save_ifs" + + if test "X$ECHO" = Xecho; then + # We didn't find a better echo, so look for alternatives. + if test "X`{ print -r '\t'; } 2>/dev/null`" = 'X\t' && + echo_testing_string=`{ print -r "$echo_test_string"; } 2>/dev/null` && + test "X$echo_testing_string" = "X$echo_test_string"; then + # This shell has a builtin print -r that does the trick. + ECHO='print -r' + elif { test -f /bin/ksh || test -f /bin/ksh$ac_exeext; } && + test "X$CONFIG_SHELL" != X/bin/ksh; then + # If we have ksh, try running configure again with it. + ORIGINAL_CONFIG_SHELL=${CONFIG_SHELL-/bin/sh} + export ORIGINAL_CONFIG_SHELL + CONFIG_SHELL=/bin/ksh + export CONFIG_SHELL + exec $CONFIG_SHELL "$0" --no-reexec ${1+"$@"} + else + # Try using printf. + ECHO='printf %s\n' + if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' && + echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` && + test "X$echo_testing_string" = "X$echo_test_string"; then + # Cool, printf works + : + elif echo_testing_string=`($ORIGINAL_CONFIG_SHELL "$0" --fallback-echo '\t') 2>/dev/null` && + test "X$echo_testing_string" = 'X\t' && + echo_testing_string=`($ORIGINAL_CONFIG_SHELL "$0" --fallback-echo "$echo_test_string") 2>/dev/null` && + test "X$echo_testing_string" = "X$echo_test_string"; then + CONFIG_SHELL=$ORIGINAL_CONFIG_SHELL + export CONFIG_SHELL + SHELL="$CONFIG_SHELL" + export SHELL + ECHO="$CONFIG_SHELL $0 --fallback-echo" + elif echo_testing_string=`($CONFIG_SHELL "$0" --fallback-echo '\t') 2>/dev/null` && + test "X$echo_testing_string" = 'X\t' && + echo_testing_string=`($CONFIG_SHELL "$0" --fallback-echo "$echo_test_string") 2>/dev/null` && + test "X$echo_testing_string" = "X$echo_test_string"; then + ECHO="$CONFIG_SHELL $0 --fallback-echo" + else + # maybe with a smaller string... + prev=: + + for cmd in 'echo test' 'sed 2q "$0"' 'sed 10q "$0"' 'sed 20q "$0"' 'sed 50q "$0"'; do + if { test "X$echo_test_string" = "X`eval $cmd`"; } 2>/dev/null + then + break + fi + prev="$cmd" + done + + if test "$prev" != 'sed 50q "$0"'; then + echo_test_string=`eval $prev` + export echo_test_string + exec ${ORIGINAL_CONFIG_SHELL-${CONFIG_SHELL-/bin/sh}} "$0" ${1+"$@"} + else + # Oops. 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Don't cache a + # value for MKDIR_P within a source directory, because that will + # break other packages using the cache if that directory is + # removed, or if the value is a relative name. + test -d ./--version && rmdir ./--version + MKDIR_P="$ac_install_sh -d" + fi +fi +{ $as_echo "$as_me:$LINENO: result: $MKDIR_P" >&5 +$as_echo "$MKDIR_P" >&6; } + +mkdir_p="$MKDIR_P" +case $mkdir_p in + [\\/$]* | ?:[\\/]*) ;; + */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;; +esac + +for ac_prog in gawk mawk nawk awk +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_AWK+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$AWK"; then + ac_cv_prog_AWK="$AWK" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_AWK="$ac_prog" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +AWK=$ac_cv_prog_AWK +if test -n "$AWK"; then + { $as_echo "$as_me:$LINENO: result: $AWK" >&5 +$as_echo "$AWK" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$AWK" && break +done + +{ $as_echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5 +$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; } +set x ${MAKE-make} +ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'` +if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.make <<\_ACEOF +SHELL = /bin/sh +all: + @echo '@@@%%%=$(MAKE)=@@@%%%' +_ACEOF +# GNU make sometimes prints "make[1]: Entering...", which would confuse us. +case `${MAKE-make} -f conftest.make 2>/dev/null` in + *@@@%%%=?*=@@@%%%*) + eval ac_cv_prog_make_${ac_make}_set=yes;; + *) + eval ac_cv_prog_make_${ac_make}_set=no;; +esac +rm -f conftest.make +fi +if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then + { $as_echo "$as_me:$LINENO: result: yes" >&5 +$as_echo "yes" >&6; } + SET_MAKE= +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } + SET_MAKE="MAKE=${MAKE-make}" +fi + +rm -rf .tst 2>/dev/null +mkdir .tst 2>/dev/null +if test -d .tst; then + am__leading_dot=. +else + am__leading_dot=_ +fi +rmdir .tst 2>/dev/null + +if test "`cd $srcdir && pwd`" != "`pwd`"; then + # Use -I$(srcdir) only when $(srcdir) != ., so that make's output + # is not polluted with repeated "-I." + am__isrc=' -I$(srcdir)' + # test to see if srcdir already configured + if test -f $srcdir/config.status; then + { { $as_echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5 +$as_echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;} + { (exit 1); exit 1; }; } + fi +fi + +# test whether we have cygpath +if test -z "$CYGPATH_W"; then + if (cygpath --version) >/dev/null 2>/dev/null; then + CYGPATH_W='cygpath -w' + else + CYGPATH_W=echo + fi +fi + + +# Define the identity of the package. + PACKAGE='clustal-omega' + VERSION='1.0.2' + + +cat >>confdefs.h <<_ACEOF +#define PACKAGE "$PACKAGE" +_ACEOF + + +cat >>confdefs.h <<_ACEOF +#define VERSION "$VERSION" +_ACEOF + +# Some tools Automake needs. + +ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"} + + +AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"} + + +AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"} + + +AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"} + + +MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"} + +install_sh=${install_sh-"\$(SHELL) $am_aux_dir/install-sh"} + +# Installed binaries are usually stripped using `strip' when the user +# run `make install-strip'. However `strip' might not be the right +# tool to use in cross-compilation environments, therefore Automake +# will honor the `STRIP' environment variable to overrule this program. +if test "$cross_compiling" != no; then + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. +set dummy ${ac_tool_prefix}strip; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_STRIP+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$STRIP"; then + ac_cv_prog_STRIP="$STRIP" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_STRIP="${ac_tool_prefix}strip" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +STRIP=$ac_cv_prog_STRIP +if test -n "$STRIP"; then + { $as_echo "$as_me:$LINENO: result: $STRIP" >&5 +$as_echo "$STRIP" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_STRIP"; then + ac_ct_STRIP=$STRIP + # Extract the first word of "strip", so it can be a program name with args. +set dummy strip; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_STRIP"; then + ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_STRIP="strip" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP +if test -n "$ac_ct_STRIP"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5 +$as_echo "$ac_ct_STRIP" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_STRIP" = x; then + STRIP=":" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + STRIP=$ac_ct_STRIP + fi +else + STRIP="$ac_cv_prog_STRIP" +fi + +fi +INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s" + +# We need awk for the "check" target. The system "awk" is bad on +# some platforms. +# Always define AMTAR for backward compatibility. + +AMTAR=${AMTAR-"${am_missing_run}tar"} + +am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -' + + + + + + +# config header: provides a way for people to customise the +# configuration for their platform, via #defines. config.h.in can be +# generated automatically with the autoheader tool. However, you need +# a stamp-h file in your project to ensure that automake regenerates +# config.h from config.h.in. Type 'touch stamp-h' to add this file to +# your project. +# +ac_config_headers="$ac_config_headers src/config.h" + + +# the following allows to install a copy config.h for libclustalo in a +# namespace like way, i.e. no name clash with your own config.h + +ac_config_commands="$ac_config_commands src/clustal-omega-config.h" + + +# This macro was introduced in Autoconf 2.60. If possible, enable +# extensions to C or Posix on hosts that normally disable the +# extensions. +DEPDIR="${am__leading_dot}deps" + +ac_config_commands="$ac_config_commands depfiles" + + +am_make=${MAKE-make} +cat > confinc << 'END' +am__doit: + @echo done +.PHONY: am__doit +END +# If we don't find an include directive, just comment out the code. +{ $as_echo "$as_me:$LINENO: checking for style of include used by $am_make" >&5 +$as_echo_n "checking for style of include used by $am_make... " >&6; } +am__include="#" +am__quote= +_am_result=none +# First try GNU make style include. +echo "include confinc" > confmf +# We grep out `Entering directory' and `Leaving directory' +# messages which can occur if `w' ends up in MAKEFLAGS. +# In particular we don't look at `^make:' because GNU make might +# be invoked under some other name (usually "gmake"), in which +# case it prints its new name instead of `make'. +if test "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then + am__include=include + am__quote= + _am_result=GNU +fi +# Now try BSD make style include. +if test "$am__include" = "#"; then + echo '.include "confinc"' > confmf + if test "`$am_make -s -f confmf 2> /dev/null`" = "done"; then + am__include=.include + am__quote="\"" + _am_result=BSD + fi +fi + + +{ $as_echo "$as_me:$LINENO: result: $_am_result" >&5 +$as_echo "$_am_result" >&6; } +rm -f confinc confmf + +# Check whether --enable-dependency-tracking was given. +if test "${enable_dependency_tracking+set}" = set; then + enableval=$enable_dependency_tracking; +fi + +if test "x$enable_dependency_tracking" != xno; then + am_depcomp="$ac_aux_dir/depcomp" + AMDEPBACKSLASH='\' +fi + if test "x$enable_dependency_tracking" != xno; then + AMDEP_TRUE= + AMDEP_FALSE='#' +else + AMDEP_TRUE='#' + AMDEP_FALSE= +fi + + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. +set dummy ${ac_tool_prefix}gcc; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_CC="${ac_tool_prefix}gcc" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:$LINENO: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "gcc", so it can be a program name with args. +set dummy gcc; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_CC="gcc" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi +else + CC="$ac_cv_prog_CC" +fi + +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. +set dummy ${ac_tool_prefix}cc; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_CC="${ac_tool_prefix}cc" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:$LINENO: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + + fi +fi +if test -z "$CC"; then + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else + ac_prog_rejected=no +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then + ac_prog_rejected=yes + continue + fi + ac_cv_prog_CC="cc" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +if test $ac_prog_rejected = yes; then + # We found a bogon in the path, so make sure we never use it. + set dummy $ac_cv_prog_CC + shift + if test $# != 0; then + # We chose a different compiler from the bogus one. + # However, it has the same basename, so the bogon will be chosen + # first if we set CC to just the basename; use the full file name. + shift + ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@" + fi +fi +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:$LINENO: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + for ac_prog in cl.exe + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_CC="$ac_tool_prefix$ac_prog" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:$LINENO: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$CC" && break + done +fi +if test -z "$CC"; then + ac_ct_CC=$CC + for ac_prog in cl.exe +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_CC="$ac_prog" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$ac_ct_CC" && break +done + + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi +fi + +fi + + +test -z "$CC" && { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } + +# Provide some information about the compiler. +$as_echo "$as_me:$LINENO: checking for C compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +{ (ac_try="$ac_compiler --version >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler --version >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -v >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -v >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -V >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -V >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } + +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +ac_clean_files_save=$ac_clean_files +ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out" +# Try to create an executable without -o first, disregard a.out. +# It will help us diagnose broken compilers, and finding out an intuition +# of exeext. +{ $as_echo "$as_me:$LINENO: checking for C compiler default output file name" >&5 +$as_echo_n "checking for C compiler default output file name... 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We should not override ac_cv_exeext if it was cached, +# so that the user can short-circuit this test for compilers unknown to +# Autoconf. +for ac_file in $ac_files '' +do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) + ;; + [ab].out ) + # We found the default executable, but exeext='' is most + # certainly right. + break;; + *.* ) + if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no; + then :; else + ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + fi + # We set ac_cv_exeext here because the later test for it is not + # safe: cross compilers may not add the suffix if given an `-o' + # argument, so we may need to know it at that point already. + # Even if this section looks crufty: it has the advantage of + # actually working. + break;; + * ) + break;; + esac +done +test "$ac_cv_exeext" = no && ac_cv_exeext= + +else + ac_file='' +fi + +{ $as_echo "$as_me:$LINENO: result: $ac_file" >&5 +$as_echo "$ac_file" >&6; } +if test -z "$ac_file"; then + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: C compiler cannot create executables +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: C compiler cannot create executables +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } +fi + +ac_exeext=$ac_cv_exeext + +# Check that the compiler produces executables we can run. 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For instance with Cygwin, `ls conftest' will +# work properly (i.e., refer to `conftest.exe'), while it won't with +# `rm'. +for ac_file in conftest.exe conftest conftest.*; do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; + *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + break;; + * ) break;; + esac +done +else + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } +fi + +rm -f conftest$ac_cv_exeext +{ $as_echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 +$as_echo "$ac_cv_exeext" >&6; } + +rm -f conftest.$ac_ext +EXEEXT=$ac_cv_exeext +ac_exeext=$EXEEXT +{ $as_echo "$as_me:$LINENO: checking for suffix of object files" >&5 +$as_echo_n "checking for suffix of object files... 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" >&6; } +if test "${ac_cv_c_compiler_gnu+set}" = set; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_compiler_gnu=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_compiler_gnu=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_c_compiler_gnu=$ac_compiler_gnu + +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 +$as_echo "$ac_cv_c_compiler_gnu" >&6; } +if test $ac_compiler_gnu = yes; then + GCC=yes +else + GCC= +fi +ac_test_CFLAGS=${CFLAGS+set} +ac_save_CFLAGS=$CFLAGS +{ $as_echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 +$as_echo_n "checking whether $CC accepts -g... " >&6; } +if test "${ac_cv_prog_cc_g+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_save_c_werror_flag=$ac_c_werror_flag + ac_c_werror_flag=yes + ac_cv_prog_cc_g=no + CFLAGS="-g" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_cv_prog_cc_g=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + CFLAGS="" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + : +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_c_werror_flag=$ac_save_c_werror_flag + CFLAGS="-g" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_cv_prog_cc_g=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_c_werror_flag=$ac_save_c_werror_flag +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 +$as_echo "$ac_cv_prog_cc_g" >&6; } +if test "$ac_test_CFLAGS" = set; then + CFLAGS=$ac_save_CFLAGS +elif test $ac_cv_prog_cc_g = yes; then + if test "$GCC" = yes; then + CFLAGS="-g -O2" + else + CFLAGS="-g" + fi +else + if test "$GCC" = yes; then + CFLAGS="-O2" + else + CFLAGS= + fi +fi +{ $as_echo "$as_me:$LINENO: checking for $CC option to accept ISO C89" >&5 +$as_echo_n "checking for $CC option to accept ISO C89... " >&6; } +if test "${ac_cv_prog_cc_c89+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_cv_prog_cc_c89=no +ac_save_CC=$CC +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#include +#include +/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ +struct buf { int x; }; +FILE * (*rcsopen) (struct buf *, struct stat *, int); +static char *e (p, i) + char **p; + int i; +{ + return p[i]; +} +static char *f (char * (*g) (char **, int), char **p, ...) +{ + char *s; + va_list v; + va_start (v,p); + s = g (p, va_arg (v,int)); + va_end (v); + return s; +} + +/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has + function prototypes and stuff, but not '\xHH' hex character constants. + These don't provoke an error unfortunately, instead are silently treated + as 'x'. The following induces an error, until -std is added to get + proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an + array size at least. It's necessary to write '\x00'==0 to get something + that's true only with -std. */ +int osf4_cc_array ['\x00' == 0 ? 1 : -1]; + +/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters + inside strings and character constants. */ +#define FOO(x) 'x' +int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1]; + +int test (int i, double x); +struct s1 {int (*f) (int a);}; +struct s2 {int (*f) (double a);}; +int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); +int argc; +char **argv; +int +main () +{ +return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; + ; + return 0; +} +_ACEOF +for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ + -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +do + CC="$ac_save_CC $ac_arg" + rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_cv_prog_cc_c89=$ac_arg +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -f core conftest.err conftest.$ac_objext + test "x$ac_cv_prog_cc_c89" != "xno" && break +done +rm -f conftest.$ac_ext +CC=$ac_save_CC + +fi +# AC_CACHE_VAL +case "x$ac_cv_prog_cc_c89" in + x) + { $as_echo "$as_me:$LINENO: result: none needed" >&5 +$as_echo "none needed" >&6; } ;; + xno) + { $as_echo "$as_me:$LINENO: result: unsupported" >&5 +$as_echo "unsupported" >&6; } ;; + *) + CC="$CC $ac_cv_prog_cc_c89" + { $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_c89" >&5 +$as_echo "$ac_cv_prog_cc_c89" >&6; } ;; +esac + + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +depcc="$CC" am_compiler_list= + +{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5 +$as_echo_n "checking dependency style of $depcc... " >&6; } +if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then + # We make a subdir and do the tests there. Otherwise we can end up + # making bogus files that we don't know about and never remove. For + # instance it was reported that on HP-UX the gcc test will end up + # making a dummy file named `D' -- because `-MD' means `put the output + # in D'. + mkdir conftest.dir + # Copy depcomp to subdir because otherwise we won't find it if we're + # using a relative directory. + cp "$am_depcomp" conftest.dir + cd conftest.dir + # We will build objects and dependencies in a subdirectory because + # it helps to detect inapplicable dependency modes. For instance + # both Tru64's cc and ICC support -MD to output dependencies as a + # side effect of compilation, but ICC will put the dependencies in + # the current directory while Tru64 will put them in the object + # directory. + mkdir sub + + am_cv_CC_dependencies_compiler_type=none + if test "$am_compiler_list" = ""; then + am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp` + fi + for depmode in $am_compiler_list; do + # Setup a source with many dependencies, because some compilers + # like to wrap large dependency lists on column 80 (with \), and + # we should not choose a depcomp mode which is confused by this. + # + # We need to recreate these files for each test, as the compiler may + # overwrite some of them when testing with obscure command lines. + # This happens at least with the AIX C compiler. + : > sub/conftest.c + for i in 1 2 3 4 5 6; do + echo '#include "conftst'$i'.h"' >> sub/conftest.c + # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with + # Solaris 8's {/usr,}/bin/sh. + touch sub/conftst$i.h + done + echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf + + case $depmode in + nosideeffect) + # after this tag, mechanisms are not by side-effect, so they'll + # only be used when explicitly requested + if test "x$enable_dependency_tracking" = xyes; then + continue + else + break + fi + ;; + none) break ;; + esac + # We check with `-c' and `-o' for the sake of the "dashmstdout" + # mode. It turns out that the SunPro C++ compiler does not properly + # handle `-M -o', and we need to detect this. + if depmode=$depmode \ + source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \ + depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \ + $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \ + >/dev/null 2>conftest.err && + grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 && + grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 && + grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 && + ${MAKE-make} -s -f confmf > /dev/null 2>&1; then + # icc doesn't choke on unknown options, it will just issue warnings + # or remarks (even with -Werror). So we grep stderr for any message + # that says an option was ignored or not supported. + # When given -MP, icc 7.0 and 7.1 complain thusly: + # icc: Command line warning: ignoring option '-M'; no argument required + # The diagnosis changed in icc 8.0: + # icc: Command line remark: option '-MP' not supported + if (grep 'ignoring option' conftest.err || + grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else + am_cv_CC_dependencies_compiler_type=$depmode + break + fi + fi + done + + cd .. + rm -rf conftest.dir +else + am_cv_CC_dependencies_compiler_type=none +fi + +fi +{ $as_echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5 +$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; } +CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type + + if + test "x$enable_dependency_tracking" != xno \ + && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then + am__fastdepCC_TRUE= + am__fastdepCC_FALSE='#' +else + am__fastdepCC_TRUE='#' + am__fastdepCC_FALSE= +fi + + + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +{ $as_echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5 +$as_echo_n "checking how to run the C preprocessor... 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Now check whether nonexistent headers + # can be detected and how. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + # Broken: success on invalid input. +continue +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Passes both tests. +ac_preproc_ok=: +break +fi + +rm -f conftest.err conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + break +fi + + done + ac_cv_prog_CPP=$CPP + +fi + CPP=$ac_cv_prog_CPP +else + ac_cv_prog_CPP=$CPP +fi +{ $as_echo "$as_me:$LINENO: result: $CPP" >&5 +$as_echo "$CPP" >&6; } +ac_preproc_ok=false +for ac_c_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + : +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Broken: fails on valid input. +continue +fi + +rm -f conftest.err conftest.$ac_ext + + # OK, works on sane cases. Now check whether nonexistent headers + # can be detected and how. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + # Broken: success on invalid input. +continue +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Passes both tests. +ac_preproc_ok=: +break +fi + +rm -f conftest.err conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + : +else + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + +{ $as_echo "$as_me:$LINENO: checking for grep that handles long lines and -e" >&5 +$as_echo_n "checking for grep that handles long lines and -e... " >&6; } +if test "${ac_cv_path_GREP+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -z "$GREP"; then + ac_path_GREP_found=false + # Loop through the user's path and test for each of PROGNAME-LIST + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_prog in grep ggrep; do + for ac_exec_ext in '' $ac_executable_extensions; do + ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext" + { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue +# Check for GNU ac_path_GREP and select it if it is found. + # Check for GNU $ac_path_GREP +case `"$ac_path_GREP" --version 2>&1` in +*GNU*) + ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;; +*) + ac_count=0 + $as_echo_n 0123456789 >"conftest.in" + while : + do + cat "conftest.in" "conftest.in" >"conftest.tmp" + mv "conftest.tmp" "conftest.in" + cp "conftest.in" "conftest.nl" + $as_echo 'GREP' >> "conftest.nl" + "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break + diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break + ac_count=`expr $ac_count + 1` + if test $ac_count -gt ${ac_path_GREP_max-0}; then + # Best one so far, save it but keep looking for a better one + ac_cv_path_GREP="$ac_path_GREP" + ac_path_GREP_max=$ac_count + fi + # 10*(2^10) chars as input seems more than enough + test $ac_count -gt 10 && break + done + rm -f conftest.in conftest.tmp conftest.nl conftest.out;; +esac + + $ac_path_GREP_found && break 3 + done + done +done +IFS=$as_save_IFS + if test -z "$ac_cv_path_GREP"; then + { { $as_echo "$as_me:$LINENO: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5 +$as_echo "$as_me: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;} + { (exit 1); exit 1; }; } + fi +else + ac_cv_path_GREP=$GREP +fi + +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_GREP" >&5 +$as_echo "$ac_cv_path_GREP" >&6; } + GREP="$ac_cv_path_GREP" + + +{ $as_echo "$as_me:$LINENO: checking for egrep" >&5 +$as_echo_n "checking for egrep... " >&6; } +if test "${ac_cv_path_EGREP+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if echo a | $GREP -E '(a|b)' >/dev/null 2>&1 + then ac_cv_path_EGREP="$GREP -E" + else + if test -z "$EGREP"; then + ac_path_EGREP_found=false + # Loop through the user's path and test for each of PROGNAME-LIST + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_prog in egrep; do + for ac_exec_ext in '' $ac_executable_extensions; do + ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext" + { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue +# Check for GNU ac_path_EGREP and select it if it is found. + # Check for GNU $ac_path_EGREP +case `"$ac_path_EGREP" --version 2>&1` in +*GNU*) + ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_found=:;; +*) + ac_count=0 + $as_echo_n 0123456789 >"conftest.in" + while : + do + cat "conftest.in" "conftest.in" >"conftest.tmp" + mv "conftest.tmp" "conftest.in" + cp "conftest.in" "conftest.nl" + $as_echo 'EGREP' >> "conftest.nl" + "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break + diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break + ac_count=`expr $ac_count + 1` + if test $ac_count -gt ${ac_path_EGREP_max-0}; then + # Best one so far, save it but keep looking for a better one + ac_cv_path_EGREP="$ac_path_EGREP" + ac_path_EGREP_max=$ac_count + fi + # 10*(2^10) chars as input seems more than enough + test $ac_count -gt 10 && break + done + rm -f conftest.in conftest.tmp conftest.nl conftest.out;; +esac + + $ac_path_EGREP_found && break 3 + done + done +done +IFS=$as_save_IFS + if test -z "$ac_cv_path_EGREP"; then + { { $as_echo "$as_me:$LINENO: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5 +$as_echo "$as_me: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;} + { (exit 1); exit 1; }; } + fi +else + ac_cv_path_EGREP=$EGREP +fi + + fi +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_EGREP" >&5 +$as_echo "$ac_cv_path_EGREP" >&6; } + EGREP="$ac_cv_path_EGREP" + + +{ $as_echo "$as_me:$LINENO: checking for ANSI C header files" >&5 +$as_echo_n "checking for ANSI C header files... " >&6; } +if test "${ac_cv_header_stdc+set}" = set; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#include +#include + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_cv_header_stdc=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_header_stdc=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + +if test $ac_cv_header_stdc = yes; then + # SunOS 4.x string.h does not declare mem*, contrary to ANSI. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "memchr" >/dev/null 2>&1; then + : +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "free" >/dev/null 2>&1; then + : +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. + if test "$cross_compiling" = yes; then + : +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#if ((' ' & 0x0FF) == 0x020) +# define ISLOWER(c) ('a' <= (c) && (c) <= 'z') +# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) +#else +# define ISLOWER(c) \ + (('a' <= (c) && (c) <= 'i') \ + || ('j' <= (c) && (c) <= 'r') \ + || ('s' <= (c) && (c) <= 'z')) +# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) +#endif + +#define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) +int +main () +{ + int i; + for (i = 0; i < 256; i++) + if (XOR (islower (i), ISLOWER (i)) + || toupper (i) != TOUPPER (i)) + return 2; + return 0; +} +_ACEOF +rm -f conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + $as_echo "$as_me: program exited with status $ac_status" >&5 +$as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +ac_cv_header_stdc=no +fi +rm -rf conftest.dSYM +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +fi + + +fi +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 +$as_echo "$ac_cv_header_stdc" >&6; } +if test $ac_cv_header_stdc = yes; then + +cat >>confdefs.h <<\_ACEOF +#define STDC_HEADERS 1 +_ACEOF + +fi + +# On IRIX 5.3, sys/types and inttypes.h are conflicting. + + + + + + + + + +for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ + inttypes.h stdint.h unistd.h +do +as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default + +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + eval "$as_ac_Header=yes" +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + eval "$as_ac_Header=no" +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +as_val=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then + cat >>confdefs.h <<_ACEOF +#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +fi + +done + + + + if test "${ac_cv_header_minix_config_h+set}" = set; then + { $as_echo "$as_me:$LINENO: checking for minix/config.h" >&5 +$as_echo_n "checking for minix/config.h... " >&6; } +if test "${ac_cv_header_minix_config_h+set}" = set; then + $as_echo_n "(cached) " >&6 +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_minix_config_h" >&5 +$as_echo "$ac_cv_header_minix_config_h" >&6; } +else + # Is the header compilable? +{ $as_echo "$as_me:$LINENO: checking minix/config.h usability" >&5 +$as_echo_n "checking minix/config.h usability... " >&6; } +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +#include +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_header_compiler=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_compiler=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5 +$as_echo "$ac_header_compiler" >&6; } + +# Is the header present? +{ $as_echo "$as_me:$LINENO: checking minix/config.h presence" >&5 +$as_echo_n "checking minix/config.h presence... " >&6; } +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + ac_header_preproc=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_preproc=no +fi + +rm -f conftest.err conftest.$ac_ext +{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 +$as_echo "$ac_header_preproc" >&6; } + +# So? What about this header? +case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in + yes:no: ) + { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: accepted by the compiler, rejected by the preprocessor!" >&5 +$as_echo "$as_me: WARNING: minix/config.h: accepted by the compiler, rejected by the preprocessor!" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: proceeding with the compiler's result" >&5 +$as_echo "$as_me: WARNING: minix/config.h: proceeding with the compiler's result" >&2;} + ac_header_preproc=yes + ;; + no:yes:* ) + { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: present but cannot be compiled" >&5 +$as_echo "$as_me: WARNING: minix/config.h: present but cannot be compiled" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: check for missing prerequisite headers?" >&5 +$as_echo "$as_me: WARNING: minix/config.h: check for missing prerequisite headers?" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: see the Autoconf documentation" >&5 +$as_echo "$as_me: WARNING: minix/config.h: see the Autoconf documentation" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: section \"Present But Cannot Be Compiled\"" >&5 +$as_echo "$as_me: WARNING: minix/config.h: section \"Present But Cannot Be Compiled\"" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: proceeding with the preprocessor's result" >&5 +$as_echo "$as_me: WARNING: minix/config.h: proceeding with the preprocessor's result" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: in the future, the compiler will take precedence" >&5 +$as_echo "$as_me: WARNING: minix/config.h: in the future, the compiler will take precedence" >&2;} + ( cat <<\_ASBOX +## ------------------------------ ## +## Report this to clustalw@ucd.ie ## +## ------------------------------ ## +_ASBOX + ) | sed "s/^/$as_me: WARNING: /" >&2 + ;; +esac +{ $as_echo "$as_me:$LINENO: checking for minix/config.h" >&5 +$as_echo_n "checking for minix/config.h... " >&6; } +if test "${ac_cv_header_minix_config_h+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_cv_header_minix_config_h=$ac_header_preproc +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_minix_config_h" >&5 +$as_echo "$ac_cv_header_minix_config_h" >&6; } + +fi +if test "x$ac_cv_header_minix_config_h" = x""yes; then + MINIX=yes +else + MINIX= +fi + + + if test "$MINIX" = yes; then + +cat >>confdefs.h <<\_ACEOF +#define _POSIX_SOURCE 1 +_ACEOF + + +cat >>confdefs.h <<\_ACEOF +#define _POSIX_1_SOURCE 2 +_ACEOF + + +cat >>confdefs.h <<\_ACEOF +#define _MINIX 1 +_ACEOF + + fi + + + + { $as_echo "$as_me:$LINENO: checking whether it is safe to define __EXTENSIONS__" >&5 +$as_echo_n "checking whether it is safe to define __EXTENSIONS__... " >&6; } +if test "${ac_cv_safe_to_define___extensions__+set}" = set; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +# define __EXTENSIONS__ 1 + $ac_includes_default +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_cv_safe_to_define___extensions__=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_safe_to_define___extensions__=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_safe_to_define___extensions__" >&5 +$as_echo "$ac_cv_safe_to_define___extensions__" >&6; } + test $ac_cv_safe_to_define___extensions__ = yes && + cat >>confdefs.h <<\_ACEOF +#define __EXTENSIONS__ 1 +_ACEOF + + cat >>confdefs.h <<\_ACEOF +#define _ALL_SOURCE 1 +_ACEOF + + cat >>confdefs.h <<\_ACEOF +#define _GNU_SOURCE 1 +_ACEOF + + cat >>confdefs.h <<\_ACEOF +#define _POSIX_PTHREAD_SEMANTICS 1 +_ACEOF + + cat >>confdefs.h <<\_ACEOF +#define _TANDEM_SOURCE 1 +_ACEOF + + + + +# for cross compilation +# +# Make sure we can run config.sub. +$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 || + { { $as_echo "$as_me:$LINENO: error: cannot run $SHELL $ac_aux_dir/config.sub" >&5 +$as_echo "$as_me: error: cannot run $SHELL $ac_aux_dir/config.sub" >&2;} + { (exit 1); exit 1; }; } + +{ $as_echo "$as_me:$LINENO: checking build system type" >&5 +$as_echo_n "checking build system type... " >&6; } +if test "${ac_cv_build+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_build_alias=$build_alias +test "x$ac_build_alias" = x && + ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"` +test "x$ac_build_alias" = x && + { { $as_echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5 +$as_echo "$as_me: error: cannot guess build type; you must specify one" >&2;} + { (exit 1); exit 1; }; } +ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` || + { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&5 +$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&2;} + { (exit 1); exit 1; }; } + +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_build" >&5 +$as_echo "$ac_cv_build" >&6; } +case $ac_cv_build in +*-*-*) ;; +*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical build" >&5 +$as_echo "$as_me: error: invalid value of canonical build" >&2;} + { (exit 1); exit 1; }; };; +esac +build=$ac_cv_build +ac_save_IFS=$IFS; IFS='-' +set x $ac_cv_build +shift +build_cpu=$1 +build_vendor=$2 +shift; shift +# Remember, the first character of IFS is used to create $*, +# except with old shells: +build_os=$* +IFS=$ac_save_IFS +case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac + + +{ $as_echo "$as_me:$LINENO: checking host system type" >&5 +$as_echo_n "checking host system type... " >&6; } +if test "${ac_cv_host+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test "x$host_alias" = x; then + ac_cv_host=$ac_cv_build +else + ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` || + { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&5 +$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&2;} + { (exit 1); exit 1; }; } +fi + +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_host" >&5 +$as_echo "$ac_cv_host" >&6; } +case $ac_cv_host in +*-*-*) ;; +*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical host" >&5 +$as_echo "$as_me: error: invalid value of canonical host" >&2;} + { (exit 1); exit 1; }; };; +esac +host=$ac_cv_host +ac_save_IFS=$IFS; IFS='-' +set x $ac_cv_host +shift +host_cpu=$1 +host_vendor=$2 +shift; shift +# Remember, the first character of IFS is used to create $*, +# except with old shells: +host_os=$* +IFS=$ac_save_IFS +case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac + + +## AC_CANONICAL_BUILD +## AC_CANONICAL_TARGET + +# Set the @SET_MAKE@ variable=make if $(MAKE) not set +{ $as_echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5 +$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; } +set x ${MAKE-make} +ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'` +if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.make <<\_ACEOF +SHELL = /bin/sh +all: + @echo '@@@%%%=$(MAKE)=@@@%%%' +_ACEOF +# GNU make sometimes prints "make[1]: Entering...", which would confuse us. +case `${MAKE-make} -f conftest.make 2>/dev/null` in + *@@@%%%=?*=@@@%%%*) + eval ac_cv_prog_make_${ac_make}_set=yes;; + *) + eval ac_cv_prog_make_${ac_make}_set=no;; +esac +rm -f conftest.make +fi +if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then + { $as_echo "$as_me:$LINENO: result: yes" >&5 +$as_echo "yes" >&6; } + SET_MAKE= +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } + SET_MAKE="MAKE=${MAKE-make}" +fi + + +# AC_PROG_RANLIB will allow you to build code in sub-directories into +# temporary libraries, which make will then link in with the rest of +# the code. +# Rendered obsolte by LT_INIT: AC_PROG_RANLIB +#AC_PROG_LIBTOOL +case `pwd` in + *\ * | *\ *) + { $as_echo "$as_me:$LINENO: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&5 +$as_echo "$as_me: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&2;} ;; +esac + + + +macro_version='2.2.6' +macro_revision='1.3012' + + + + + + + + + + + + + +ltmain="$ac_aux_dir/ltmain.sh" + +{ $as_echo "$as_me:$LINENO: checking for a sed that does not truncate output" >&5 +$as_echo_n "checking for a sed that does not truncate output... " >&6; } +if test "${ac_cv_path_SED+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_script=s/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb/ + for ac_i in 1 2 3 4 5 6 7; do + ac_script="$ac_script$as_nl$ac_script" + done + echo "$ac_script" 2>/dev/null | sed 99q >conftest.sed + $as_unset ac_script || ac_script= + if test -z "$SED"; then + ac_path_SED_found=false + # Loop through the user's path and test for each of PROGNAME-LIST + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_prog in sed gsed; do + for ac_exec_ext in '' $ac_executable_extensions; do + ac_path_SED="$as_dir/$ac_prog$ac_exec_ext" + { test -f "$ac_path_SED" && $as_test_x "$ac_path_SED"; } || continue +# Check for GNU ac_path_SED and select it if it is found. + # Check for GNU $ac_path_SED +case `"$ac_path_SED" --version 2>&1` in +*GNU*) + ac_cv_path_SED="$ac_path_SED" ac_path_SED_found=:;; +*) + ac_count=0 + $as_echo_n 0123456789 >"conftest.in" + while : + do + cat "conftest.in" "conftest.in" >"conftest.tmp" + mv "conftest.tmp" "conftest.in" + cp "conftest.in" "conftest.nl" + $as_echo '' >> "conftest.nl" + "$ac_path_SED" -f conftest.sed < "conftest.nl" >"conftest.out" 2>/dev/null || break + diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break + ac_count=`expr $ac_count + 1` + if test $ac_count -gt ${ac_path_SED_max-0}; then + # Best one so far, save it but keep looking for a better one + ac_cv_path_SED="$ac_path_SED" + ac_path_SED_max=$ac_count + fi + # 10*(2^10) chars as input seems more than enough + test $ac_count -gt 10 && break + done + rm -f conftest.in conftest.tmp conftest.nl conftest.out;; +esac + + $ac_path_SED_found && break 3 + done + done +done +IFS=$as_save_IFS + if test -z "$ac_cv_path_SED"; then + { { $as_echo "$as_me:$LINENO: error: no acceptable sed could be found in \$PATH" >&5 +$as_echo "$as_me: error: no acceptable sed could be found in \$PATH" >&2;} + { (exit 1); exit 1; }; } + fi +else + ac_cv_path_SED=$SED +fi + +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_SED" >&5 +$as_echo "$ac_cv_path_SED" >&6; } + SED="$ac_cv_path_SED" + rm -f conftest.sed + +test -z "$SED" && SED=sed +Xsed="$SED -e 1s/^X//" + + + + + + + + + + + +{ $as_echo "$as_me:$LINENO: checking for fgrep" >&5 +$as_echo_n "checking for fgrep... " >&6; } +if test "${ac_cv_path_FGREP+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if echo 'ab*c' | $GREP -F 'ab*c' >/dev/null 2>&1 + then ac_cv_path_FGREP="$GREP -F" + else + if test -z "$FGREP"; then + ac_path_FGREP_found=false + # Loop through the user's path and test for each of PROGNAME-LIST + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_prog in fgrep; do + for ac_exec_ext in '' $ac_executable_extensions; do + ac_path_FGREP="$as_dir/$ac_prog$ac_exec_ext" + { test -f "$ac_path_FGREP" && $as_test_x "$ac_path_FGREP"; } || continue +# Check for GNU ac_path_FGREP and select it if it is found. + # Check for GNU $ac_path_FGREP +case `"$ac_path_FGREP" --version 2>&1` in +*GNU*) + ac_cv_path_FGREP="$ac_path_FGREP" ac_path_FGREP_found=:;; +*) + ac_count=0 + $as_echo_n 0123456789 >"conftest.in" + while : + do + cat "conftest.in" "conftest.in" >"conftest.tmp" + mv "conftest.tmp" "conftest.in" + cp "conftest.in" "conftest.nl" + $as_echo 'FGREP' >> "conftest.nl" + "$ac_path_FGREP" FGREP < "conftest.nl" >"conftest.out" 2>/dev/null || break + diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break + ac_count=`expr $ac_count + 1` + if test $ac_count -gt ${ac_path_FGREP_max-0}; then + # Best one so far, save it but keep looking for a better one + ac_cv_path_FGREP="$ac_path_FGREP" + ac_path_FGREP_max=$ac_count + fi + # 10*(2^10) chars as input seems more than enough + test $ac_count -gt 10 && break + done + rm -f conftest.in conftest.tmp conftest.nl conftest.out;; +esac + + $ac_path_FGREP_found && break 3 + done + done +done +IFS=$as_save_IFS + if test -z "$ac_cv_path_FGREP"; then + { { $as_echo "$as_me:$LINENO: error: no acceptable fgrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5 +$as_echo "$as_me: error: no acceptable fgrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;} + { (exit 1); exit 1; }; } + fi +else + ac_cv_path_FGREP=$FGREP +fi + + fi +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_FGREP" >&5 +$as_echo "$ac_cv_path_FGREP" >&6; } + FGREP="$ac_cv_path_FGREP" + + +test -z "$GREP" && GREP=grep + + + + + + + + + + + + + + + + + + + +# Check whether --with-gnu-ld was given. +if test "${with_gnu_ld+set}" = set; then + withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes +else + with_gnu_ld=no +fi + +ac_prog=ld +if test "$GCC" = yes; then + # Check if gcc -print-prog-name=ld gives a path. + { $as_echo "$as_me:$LINENO: checking for ld used by $CC" >&5 +$as_echo_n "checking for ld used by $CC... " >&6; } + case $host in + *-*-mingw*) + # gcc leaves a trailing carriage return which upsets mingw + ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;; + *) + ac_prog=`($CC -print-prog-name=ld) 2>&5` ;; + esac + case $ac_prog in + # Accept absolute paths. + [\\/]* | ?:[\\/]*) + re_direlt='/[^/][^/]*/\.\./' + # Canonicalize the pathname of ld + ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'` + while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do + ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"` + done + test -z "$LD" && LD="$ac_prog" + ;; + "") + # If it fails, then pretend we aren't using GCC. + ac_prog=ld + ;; + *) + # If it is relative, then search for the first ld in PATH. + with_gnu_ld=unknown + ;; + esac +elif test "$with_gnu_ld" = yes; then + { $as_echo "$as_me:$LINENO: checking for GNU ld" >&5 +$as_echo_n "checking for GNU ld... " >&6; } +else + { $as_echo "$as_me:$LINENO: checking for non-GNU ld" >&5 +$as_echo_n "checking for non-GNU ld... " >&6; } +fi +if test "${lt_cv_path_LD+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -z "$LD"; then + lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR + for ac_dir in $PATH; do + IFS="$lt_save_ifs" + test -z "$ac_dir" && ac_dir=. + if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then + lt_cv_path_LD="$ac_dir/$ac_prog" + # Check to see if the program is GNU ld. I'd rather use --version, + # but apparently some variants of GNU ld only accept -v. + # Break only if it was the GNU/non-GNU ld that we prefer. + case `"$lt_cv_path_LD" -v 2>&1 &5 +$as_echo "$LD" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi +test -z "$LD" && { { $as_echo "$as_me:$LINENO: error: no acceptable ld found in \$PATH" >&5 +$as_echo "$as_me: error: no acceptable ld found in \$PATH" >&2;} + { (exit 1); exit 1; }; } +{ $as_echo "$as_me:$LINENO: checking if the linker ($LD) is GNU ld" >&5 +$as_echo_n "checking if the linker ($LD) is GNU ld... " >&6; } +if test "${lt_cv_prog_gnu_ld+set}" = set; then + $as_echo_n "(cached) " >&6 +else + # I'd rather use --version here, but apparently some GNU lds only accept -v. +case `$LD -v 2>&1 &5 +$as_echo "$lt_cv_prog_gnu_ld" >&6; } +with_gnu_ld=$lt_cv_prog_gnu_ld + + + + + + + + + +{ $as_echo "$as_me:$LINENO: checking for BSD- or MS-compatible name lister (nm)" >&5 +$as_echo_n "checking for BSD- or MS-compatible name lister (nm)... " >&6; } +if test "${lt_cv_path_NM+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$NM"; then + # Let the user override the test. + lt_cv_path_NM="$NM" +else + lt_nm_to_check="${ac_tool_prefix}nm" + if test -n "$ac_tool_prefix" && test "$build" = "$host"; then + lt_nm_to_check="$lt_nm_to_check nm" + fi + for lt_tmp_nm in $lt_nm_to_check; do + lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR + for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do + IFS="$lt_save_ifs" + test -z "$ac_dir" && ac_dir=. + tmp_nm="$ac_dir/$lt_tmp_nm" + if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then + # Check to see if the nm accepts a BSD-compat flag. + # Adding the `sed 1q' prevents false positives on HP-UX, which says: + # nm: unknown option "B" ignored + # Tru64's nm complains that /dev/null is an invalid object file + case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in + */dev/null* | *'Invalid file or object type'*) + lt_cv_path_NM="$tmp_nm -B" + break + ;; + *) + case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in + */dev/null*) + lt_cv_path_NM="$tmp_nm -p" + break + ;; + *) + lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but + continue # so that we can try to find one that supports BSD flags + ;; + esac + ;; + esac + fi + done + IFS="$lt_save_ifs" + done + : ${lt_cv_path_NM=no} +fi +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_path_NM" >&5 +$as_echo "$lt_cv_path_NM" >&6; } +if test "$lt_cv_path_NM" != "no"; then + NM="$lt_cv_path_NM" +else + # Didn't find any BSD compatible name lister, look for dumpbin. + if test -n "$ac_tool_prefix"; then + for ac_prog in "dumpbin -symbols" "link -dump -symbols" + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_DUMPBIN+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$DUMPBIN"; then + ac_cv_prog_DUMPBIN="$DUMPBIN" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_DUMPBIN="$ac_tool_prefix$ac_prog" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +DUMPBIN=$ac_cv_prog_DUMPBIN +if test -n "$DUMPBIN"; then + { $as_echo "$as_me:$LINENO: result: $DUMPBIN" >&5 +$as_echo "$DUMPBIN" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$DUMPBIN" && break + done +fi +if test -z "$DUMPBIN"; then + ac_ct_DUMPBIN=$DUMPBIN + for ac_prog in "dumpbin -symbols" "link -dump -symbols" +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_DUMPBIN+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_DUMPBIN"; then + ac_cv_prog_ac_ct_DUMPBIN="$ac_ct_DUMPBIN" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_DUMPBIN="$ac_prog" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_DUMPBIN=$ac_cv_prog_ac_ct_DUMPBIN +if test -n "$ac_ct_DUMPBIN"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_DUMPBIN" >&5 +$as_echo "$ac_ct_DUMPBIN" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$ac_ct_DUMPBIN" && break +done + + if test "x$ac_ct_DUMPBIN" = x; then + DUMPBIN=":" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + DUMPBIN=$ac_ct_DUMPBIN + fi +fi + + + if test "$DUMPBIN" != ":"; then + NM="$DUMPBIN" + fi +fi +test -z "$NM" && NM=nm + + + + + + +{ $as_echo "$as_me:$LINENO: checking the name lister ($NM) interface" >&5 +$as_echo_n "checking the name lister ($NM) interface... " >&6; } +if test "${lt_cv_nm_interface+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_nm_interface="BSD nm" + echo "int some_variable = 0;" > conftest.$ac_ext + (eval echo "\"\$as_me:5230: $ac_compile\"" >&5) + (eval "$ac_compile" 2>conftest.err) + cat conftest.err >&5 + (eval echo "\"\$as_me:5233: $NM \\\"conftest.$ac_objext\\\"\"" >&5) + (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out) + cat conftest.err >&5 + (eval echo "\"\$as_me:5236: output\"" >&5) + cat conftest.out >&5 + if $GREP 'External.*some_variable' conftest.out > /dev/null; then + lt_cv_nm_interface="MS dumpbin" + fi + rm -f conftest* +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_nm_interface" >&5 +$as_echo "$lt_cv_nm_interface" >&6; } + +{ $as_echo "$as_me:$LINENO: checking whether ln -s works" >&5 +$as_echo_n "checking whether ln -s works... " >&6; } +LN_S=$as_ln_s +if test "$LN_S" = "ln -s"; then + { $as_echo "$as_me:$LINENO: result: yes" >&5 +$as_echo "yes" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no, using $LN_S" >&5 +$as_echo "no, using $LN_S" >&6; } +fi + +# find the maximum length of command line arguments +{ $as_echo "$as_me:$LINENO: checking the maximum length of command line arguments" >&5 +$as_echo_n "checking the maximum length of command line arguments... " >&6; } +if test "${lt_cv_sys_max_cmd_len+set}" = set; then + $as_echo_n "(cached) " >&6 +else + i=0 + teststring="ABCD" + + case $build_os in + msdosdjgpp*) + # On DJGPP, this test can blow up pretty badly due to problems in libc + # (any single argument exceeding 2000 bytes causes a buffer overrun + # during glob expansion). Even if it were fixed, the result of this + # check would be larger than it should be. + lt_cv_sys_max_cmd_len=12288; # 12K is about right + ;; + + gnu*) + # Under GNU Hurd, this test is not required because there is + # no limit to the length of command line arguments. + # Libtool will interpret -1 as no limit whatsoever + lt_cv_sys_max_cmd_len=-1; + ;; + + cygwin* | mingw* | cegcc*) + # On Win9x/ME, this test blows up -- it succeeds, but takes + # about 5 minutes as the teststring grows exponentially. + # Worse, since 9x/ME are not pre-emptively multitasking, + # you end up with a "frozen" computer, even though with patience + # the test eventually succeeds (with a max line length of 256k). + # Instead, let's just punt: use the minimum linelength reported by + # all of the supported platforms: 8192 (on NT/2K/XP). + lt_cv_sys_max_cmd_len=8192; + ;; + + amigaos*) + # On AmigaOS with pdksh, this test takes hours, literally. + # So we just punt and use a minimum line length of 8192. + lt_cv_sys_max_cmd_len=8192; + ;; + + netbsd* | freebsd* | openbsd* | darwin* | dragonfly*) + # This has been around since 386BSD, at least. Likely further. + if test -x /sbin/sysctl; then + lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax` + elif test -x /usr/sbin/sysctl; then + lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax` + else + lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs + fi + # And add a safety zone + lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` + lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` + ;; + + interix*) + # We know the value 262144 and hardcode it with a safety zone (like BSD) + lt_cv_sys_max_cmd_len=196608 + ;; + + osf*) + # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure + # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not + # nice to cause kernel panics so lets avoid the loop below. + # First set a reasonable default. + lt_cv_sys_max_cmd_len=16384 + # + if test -x /sbin/sysconfig; then + case `/sbin/sysconfig -q proc exec_disable_arg_limit` in + *1*) lt_cv_sys_max_cmd_len=-1 ;; + esac + fi + ;; + sco3.2v5*) + lt_cv_sys_max_cmd_len=102400 + ;; + sysv5* | sco5v6* | sysv4.2uw2*) + kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null` + if test -n "$kargmax"; then + lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[ ]//'` + else + lt_cv_sys_max_cmd_len=32768 + fi + ;; + *) + lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null` + if test -n "$lt_cv_sys_max_cmd_len"; then + lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` + lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` + else + # Make teststring a little bigger before we do anything with it. + # a 1K string should be a reasonable start. + for i in 1 2 3 4 5 6 7 8 ; do + teststring=$teststring$teststring + done + SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}} + # If test is not a shell built-in, we'll probably end up computing a + # maximum length that is only half of the actual maximum length, but + # we can't tell. + while { test "X"`$SHELL $0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \ + = "XX$teststring$teststring"; } >/dev/null 2>&1 && + test $i != 17 # 1/2 MB should be enough + do + i=`expr $i + 1` + teststring=$teststring$teststring + done + # Only check the string length outside the loop. + lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1` + teststring= + # Add a significant safety factor because C++ compilers can tack on + # massive amounts of additional arguments before passing them to the + # linker. It appears as though 1/2 is a usable value. + lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2` + fi + ;; + esac + +fi + +if test -n $lt_cv_sys_max_cmd_len ; then + { $as_echo "$as_me:$LINENO: result: $lt_cv_sys_max_cmd_len" >&5 +$as_echo "$lt_cv_sys_max_cmd_len" >&6; } +else + { $as_echo "$as_me:$LINENO: result: none" >&5 +$as_echo "none" >&6; } +fi +max_cmd_len=$lt_cv_sys_max_cmd_len + + + + + + +: ${CP="cp -f"} +: ${MV="mv -f"} +: ${RM="rm -f"} + +{ $as_echo "$as_me:$LINENO: checking whether the shell understands some XSI constructs" >&5 +$as_echo_n "checking whether the shell understands some XSI constructs... " >&6; } +# Try some XSI features +xsi_shell=no +( _lt_dummy="a/b/c" + test "${_lt_dummy##*/},${_lt_dummy%/*},"${_lt_dummy%"$_lt_dummy"}, \ + = c,a/b,, \ + && eval 'test $(( 1 + 1 )) -eq 2 \ + && test "${#_lt_dummy}" -eq 5' ) >/dev/null 2>&1 \ + && xsi_shell=yes +{ $as_echo "$as_me:$LINENO: result: $xsi_shell" >&5 +$as_echo "$xsi_shell" >&6; } + + +{ $as_echo "$as_me:$LINENO: checking whether the shell understands \"+=\"" >&5 +$as_echo_n "checking whether the shell understands \"+=\"... " >&6; } +lt_shell_append=no +( foo=bar; set foo baz; eval "$1+=\$2" && test "$foo" = barbaz ) \ + >/dev/null 2>&1 \ + && lt_shell_append=yes +{ $as_echo "$as_me:$LINENO: result: $lt_shell_append" >&5 +$as_echo "$lt_shell_append" >&6; } + + +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + lt_unset=unset +else + lt_unset=false +fi + + + + + +# test EBCDIC or ASCII +case `echo X|tr X '\101'` in + A) # ASCII based system + # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr + lt_SP2NL='tr \040 \012' + lt_NL2SP='tr \015\012 \040\040' + ;; + *) # EBCDIC based system + lt_SP2NL='tr \100 \n' + lt_NL2SP='tr \r\n \100\100' + ;; +esac + + + + + + + + + +{ $as_echo "$as_me:$LINENO: checking for $LD option to reload object files" >&5 +$as_echo_n "checking for $LD option to reload object files... " >&6; } +if test "${lt_cv_ld_reload_flag+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_ld_reload_flag='-r' +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_ld_reload_flag" >&5 +$as_echo "$lt_cv_ld_reload_flag" >&6; } +reload_flag=$lt_cv_ld_reload_flag +case $reload_flag in +"" | " "*) ;; +*) reload_flag=" $reload_flag" ;; +esac +reload_cmds='$LD$reload_flag -o $output$reload_objs' +case $host_os in + darwin*) + if test "$GCC" = yes; then + reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs' + else + reload_cmds='$LD$reload_flag -o $output$reload_objs' + fi + ;; +esac + + + + + + + + + +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}objdump", so it can be a program name with args. +set dummy ${ac_tool_prefix}objdump; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_OBJDUMP+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$OBJDUMP"; then + ac_cv_prog_OBJDUMP="$OBJDUMP" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_OBJDUMP="${ac_tool_prefix}objdump" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +OBJDUMP=$ac_cv_prog_OBJDUMP +if test -n "$OBJDUMP"; then + { $as_echo "$as_me:$LINENO: result: $OBJDUMP" >&5 +$as_echo "$OBJDUMP" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_OBJDUMP"; then + ac_ct_OBJDUMP=$OBJDUMP + # Extract the first word of "objdump", so it can be a program name with args. +set dummy objdump; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_OBJDUMP+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_OBJDUMP"; then + ac_cv_prog_ac_ct_OBJDUMP="$ac_ct_OBJDUMP" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_OBJDUMP="objdump" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_OBJDUMP=$ac_cv_prog_ac_ct_OBJDUMP +if test -n "$ac_ct_OBJDUMP"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_OBJDUMP" >&5 +$as_echo "$ac_ct_OBJDUMP" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_OBJDUMP" = x; then + OBJDUMP="false" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + OBJDUMP=$ac_ct_OBJDUMP + fi +else + OBJDUMP="$ac_cv_prog_OBJDUMP" +fi + +test -z "$OBJDUMP" && OBJDUMP=objdump + + + + + + + + + +{ $as_echo "$as_me:$LINENO: checking how to recognize dependent libraries" >&5 +$as_echo_n "checking how to recognize dependent libraries... " >&6; } +if test "${lt_cv_deplibs_check_method+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_file_magic_cmd='$MAGIC_CMD' +lt_cv_file_magic_test_file= +lt_cv_deplibs_check_method='unknown' +# Need to set the preceding variable on all platforms that support +# interlibrary dependencies. +# 'none' -- dependencies not supported. +# `unknown' -- same as none, but documents that we really don't know. +# 'pass_all' -- all dependencies passed with no checks. +# 'test_compile' -- check by making test program. +# 'file_magic [[regex]]' -- check by looking for files in library path +# which responds to the $file_magic_cmd with a given extended regex. +# If you have `file' or equivalent on your system and you're not sure +# whether `pass_all' will *always* work, you probably want this one. + +case $host_os in +aix[4-9]*) + lt_cv_deplibs_check_method=pass_all + ;; + +beos*) + lt_cv_deplibs_check_method=pass_all + ;; + +bsdi[45]*) + lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib)' + lt_cv_file_magic_cmd='/usr/bin/file -L' + lt_cv_file_magic_test_file=/shlib/libc.so + ;; + +cygwin*) + # func_win32_libid is a shell function defined in ltmain.sh + lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' + lt_cv_file_magic_cmd='func_win32_libid' + ;; + +mingw* | pw32*) + # Base MSYS/MinGW do not provide the 'file' command needed by + # func_win32_libid shell function, so use a weaker test based on 'objdump', + # unless we find 'file', for example because we are cross-compiling. + if ( file / ) >/dev/null 2>&1; then + lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' + lt_cv_file_magic_cmd='func_win32_libid' + else + lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?' + lt_cv_file_magic_cmd='$OBJDUMP -f' + fi + ;; + +cegcc) + # use the weaker test based on 'objdump'. See mingw*. + lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?' + lt_cv_file_magic_cmd='$OBJDUMP -f' + ;; + +darwin* | rhapsody*) + lt_cv_deplibs_check_method=pass_all + ;; + +freebsd* | dragonfly*) + if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then + case $host_cpu in + i*86 ) + # Not sure whether the presence of OpenBSD here was a mistake. + # Let's accept both of them until this is cleared up. + lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library' + lt_cv_file_magic_cmd=/usr/bin/file + lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*` + ;; + esac + else + lt_cv_deplibs_check_method=pass_all + fi + ;; + +gnu*) + lt_cv_deplibs_check_method=pass_all + ;; + +hpux10.20* | hpux11*) + lt_cv_file_magic_cmd=/usr/bin/file + case $host_cpu in + ia64*) + lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64' + lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so + ;; + hppa*64*) + lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]' + lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl + ;; + *) + lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9].[0-9]) shared library' + lt_cv_file_magic_test_file=/usr/lib/libc.sl + ;; + esac + ;; + +interix[3-9]*) + # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here + lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$' + ;; + +irix5* | irix6* | nonstopux*) + case $LD in + *-32|*"-32 ") libmagic=32-bit;; + *-n32|*"-n32 ") libmagic=N32;; + *-64|*"-64 ") libmagic=64-bit;; + *) libmagic=never-match;; + esac + lt_cv_deplibs_check_method=pass_all + ;; + +# This must be Linux ELF. +linux* | k*bsd*-gnu) + lt_cv_deplibs_check_method=pass_all + ;; + +netbsd* | netbsdelf*-gnu) + if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then + lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' + else + lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$' + fi + ;; + +newos6*) + lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)' + lt_cv_file_magic_cmd=/usr/bin/file + lt_cv_file_magic_test_file=/usr/lib/libnls.so + ;; + +*nto* | *qnx*) + lt_cv_deplibs_check_method=pass_all + ;; + +openbsd*) + if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then + lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$' + else + lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' + fi + ;; + +osf3* | osf4* | osf5*) + lt_cv_deplibs_check_method=pass_all + ;; + +rdos*) + lt_cv_deplibs_check_method=pass_all + ;; + +solaris*) + lt_cv_deplibs_check_method=pass_all + ;; + +sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) + lt_cv_deplibs_check_method=pass_all + ;; + +sysv4 | sysv4.3*) + case $host_vendor in + motorola) + lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]' + lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` + ;; + ncr) + lt_cv_deplibs_check_method=pass_all + ;; + sequent) + lt_cv_file_magic_cmd='/bin/file' + lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )' + ;; + sni) + lt_cv_file_magic_cmd='/bin/file' + lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib" + lt_cv_file_magic_test_file=/lib/libc.so + ;; + siemens) + lt_cv_deplibs_check_method=pass_all + ;; + pc) + lt_cv_deplibs_check_method=pass_all + ;; + esac + ;; + +tpf*) + lt_cv_deplibs_check_method=pass_all + ;; +esac + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_deplibs_check_method" >&5 +$as_echo "$lt_cv_deplibs_check_method" >&6; } +file_magic_cmd=$lt_cv_file_magic_cmd +deplibs_check_method=$lt_cv_deplibs_check_method +test -z "$deplibs_check_method" && deplibs_check_method=unknown + + + + + + + + + + + + +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}ar", so it can be a program name with args. +set dummy ${ac_tool_prefix}ar; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_AR+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$AR"; then + ac_cv_prog_AR="$AR" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_AR="${ac_tool_prefix}ar" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +AR=$ac_cv_prog_AR +if test -n "$AR"; then + { $as_echo "$as_me:$LINENO: result: $AR" >&5 +$as_echo "$AR" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_AR"; then + ac_ct_AR=$AR + # Extract the first word of "ar", so it can be a program name with args. +set dummy ar; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_AR+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_AR"; then + ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_AR="ar" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_AR=$ac_cv_prog_ac_ct_AR +if test -n "$ac_ct_AR"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_AR" >&5 +$as_echo "$ac_ct_AR" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_AR" = x; then + AR="false" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + AR=$ac_ct_AR + fi +else + AR="$ac_cv_prog_AR" +fi + +test -z "$AR" && AR=ar +test -z "$AR_FLAGS" && AR_FLAGS=cru + + + + + + + + + + + +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. +set dummy ${ac_tool_prefix}strip; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_STRIP+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$STRIP"; then + ac_cv_prog_STRIP="$STRIP" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_STRIP="${ac_tool_prefix}strip" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +STRIP=$ac_cv_prog_STRIP +if test -n "$STRIP"; then + { $as_echo "$as_me:$LINENO: result: $STRIP" >&5 +$as_echo "$STRIP" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_STRIP"; then + ac_ct_STRIP=$STRIP + # Extract the first word of "strip", so it can be a program name with args. +set dummy strip; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_STRIP"; then + ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_STRIP="strip" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP +if test -n "$ac_ct_STRIP"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5 +$as_echo "$ac_ct_STRIP" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_STRIP" = x; then + STRIP=":" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + STRIP=$ac_ct_STRIP + fi +else + STRIP="$ac_cv_prog_STRIP" +fi + +test -z "$STRIP" && STRIP=: + + + + + + +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. +set dummy ${ac_tool_prefix}ranlib; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_RANLIB+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$RANLIB"; then + ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +RANLIB=$ac_cv_prog_RANLIB +if test -n "$RANLIB"; then + { $as_echo "$as_me:$LINENO: result: $RANLIB" >&5 +$as_echo "$RANLIB" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_RANLIB"; then + ac_ct_RANLIB=$RANLIB + # Extract the first word of "ranlib", so it can be a program name with args. +set dummy ranlib; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_RANLIB"; then + ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_RANLIB="ranlib" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB +if test -n "$ac_ct_RANLIB"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_RANLIB" >&5 +$as_echo "$ac_ct_RANLIB" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_RANLIB" = x; then + RANLIB=":" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + RANLIB=$ac_ct_RANLIB + fi +else + RANLIB="$ac_cv_prog_RANLIB" +fi + +test -z "$RANLIB" && RANLIB=: + + + + + + +# Determine commands to create old-style static archives. +old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs' +old_postinstall_cmds='chmod 644 $oldlib' +old_postuninstall_cmds= + +if test -n "$RANLIB"; then + case $host_os in + openbsd*) + old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib" + ;; + *) + old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib" + ;; + esac + old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib" +fi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +# If no C compiler was specified, use CC. +LTCC=${LTCC-"$CC"} + +# If no C compiler flags were specified, use CFLAGS. +LTCFLAGS=${LTCFLAGS-"$CFLAGS"} + +# Allow CC to be a program name with arguments. +compiler=$CC + + +# Check for command to grab the raw symbol name followed by C symbol from nm. +{ $as_echo "$as_me:$LINENO: checking command to parse $NM output from $compiler object" >&5 +$as_echo_n "checking command to parse $NM output from $compiler object... " >&6; } +if test "${lt_cv_sys_global_symbol_pipe+set}" = set; then + $as_echo_n "(cached) " >&6 +else + +# These are sane defaults that work on at least a few old systems. +# [They come from Ultrix. What could be older than Ultrix?!! ;)] + +# Character class describing NM global symbol codes. +symcode='[BCDEGRST]' + +# Regexp to match symbols that can be accessed directly from C. +sympat='\([_A-Za-z][_A-Za-z0-9]*\)' + +# Define system-specific variables. +case $host_os in +aix*) + symcode='[BCDT]' + ;; +cygwin* | mingw* | pw32* | cegcc*) + symcode='[ABCDGISTW]' + ;; +hpux*) + if test "$host_cpu" = ia64; then + symcode='[ABCDEGRST]' + fi + ;; +irix* | nonstopux*) + symcode='[BCDEGRST]' + ;; +osf*) + symcode='[BCDEGQRST]' + ;; +solaris*) + symcode='[BDRT]' + ;; +sco3.2v5*) + symcode='[DT]' + ;; +sysv4.2uw2*) + symcode='[DT]' + ;; +sysv5* | sco5v6* | unixware* | OpenUNIX*) + symcode='[ABDT]' + ;; +sysv4) + symcode='[DFNSTU]' + ;; +esac + +# If we're using GNU nm, then use its standard symbol codes. +case `$NM -V 2>&1` in +*GNU* | *'with BFD'*) + symcode='[ABCDGIRSTW]' ;; +esac + +# Transform an extracted symbol line into a proper C declaration. +# Some systems (esp. on ia64) link data and code symbols differently, +# so use this general approach. +lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" + +# Transform an extracted symbol line into symbol name and symbol address +lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (void *) \&\2},/p'" +lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \(lib[^ ]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"lib\2\", (void *) \&\2},/p'" + +# Handle CRLF in mingw tool chain +opt_cr= +case $build_os in +mingw*) + opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp + ;; +esac + +# Try without a prefix underscore, then with it. +for ac_symprfx in "" "_"; do + + # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. + symxfrm="\\1 $ac_symprfx\\2 \\2" + + # Write the raw and C identifiers. + if test "$lt_cv_nm_interface" = "MS dumpbin"; then + # Fake it for dumpbin and say T for any non-static function + # and D for any global variable. + # Also find C++ and __fastcall symbols from MSVC++, + # which start with @ or ?. + lt_cv_sys_global_symbol_pipe="$AWK '"\ +" {last_section=section; section=\$ 3};"\ +" /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ +" \$ 0!~/External *\|/{next};"\ +" / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ +" {if(hide[section]) next};"\ +" {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ +" {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ +" s[1]~/^[@?]/{print s[1], s[1]; next};"\ +" s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ +" ' prfx=^$ac_symprfx" + else + lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" + fi + + # Check to see that the pipe works correctly. + pipe_works=no + + rm -f conftest* + cat > conftest.$ac_ext <<_LT_EOF +#ifdef __cplusplus +extern "C" { +#endif +char nm_test_var; +void nm_test_func(void); +void nm_test_func(void){} +#ifdef __cplusplus +} +#endif +int main(){nm_test_var='a';nm_test_func();return(0);} +_LT_EOF + + if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # Now try to grab the symbols. + nlist=conftest.nm + if { (eval echo "$as_me:$LINENO: \"$NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist\"") >&5 + (eval $NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && test -s "$nlist"; then + # Try sorting and uniquifying the output. + if sort "$nlist" | uniq > "$nlist"T; then + mv -f "$nlist"T "$nlist" + else + rm -f "$nlist"T + fi + + # Make sure that we snagged all the symbols we need. + if $GREP ' nm_test_var$' "$nlist" >/dev/null; then + if $GREP ' nm_test_func$' "$nlist" >/dev/null; then + cat <<_LT_EOF > conftest.$ac_ext +#ifdef __cplusplus +extern "C" { +#endif + +_LT_EOF + # Now generate the symbol file. + eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' + + cat <<_LT_EOF >> conftest.$ac_ext + +/* The mapping between symbol names and symbols. */ +const struct { + const char *name; + void *address; +} +lt__PROGRAM__LTX_preloaded_symbols[] = +{ + { "@PROGRAM@", (void *) 0 }, +_LT_EOF + $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext + cat <<\_LT_EOF >> conftest.$ac_ext + {0, (void *) 0} +}; + +/* This works around a problem in FreeBSD linker */ +#ifdef FREEBSD_WORKAROUND +static const void *lt_preloaded_setup() { + return lt__PROGRAM__LTX_preloaded_symbols; +} +#endif + +#ifdef __cplusplus +} +#endif +_LT_EOF + # Now try linking the two files. + mv conftest.$ac_objext conftstm.$ac_objext + lt_save_LIBS="$LIBS" + lt_save_CFLAGS="$CFLAGS" + LIBS="conftstm.$ac_objext" + CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag" + if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && test -s conftest${ac_exeext}; then + pipe_works=yes + fi + LIBS="$lt_save_LIBS" + CFLAGS="$lt_save_CFLAGS" + else + echo "cannot find nm_test_func in $nlist" >&5 + fi + else + echo "cannot find nm_test_var in $nlist" >&5 + fi + else + echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5 + fi + else + echo "$progname: failed program was:" >&5 + cat conftest.$ac_ext >&5 + fi + rm -rf conftest* conftst* + + # Do not use the global_symbol_pipe unless it works. + if test "$pipe_works" = yes; then + break + else + lt_cv_sys_global_symbol_pipe= + fi +done + +fi + +if test -z "$lt_cv_sys_global_symbol_pipe"; then + lt_cv_sys_global_symbol_to_cdecl= +fi +if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then + { $as_echo "$as_me:$LINENO: result: failed" >&5 +$as_echo "failed" >&6; } +else + { $as_echo "$as_me:$LINENO: result: ok" >&5 +$as_echo "ok" >&6; } +fi + + + + + + + + + + + + + + + + + + + + + + +# Check whether --enable-libtool-lock was given. +if test "${enable_libtool_lock+set}" = set; then + enableval=$enable_libtool_lock; +fi + +test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes + +# Some flags need to be propagated to the compiler or linker for good +# libtool support. +case $host in +ia64-*-hpux*) + # Find out which ABI we are using. + echo 'int i;' > conftest.$ac_ext + if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + case `/usr/bin/file conftest.$ac_objext` in + *ELF-32*) + HPUX_IA64_MODE="32" + ;; + *ELF-64*) + HPUX_IA64_MODE="64" + ;; + esac + fi + rm -rf conftest* + ;; +*-*-irix6*) + # Find out which ABI we are using. + echo '#line 6441 "configure"' > conftest.$ac_ext + if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + if test "$lt_cv_prog_gnu_ld" = yes; then + case `/usr/bin/file conftest.$ac_objext` in + *32-bit*) + LD="${LD-ld} -melf32bsmip" + ;; + *N32*) + LD="${LD-ld} -melf32bmipn32" + ;; + *64-bit*) + LD="${LD-ld} -melf64bmip" + ;; + esac + else + case `/usr/bin/file conftest.$ac_objext` in + *32-bit*) + LD="${LD-ld} -32" + ;; + *N32*) + LD="${LD-ld} -n32" + ;; + *64-bit*) + LD="${LD-ld} -64" + ;; + esac + fi + fi + rm -rf conftest* + ;; + +x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \ +s390*-*linux*|s390*-*tpf*|sparc*-*linux*) + # Find out which ABI we are using. + echo 'int i;' > conftest.$ac_ext + if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + case `/usr/bin/file conftest.o` in + *32-bit*) + case $host in + x86_64-*kfreebsd*-gnu) + LD="${LD-ld} -m elf_i386_fbsd" + ;; + x86_64-*linux*) + LD="${LD-ld} -m elf_i386" + ;; + ppc64-*linux*|powerpc64-*linux*) + LD="${LD-ld} -m elf32ppclinux" + ;; + s390x-*linux*) + LD="${LD-ld} -m elf_s390" + ;; + sparc64-*linux*) + LD="${LD-ld} -m elf32_sparc" + ;; + esac + ;; + *64-bit*) + case $host in + x86_64-*kfreebsd*-gnu) + LD="${LD-ld} -m elf_x86_64_fbsd" + ;; + x86_64-*linux*) + LD="${LD-ld} -m elf_x86_64" + ;; + ppc*-*linux*|powerpc*-*linux*) + LD="${LD-ld} -m elf64ppc" + ;; + s390*-*linux*|s390*-*tpf*) + LD="${LD-ld} -m elf64_s390" + ;; + sparc*-*linux*) + LD="${LD-ld} -m elf64_sparc" + ;; + esac + ;; + esac + fi + rm -rf conftest* + ;; + +*-*-sco3.2v5*) + # On SCO OpenServer 5, we need -belf to get full-featured binaries. + SAVE_CFLAGS="$CFLAGS" + CFLAGS="$CFLAGS -belf" + { $as_echo "$as_me:$LINENO: checking whether the C compiler needs -belf" >&5 +$as_echo_n "checking whether the C compiler needs -belf... " >&6; } +if test "${lt_cv_cc_needs_belf+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + lt_cv_cc_needs_belf=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + lt_cv_cc_needs_belf=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext + ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_cc_needs_belf" >&5 +$as_echo "$lt_cv_cc_needs_belf" >&6; } + if test x"$lt_cv_cc_needs_belf" != x"yes"; then + # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf + CFLAGS="$SAVE_CFLAGS" + fi + ;; +sparc*-*solaris*) + # Find out which ABI we are using. + echo 'int i;' > conftest.$ac_ext + if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + case `/usr/bin/file conftest.o` in + *64-bit*) + case $lt_cv_prog_gnu_ld in + yes*) LD="${LD-ld} -m elf64_sparc" ;; + *) + if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then + LD="${LD-ld} -64" + fi + ;; + esac + ;; + esac + fi + rm -rf conftest* + ;; +esac + +need_locks="$enable_libtool_lock" + + + case $host_os in + rhapsody* | darwin*) + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args. +set dummy ${ac_tool_prefix}dsymutil; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_DSYMUTIL+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$DSYMUTIL"; then + ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +DSYMUTIL=$ac_cv_prog_DSYMUTIL +if test -n "$DSYMUTIL"; then + { $as_echo "$as_me:$LINENO: result: $DSYMUTIL" >&5 +$as_echo "$DSYMUTIL" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_DSYMUTIL"; then + ac_ct_DSYMUTIL=$DSYMUTIL + # Extract the first word of "dsymutil", so it can be a program name with args. +set dummy dsymutil; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_DSYMUTIL+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_DSYMUTIL"; then + ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_DSYMUTIL="dsymutil" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL +if test -n "$ac_ct_DSYMUTIL"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_DSYMUTIL" >&5 +$as_echo "$ac_ct_DSYMUTIL" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_DSYMUTIL" = x; then + DSYMUTIL=":" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + DSYMUTIL=$ac_ct_DSYMUTIL + fi +else + DSYMUTIL="$ac_cv_prog_DSYMUTIL" +fi + + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args. +set dummy ${ac_tool_prefix}nmedit; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_NMEDIT+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$NMEDIT"; then + ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +NMEDIT=$ac_cv_prog_NMEDIT +if test -n "$NMEDIT"; then + { $as_echo "$as_me:$LINENO: result: $NMEDIT" >&5 +$as_echo "$NMEDIT" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_NMEDIT"; then + ac_ct_NMEDIT=$NMEDIT + # Extract the first word of "nmedit", so it can be a program name with args. +set dummy nmedit; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_NMEDIT+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_NMEDIT"; then + ac_cv_prog_ac_ct_NMEDIT="$ac_ct_NMEDIT" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_NMEDIT="nmedit" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_NMEDIT=$ac_cv_prog_ac_ct_NMEDIT +if test -n "$ac_ct_NMEDIT"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_NMEDIT" >&5 +$as_echo "$ac_ct_NMEDIT" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_NMEDIT" = x; then + NMEDIT=":" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + NMEDIT=$ac_ct_NMEDIT + fi +else + NMEDIT="$ac_cv_prog_NMEDIT" +fi + + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}lipo", so it can be a program name with args. +set dummy ${ac_tool_prefix}lipo; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_LIPO+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$LIPO"; then + ac_cv_prog_LIPO="$LIPO" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_LIPO="${ac_tool_prefix}lipo" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +LIPO=$ac_cv_prog_LIPO +if test -n "$LIPO"; then + { $as_echo "$as_me:$LINENO: result: $LIPO" >&5 +$as_echo "$LIPO" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_LIPO"; then + ac_ct_LIPO=$LIPO + # Extract the first word of "lipo", so it can be a program name with args. +set dummy lipo; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_LIPO+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_LIPO"; then + ac_cv_prog_ac_ct_LIPO="$ac_ct_LIPO" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_LIPO="lipo" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_LIPO=$ac_cv_prog_ac_ct_LIPO +if test -n "$ac_ct_LIPO"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_LIPO" >&5 +$as_echo "$ac_ct_LIPO" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_LIPO" = x; then + LIPO=":" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + LIPO=$ac_ct_LIPO + fi +else + LIPO="$ac_cv_prog_LIPO" +fi + + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}otool", so it can be a program name with args. +set dummy ${ac_tool_prefix}otool; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_OTOOL+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$OTOOL"; then + ac_cv_prog_OTOOL="$OTOOL" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_OTOOL="${ac_tool_prefix}otool" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +OTOOL=$ac_cv_prog_OTOOL +if test -n "$OTOOL"; then + { $as_echo "$as_me:$LINENO: result: $OTOOL" >&5 +$as_echo "$OTOOL" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_OTOOL"; then + ac_ct_OTOOL=$OTOOL + # Extract the first word of "otool", so it can be a program name with args. +set dummy otool; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_OTOOL+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_OTOOL"; then + ac_cv_prog_ac_ct_OTOOL="$ac_ct_OTOOL" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_OTOOL="otool" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_OTOOL=$ac_cv_prog_ac_ct_OTOOL +if test -n "$ac_ct_OTOOL"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_OTOOL" >&5 +$as_echo "$ac_ct_OTOOL" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_OTOOL" = x; then + OTOOL=":" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + OTOOL=$ac_ct_OTOOL + fi +else + OTOOL="$ac_cv_prog_OTOOL" +fi + + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}otool64", so it can be a program name with args. +set dummy ${ac_tool_prefix}otool64; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_OTOOL64+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$OTOOL64"; then + ac_cv_prog_OTOOL64="$OTOOL64" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_OTOOL64="${ac_tool_prefix}otool64" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +OTOOL64=$ac_cv_prog_OTOOL64 +if test -n "$OTOOL64"; then + { $as_echo "$as_me:$LINENO: result: $OTOOL64" >&5 +$as_echo "$OTOOL64" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_OTOOL64"; then + ac_ct_OTOOL64=$OTOOL64 + # Extract the first word of "otool64", so it can be a program name with args. +set dummy otool64; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_OTOOL64+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_OTOOL64"; then + ac_cv_prog_ac_ct_OTOOL64="$ac_ct_OTOOL64" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_OTOOL64="otool64" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_OTOOL64=$ac_cv_prog_ac_ct_OTOOL64 +if test -n "$ac_ct_OTOOL64"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_OTOOL64" >&5 +$as_echo "$ac_ct_OTOOL64" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_OTOOL64" = x; then + OTOOL64=":" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + OTOOL64=$ac_ct_OTOOL64 + fi +else + OTOOL64="$ac_cv_prog_OTOOL64" +fi + + + + + + + + + + + + + + + + + + + + + + + + + + + + { $as_echo "$as_me:$LINENO: checking for -single_module linker flag" >&5 +$as_echo_n "checking for -single_module linker flag... " >&6; } +if test "${lt_cv_apple_cc_single_mod+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_apple_cc_single_mod=no + if test -z "${LT_MULTI_MODULE}"; then + # By default we will add the -single_module flag. You can override + # by either setting the environment variable LT_MULTI_MODULE + # non-empty at configure time, or by adding -multi_module to the + # link flags. + rm -rf libconftest.dylib* + echo "int foo(void){return 1;}" > conftest.c + echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ +-dynamiclib -Wl,-single_module conftest.c" >&5 + $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ + -dynamiclib -Wl,-single_module conftest.c 2>conftest.err + _lt_result=$? + if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then + lt_cv_apple_cc_single_mod=yes + else + cat conftest.err >&5 + fi + rm -rf libconftest.dylib* + rm -f conftest.* + fi +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_apple_cc_single_mod" >&5 +$as_echo "$lt_cv_apple_cc_single_mod" >&6; } + { $as_echo "$as_me:$LINENO: checking for -exported_symbols_list linker flag" >&5 +$as_echo_n "checking for -exported_symbols_list linker flag... " >&6; } +if test "${lt_cv_ld_exported_symbols_list+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_ld_exported_symbols_list=no + save_LDFLAGS=$LDFLAGS + echo "_main" > conftest.sym + LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + lt_cv_ld_exported_symbols_list=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + lt_cv_ld_exported_symbols_list=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext + LDFLAGS="$save_LDFLAGS" + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_ld_exported_symbols_list" >&5 +$as_echo "$lt_cv_ld_exported_symbols_list" >&6; } + case $host_os in + rhapsody* | darwin1.[012]) + _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;; + darwin1.*) + _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; + darwin*) # darwin 5.x on + # if running on 10.5 or later, the deployment target defaults + # to the OS version, if on x86, and 10.4, the deployment + # target defaults to 10.4. Don't you love it? + case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in + 10.0,*86*-darwin8*|10.0,*-darwin[91]*) + _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; + 10.[012]*) + _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; + 10.*) + _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; + esac + ;; + esac + if test "$lt_cv_apple_cc_single_mod" = "yes"; then + _lt_dar_single_mod='$single_module' + fi + if test "$lt_cv_ld_exported_symbols_list" = "yes"; then + _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym' + else + _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}' + fi + if test "$DSYMUTIL" != ":"; then + _lt_dsymutil='~$DSYMUTIL $lib || :' + else + _lt_dsymutil= + fi + ;; + esac + + +for ac_header in dlfcn.h +do +as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default + +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + eval "$as_ac_Header=yes" +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + eval "$as_ac_Header=no" +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +as_val=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then + cat >>confdefs.h <<_ACEOF +#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +fi + +done + + + +# Set options + + + + enable_dlopen=no + + + enable_win32_dll=no + + + # Check whether --enable-shared was given. +if test "${enable_shared+set}" = set; then + enableval=$enable_shared; p=${PACKAGE-default} + case $enableval in + yes) enable_shared=yes ;; + no) enable_shared=no ;; + *) + enable_shared=no + # Look at the argument we got. We use all the common list separators. + lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," + for pkg in $enableval; do + IFS="$lt_save_ifs" + if test "X$pkg" = "X$p"; then + enable_shared=yes + fi + done + IFS="$lt_save_ifs" + ;; + esac +else + enable_shared=yes +fi + + + + + + + + + + # Check whether --enable-static was given. +if test "${enable_static+set}" = set; then + enableval=$enable_static; p=${PACKAGE-default} + case $enableval in + yes) enable_static=yes ;; + no) enable_static=no ;; + *) + enable_static=no + # Look at the argument we got. We use all the common list separators. + lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," + for pkg in $enableval; do + IFS="$lt_save_ifs" + if test "X$pkg" = "X$p"; then + enable_static=yes + fi + done + IFS="$lt_save_ifs" + ;; + esac +else + enable_static=yes +fi + + + + + + + + + + +# Check whether --with-pic was given. +if test "${with_pic+set}" = set; then + withval=$with_pic; pic_mode="$withval" +else + pic_mode=default +fi + + +test -z "$pic_mode" && pic_mode=default + + + + + + + + # Check whether --enable-fast-install was given. +if test "${enable_fast_install+set}" = set; then + enableval=$enable_fast_install; p=${PACKAGE-default} + case $enableval in + yes) enable_fast_install=yes ;; + no) enable_fast_install=no ;; + *) + enable_fast_install=no + # Look at the argument we got. We use all the common list separators. + lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," + for pkg in $enableval; do + IFS="$lt_save_ifs" + if test "X$pkg" = "X$p"; then + enable_fast_install=yes + fi + done + IFS="$lt_save_ifs" + ;; + esac +else + enable_fast_install=yes +fi + + + + + + + + + + + +# This can be used to rebuild libtool when needed +LIBTOOL_DEPS="$ltmain" + +# Always use our own libtool. +LIBTOOL='$(SHELL) $(top_builddir)/libtool' + + + + + + + + + + + + + + + + + + + + + + + + + +test -z "$LN_S" && LN_S="ln -s" + + + + + + + + + + + + + + +if test -n "${ZSH_VERSION+set}" ; then + setopt NO_GLOB_SUBST +fi + +{ $as_echo "$as_me:$LINENO: checking for objdir" >&5 +$as_echo_n "checking for objdir... " >&6; } +if test "${lt_cv_objdir+set}" = set; then + $as_echo_n "(cached) " >&6 +else + rm -f .libs 2>/dev/null +mkdir .libs 2>/dev/null +if test -d .libs; then + lt_cv_objdir=.libs +else + # MS-DOS does not allow filenames that begin with a dot. + lt_cv_objdir=_libs +fi +rmdir .libs 2>/dev/null +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_objdir" >&5 +$as_echo "$lt_cv_objdir" >&6; } +objdir=$lt_cv_objdir + + + + + +cat >>confdefs.h <<_ACEOF +#define LT_OBJDIR "$lt_cv_objdir/" +_ACEOF + + + + + + + + + + + + + + + + + +case $host_os in +aix3*) + # AIX sometimes has problems with the GCC collect2 program. For some + # reason, if we set the COLLECT_NAMES environment variable, the problems + # vanish in a puff of smoke. + if test "X${COLLECT_NAMES+set}" != Xset; then + COLLECT_NAMES= + export COLLECT_NAMES + fi + ;; +esac + +# Sed substitution that helps us do robust quoting. It backslashifies +# metacharacters that are still active within double-quoted strings. +sed_quote_subst='s/\(["`$\\]\)/\\\1/g' + +# Same as above, but do not quote variable references. +double_quote_subst='s/\(["`\\]\)/\\\1/g' + +# Sed substitution to delay expansion of an escaped shell variable in a +# double_quote_subst'ed string. +delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g' + +# Sed substitution to delay expansion of an escaped single quote. +delay_single_quote_subst='s/'\''/'\'\\\\\\\'\''/g' + +# Sed substitution to avoid accidental globbing in evaled expressions +no_glob_subst='s/\*/\\\*/g' + +# Global variables: +ofile=libtool +can_build_shared=yes + +# All known linkers require a `.a' archive for static linking (except MSVC, +# which needs '.lib'). +libext=a + +with_gnu_ld="$lt_cv_prog_gnu_ld" + +old_CC="$CC" +old_CFLAGS="$CFLAGS" + +# Set sane defaults for various variables +test -z "$CC" && CC=cc +test -z "$LTCC" && LTCC=$CC +test -z "$LTCFLAGS" && LTCFLAGS=$CFLAGS +test -z "$LD" && LD=ld +test -z "$ac_objext" && ac_objext=o + +for cc_temp in $compiler""; do + case $cc_temp in + compile | *[\\/]compile | ccache | *[\\/]ccache ) ;; + distcc | *[\\/]distcc | purify | *[\\/]purify ) ;; + \-*) ;; + *) break;; + esac +done +cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"` + + +# Only perform the check for file, if the check method requires it +test -z "$MAGIC_CMD" && MAGIC_CMD=file +case $deplibs_check_method in +file_magic*) + if test "$file_magic_cmd" = '$MAGIC_CMD'; then + { $as_echo "$as_me:$LINENO: checking for ${ac_tool_prefix}file" >&5 +$as_echo_n "checking for ${ac_tool_prefix}file... " >&6; } +if test "${lt_cv_path_MAGIC_CMD+set}" = set; then + $as_echo_n "(cached) " >&6 +else + case $MAGIC_CMD in +[\\/*] | ?:[\\/]*) + lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path. + ;; +*) + lt_save_MAGIC_CMD="$MAGIC_CMD" + lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR + ac_dummy="/usr/bin$PATH_SEPARATOR$PATH" + for ac_dir in $ac_dummy; do + IFS="$lt_save_ifs" + test -z "$ac_dir" && ac_dir=. + if test -f $ac_dir/${ac_tool_prefix}file; then + lt_cv_path_MAGIC_CMD="$ac_dir/${ac_tool_prefix}file" + if test -n "$file_magic_test_file"; then + case $deplibs_check_method in + "file_magic "*) + file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"` + MAGIC_CMD="$lt_cv_path_MAGIC_CMD" + if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null | + $EGREP "$file_magic_regex" > /dev/null; then + : + else + cat <<_LT_EOF 1>&2 + +*** Warning: the command libtool uses to detect shared libraries, +*** $file_magic_cmd, produces output that libtool cannot recognize. +*** The result is that libtool may fail to recognize shared libraries +*** as such. This will affect the creation of libtool libraries that +*** depend on shared libraries, but programs linked with such libtool +*** libraries will work regardless of this problem. Nevertheless, you +*** may want to report the problem to your system manager and/or to +*** bug-libtool@gnu.org + +_LT_EOF + fi ;; + esac + fi + break + fi + done + IFS="$lt_save_ifs" + MAGIC_CMD="$lt_save_MAGIC_CMD" + ;; +esac +fi + +MAGIC_CMD="$lt_cv_path_MAGIC_CMD" +if test -n "$MAGIC_CMD"; then + { $as_echo "$as_me:$LINENO: result: $MAGIC_CMD" >&5 +$as_echo "$MAGIC_CMD" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + + + + +if test -z "$lt_cv_path_MAGIC_CMD"; then + if test -n "$ac_tool_prefix"; then + { $as_echo "$as_me:$LINENO: checking for file" >&5 +$as_echo_n "checking for file... " >&6; } +if test "${lt_cv_path_MAGIC_CMD+set}" = set; then + $as_echo_n "(cached) " >&6 +else + case $MAGIC_CMD in +[\\/*] | ?:[\\/]*) + lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path. + ;; +*) + lt_save_MAGIC_CMD="$MAGIC_CMD" + lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR + ac_dummy="/usr/bin$PATH_SEPARATOR$PATH" + for ac_dir in $ac_dummy; do + IFS="$lt_save_ifs" + test -z "$ac_dir" && ac_dir=. + if test -f $ac_dir/file; then + lt_cv_path_MAGIC_CMD="$ac_dir/file" + if test -n "$file_magic_test_file"; then + case $deplibs_check_method in + "file_magic "*) + file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"` + MAGIC_CMD="$lt_cv_path_MAGIC_CMD" + if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null | + $EGREP "$file_magic_regex" > /dev/null; then + : + else + cat <<_LT_EOF 1>&2 + +*** Warning: the command libtool uses to detect shared libraries, +*** $file_magic_cmd, produces output that libtool cannot recognize. +*** The result is that libtool may fail to recognize shared libraries +*** as such. This will affect the creation of libtool libraries that +*** depend on shared libraries, but programs linked with such libtool +*** libraries will work regardless of this problem. Nevertheless, you +*** may want to report the problem to your system manager and/or to +*** bug-libtool@gnu.org + +_LT_EOF + fi ;; + esac + fi + break + fi + done + IFS="$lt_save_ifs" + MAGIC_CMD="$lt_save_MAGIC_CMD" + ;; +esac +fi + +MAGIC_CMD="$lt_cv_path_MAGIC_CMD" +if test -n "$MAGIC_CMD"; then + { $as_echo "$as_me:$LINENO: result: $MAGIC_CMD" >&5 +$as_echo "$MAGIC_CMD" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + + else + MAGIC_CMD=: + fi +fi + + fi + ;; +esac + +# Use C for the default configuration in the libtool script + +lt_save_CC="$CC" +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + +# Source file extension for C test sources. +ac_ext=c + +# Object file extension for compiled C test sources. +objext=o +objext=$objext + +# Code to be used in simple compile tests +lt_simple_compile_test_code="int some_variable = 0;" + +# Code to be used in simple link tests +lt_simple_link_test_code='int main(){return(0);}' + + + + + + + +# If no C compiler was specified, use CC. +LTCC=${LTCC-"$CC"} + +# If no C compiler flags were specified, use CFLAGS. +LTCFLAGS=${LTCFLAGS-"$CFLAGS"} + +# Allow CC to be a program name with arguments. +compiler=$CC + +# Save the default compiler, since it gets overwritten when the other +# tags are being tested, and _LT_TAGVAR(compiler, []) is a NOP. +compiler_DEFAULT=$CC + +# save warnings/boilerplate of simple test code +ac_outfile=conftest.$ac_objext +echo "$lt_simple_compile_test_code" >conftest.$ac_ext +eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err +_lt_compiler_boilerplate=`cat conftest.err` +$RM conftest* + +ac_outfile=conftest.$ac_objext +echo "$lt_simple_link_test_code" >conftest.$ac_ext +eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err +_lt_linker_boilerplate=`cat conftest.err` +$RM -r conftest* + + +## CAVEAT EMPTOR: +## There is no encapsulation within the following macros, do not change +## the running order or otherwise move them around unless you know exactly +## what you are doing... +if test -n "$compiler"; then + +lt_prog_compiler_no_builtin_flag= + +if test "$GCC" = yes; then + lt_prog_compiler_no_builtin_flag=' -fno-builtin' + + { $as_echo "$as_me:$LINENO: checking if $compiler supports -fno-rtti -fno-exceptions" >&5 +$as_echo_n "checking if $compiler supports -fno-rtti -fno-exceptions... " >&6; } +if test "${lt_cv_prog_compiler_rtti_exceptions+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_prog_compiler_rtti_exceptions=no + ac_outfile=conftest.$ac_objext + echo "$lt_simple_compile_test_code" > conftest.$ac_ext + lt_compiler_flag="-fno-rtti -fno-exceptions" + # Insert the option either (1) after the last *FLAGS variable, or + # (2) before a word containing "conftest.", or (3) at the end. + # Note that $ac_compile itself does not contain backslashes and begins + # with a dollar sign (not a hyphen), so the echo should work correctly. + # The option is referenced via a variable to avoid confusing sed. + lt_compile=`echo "$ac_compile" | $SED \ + -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \ + -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \ + -e 's:$: $lt_compiler_flag:'` + (eval echo "\"\$as_me:7810: $lt_compile\"" >&5) + (eval "$lt_compile" 2>conftest.err) + ac_status=$? + cat conftest.err >&5 + echo "$as_me:7814: \$? = $ac_status" >&5 + if (exit $ac_status) && test -s "$ac_outfile"; then + # The compiler can only warn and ignore the option if not recognized + # So say no if there are warnings other than the usual output. + $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp + $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2 + if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then + lt_cv_prog_compiler_rtti_exceptions=yes + fi + fi + $RM conftest* + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_rtti_exceptions" >&5 +$as_echo "$lt_cv_prog_compiler_rtti_exceptions" >&6; } + +if test x"$lt_cv_prog_compiler_rtti_exceptions" = xyes; then + lt_prog_compiler_no_builtin_flag="$lt_prog_compiler_no_builtin_flag -fno-rtti -fno-exceptions" +else + : +fi + +fi + + + + + + + lt_prog_compiler_wl= +lt_prog_compiler_pic= +lt_prog_compiler_static= + +{ $as_echo "$as_me:$LINENO: checking for $compiler option to produce PIC" >&5 +$as_echo_n "checking for $compiler option to produce PIC... " >&6; } + + if test "$GCC" = yes; then + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_static='-static' + + case $host_os in + aix*) + # All AIX code is PIC. + if test "$host_cpu" = ia64; then + # AIX 5 now supports IA64 processor + lt_prog_compiler_static='-Bstatic' + fi + ;; + + amigaos*) + case $host_cpu in + powerpc) + # see comment about AmigaOS4 .so support + lt_prog_compiler_pic='-fPIC' + ;; + m68k) + # FIXME: we need at least 68020 code to build shared libraries, but + # adding the `-m68020' flag to GCC prevents building anything better, + # like `-m68040'. + lt_prog_compiler_pic='-m68020 -resident32 -malways-restore-a4' + ;; + esac + ;; + + beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) + # PIC is the default for these OSes. + ;; + + mingw* | cygwin* | pw32* | os2* | cegcc*) + # This hack is so that the source file can tell whether it is being + # built for inclusion in a dll (and should export symbols for example). + # Although the cygwin gcc ignores -fPIC, still need this for old-style + # (--disable-auto-import) libraries + lt_prog_compiler_pic='-DDLL_EXPORT' + ;; + + darwin* | rhapsody*) + # PIC is the default on this platform + # Common symbols not allowed in MH_DYLIB files + lt_prog_compiler_pic='-fno-common' + ;; + + hpux*) + # PIC is the default for 64-bit PA HP-UX, but not for 32-bit + # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag + # sets the default TLS model and affects inlining. + case $host_cpu in + hppa*64*) + # +Z the default + ;; + *) + lt_prog_compiler_pic='-fPIC' + ;; + esac + ;; + + interix[3-9]*) + # Interix 3.x gcc -fpic/-fPIC options generate broken code. + # Instead, we relocate shared libraries at runtime. + ;; + + msdosdjgpp*) + # Just because we use GCC doesn't mean we suddenly get shared libraries + # on systems that don't support them. + lt_prog_compiler_can_build_shared=no + enable_shared=no + ;; + + *nto* | *qnx*) + # QNX uses GNU C++, but need to define -shared option too, otherwise + # it will coredump. + lt_prog_compiler_pic='-fPIC -shared' + ;; + + sysv4*MP*) + if test -d /usr/nec; then + lt_prog_compiler_pic=-Kconform_pic + fi + ;; + + *) + lt_prog_compiler_pic='-fPIC' + ;; + esac + else + # PORTME Check for flag to pass linker flags through the system compiler. + case $host_os in + aix*) + lt_prog_compiler_wl='-Wl,' + if test "$host_cpu" = ia64; then + # AIX 5 now supports IA64 processor + lt_prog_compiler_static='-Bstatic' + else + lt_prog_compiler_static='-bnso -bI:/lib/syscalls.exp' + fi + ;; + + mingw* | cygwin* | pw32* | os2* | cegcc*) + # This hack is so that the source file can tell whether it is being + # built for inclusion in a dll (and should export symbols for example). + lt_prog_compiler_pic='-DDLL_EXPORT' + ;; + + hpux9* | hpux10* | hpux11*) + lt_prog_compiler_wl='-Wl,' + # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but + # not for PA HP-UX. + case $host_cpu in + hppa*64*|ia64*) + # +Z the default + ;; + *) + lt_prog_compiler_pic='+Z' + ;; + esac + # Is there a better lt_prog_compiler_static that works with the bundled CC? + lt_prog_compiler_static='${wl}-a ${wl}archive' + ;; + + irix5* | irix6* | nonstopux*) + lt_prog_compiler_wl='-Wl,' + # PIC (with -KPIC) is the default. + lt_prog_compiler_static='-non_shared' + ;; + + linux* | k*bsd*-gnu) + case $cc_basename in + # old Intel for x86_64 which still supported -KPIC. + ecc*) + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_pic='-KPIC' + lt_prog_compiler_static='-static' + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. + icc* | ifort*) + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_pic='-fPIC' + lt_prog_compiler_static='-static' + ;; + # Lahey Fortran 8.1. + lf95*) + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_pic='--shared' + lt_prog_compiler_static='--static' + ;; + pgcc* | pgf77* | pgf90* | pgf95*) + # Portland Group compilers (*not* the Pentium gcc compiler, + # which looks to be a dead project) + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_pic='-fpic' + lt_prog_compiler_static='-Bstatic' + ;; + ccc*) + lt_prog_compiler_wl='-Wl,' + # All Alpha code is PIC. + lt_prog_compiler_static='-non_shared' + ;; + xl*) + # IBM XL C 8.0/Fortran 10.1 on PPC + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_pic='-qpic' + lt_prog_compiler_static='-qstaticlink' + ;; + *) + case `$CC -V 2>&1 | sed 5q` in + *Sun\ C*) + # Sun C 5.9 + lt_prog_compiler_pic='-KPIC' + lt_prog_compiler_static='-Bstatic' + lt_prog_compiler_wl='-Wl,' + ;; + *Sun\ F*) + # Sun Fortran 8.3 passes all unrecognized flags to the linker + lt_prog_compiler_pic='-KPIC' + lt_prog_compiler_static='-Bstatic' + lt_prog_compiler_wl='' + ;; + esac + ;; + esac + ;; + + newsos6) + lt_prog_compiler_pic='-KPIC' + lt_prog_compiler_static='-Bstatic' + ;; + + *nto* | *qnx*) + # QNX uses GNU C++, but need to define -shared option too, otherwise + # it will coredump. + lt_prog_compiler_pic='-fPIC -shared' + ;; + + osf3* | osf4* | osf5*) + lt_prog_compiler_wl='-Wl,' + # All OSF/1 code is PIC. + lt_prog_compiler_static='-non_shared' + ;; + + rdos*) + lt_prog_compiler_static='-non_shared' + ;; + + solaris*) + lt_prog_compiler_pic='-KPIC' + lt_prog_compiler_static='-Bstatic' + case $cc_basename in + f77* | f90* | f95*) + lt_prog_compiler_wl='-Qoption ld ';; + *) + lt_prog_compiler_wl='-Wl,';; + esac + ;; + + sunos4*) + lt_prog_compiler_wl='-Qoption ld ' + lt_prog_compiler_pic='-PIC' + lt_prog_compiler_static='-Bstatic' + ;; + + sysv4 | sysv4.2uw2* | sysv4.3*) + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_pic='-KPIC' + lt_prog_compiler_static='-Bstatic' + ;; + + sysv4*MP*) + if test -d /usr/nec ;then + lt_prog_compiler_pic='-Kconform_pic' + lt_prog_compiler_static='-Bstatic' + fi + ;; + + sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*) + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_pic='-KPIC' + lt_prog_compiler_static='-Bstatic' + ;; + + unicos*) + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_can_build_shared=no + ;; + + uts4*) + lt_prog_compiler_pic='-pic' + lt_prog_compiler_static='-Bstatic' + ;; + + *) + lt_prog_compiler_can_build_shared=no + ;; + esac + fi + +case $host_os in + # For platforms which do not support PIC, -DPIC is meaningless: + *djgpp*) + lt_prog_compiler_pic= + ;; + *) + lt_prog_compiler_pic="$lt_prog_compiler_pic -DPIC" + ;; +esac +{ $as_echo "$as_me:$LINENO: result: $lt_prog_compiler_pic" >&5 +$as_echo "$lt_prog_compiler_pic" >&6; } + + + + + + +# +# Check to make sure the PIC flag actually works. +# +if test -n "$lt_prog_compiler_pic"; then + { $as_echo "$as_me:$LINENO: checking if $compiler PIC flag $lt_prog_compiler_pic works" >&5 +$as_echo_n "checking if $compiler PIC flag $lt_prog_compiler_pic works... " >&6; } +if test "${lt_cv_prog_compiler_pic_works+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_prog_compiler_pic_works=no + ac_outfile=conftest.$ac_objext + echo "$lt_simple_compile_test_code" > conftest.$ac_ext + lt_compiler_flag="$lt_prog_compiler_pic -DPIC" + # Insert the option either (1) after the last *FLAGS variable, or + # (2) before a word containing "conftest.", or (3) at the end. + # Note that $ac_compile itself does not contain backslashes and begins + # with a dollar sign (not a hyphen), so the echo should work correctly. + # The option is referenced via a variable to avoid confusing sed. + lt_compile=`echo "$ac_compile" | $SED \ + -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \ + -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \ + -e 's:$: $lt_compiler_flag:'` + (eval echo "\"\$as_me:8149: $lt_compile\"" >&5) + (eval "$lt_compile" 2>conftest.err) + ac_status=$? + cat conftest.err >&5 + echo "$as_me:8153: \$? = $ac_status" >&5 + if (exit $ac_status) && test -s "$ac_outfile"; then + # The compiler can only warn and ignore the option if not recognized + # So say no if there are warnings other than the usual output. + $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp + $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2 + if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then + lt_cv_prog_compiler_pic_works=yes + fi + fi + $RM conftest* + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_pic_works" >&5 +$as_echo "$lt_cv_prog_compiler_pic_works" >&6; } + +if test x"$lt_cv_prog_compiler_pic_works" = xyes; then + case $lt_prog_compiler_pic in + "" | " "*) ;; + *) lt_prog_compiler_pic=" $lt_prog_compiler_pic" ;; + esac +else + lt_prog_compiler_pic= + lt_prog_compiler_can_build_shared=no +fi + +fi + + + + + + +# +# Check to make sure the static flag actually works. +# +wl=$lt_prog_compiler_wl eval lt_tmp_static_flag=\"$lt_prog_compiler_static\" +{ $as_echo "$as_me:$LINENO: checking if $compiler static flag $lt_tmp_static_flag works" >&5 +$as_echo_n "checking if $compiler static flag $lt_tmp_static_flag works... " >&6; } +if test "${lt_cv_prog_compiler_static_works+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_prog_compiler_static_works=no + save_LDFLAGS="$LDFLAGS" + LDFLAGS="$LDFLAGS $lt_tmp_static_flag" + echo "$lt_simple_link_test_code" > conftest.$ac_ext + if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then + # The linker can only warn and ignore the option if not recognized + # So say no if there are warnings + if test -s conftest.err; then + # Append any errors to the config.log. + cat conftest.err 1>&5 + $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp + $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2 + if diff conftest.exp conftest.er2 >/dev/null; then + lt_cv_prog_compiler_static_works=yes + fi + else + lt_cv_prog_compiler_static_works=yes + fi + fi + $RM -r conftest* + LDFLAGS="$save_LDFLAGS" + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_static_works" >&5 +$as_echo "$lt_cv_prog_compiler_static_works" >&6; } + +if test x"$lt_cv_prog_compiler_static_works" = xyes; then + : +else + lt_prog_compiler_static= +fi + + + + + + + + { $as_echo "$as_me:$LINENO: checking if $compiler supports -c -o file.$ac_objext" >&5 +$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; } +if test "${lt_cv_prog_compiler_c_o+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_prog_compiler_c_o=no + $RM -r conftest 2>/dev/null + mkdir conftest + cd conftest + mkdir out + echo "$lt_simple_compile_test_code" > conftest.$ac_ext + + lt_compiler_flag="-o out/conftest2.$ac_objext" + # Insert the option either (1) after the last *FLAGS variable, or + # (2) before a word containing "conftest.", or (3) at the end. + # Note that $ac_compile itself does not contain backslashes and begins + # with a dollar sign (not a hyphen), so the echo should work correctly. + lt_compile=`echo "$ac_compile" | $SED \ + -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \ + -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \ + -e 's:$: $lt_compiler_flag:'` + (eval echo "\"\$as_me:8254: $lt_compile\"" >&5) + (eval "$lt_compile" 2>out/conftest.err) + ac_status=$? + cat out/conftest.err >&5 + echo "$as_me:8258: \$? = $ac_status" >&5 + if (exit $ac_status) && test -s out/conftest2.$ac_objext + then + # The compiler can only warn and ignore the option if not recognized + # So say no if there are warnings + $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp + $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2 + if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then + lt_cv_prog_compiler_c_o=yes + fi + fi + chmod u+w . 2>&5 + $RM conftest* + # SGI C++ compiler will create directory out/ii_files/ for + # template instantiation + test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files + $RM out/* && rmdir out + cd .. + $RM -r conftest + $RM conftest* + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_c_o" >&5 +$as_echo "$lt_cv_prog_compiler_c_o" >&6; } + + + + + + + { $as_echo "$as_me:$LINENO: checking if $compiler supports -c -o file.$ac_objext" >&5 +$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; } +if test "${lt_cv_prog_compiler_c_o+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_prog_compiler_c_o=no + $RM -r conftest 2>/dev/null + mkdir conftest + cd conftest + mkdir out + echo "$lt_simple_compile_test_code" > conftest.$ac_ext + + lt_compiler_flag="-o out/conftest2.$ac_objext" + # Insert the option either (1) after the last *FLAGS variable, or + # (2) before a word containing "conftest.", or (3) at the end. + # Note that $ac_compile itself does not contain backslashes and begins + # with a dollar sign (not a hyphen), so the echo should work correctly. + lt_compile=`echo "$ac_compile" | $SED \ + -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \ + -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \ + -e 's:$: $lt_compiler_flag:'` + (eval echo "\"\$as_me:8309: $lt_compile\"" >&5) + (eval "$lt_compile" 2>out/conftest.err) + ac_status=$? + cat out/conftest.err >&5 + echo "$as_me:8313: \$? = $ac_status" >&5 + if (exit $ac_status) && test -s out/conftest2.$ac_objext + then + # The compiler can only warn and ignore the option if not recognized + # So say no if there are warnings + $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp + $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2 + if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then + lt_cv_prog_compiler_c_o=yes + fi + fi + chmod u+w . 2>&5 + $RM conftest* + # SGI C++ compiler will create directory out/ii_files/ for + # template instantiation + test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files + $RM out/* && rmdir out + cd .. + $RM -r conftest + $RM conftest* + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_c_o" >&5 +$as_echo "$lt_cv_prog_compiler_c_o" >&6; } + + + + +hard_links="nottested" +if test "$lt_cv_prog_compiler_c_o" = no && test "$need_locks" != no; then + # do not overwrite the value of need_locks provided by the user + { $as_echo "$as_me:$LINENO: checking if we can lock with hard links" >&5 +$as_echo_n "checking if we can lock with hard links... " >&6; } + hard_links=yes + $RM conftest* + ln conftest.a conftest.b 2>/dev/null && hard_links=no + touch conftest.a + ln conftest.a conftest.b 2>&5 || hard_links=no + ln conftest.a conftest.b 2>/dev/null && hard_links=no + { $as_echo "$as_me:$LINENO: result: $hard_links" >&5 +$as_echo "$hard_links" >&6; } + if test "$hard_links" = no; then + { $as_echo "$as_me:$LINENO: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&5 +$as_echo "$as_me: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&2;} + need_locks=warn + fi +else + need_locks=no +fi + + + + + + + { $as_echo "$as_me:$LINENO: checking whether the $compiler linker ($LD) supports shared libraries" >&5 +$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; } + + runpath_var= + allow_undefined_flag= + always_export_symbols=no + archive_cmds= + archive_expsym_cmds= + compiler_needs_object=no + enable_shared_with_static_runtimes=no + export_dynamic_flag_spec= + export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols' + hardcode_automatic=no + hardcode_direct=no + hardcode_direct_absolute=no + hardcode_libdir_flag_spec= + hardcode_libdir_flag_spec_ld= + hardcode_libdir_separator= + hardcode_minus_L=no + hardcode_shlibpath_var=unsupported + inherit_rpath=no + link_all_deplibs=unknown + module_cmds= + module_expsym_cmds= + old_archive_from_new_cmds= + old_archive_from_expsyms_cmds= + thread_safe_flag_spec= + whole_archive_flag_spec= + # include_expsyms should be a list of space-separated symbols to be *always* + # included in the symbol list + include_expsyms= + # exclude_expsyms can be an extended regexp of symbols to exclude + # it will be wrapped by ` (' and `)$', so one must not match beginning or + # end of line. Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc', + # as well as any symbol that contains `d'. + exclude_expsyms='_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*' + # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out + # platforms (ab)use it in PIC code, but their linkers get confused if + # the symbol is explicitly referenced. Since portable code cannot + # rely on this symbol name, it's probably fine to never include it in + # preloaded symbol tables. + # Exclude shared library initialization/finalization symbols. + extract_expsyms_cmds= + + case $host_os in + cygwin* | mingw* | pw32* | cegcc*) + # FIXME: the MSVC++ port hasn't been tested in a loooong time + # When not using gcc, we currently assume that we are using + # Microsoft Visual C++. + if test "$GCC" != yes; then + with_gnu_ld=no + fi + ;; + interix*) + # we just hope/assume this is gcc and not c89 (= MSVC++) + with_gnu_ld=yes + ;; + openbsd*) + with_gnu_ld=no + ;; + esac + + ld_shlibs=yes + if test "$with_gnu_ld" = yes; then + # If archive_cmds runs LD, not CC, wlarc should be empty + wlarc='${wl}' + + # Set some defaults for GNU ld with shared library support. These + # are reset later if shared libraries are not supported. Putting them + # here allows them to be overridden if necessary. + runpath_var=LD_RUN_PATH + hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' + export_dynamic_flag_spec='${wl}--export-dynamic' + # ancient GNU ld didn't support --whole-archive et. al. + if $LD --help 2>&1 | $GREP 'no-whole-archive' > /dev/null; then + whole_archive_flag_spec="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive' + else + whole_archive_flag_spec= + fi + supports_anon_versioning=no + case `$LD -v 2>&1` in + *\ [01].* | *\ 2.[0-9].* | *\ 2.10.*) ;; # catch versions < 2.11 + *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ... + *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ... + *\ 2.11.*) ;; # other 2.11 versions + *) supports_anon_versioning=yes ;; + esac + + # See if GNU ld supports shared libraries. + case $host_os in + aix[3-9]*) + # On AIX/PPC, the GNU linker is very broken + if test "$host_cpu" != ia64; then + ld_shlibs=no + cat <<_LT_EOF 1>&2 + +*** Warning: the GNU linker, at least up to release 2.9.1, is reported +*** to be unable to reliably create shared libraries on AIX. +*** Therefore, libtool is disabling shared libraries support. If you +*** really care for shared libraries, you may want to modify your PATH +*** so that a non-GNU linker is found, and then restart. + +_LT_EOF + fi + ;; + + amigaos*) + case $host_cpu in + powerpc) + # see comment about AmigaOS4 .so support + archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + archive_expsym_cmds='' + ;; + m68k) + archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' + hardcode_libdir_flag_spec='-L$libdir' + hardcode_minus_L=yes + ;; + esac + ;; + + beos*) + if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then + allow_undefined_flag=unsupported + # Joseph Beckenbach says some releases of gcc + # support --undefined. This deserves some investigation. FIXME + archive_cmds='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + else + ld_shlibs=no + fi + ;; + + cygwin* | mingw* | pw32* | cegcc*) + # _LT_TAGVAR(hardcode_libdir_flag_spec, ) is actually meaningless, + # as there is no search path for DLLs. + hardcode_libdir_flag_spec='-L$libdir' + allow_undefined_flag=unsupported + always_export_symbols=no + enable_shared_with_static_runtimes=yes + export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/'\'' | $SED -e '\''/^[AITW][ ]/s/.*[ ]//'\'' | sort | uniq > $export_symbols' + + if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then + archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' + # If the export-symbols file already is a .def file (1st line + # is EXPORTS), use it as is; otherwise, prepend... + archive_expsym_cmds='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then + cp $export_symbols $output_objdir/$soname.def; + else + echo EXPORTS > $output_objdir/$soname.def; + cat $export_symbols >> $output_objdir/$soname.def; + fi~ + $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' + else + ld_shlibs=no + fi + ;; + + interix[3-9]*) + hardcode_direct=no + hardcode_shlibpath_var=no + hardcode_libdir_flag_spec='${wl}-rpath,$libdir' + export_dynamic_flag_spec='${wl}-E' + # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc. + # Instead, shared libraries are loaded at an image base (0x10000000 by + # default) and relocated if they conflict, which is a slow very memory + # consuming and fragmenting process. To avoid this, we pick a random, + # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link + # time. Moving up from 0x10000000 also allows more sbrk(2) space. + archive_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib' + archive_expsym_cmds='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib' + ;; + + gnu* | linux* | tpf* | k*bsd*-gnu) + tmp_diet=no + if test "$host_os" = linux-dietlibc; then + case $cc_basename in + diet\ *) tmp_diet=yes;; # linux-dietlibc with static linking (!diet-dyn) + esac + fi + if $LD --help 2>&1 | $EGREP ': supported targets:.* elf' > /dev/null \ + && test "$tmp_diet" = no + then + tmp_addflag= + tmp_sharedflag='-shared' + case $cc_basename,$host_cpu in + pgcc*) # Portland Group C compiler + whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag' + ;; + pgf77* | pgf90* | pgf95*) # Portland Group f77 and f90 compilers + whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag -Mnomain' ;; + ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; + efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; + ifc* | ifort*) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec= + tmp_sharedflag='--shared' ;; + xl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' + tmp_addflag= ;; + esac + case `$CC -V 2>&1 | sed 5q` in + *Sun\ C*) # Sun C 5.9 + whole_archive_flag_spec='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' + compiler_needs_object=yes + tmp_sharedflag='-G' ;; + *Sun\ F*) # Sun Fortran 8.3 + tmp_sharedflag='-G' ;; + esac + archive_cmds='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + + if test "x$supports_anon_versioning" = xyes; then + archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~ + cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ + echo "local: *; };" >> $output_objdir/$libname.ver~ + $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib' + fi + + case $cc_basename in + xlf*) + # IBM XL Fortran 10.1 on PPC cannot create shared libs itself + whole_archive_flag_spec='--whole-archive$convenience --no-whole-archive' + hardcode_libdir_flag_spec= + hardcode_libdir_flag_spec_ld='-rpath $libdir' + archive_cmds='$LD -shared $libobjs $deplibs $compiler_flags -soname $soname -o $lib' + if test "x$supports_anon_versioning" = xyes; then + archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~ + cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ + echo "local: *; };" >> $output_objdir/$libname.ver~ + $LD -shared $libobjs $deplibs $compiler_flags -soname $soname -version-script $output_objdir/$libname.ver -o $lib' + fi + ;; + esac + else + ld_shlibs=no + fi + ;; + + netbsd* | netbsdelf*-gnu) + if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then + archive_cmds='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib' + wlarc= + else + archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' + fi + ;; + + solaris*) + if $LD -v 2>&1 | $GREP 'BFD 2\.8' > /dev/null; then + ld_shlibs=no + cat <<_LT_EOF 1>&2 + +*** Warning: The releases 2.8.* of the GNU linker cannot reliably +*** create shared libraries on Solaris systems. Therefore, libtool +*** is disabling shared libraries support. We urge you to upgrade GNU +*** binutils to release 2.9.1 or newer. Another option is to modify +*** your PATH or compiler configuration so that the native linker is +*** used, and then restart. + +_LT_EOF + elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then + archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' + else + ld_shlibs=no + fi + ;; + + sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*) + case `$LD -v 2>&1` in + *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*) + ld_shlibs=no + cat <<_LT_EOF 1>&2 + +*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not +*** reliably create shared libraries on SCO systems. Therefore, libtool +*** is disabling shared libraries support. We urge you to upgrade GNU +*** binutils to release 2.16.91.0.3 or newer. Another option is to modify +*** your PATH or compiler configuration so that the native linker is +*** used, and then restart. + +_LT_EOF + ;; + *) + # For security reasons, it is highly recommended that you always + # use absolute paths for naming shared libraries, and exclude the + # DT_RUNPATH tag from executables and libraries. But doing so + # requires that you compile everything twice, which is a pain. + if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then + hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' + archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' + else + ld_shlibs=no + fi + ;; + esac + ;; + + sunos4*) + archive_cmds='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags' + wlarc= + hardcode_direct=yes + hardcode_shlibpath_var=no + ;; + + *) + if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then + archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' + else + ld_shlibs=no + fi + ;; + esac + + if test "$ld_shlibs" = no; then + runpath_var= + hardcode_libdir_flag_spec= + export_dynamic_flag_spec= + whole_archive_flag_spec= + fi + else + # PORTME fill in a description of your system's linker (not GNU ld) + case $host_os in + aix3*) + allow_undefined_flag=unsupported + always_export_symbols=yes + archive_expsym_cmds='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname' + # Note: this linker hardcodes the directories in LIBPATH if there + # are no directories specified by -L. + hardcode_minus_L=yes + if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then + # Neither direct hardcoding nor static linking is supported with a + # broken collect2. + hardcode_direct=unsupported + fi + ;; + + aix[4-9]*) + if test "$host_cpu" = ia64; then + # On IA64, the linker does run time linking by default, so we don't + # have to do anything special. + aix_use_runtimelinking=no + exp_sym_flag='-Bexport' + no_entry_flag="" + else + # If we're using GNU nm, then we don't want the "-C" option. + # -C means demangle to AIX nm, but means don't demangle with GNU nm + if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then + export_symbols_cmds='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols' + else + export_symbols_cmds='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols' + fi + aix_use_runtimelinking=no + + # Test if we are trying to use run time linking or normal + # AIX style linking. If -brtl is somewhere in LDFLAGS, we + # need to do runtime linking. + case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*) + for ld_flag in $LDFLAGS; do + if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then + aix_use_runtimelinking=yes + break + fi + done + ;; + esac + + exp_sym_flag='-bexport' + no_entry_flag='-bnoentry' + fi + + # When large executables or shared objects are built, AIX ld can + # have problems creating the table of contents. If linking a library + # or program results in "error TOC overflow" add -mminimal-toc to + # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not + # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS. + + archive_cmds='' + hardcode_direct=yes + hardcode_direct_absolute=yes + hardcode_libdir_separator=':' + link_all_deplibs=yes + file_list_spec='${wl}-f,' + + if test "$GCC" = yes; then + case $host_os in aix4.[012]|aix4.[012].*) + # We only want to do this on AIX 4.2 and lower, the check + # below for broken collect2 doesn't work under 4.3+ + collect2name=`${CC} -print-prog-name=collect2` + if test -f "$collect2name" && + strings "$collect2name" | $GREP resolve_lib_name >/dev/null + then + # We have reworked collect2 + : + else + # We have old collect2 + hardcode_direct=unsupported + # It fails to find uninstalled libraries when the uninstalled + # path is not listed in the libpath. Setting hardcode_minus_L + # to unsupported forces relinking + hardcode_minus_L=yes + hardcode_libdir_flag_spec='-L$libdir' + hardcode_libdir_separator= + fi + ;; + esac + shared_flag='-shared' + if test "$aix_use_runtimelinking" = yes; then + shared_flag="$shared_flag "'${wl}-G' + fi + link_all_deplibs=no + else + # not using gcc + if test "$host_cpu" = ia64; then + # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release + # chokes on -Wl,-G. The following line is correct: + shared_flag='-G' + else + if test "$aix_use_runtimelinking" = yes; then + shared_flag='${wl}-G' + else + shared_flag='${wl}-bM:SRE' + fi + fi + fi + + export_dynamic_flag_spec='${wl}-bexpall' + # It seems that -bexpall does not export symbols beginning with + # underscore (_), so it is better to generate a list of symbols to export. + always_export_symbols=yes + if test "$aix_use_runtimelinking" = yes; then + # Warning - without using the other runtime loading flags (-brtl), + # -berok will link without error, but may produce a broken library. + allow_undefined_flag='-berok' + # Determine the default libpath from the value encoded in an + # empty executable. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + +lt_aix_libpath_sed=' + /Import File Strings/,/^$/ { + /^0/ { + s/^0 *\(.*\)$/\1/ + p + } + }' +aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` +# Check for a 64-bit object if we didn't find anything. +if test -z "$aix_libpath"; then + aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` +fi +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi + + hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" + archive_expsym_cmds='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" + else + if test "$host_cpu" = ia64; then + hardcode_libdir_flag_spec='${wl}-R $libdir:/usr/lib:/lib' + allow_undefined_flag="-z nodefs" + archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" + else + # Determine the default libpath from the value encoded in an + # empty executable. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + +lt_aix_libpath_sed=' + /Import File Strings/,/^$/ { + /^0/ { + s/^0 *\(.*\)$/\1/ + p + } + }' +aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` +# Check for a 64-bit object if we didn't find anything. +if test -z "$aix_libpath"; then + aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` +fi +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi + + hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" + # Warning - without using the other run time loading flags, + # -berok will link without error, but may produce a broken library. + no_undefined_flag=' ${wl}-bernotok' + allow_undefined_flag=' ${wl}-berok' + # Exported symbols can be pulled into shared objects from archives + whole_archive_flag_spec='$convenience' + archive_cmds_need_lc=yes + # This is similar to how AIX traditionally builds its shared libraries. + archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' + fi + fi + ;; + + amigaos*) + case $host_cpu in + powerpc) + # see comment about AmigaOS4 .so support + archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + archive_expsym_cmds='' + ;; + m68k) + archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' + hardcode_libdir_flag_spec='-L$libdir' + hardcode_minus_L=yes + ;; + esac + ;; + + bsdi[45]*) + export_dynamic_flag_spec=-rdynamic + ;; + + cygwin* | mingw* | pw32* | cegcc*) + # When not using gcc, we currently assume that we are using + # Microsoft Visual C++. + # hardcode_libdir_flag_spec is actually meaningless, as there is + # no search path for DLLs. + hardcode_libdir_flag_spec=' ' + allow_undefined_flag=unsupported + # Tell ltmain to make .lib files, not .a files. + libext=lib + # Tell ltmain to make .dll files, not .so files. + shrext_cmds=".dll" + # FIXME: Setting linknames here is a bad hack. + archive_cmds='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames=' + # The linker will automatically build a .lib file if we build a DLL. + old_archive_from_new_cmds='true' + # FIXME: Should let the user specify the lib program. + old_archive_cmds='lib -OUT:$oldlib$oldobjs$old_deplibs' + fix_srcfile_path='`cygpath -w "$srcfile"`' + enable_shared_with_static_runtimes=yes + ;; + + darwin* | rhapsody*) + + + archive_cmds_need_lc=no + hardcode_direct=no + hardcode_automatic=yes + hardcode_shlibpath_var=unsupported + whole_archive_flag_spec='' + link_all_deplibs=yes + allow_undefined_flag="$_lt_dar_allow_undefined" + case $cc_basename in + ifort*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then + output_verbose_link_cmd=echo + archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}" + module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}" + archive_expsym_cmds="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}" + module_expsym_cmds="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}" + + else + ld_shlibs=no + fi + + ;; + + dgux*) + archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + hardcode_libdir_flag_spec='-L$libdir' + hardcode_shlibpath_var=no + ;; + + freebsd1*) + ld_shlibs=no + ;; + + # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor + # support. Future versions do this automatically, but an explicit c++rt0.o + # does not break anything, and helps significantly (at the cost of a little + # extra space). + freebsd2.2*) + archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' + hardcode_libdir_flag_spec='-R$libdir' + hardcode_direct=yes + hardcode_shlibpath_var=no + ;; + + # Unfortunately, older versions of FreeBSD 2 do not have this feature. + freebsd2*) + archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' + hardcode_direct=yes + hardcode_minus_L=yes + hardcode_shlibpath_var=no + ;; + + # FreeBSD 3 and greater uses gcc -shared to do shared libraries. + freebsd* | dragonfly*) + archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' + hardcode_libdir_flag_spec='-R$libdir' + hardcode_direct=yes + hardcode_shlibpath_var=no + ;; + + hpux9*) + if test "$GCC" = yes; then + archive_cmds='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' + else + archive_cmds='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' + fi + hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' + hardcode_libdir_separator=: + hardcode_direct=yes + + # hardcode_minus_L: Not really in the search PATH, + # but as the default location of the library. + hardcode_minus_L=yes + export_dynamic_flag_spec='${wl}-E' + ;; + + hpux10*) + if test "$GCC" = yes -a "$with_gnu_ld" = no; then + archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' + else + archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' + fi + if test "$with_gnu_ld" = no; then + hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' + hardcode_libdir_flag_spec_ld='+b $libdir' + hardcode_libdir_separator=: + hardcode_direct=yes + hardcode_direct_absolute=yes + export_dynamic_flag_spec='${wl}-E' + # hardcode_minus_L: Not really in the search PATH, + # but as the default location of the library. + hardcode_minus_L=yes + fi + ;; + + hpux11*) + if test "$GCC" = yes -a "$with_gnu_ld" = no; then + case $host_cpu in + hppa*64*) + archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' + ;; + ia64*) + archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' + ;; + *) + archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' + ;; + esac + else + case $host_cpu in + hppa*64*) + archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' + ;; + ia64*) + archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' + ;; + *) + archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' + ;; + esac + fi + if test "$with_gnu_ld" = no; then + hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' + hardcode_libdir_separator=: + + case $host_cpu in + hppa*64*|ia64*) + hardcode_direct=no + hardcode_shlibpath_var=no + ;; + *) + hardcode_direct=yes + hardcode_direct_absolute=yes + export_dynamic_flag_spec='${wl}-E' + + # hardcode_minus_L: Not really in the search PATH, + # but as the default location of the library. + hardcode_minus_L=yes + ;; + esac + fi + ;; + + irix5* | irix6* | nonstopux*) + if test "$GCC" = yes; then + archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' + # Try to use the -exported_symbol ld option, if it does not + # work, assume that -exports_file does not work either and + # implicitly export all symbols. + save_LDFLAGS="$LDFLAGS" + LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null" + cat >conftest.$ac_ext <<_ACEOF +int foo(void) {} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib' + +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext + LDFLAGS="$save_LDFLAGS" + else + archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' + archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib' + fi + archive_cmds_need_lc='no' + hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' + hardcode_libdir_separator=: + inherit_rpath=yes + link_all_deplibs=yes + ;; + + netbsd* | netbsdelf*-gnu) + if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then + archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out + else + archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF + fi + hardcode_libdir_flag_spec='-R$libdir' + hardcode_direct=yes + hardcode_shlibpath_var=no + ;; + + newsos6) + archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + hardcode_direct=yes + hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' + hardcode_libdir_separator=: + hardcode_shlibpath_var=no + ;; + + *nto* | *qnx*) + ;; + + openbsd*) + if test -f /usr/libexec/ld.so; then + hardcode_direct=yes + hardcode_shlibpath_var=no + hardcode_direct_absolute=yes + if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then + archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' + archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' + hardcode_libdir_flag_spec='${wl}-rpath,$libdir' + export_dynamic_flag_spec='${wl}-E' + else + case $host_os in + openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*) + archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' + hardcode_libdir_flag_spec='-R$libdir' + ;; + *) + archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' + hardcode_libdir_flag_spec='${wl}-rpath,$libdir' + ;; + esac + fi + else + ld_shlibs=no + fi + ;; + + os2*) + hardcode_libdir_flag_spec='-L$libdir' + hardcode_minus_L=yes + allow_undefined_flag=unsupported + archive_cmds='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' + old_archive_from_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' + ;; + + osf3*) + if test "$GCC" = yes; then + allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' + archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' + else + allow_undefined_flag=' -expect_unresolved \*' + archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' + fi + archive_cmds_need_lc='no' + hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' + hardcode_libdir_separator=: + ;; + + osf4* | osf5*) # as osf3* with the addition of -msym flag + if test "$GCC" = yes; then + allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' + archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' + hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' + else + allow_undefined_flag=' -expect_unresolved \*' + archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' + archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~ + $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp' + + # Both c and cxx compiler support -rpath directly + hardcode_libdir_flag_spec='-rpath $libdir' + fi + archive_cmds_need_lc='no' + hardcode_libdir_separator=: + ;; + + solaris*) + no_undefined_flag=' -z defs' + if test "$GCC" = yes; then + wlarc='${wl}' + archive_cmds='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' + archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ + $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' + else + case `$CC -V 2>&1` in + *"Compilers 5.0"*) + wlarc='' + archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' + archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ + $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp' + ;; + *) + wlarc='${wl}' + archive_cmds='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags' + archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ + $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' + ;; + esac + fi + hardcode_libdir_flag_spec='-R$libdir' + hardcode_shlibpath_var=no + case $host_os in + solaris2.[0-5] | solaris2.[0-5].*) ;; + *) + # The compiler driver will combine and reorder linker options, + # but understands `-z linker_flag'. GCC discards it without `$wl', + # but is careful enough not to reorder. + # Supported since Solaris 2.6 (maybe 2.5.1?) + if test "$GCC" = yes; then + whole_archive_flag_spec='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract' + else + whole_archive_flag_spec='-z allextract$convenience -z defaultextract' + fi + ;; + esac + link_all_deplibs=yes + ;; + + sunos4*) + if test "x$host_vendor" = xsequent; then + # Use $CC to link under sequent, because it throws in some extra .o + # files that make .init and .fini sections work. + archive_cmds='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags' + else + archive_cmds='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags' + fi + hardcode_libdir_flag_spec='-L$libdir' + hardcode_direct=yes + hardcode_minus_L=yes + hardcode_shlibpath_var=no + ;; + + sysv4) + case $host_vendor in + sni) + archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + hardcode_direct=yes # is this really true??? + ;; + siemens) + ## LD is ld it makes a PLAMLIB + ## CC just makes a GrossModule. + archive_cmds='$LD -G -o $lib $libobjs $deplibs $linker_flags' + reload_cmds='$CC -r -o $output$reload_objs' + hardcode_direct=no + ;; + motorola) + archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + hardcode_direct=no #Motorola manual says yes, but my tests say they lie + ;; + esac + runpath_var='LD_RUN_PATH' + hardcode_shlibpath_var=no + ;; + + sysv4.3*) + archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + hardcode_shlibpath_var=no + export_dynamic_flag_spec='-Bexport' + ;; + + sysv4*MP*) + if test -d /usr/nec; then + archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + hardcode_shlibpath_var=no + runpath_var=LD_RUN_PATH + hardcode_runpath_var=yes + ld_shlibs=yes + fi + ;; + + sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*) + no_undefined_flag='${wl}-z,text' + archive_cmds_need_lc=no + hardcode_shlibpath_var=no + runpath_var='LD_RUN_PATH' + + if test "$GCC" = yes; then + archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + else + archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + fi + ;; + + sysv5* | sco3.2v5* | sco5v6*) + # Note: We can NOT use -z defs as we might desire, because we do not + # link with -lc, and that would cause any symbols used from libc to + # always be unresolved, which means just about no library would + # ever link correctly. If we're not using GNU ld we use -z text + # though, which does catch some bad symbols but isn't as heavy-handed + # as -z defs. + no_undefined_flag='${wl}-z,text' + allow_undefined_flag='${wl}-z,nodefs' + archive_cmds_need_lc=no + hardcode_shlibpath_var=no + hardcode_libdir_flag_spec='${wl}-R,$libdir' + hardcode_libdir_separator=':' + link_all_deplibs=yes + export_dynamic_flag_spec='${wl}-Bexport' + runpath_var='LD_RUN_PATH' + + if test "$GCC" = yes; then + archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + else + archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + fi + ;; + + uts4*) + archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + hardcode_libdir_flag_spec='-L$libdir' + hardcode_shlibpath_var=no + ;; + + *) + ld_shlibs=no + ;; + esac + + if test x$host_vendor = xsni; then + case $host in + sysv4 | sysv4.2uw2* | sysv4.3* | sysv5*) + export_dynamic_flag_spec='${wl}-Blargedynsym' + ;; + esac + fi + fi + +{ $as_echo "$as_me:$LINENO: result: $ld_shlibs" >&5 +$as_echo "$ld_shlibs" >&6; } +test "$ld_shlibs" = no && can_build_shared=no + +with_gnu_ld=$with_gnu_ld + + + + + + + + + + + + + + + +# +# Do we need to explicitly link libc? +# +case "x$archive_cmds_need_lc" in +x|xyes) + # Assume -lc should be added + archive_cmds_need_lc=yes + + if test "$enable_shared" = yes && test "$GCC" = yes; then + case $archive_cmds in + *'~'*) + # FIXME: we may have to deal with multi-command sequences. + ;; + '$CC '*) + # Test whether the compiler implicitly links with -lc since on some + # systems, -lgcc has to come before -lc. If gcc already passes -lc + # to ld, don't add -lc before -lgcc. + { $as_echo "$as_me:$LINENO: checking whether -lc should be explicitly linked in" >&5 +$as_echo_n "checking whether -lc should be explicitly linked in... " >&6; } + $RM conftest* + echo "$lt_simple_compile_test_code" > conftest.$ac_ext + + if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } 2>conftest.err; then + soname=conftest + lib=conftest + libobjs=conftest.$ac_objext + deplibs= + wl=$lt_prog_compiler_wl + pic_flag=$lt_prog_compiler_pic + compiler_flags=-v + linker_flags=-v + verstring= + output_objdir=. + libname=conftest + lt_save_allow_undefined_flag=$allow_undefined_flag + allow_undefined_flag= + if { (eval echo "$as_me:$LINENO: \"$archive_cmds 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1\"") >&5 + (eval $archive_cmds 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } + then + archive_cmds_need_lc=no + else + archive_cmds_need_lc=yes + fi + allow_undefined_flag=$lt_save_allow_undefined_flag + else + cat conftest.err 1>&5 + fi + $RM conftest* + { $as_echo "$as_me:$LINENO: result: $archive_cmds_need_lc" >&5 +$as_echo "$archive_cmds_need_lc" >&6; } + ;; + esac + fi + ;; +esac + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + { $as_echo "$as_me:$LINENO: checking dynamic linker characteristics" >&5 +$as_echo_n "checking dynamic linker characteristics... " >&6; } + +if test "$GCC" = yes; then + case $host_os in + darwin*) lt_awk_arg="/^libraries:/,/LR/" ;; + *) lt_awk_arg="/^libraries:/" ;; + esac + lt_search_path_spec=`$CC -print-search-dirs | awk $lt_awk_arg | $SED -e "s/^libraries://" -e "s,=/,/,g"` + if $ECHO "$lt_search_path_spec" | $GREP ';' >/dev/null ; then + # if the path contains ";" then we assume it to be the separator + # otherwise default to the standard path separator (i.e. ":") - it is + # assumed that no part of a normal pathname contains ";" but that should + # okay in the real world where ";" in dirpaths is itself problematic. + lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e 's/;/ /g'` + else + lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"` + fi + # Ok, now we have the path, separated by spaces, we can step through it + # and add multilib dir if necessary. + lt_tmp_lt_search_path_spec= + lt_multi_os_dir=`$CC $CPPFLAGS $CFLAGS $LDFLAGS -print-multi-os-directory 2>/dev/null` + for lt_sys_path in $lt_search_path_spec; do + if test -d "$lt_sys_path/$lt_multi_os_dir"; then + lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path/$lt_multi_os_dir" + else + test -d "$lt_sys_path" && \ + lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path" + fi + done + lt_search_path_spec=`$ECHO $lt_tmp_lt_search_path_spec | awk ' +BEGIN {RS=" "; FS="/|\n";} { + lt_foo=""; + lt_count=0; + for (lt_i = NF; lt_i > 0; lt_i--) { + if ($lt_i != "" && $lt_i != ".") { + if ($lt_i == "..") { + lt_count++; + } else { + if (lt_count == 0) { + lt_foo="/" $lt_i lt_foo; + } else { + lt_count--; + } + } + } + } + if (lt_foo != "") { lt_freq[lt_foo]++; } + if (lt_freq[lt_foo] == 1) { print lt_foo; } +}'` + sys_lib_search_path_spec=`$ECHO $lt_search_path_spec` +else + sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib" +fi +library_names_spec= +libname_spec='lib$name' +soname_spec= +shrext_cmds=".so" +postinstall_cmds= +postuninstall_cmds= +finish_cmds= +finish_eval= +shlibpath_var= +shlibpath_overrides_runpath=unknown +version_type=none +dynamic_linker="$host_os ld.so" +sys_lib_dlsearch_path_spec="/lib /usr/lib" +need_lib_prefix=unknown +hardcode_into_libs=no + +# when you set need_version to no, make sure it does not cause -set_version +# flags to be left without arguments +need_version=unknown + +case $host_os in +aix3*) + version_type=linux + library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a' + shlibpath_var=LIBPATH + + # AIX 3 has no versioning support, so we append a major version to the name. + soname_spec='${libname}${release}${shared_ext}$major' + ;; + +aix[4-9]*) + version_type=linux + need_lib_prefix=no + need_version=no + hardcode_into_libs=yes + if test "$host_cpu" = ia64; then + # AIX 5 supports IA64 + library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}' + shlibpath_var=LD_LIBRARY_PATH + else + # With GCC up to 2.95.x, collect2 would create an import file + # for dependence libraries. The import file would start with + # the line `#! .'. This would cause the generated library to + # depend on `.', always an invalid library. This was fixed in + # development snapshots of GCC prior to 3.0. + case $host_os in + aix4 | aix4.[01] | aix4.[01].*) + if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)' + echo ' yes ' + echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then + : + else + can_build_shared=no + fi + ;; + esac + # AIX (on Power*) has no versioning support, so currently we can not hardcode correct + # soname into executable. Probably we can add versioning support to + # collect2, so additional links can be useful in future. + if test "$aix_use_runtimelinking" = yes; then + # If using run time linking (on AIX 4.2 or later) use lib.so + # instead of lib.a to let people know that these are not + # typical AIX shared libraries. + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + else + # We preserve .a as extension for shared libraries through AIX4.2 + # and later when we are not doing run time linking. + library_names_spec='${libname}${release}.a $libname.a' + soname_spec='${libname}${release}${shared_ext}$major' + fi + shlibpath_var=LIBPATH + fi + ;; + +amigaos*) + case $host_cpu in + powerpc) + # Since July 2007 AmigaOS4 officially supports .so libraries. + # When compiling the executable, add -use-dynld -Lsobjs: to the compileline. + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + ;; + m68k) + library_names_spec='$libname.ixlibrary $libname.a' + # Create ${libname}_ixlibrary.a entries in /sys/libs. + finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done' + ;; + esac + ;; + +beos*) + library_names_spec='${libname}${shared_ext}' + dynamic_linker="$host_os ld.so" + shlibpath_var=LIBRARY_PATH + ;; + +bsdi[45]*) + version_type=linux + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir' + shlibpath_var=LD_LIBRARY_PATH + sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib" + sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib" + # the default ld.so.conf also contains /usr/contrib/lib and + # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow + # libtool to hard-code these into programs + ;; + +cygwin* | mingw* | pw32* | cegcc*) + version_type=windows + shrext_cmds=".dll" + need_version=no + need_lib_prefix=no + + case $GCC,$host_os in + yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*) + library_names_spec='$libname.dll.a' + # DLL is installed to $(libdir)/../bin by postinstall_cmds + postinstall_cmds='base_file=`basename \${file}`~ + dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~ + dldir=$destdir/`dirname \$dlpath`~ + test -d \$dldir || mkdir -p \$dldir~ + $install_prog $dir/$dlname \$dldir/$dlname~ + chmod a+x \$dldir/$dlname~ + if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then + eval '\''$striplib \$dldir/$dlname'\'' || exit \$?; + fi' + postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~ + dlpath=$dir/\$dldll~ + $RM \$dlpath' + shlibpath_overrides_runpath=yes + + case $host_os in + cygwin*) + # Cygwin DLLs use 'cyg' prefix rather than 'lib' + soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}' + sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib" + ;; + mingw* | cegcc*) + # MinGW DLLs use traditional 'lib' prefix + soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}' + sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"` + if $ECHO "$sys_lib_search_path_spec" | $GREP ';[c-zC-Z]:/' >/dev/null; then + # It is most probably a Windows format PATH printed by + # mingw gcc, but we are running on Cygwin. Gcc prints its search + # path with ; separators, and with drive letters. We can handle the + # drive letters (cygwin fileutils understands them), so leave them, + # especially as we might pass files found there to a mingw objdump, + # which wouldn't understand a cygwinified path. Ahh. + sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'` + else + sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"` + fi + ;; + pw32*) + # pw32 DLLs use 'pw' prefix rather than 'lib' + library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}' + ;; + esac + ;; + + *) + library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib' + ;; + esac + dynamic_linker='Win32 ld.exe' + # FIXME: first we should search . and the directory the executable is in + shlibpath_var=PATH + ;; + +darwin* | rhapsody*) + dynamic_linker="$host_os dyld" + version_type=darwin + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext' + soname_spec='${libname}${release}${major}$shared_ext' + shlibpath_overrides_runpath=yes + shlibpath_var=DYLD_LIBRARY_PATH + shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`' + + sys_lib_search_path_spec="$sys_lib_search_path_spec /usr/local/lib" + sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib' + ;; + +dgux*) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + ;; + +freebsd1*) + dynamic_linker=no + ;; + +freebsd* | dragonfly*) + # DragonFly does not have aout. When/if they implement a new + # versioning mechanism, adjust this. + if test -x /usr/bin/objformat; then + objformat=`/usr/bin/objformat` + else + case $host_os in + freebsd[123]*) objformat=aout ;; + *) objformat=elf ;; + esac + fi + version_type=freebsd-$objformat + case $version_type in + freebsd-elf*) + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' + need_version=no + need_lib_prefix=no + ;; + freebsd-*) + library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix' + need_version=yes + ;; + esac + shlibpath_var=LD_LIBRARY_PATH + case $host_os in + freebsd2*) + shlibpath_overrides_runpath=yes + ;; + freebsd3.[01]* | freebsdelf3.[01]*) + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + ;; + freebsd3.[2-9]* | freebsdelf3.[2-9]* | \ + freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1) + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + ;; + *) # from 4.6 on, and DragonFly + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + ;; + esac + ;; + +gnu*) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + hardcode_into_libs=yes + ;; + +hpux9* | hpux10* | hpux11*) + # Give a soname corresponding to the major version so that dld.sl refuses to + # link against other versions. + version_type=sunos + need_lib_prefix=no + need_version=no + case $host_cpu in + ia64*) + shrext_cmds='.so' + hardcode_into_libs=yes + dynamic_linker="$host_os dld.so" + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + if test "X$HPUX_IA64_MODE" = X32; then + sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib" + else + sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64" + fi + sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec + ;; + hppa*64*) + shrext_cmds='.sl' + hardcode_into_libs=yes + dynamic_linker="$host_os dld.sl" + shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH + shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64" + sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec + ;; + *) + shrext_cmds='.sl' + dynamic_linker="$host_os dld.sl" + shlibpath_var=SHLIB_PATH + shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + ;; + esac + # HP-UX runs *really* slowly unless shared libraries are mode 555. + postinstall_cmds='chmod 555 $lib' + ;; + +interix[3-9]*) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + ;; + +irix5* | irix6* | nonstopux*) + case $host_os in + nonstopux*) version_type=nonstopux ;; + *) + if test "$lt_cv_prog_gnu_ld" = yes; then + version_type=linux + else + version_type=irix + fi ;; + esac + need_lib_prefix=no + need_version=no + soname_spec='${libname}${release}${shared_ext}$major' + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}' + case $host_os in + irix5* | nonstopux*) + libsuff= shlibsuff= + ;; + *) + case $LD in # libtool.m4 will add one of these switches to LD + *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") + libsuff= shlibsuff= libmagic=32-bit;; + *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ") + libsuff=32 shlibsuff=N32 libmagic=N32;; + *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ") + libsuff=64 shlibsuff=64 libmagic=64-bit;; + *) libsuff= shlibsuff= libmagic=never-match;; + esac + ;; + esac + shlibpath_var=LD_LIBRARY${shlibsuff}_PATH + shlibpath_overrides_runpath=no + sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}" + sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}" + hardcode_into_libs=yes + ;; + +# No shared lib support for Linux oldld, aout, or coff. +linux*oldld* | linux*aout* | linux*coff*) + dynamic_linker=no + ;; + +# This must be Linux ELF. +linux* | k*bsd*-gnu) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + # Some binutils ld are patched to set DT_RUNPATH + save_LDFLAGS=$LDFLAGS + save_libdir=$libdir + eval "libdir=/foo; wl=\"$lt_prog_compiler_wl\"; \ + LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec\"" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then + shlibpath_overrides_runpath=yes +fi + +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext + LDFLAGS=$save_LDFLAGS + libdir=$save_libdir + + # This implies no fast_install, which is unacceptable. + # Some rework will be needed to allow for fast_install + # before this can be enabled. + hardcode_into_libs=yes + + # Append ld.so.conf contents to the search path + if test -f /etc/ld.so.conf; then + lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '` + sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra" + fi + + # We used to test for /lib/ld.so.1 and disable shared libraries on + # powerpc, because MkLinux only supported shared libraries with the + # GNU dynamic linker. Since this was broken with cross compilers, + # most powerpc-linux boxes support dynamic linking these days and + # people can always --disable-shared, the test was removed, and we + # assume the GNU/Linux dynamic linker is in use. + dynamic_linker='GNU/Linux ld.so' + ;; + +netbsdelf*-gnu) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + dynamic_linker='NetBSD ld.elf_so' + ;; + +netbsd*) + version_type=sunos + need_lib_prefix=no + need_version=no + if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' + finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' + dynamic_linker='NetBSD (a.out) ld.so' + else + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + dynamic_linker='NetBSD ld.elf_so' + fi + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + ;; + +newsos6) + version_type=linux + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + ;; + +*nto* | *qnx*) + version_type=qnx + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + dynamic_linker='ldqnx.so' + ;; + +openbsd*) + version_type=sunos + sys_lib_dlsearch_path_spec="/usr/lib" + need_lib_prefix=no + # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs. + case $host_os in + openbsd3.3 | openbsd3.3.*) need_version=yes ;; + *) need_version=no ;; + esac + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' + finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' + shlibpath_var=LD_LIBRARY_PATH + if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then + case $host_os in + openbsd2.[89] | openbsd2.[89].*) + shlibpath_overrides_runpath=no + ;; + *) + shlibpath_overrides_runpath=yes + ;; + esac + else + shlibpath_overrides_runpath=yes + fi + ;; + +os2*) + libname_spec='$name' + shrext_cmds=".dll" + need_lib_prefix=no + library_names_spec='$libname${shared_ext} $libname.a' + dynamic_linker='OS/2 ld.exe' + shlibpath_var=LIBPATH + ;; + +osf3* | osf4* | osf5*) + version_type=osf + need_lib_prefix=no + need_version=no + soname_spec='${libname}${release}${shared_ext}$major' + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + shlibpath_var=LD_LIBRARY_PATH + sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib" + sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec" + ;; + +rdos*) + dynamic_linker=no + ;; + +solaris*) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + # ldd complains unless libraries are executable + postinstall_cmds='chmod +x $lib' + ;; + +sunos4*) + version_type=sunos + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' + finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + if test "$with_gnu_ld" = yes; then + need_lib_prefix=no + fi + need_version=yes + ;; + +sysv4 | sysv4.3*) + version_type=linux + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + case $host_vendor in + sni) + shlibpath_overrides_runpath=no + need_lib_prefix=no + runpath_var=LD_RUN_PATH + ;; + siemens) + need_lib_prefix=no + ;; + motorola) + need_lib_prefix=no + need_version=no + shlibpath_overrides_runpath=no + sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib' + ;; + esac + ;; + +sysv4*MP*) + if test -d /usr/nec ;then + version_type=linux + library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}' + soname_spec='$libname${shared_ext}.$major' + shlibpath_var=LD_LIBRARY_PATH + fi + ;; + +sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) + version_type=freebsd-elf + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + if test "$with_gnu_ld" = yes; then + sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib' + else + sys_lib_search_path_spec='/usr/ccs/lib /usr/lib' + case $host_os in + sco3.2v5*) + sys_lib_search_path_spec="$sys_lib_search_path_spec /lib" + ;; + esac + fi + sys_lib_dlsearch_path_spec='/usr/lib' + ;; + +tpf*) + # TPF is a cross-target only. Preferred cross-host = GNU/Linux. + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + ;; + +uts4*) + version_type=linux + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + ;; + +*) + dynamic_linker=no + ;; +esac +{ $as_echo "$as_me:$LINENO: result: $dynamic_linker" >&5 +$as_echo "$dynamic_linker" >&6; } +test "$dynamic_linker" = no && can_build_shared=no + +variables_saved_for_relink="PATH $shlibpath_var $runpath_var" +if test "$GCC" = yes; then + variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH" +fi + +if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then + sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec" +fi +if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then + sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec" +fi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + { $as_echo "$as_me:$LINENO: checking how to hardcode library paths into programs" >&5 +$as_echo_n "checking how to hardcode library paths into programs... " >&6; } +hardcode_action= +if test -n "$hardcode_libdir_flag_spec" || + test -n "$runpath_var" || + test "X$hardcode_automatic" = "Xyes" ; then + + # We can hardcode non-existent directories. + if test "$hardcode_direct" != no && + # If the only mechanism to avoid hardcoding is shlibpath_var, we + # have to relink, otherwise we might link with an installed library + # when we should be linking with a yet-to-be-installed one + ## test "$_LT_TAGVAR(hardcode_shlibpath_var, )" != no && + test "$hardcode_minus_L" != no; then + # Linking always hardcodes the temporary library directory. + hardcode_action=relink + else + # We can link without hardcoding, and we can hardcode nonexisting dirs. + hardcode_action=immediate + fi +else + # We cannot hardcode anything, or else we can only hardcode existing + # directories. + hardcode_action=unsupported +fi +{ $as_echo "$as_me:$LINENO: result: $hardcode_action" >&5 +$as_echo "$hardcode_action" >&6; } + +if test "$hardcode_action" = relink || + test "$inherit_rpath" = yes; then + # Fast installation is not supported + enable_fast_install=no +elif test "$shlibpath_overrides_runpath" = yes || + test "$enable_shared" = no; then + # Fast installation is not necessary + enable_fast_install=needless +fi + + + + + + + if test "x$enable_dlopen" != xyes; then + enable_dlopen=unknown + enable_dlopen_self=unknown + enable_dlopen_self_static=unknown +else + lt_cv_dlopen=no + lt_cv_dlopen_libs= + + case $host_os in + beos*) + lt_cv_dlopen="load_add_on" + lt_cv_dlopen_libs= + lt_cv_dlopen_self=yes + ;; + + mingw* | pw32* | cegcc*) + lt_cv_dlopen="LoadLibrary" + lt_cv_dlopen_libs= + ;; + + cygwin*) + lt_cv_dlopen="dlopen" + lt_cv_dlopen_libs= + ;; + + darwin*) + # if libdl is installed we need to link against it + { $as_echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5 +$as_echo_n "checking for dlopen in -ldl... " >&6; } +if test "${ac_cv_lib_dl_dlopen+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-ldl $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char dlopen (); +int +main () +{ +return dlopen (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ac_cv_lib_dl_dlopen=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_dl_dlopen=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_dl_dlopen" >&5 +$as_echo "$ac_cv_lib_dl_dlopen" >&6; } +if test "x$ac_cv_lib_dl_dlopen" = x""yes; then + lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" +else + + lt_cv_dlopen="dyld" + lt_cv_dlopen_libs= + lt_cv_dlopen_self=yes + +fi + + ;; + + *) + { $as_echo "$as_me:$LINENO: checking for shl_load" >&5 +$as_echo_n "checking for shl_load... " >&6; } +if test "${ac_cv_func_shl_load+set}" = set; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define shl_load to an innocuous variant, in case declares shl_load. + For example, HP-UX 11i declares gettimeofday. */ +#define shl_load innocuous_shl_load + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char shl_load (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef shl_load + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char shl_load (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined __stub_shl_load || defined __stub___shl_load +choke me +#endif + +int +main () +{ +return shl_load (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ac_cv_func_shl_load=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_func_shl_load=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_func_shl_load" >&5 +$as_echo "$ac_cv_func_shl_load" >&6; } +if test "x$ac_cv_func_shl_load" = x""yes; then + lt_cv_dlopen="shl_load" +else + { $as_echo "$as_me:$LINENO: checking for shl_load in -ldld" >&5 +$as_echo_n "checking for shl_load in -ldld... " >&6; } +if test "${ac_cv_lib_dld_shl_load+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-ldld $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char shl_load (); +int +main () +{ +return shl_load (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ac_cv_lib_dld_shl_load=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_dld_shl_load=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_dld_shl_load" >&5 +$as_echo "$ac_cv_lib_dld_shl_load" >&6; } +if test "x$ac_cv_lib_dld_shl_load" = x""yes; then + lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld" +else + { $as_echo "$as_me:$LINENO: checking for dlopen" >&5 +$as_echo_n "checking for dlopen... " >&6; } +if test "${ac_cv_func_dlopen+set}" = set; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define dlopen to an innocuous variant, in case declares dlopen. + For example, HP-UX 11i declares gettimeofday. */ +#define dlopen innocuous_dlopen + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char dlopen (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef dlopen + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char dlopen (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined __stub_dlopen || defined __stub___dlopen +choke me +#endif + +int +main () +{ +return dlopen (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ac_cv_func_dlopen=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_func_dlopen=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_func_dlopen" >&5 +$as_echo "$ac_cv_func_dlopen" >&6; } +if test "x$ac_cv_func_dlopen" = x""yes; then + lt_cv_dlopen="dlopen" +else + { $as_echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5 +$as_echo_n "checking for dlopen in -ldl... " >&6; } +if test "${ac_cv_lib_dl_dlopen+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-ldl $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char dlopen (); +int +main () +{ +return dlopen (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ac_cv_lib_dl_dlopen=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_dl_dlopen=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_dl_dlopen" >&5 +$as_echo "$ac_cv_lib_dl_dlopen" >&6; } +if test "x$ac_cv_lib_dl_dlopen" = x""yes; then + lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" +else + { $as_echo "$as_me:$LINENO: checking for dlopen in -lsvld" >&5 +$as_echo_n "checking for dlopen in -lsvld... " >&6; } +if test "${ac_cv_lib_svld_dlopen+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lsvld $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char dlopen (); +int +main () +{ +return dlopen (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ac_cv_lib_svld_dlopen=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_svld_dlopen=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_svld_dlopen" >&5 +$as_echo "$ac_cv_lib_svld_dlopen" >&6; } +if test "x$ac_cv_lib_svld_dlopen" = x""yes; then + lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld" +else + { $as_echo "$as_me:$LINENO: checking for dld_link in -ldld" >&5 +$as_echo_n "checking for dld_link in -ldld... " >&6; } +if test "${ac_cv_lib_dld_dld_link+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-ldld $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char dld_link (); +int +main () +{ +return dld_link (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ac_cv_lib_dld_dld_link=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_dld_dld_link=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_dld_dld_link" >&5 +$as_echo "$ac_cv_lib_dld_dld_link" >&6; } +if test "x$ac_cv_lib_dld_dld_link" = x""yes; then + lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld" +fi + + +fi + + +fi + + +fi + + +fi + + +fi + + ;; + esac + + if test "x$lt_cv_dlopen" != xno; then + enable_dlopen=yes + else + enable_dlopen=no + fi + + case $lt_cv_dlopen in + dlopen) + save_CPPFLAGS="$CPPFLAGS" + test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H" + + save_LDFLAGS="$LDFLAGS" + wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\" + + save_LIBS="$LIBS" + LIBS="$lt_cv_dlopen_libs $LIBS" + + { $as_echo "$as_me:$LINENO: checking whether a program can dlopen itself" >&5 +$as_echo_n "checking whether a program can dlopen itself... " >&6; } +if test "${lt_cv_dlopen_self+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test "$cross_compiling" = yes; then : + lt_cv_dlopen_self=cross +else + lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2 + lt_status=$lt_dlunknown + cat > conftest.$ac_ext <<_LT_EOF +#line 11122 "configure" +#include "confdefs.h" + +#if HAVE_DLFCN_H +#include +#endif + +#include + +#ifdef RTLD_GLOBAL +# define LT_DLGLOBAL RTLD_GLOBAL +#else +# ifdef DL_GLOBAL +# define LT_DLGLOBAL DL_GLOBAL +# else +# define LT_DLGLOBAL 0 +# endif +#endif + +/* We may have to define LT_DLLAZY_OR_NOW in the command line if we + find out it does not work in some platform. */ +#ifndef LT_DLLAZY_OR_NOW +# ifdef RTLD_LAZY +# define LT_DLLAZY_OR_NOW RTLD_LAZY +# else +# ifdef DL_LAZY +# define LT_DLLAZY_OR_NOW DL_LAZY +# else +# ifdef RTLD_NOW +# define LT_DLLAZY_OR_NOW RTLD_NOW +# else +# ifdef DL_NOW +# define LT_DLLAZY_OR_NOW DL_NOW +# else +# define LT_DLLAZY_OR_NOW 0 +# endif +# endif +# endif +# endif +#endif + +void fnord() { int i=42;} +int main () +{ + void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW); + int status = $lt_dlunknown; + + if (self) + { + if (dlsym (self,"fnord")) status = $lt_dlno_uscore; + else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore; + /* dlclose (self); */ + } + else + puts (dlerror ()); + + return status; +} +_LT_EOF + if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && test -s conftest${ac_exeext} 2>/dev/null; then + (./conftest; exit; ) >&5 2>/dev/null + lt_status=$? + case x$lt_status in + x$lt_dlno_uscore) lt_cv_dlopen_self=yes ;; + x$lt_dlneed_uscore) lt_cv_dlopen_self=yes ;; + x$lt_dlunknown|x*) lt_cv_dlopen_self=no ;; + esac + else : + # compilation failed + lt_cv_dlopen_self=no + fi +fi +rm -fr conftest* + + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_dlopen_self" >&5 +$as_echo "$lt_cv_dlopen_self" >&6; } + + if test "x$lt_cv_dlopen_self" = xyes; then + wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\" + { $as_echo "$as_me:$LINENO: checking whether a statically linked program can dlopen itself" >&5 +$as_echo_n "checking whether a statically linked program can dlopen itself... " >&6; } +if test "${lt_cv_dlopen_self_static+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test "$cross_compiling" = yes; then : + lt_cv_dlopen_self_static=cross +else + lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2 + lt_status=$lt_dlunknown + cat > conftest.$ac_ext <<_LT_EOF +#line 11218 "configure" +#include "confdefs.h" + +#if HAVE_DLFCN_H +#include +#endif + +#include + +#ifdef RTLD_GLOBAL +# define LT_DLGLOBAL RTLD_GLOBAL +#else +# ifdef DL_GLOBAL +# define LT_DLGLOBAL DL_GLOBAL +# else +# define LT_DLGLOBAL 0 +# endif +#endif + +/* We may have to define LT_DLLAZY_OR_NOW in the command line if we + find out it does not work in some platform. */ +#ifndef LT_DLLAZY_OR_NOW +# ifdef RTLD_LAZY +# define LT_DLLAZY_OR_NOW RTLD_LAZY +# else +# ifdef DL_LAZY +# define LT_DLLAZY_OR_NOW DL_LAZY +# else +# ifdef RTLD_NOW +# define LT_DLLAZY_OR_NOW RTLD_NOW +# else +# ifdef DL_NOW +# define LT_DLLAZY_OR_NOW DL_NOW +# else +# define LT_DLLAZY_OR_NOW 0 +# endif +# endif +# endif +# endif +#endif + +void fnord() { int i=42;} +int main () +{ + void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW); + int status = $lt_dlunknown; + + if (self) + { + if (dlsym (self,"fnord")) status = $lt_dlno_uscore; + else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore; + /* dlclose (self); */ + } + else + puts (dlerror ()); + + return status; +} +_LT_EOF + if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 + (eval $ac_link) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && test -s conftest${ac_exeext} 2>/dev/null; then + (./conftest; exit; ) >&5 2>/dev/null + lt_status=$? + case x$lt_status in + x$lt_dlno_uscore) lt_cv_dlopen_self_static=yes ;; + x$lt_dlneed_uscore) lt_cv_dlopen_self_static=yes ;; + x$lt_dlunknown|x*) lt_cv_dlopen_self_static=no ;; + esac + else : + # compilation failed + lt_cv_dlopen_self_static=no + fi +fi +rm -fr conftest* + + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_dlopen_self_static" >&5 +$as_echo "$lt_cv_dlopen_self_static" >&6; } + fi + + CPPFLAGS="$save_CPPFLAGS" + LDFLAGS="$save_LDFLAGS" + LIBS="$save_LIBS" + ;; + esac + + case $lt_cv_dlopen_self in + yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;; + *) enable_dlopen_self=unknown ;; + esac + + case $lt_cv_dlopen_self_static in + yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;; + *) enable_dlopen_self_static=unknown ;; + esac +fi + + + + + + + + + + + + + + + + + +striplib= +old_striplib= +{ $as_echo "$as_me:$LINENO: checking whether stripping libraries is possible" >&5 +$as_echo_n "checking whether stripping libraries is possible... " >&6; } +if test -n "$STRIP" && $STRIP -V 2>&1 | $GREP "GNU strip" >/dev/null; then + test -z "$old_striplib" && old_striplib="$STRIP --strip-debug" + test -z "$striplib" && striplib="$STRIP --strip-unneeded" + { $as_echo "$as_me:$LINENO: result: yes" >&5 +$as_echo "yes" >&6; } +else +# FIXME - insert some real tests, host_os isn't really good enough + case $host_os in + darwin*) + if test -n "$STRIP" ; then + striplib="$STRIP -x" + old_striplib="$STRIP -S" + { $as_echo "$as_me:$LINENO: result: yes" >&5 +$as_echo "yes" >&6; } + else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } + fi + ;; + *) + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } + ;; + esac +fi + + + + + + + + + + + + + # Report which library types will actually be built + { $as_echo "$as_me:$LINENO: checking if libtool supports shared libraries" >&5 +$as_echo_n "checking if libtool supports shared libraries... " >&6; } + { $as_echo "$as_me:$LINENO: result: $can_build_shared" >&5 +$as_echo "$can_build_shared" >&6; } + + { $as_echo "$as_me:$LINENO: checking whether to build shared libraries" >&5 +$as_echo_n "checking whether to build shared libraries... " >&6; } + test "$can_build_shared" = "no" && enable_shared=no + + # On AIX, shared libraries and static libraries use the same namespace, and + # are all built from PIC. + case $host_os in + aix3*) + test "$enable_shared" = yes && enable_static=no + if test -n "$RANLIB"; then + archive_cmds="$archive_cmds~\$RANLIB \$lib" + postinstall_cmds='$RANLIB $lib' + fi + ;; + + aix[4-9]*) + if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then + test "$enable_shared" = yes && enable_static=no + fi + ;; + esac + { $as_echo "$as_me:$LINENO: result: $enable_shared" >&5 +$as_echo "$enable_shared" >&6; } + + { $as_echo "$as_me:$LINENO: checking whether to build static libraries" >&5 +$as_echo_n "checking whether to build static libraries... " >&6; } + # Make sure either enable_shared or enable_static is yes. + test "$enable_shared" = yes || enable_static=yes + { $as_echo "$as_me:$LINENO: result: $enable_static" >&5 +$as_echo "$enable_static" >&6; } + + + + +fi +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +CC="$lt_save_CC" + + + + + + + + + + + + + + ac_config_commands="$ac_config_commands libtool" + + + + +# Only expand once: + + + +# AC_PROG_INSTALL will generate an install target so that users may +# just type 'make install' to install the software. +# Find a good install program. We prefer a C program (faster), +# so one script is as good as another. But avoid the broken or +# incompatible versions: +# SysV /etc/install, /usr/sbin/install +# SunOS /usr/etc/install +# IRIX /sbin/install +# AIX /bin/install +# AmigaOS /C/install, which installs bootblocks on floppy discs +# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag +# AFS /usr/afsws/bin/install, which mishandles nonexistent args +# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff" +# OS/2's system install, which has a completely different semantic +# ./install, which can be erroneously created by make from ./install.sh. +# Reject install programs that cannot install multiple files. +{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5 +$as_echo_n "checking for a BSD-compatible install... " >&6; } +if test -z "$INSTALL"; then +if test "${ac_cv_path_install+set}" = set; then + $as_echo_n "(cached) " >&6 +else + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in + ./ | .// | /cC/* | \ + /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ + ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \ + /usr/ucb/* ) ;; + *) + # OSF1 and SCO ODT 3.0 have their own names for install. + # Don't use installbsd from OSF since it installs stuff as root + # by default. + for ac_prog in ginstall scoinst install; do + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then + if test $ac_prog = install && + grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # AIX install. It has an incompatible calling convention. + : + elif test $ac_prog = install && + grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # program-specific install script used by HP pwplus--don't use. + : + else + rm -rf conftest.one conftest.two conftest.dir + echo one > conftest.one + echo two > conftest.two + mkdir conftest.dir + if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" && + test -s conftest.one && test -s conftest.two && + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then + ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" + break 3 + fi + fi + fi + done + done + ;; +esac + +done +IFS=$as_save_IFS + +rm -rf conftest.one conftest.two conftest.dir + +fi + if test "${ac_cv_path_install+set}" = set; then + INSTALL=$ac_cv_path_install + else + # As a last resort, use the slow shell script. Don't cache a + # value for INSTALL within a source directory, because that will + # break other packages using the cache if that directory is + # removed, or if the value is a relative name. + INSTALL=$ac_install_sh + fi +fi +{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5 +$as_echo "$INSTALL" >&6; } + +# Use test -z because SunOS4 sh mishandles braces in ${var-val}. +# It thinks the first close brace ends the variable substitution. +test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}' + +test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' + +test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' + + +# check for C++ preprocessor and compiler and the library compiler +# (might change the compiler flags) +# +# Determine a C compiler to use. If using the GNU C compiler, set +# shell variable GCC to `yes'. If output variable CFLAGS was not +# already set, set it to `-g -O2' for the GNU C compiler (`-O2' on +# systems where GCC does not accept `-g'), or `-g' for other +# compilers. +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. +set dummy ${ac_tool_prefix}gcc; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_CC="${ac_tool_prefix}gcc" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:$LINENO: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$ac_cv_prog_CC"; then + ac_ct_CC=$CC + # Extract the first word of "gcc", so it can be a program name with args. +set dummy gcc; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_CC="gcc" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi +else + CC="$ac_cv_prog_CC" +fi + +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. +set dummy ${ac_tool_prefix}cc; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_CC="${ac_tool_prefix}cc" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:$LINENO: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + + fi +fi +if test -z "$CC"; then + # Extract the first word of "cc", so it can be a program name with args. +set dummy cc; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else + ac_prog_rejected=no +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then + ac_prog_rejected=yes + continue + fi + ac_cv_prog_CC="cc" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +if test $ac_prog_rejected = yes; then + # We found a bogon in the path, so make sure we never use it. + set dummy $ac_cv_prog_CC + shift + if test $# != 0; then + # We chose a different compiler from the bogus one. + # However, it has the same basename, so the bogon will be chosen + # first if we set CC to just the basename; use the full file name. + shift + ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@" + fi +fi +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:$LINENO: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + +fi +if test -z "$CC"; then + if test -n "$ac_tool_prefix"; then + for ac_prog in cl.exe + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. +set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_CC+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$CC"; then + ac_cv_prog_CC="$CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_CC="$ac_tool_prefix$ac_prog" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +CC=$ac_cv_prog_CC +if test -n "$CC"; then + { $as_echo "$as_me:$LINENO: result: $CC" >&5 +$as_echo "$CC" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$CC" && break + done +fi +if test -z "$CC"; then + ac_ct_CC=$CC + for ac_prog in cl.exe +do + # Extract the first word of "$ac_prog", so it can be a program name with args. +set dummy $ac_prog; ac_word=$2 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 +$as_echo_n "checking for $ac_word... " >&6; } +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -n "$ac_ct_CC"; then + ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. +else +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then + ac_cv_prog_ac_ct_CC="$ac_prog" + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi +done +done +IFS=$as_save_IFS + +fi +fi +ac_ct_CC=$ac_cv_prog_ac_ct_CC +if test -n "$ac_ct_CC"; then + { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 +$as_echo "$ac_ct_CC" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + + test -n "$ac_ct_CC" && break +done + + if test "x$ac_ct_CC" = x; then + CC="" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 +$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} +ac_tool_warned=yes ;; +esac + CC=$ac_ct_CC + fi +fi + +fi + + +test -z "$CC" && { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } + +# Provide some information about the compiler. +$as_echo "$as_me:$LINENO: checking for C compiler version" >&5 +set X $ac_compile +ac_compiler=$2 +{ (ac_try="$ac_compiler --version >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler --version >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -v >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -v >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -V >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -V >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } + +{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 +$as_echo_n "checking whether we are using the GNU C compiler... " >&6; } +if test "${ac_cv_c_compiler_gnu+set}" = set; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +#ifndef __GNUC__ + choke me +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_compiler_gnu=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_compiler_gnu=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +ac_cv_c_compiler_gnu=$ac_compiler_gnu + +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 +$as_echo "$ac_cv_c_compiler_gnu" >&6; } +if test $ac_compiler_gnu = yes; then + GCC=yes +else + GCC= +fi +ac_test_CFLAGS=${CFLAGS+set} +ac_save_CFLAGS=$CFLAGS +{ $as_echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 +$as_echo_n "checking whether $CC accepts -g... " >&6; } +if test "${ac_cv_prog_cc_g+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_save_c_werror_flag=$ac_c_werror_flag + ac_c_werror_flag=yes + ac_cv_prog_cc_g=no + CFLAGS="-g" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_cv_prog_cc_g=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + CFLAGS="" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + : +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_c_werror_flag=$ac_save_c_werror_flag + CFLAGS="-g" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_cv_prog_cc_g=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + ac_c_werror_flag=$ac_save_c_werror_flag +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 +$as_echo "$ac_cv_prog_cc_g" >&6; } +if test "$ac_test_CFLAGS" = set; then + CFLAGS=$ac_save_CFLAGS +elif test $ac_cv_prog_cc_g = yes; then + if test "$GCC" = yes; then + CFLAGS="-g -O2" + else + CFLAGS="-g" + fi +else + if test "$GCC" = yes; then + CFLAGS="-O2" + else + CFLAGS= + fi +fi +{ $as_echo "$as_me:$LINENO: checking for $CC option to accept ISO C89" >&5 +$as_echo_n "checking for $CC option to accept ISO C89... " >&6; } +if test "${ac_cv_prog_cc_c89+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_cv_prog_cc_c89=no +ac_save_CC=$CC +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#include +#include +/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ +struct buf { int x; }; +FILE * (*rcsopen) (struct buf *, struct stat *, int); +static char *e (p, i) + char **p; + int i; +{ + return p[i]; +} +static char *f (char * (*g) (char **, int), char **p, ...) +{ + char *s; + va_list v; + va_start (v,p); + s = g (p, va_arg (v,int)); + va_end (v); + return s; +} + +/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has + function prototypes and stuff, but not '\xHH' hex character constants. + These don't provoke an error unfortunately, instead are silently treated + as 'x'. The following induces an error, until -std is added to get + proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an + array size at least. It's necessary to write '\x00'==0 to get something + that's true only with -std. */ +int osf4_cc_array ['\x00' == 0 ? 1 : -1]; + +/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters + inside strings and character constants. */ +#define FOO(x) 'x' +int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1]; + +int test (int i, double x); +struct s1 {int (*f) (int a);}; +struct s2 {int (*f) (double a);}; +int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); +int argc; +char **argv; +int +main () +{ +return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; + ; + return 0; +} +_ACEOF +for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ + -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" +do + CC="$ac_save_CC $ac_arg" + rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_cv_prog_cc_c89=$ac_arg +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -f core conftest.err conftest.$ac_objext + test "x$ac_cv_prog_cc_c89" != "xno" && break +done +rm -f conftest.$ac_ext +CC=$ac_save_CC + +fi +# AC_CACHE_VAL +case "x$ac_cv_prog_cc_c89" in + x) + { $as_echo "$as_me:$LINENO: result: none needed" >&5 +$as_echo "none needed" >&6; } ;; + xno) + { $as_echo "$as_me:$LINENO: result: unsupported" >&5 +$as_echo "unsupported" >&6; } ;; + *) + CC="$CC $ac_cv_prog_cc_c89" + { $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_c89" >&5 +$as_echo "$ac_cv_prog_cc_c89" >&6; } ;; +esac + + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +depcc="$CC" am_compiler_list= + +{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5 +$as_echo_n "checking dependency style of $depcc... " >&6; } +if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then + # We make a subdir and do the tests there. Otherwise we can end up + # making bogus files that we don't know about and never remove. For + # instance it was reported that on HP-UX the gcc test will end up + # making a dummy file named `D' -- because `-MD' means `put the output + # in D'. + mkdir conftest.dir + # Copy depcomp to subdir because otherwise we won't find it if we're + # using a relative directory. + cp "$am_depcomp" conftest.dir + cd conftest.dir + # We will build objects and dependencies in a subdirectory because + # it helps to detect inapplicable dependency modes. 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Now check whether nonexistent headers + # can be detected and how. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + # Broken: success on invalid input. +continue +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Passes both tests. +ac_preproc_ok=: +break +fi + +rm -f conftest.err conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + break +fi + + done + ac_cv_prog_CPP=$CPP + +fi + CPP=$ac_cv_prog_CPP +else + ac_cv_prog_CPP=$CPP +fi +{ $as_echo "$as_me:$LINENO: result: $CPP" >&5 +$as_echo "$CPP" >&6; } +ac_preproc_ok=false +for ac_c_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + : +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Broken: fails on valid input. +continue +fi + +rm -f conftest.err conftest.$ac_ext + + # OK, works on sane cases. 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Some variables (like enable_shared) +# are currently assumed to apply to all compilers on this platform, +# and will be corrupted by setting them based on a non-working compiler. +if test "$_lt_caught_CXX_error" != yes; then + # Code to be used in simple compile tests + lt_simple_compile_test_code="int some_variable = 0;" + + # Code to be used in simple link tests + lt_simple_link_test_code='int main(int, char *[]) { return(0); }' + + # ltmain only uses $CC for tagged configurations so make sure $CC is set. + + + + + + +# If no C compiler was specified, use CC. +LTCC=${LTCC-"$CC"} + +# If no C compiler flags were specified, use CFLAGS. +LTCFLAGS=${LTCFLAGS-"$CFLAGS"} + +# Allow CC to be a program name with arguments. +compiler=$CC + + + # save warnings/boilerplate of simple test code + ac_outfile=conftest.$ac_objext +echo "$lt_simple_compile_test_code" >conftest.$ac_ext +eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err +_lt_compiler_boilerplate=`cat conftest.err` +$RM conftest* + + ac_outfile=conftest.$ac_objext +echo "$lt_simple_link_test_code" >conftest.$ac_ext +eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err +_lt_linker_boilerplate=`cat conftest.err` +$RM -r conftest* + + + # Allow CC to be a program name with arguments. + lt_save_CC=$CC + lt_save_LD=$LD + lt_save_GCC=$GCC + GCC=$GXX + lt_save_with_gnu_ld=$with_gnu_ld + lt_save_path_LD=$lt_cv_path_LD + if test -n "${lt_cv_prog_gnu_ldcxx+set}"; then + lt_cv_prog_gnu_ld=$lt_cv_prog_gnu_ldcxx + else + $as_unset lt_cv_prog_gnu_ld + fi + if test -n "${lt_cv_path_LDCXX+set}"; then + lt_cv_path_LD=$lt_cv_path_LDCXX + else + $as_unset lt_cv_path_LD + fi + test -z "${LDCXX+set}" || LD=$LDCXX + CC=${CXX-"c++"} + compiler=$CC + compiler_CXX=$CC + for cc_temp in $compiler""; do + case $cc_temp in + compile | *[\\/]compile | ccache | *[\\/]ccache ) ;; + distcc | *[\\/]distcc | purify | *[\\/]purify ) ;; + \-*) ;; + *) break;; + esac +done +cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"` + + + if test -n "$compiler"; then + # We don't want -fno-exception when compiling C++ code, so set the + # no_builtin_flag separately + if test "$GXX" = yes; then + lt_prog_compiler_no_builtin_flag_CXX=' -fno-builtin' + else + lt_prog_compiler_no_builtin_flag_CXX= + fi + + if test "$GXX" = yes; then + # Set up default GNU C++ configuration + + + +# Check whether --with-gnu-ld was given. +if test "${with_gnu_ld+set}" = set; then + withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes +else + with_gnu_ld=no +fi + +ac_prog=ld +if test "$GCC" = yes; then + # Check if gcc -print-prog-name=ld gives a path. + { $as_echo "$as_me:$LINENO: checking for ld used by $CC" >&5 +$as_echo_n "checking for ld used by $CC... " >&6; } + case $host in + *-*-mingw*) + # gcc leaves a trailing carriage return which upsets mingw + ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;; + *) + ac_prog=`($CC -print-prog-name=ld) 2>&5` ;; + esac + case $ac_prog in + # Accept absolute paths. + [\\/]* | ?:[\\/]*) + re_direlt='/[^/][^/]*/\.\./' + # Canonicalize the pathname of ld + ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'` + while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do + ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"` + done + test -z "$LD" && LD="$ac_prog" + ;; + "") + # If it fails, then pretend we aren't using GCC. + ac_prog=ld + ;; + *) + # If it is relative, then search for the first ld in PATH. + with_gnu_ld=unknown + ;; + esac +elif test "$with_gnu_ld" = yes; then + { $as_echo "$as_me:$LINENO: checking for GNU ld" >&5 +$as_echo_n "checking for GNU ld... " >&6; } +else + { $as_echo "$as_me:$LINENO: checking for non-GNU ld" >&5 +$as_echo_n "checking for non-GNU ld... " >&6; } +fi +if test "${lt_cv_path_LD+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test -z "$LD"; then + lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR + for ac_dir in $PATH; do + IFS="$lt_save_ifs" + test -z "$ac_dir" && ac_dir=. + if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then + lt_cv_path_LD="$ac_dir/$ac_prog" + # Check to see if the program is GNU ld. I'd rather use --version, + # but apparently some variants of GNU ld only accept -v. + # Break only if it was the GNU/non-GNU ld that we prefer. + case `"$lt_cv_path_LD" -v 2>&1 &5 +$as_echo "$LD" >&6; } +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi +test -z "$LD" && { { $as_echo "$as_me:$LINENO: error: no acceptable ld found in \$PATH" >&5 +$as_echo "$as_me: error: no acceptable ld found in \$PATH" >&2;} + { (exit 1); exit 1; }; } +{ $as_echo "$as_me:$LINENO: checking if the linker ($LD) is GNU ld" >&5 +$as_echo_n "checking if the linker ($LD) is GNU ld... " >&6; } +if test "${lt_cv_prog_gnu_ld+set}" = set; then + $as_echo_n "(cached) " >&6 +else + # I'd rather use --version here, but apparently some GNU lds only accept -v. +case `$LD -v 2>&1 &5 +$as_echo "$lt_cv_prog_gnu_ld" >&6; } +with_gnu_ld=$lt_cv_prog_gnu_ld + + + + + + + + # Check if GNU C++ uses GNU ld as the underlying linker, since the + # archiving commands below assume that GNU ld is being used. + if test "$with_gnu_ld" = yes; then + archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib' + archive_expsym_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' + + hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir' + export_dynamic_flag_spec_CXX='${wl}--export-dynamic' + + # If archive_cmds runs LD, not CC, wlarc should be empty + # XXX I think wlarc can be eliminated in ltcf-cxx, but I need to + # investigate it a little bit more. (MM) + wlarc='${wl}' + + # ancient GNU ld didn't support --whole-archive et. al. + if eval "`$CC -print-prog-name=ld` --help 2>&1" | + $GREP 'no-whole-archive' > /dev/null; then + whole_archive_flag_spec_CXX="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive' + else + whole_archive_flag_spec_CXX= + fi + else + with_gnu_ld=no + wlarc= + + # A generic and very simple default shared library creation + # command for GNU C++ for the case where it uses the native + # linker, instead of GNU ld. If possible, this setting should + # overridden to take advantage of the native linker features on + # the platform it is being used on. + archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib' + fi + + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"' + + else + GXX=no + with_gnu_ld=no + wlarc= + fi + + # PORTME: fill in a description of your system's C++ link characteristics + { $as_echo "$as_me:$LINENO: checking whether the $compiler linker ($LD) supports shared libraries" >&5 +$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; } + ld_shlibs_CXX=yes + case $host_os in + aix3*) + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + aix[4-9]*) + if test "$host_cpu" = ia64; then + # On IA64, the linker does run time linking by default, so we don't + # have to do anything special. + aix_use_runtimelinking=no + exp_sym_flag='-Bexport' + no_entry_flag="" + else + aix_use_runtimelinking=no + + # Test if we are trying to use run time linking or normal + # AIX style linking. If -brtl is somewhere in LDFLAGS, we + # need to do runtime linking. + case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*) + for ld_flag in $LDFLAGS; do + case $ld_flag in + *-brtl*) + aix_use_runtimelinking=yes + break + ;; + esac + done + ;; + esac + + exp_sym_flag='-bexport' + no_entry_flag='-bnoentry' + fi + + # When large executables or shared objects are built, AIX ld can + # have problems creating the table of contents. If linking a library + # or program results in "error TOC overflow" add -mminimal-toc to + # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not + # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS. + + archive_cmds_CXX='' + hardcode_direct_CXX=yes + hardcode_direct_absolute_CXX=yes + hardcode_libdir_separator_CXX=':' + link_all_deplibs_CXX=yes + file_list_spec_CXX='${wl}-f,' + + if test "$GXX" = yes; then + case $host_os in aix4.[012]|aix4.[012].*) + # We only want to do this on AIX 4.2 and lower, the check + # below for broken collect2 doesn't work under 4.3+ + collect2name=`${CC} -print-prog-name=collect2` + if test -f "$collect2name" && + strings "$collect2name" | $GREP resolve_lib_name >/dev/null + then + # We have reworked collect2 + : + else + # We have old collect2 + hardcode_direct_CXX=unsupported + # It fails to find uninstalled libraries when the uninstalled + # path is not listed in the libpath. Setting hardcode_minus_L + # to unsupported forces relinking + hardcode_minus_L_CXX=yes + hardcode_libdir_flag_spec_CXX='-L$libdir' + hardcode_libdir_separator_CXX= + fi + esac + shared_flag='-shared' + if test "$aix_use_runtimelinking" = yes; then + shared_flag="$shared_flag "'${wl}-G' + fi + else + # not using gcc + if test "$host_cpu" = ia64; then + # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release + # chokes on -Wl,-G. The following line is correct: + shared_flag='-G' + else + if test "$aix_use_runtimelinking" = yes; then + shared_flag='${wl}-G' + else + shared_flag='${wl}-bM:SRE' + fi + fi + fi + + export_dynamic_flag_spec_CXX='${wl}-bexpall' + # It seems that -bexpall does not export symbols beginning with + # underscore (_), so it is better to generate a list of symbols to + # export. + always_export_symbols_CXX=yes + if test "$aix_use_runtimelinking" = yes; then + # Warning - without using the other runtime loading flags (-brtl), + # -berok will link without error, but may produce a broken library. + allow_undefined_flag_CXX='-berok' + # Determine the default libpath from the value encoded in an empty + # executable. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + +lt_aix_libpath_sed=' + /Import File Strings/,/^$/ { + /^0/ { + s/^0 *\(.*\)$/\1/ + p + } + }' +aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` +# Check for a 64-bit object if we didn't find anything. +if test -z "$aix_libpath"; then + aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` +fi +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi + + hardcode_libdir_flag_spec_CXX='${wl}-blibpath:$libdir:'"$aix_libpath" + + archive_expsym_cmds_CXX='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" + else + if test "$host_cpu" = ia64; then + hardcode_libdir_flag_spec_CXX='${wl}-R $libdir:/usr/lib:/lib' + allow_undefined_flag_CXX="-z nodefs" + archive_expsym_cmds_CXX="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" + else + # Determine the default libpath from the value encoded in an + # empty executable. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + +lt_aix_libpath_sed=' + /Import File Strings/,/^$/ { + /^0/ { + s/^0 *\(.*\)$/\1/ + p + } + }' +aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` +# Check for a 64-bit object if we didn't find anything. +if test -z "$aix_libpath"; then + aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` +fi +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi + + hardcode_libdir_flag_spec_CXX='${wl}-blibpath:$libdir:'"$aix_libpath" + # Warning - without using the other run time loading flags, + # -berok will link without error, but may produce a broken library. + no_undefined_flag_CXX=' ${wl}-bernotok' + allow_undefined_flag_CXX=' ${wl}-berok' + # Exported symbols can be pulled into shared objects from archives + whole_archive_flag_spec_CXX='$convenience' + archive_cmds_need_lc_CXX=yes + # This is similar to how AIX traditionally builds its shared + # libraries. + archive_expsym_cmds_CXX="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' + fi + fi + ;; + + beos*) + if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then + allow_undefined_flag_CXX=unsupported + # Joseph Beckenbach says some releases of gcc + # support --undefined. This deserves some investigation. 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To avoid this, we pick a random, + # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link + # time. 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(KAI) C++ Compiler + + # KCC will only create a shared library if the output file + # ends with ".so" (or ".sl" for HP-UX), so rename the library + # to its proper name (with version) after linking. + archive_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib' + archive_expsym_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib' + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + # + # There doesn't appear to be a way to prevent this compiler from + # explicitly linking system object files so we need to strip them + # from the output so that they don't get included in the library + # dependencies. + output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | $GREP "ld"`; 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+ *) # Version 6 will use weak symbols + archive_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib' + archive_expsym_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib' + ;; + esac + + hardcode_libdir_flag_spec_CXX='${wl}--rpath ${wl}$libdir' + export_dynamic_flag_spec_CXX='${wl}--export-dynamic' + whole_archive_flag_spec_CXX='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' + ;; + cxx*) + # Compaq C++ + archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib' + archive_expsym_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib ${wl}-retain-symbols-file $wl$export_symbols' + + runpath_var=LD_RUN_PATH + hardcode_libdir_flag_spec_CXX='-rpath $libdir' + hardcode_libdir_separator_CXX=: + + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + # + # There doesn't appear to be a way to prevent this compiler from + # explicitly linking system object files so we need to strip them + # from the output so that they don't get included in the library + # dependencies. + output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld .*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed' + ;; + xl*) + # IBM XL 8.0 on PPC, with GNU ld + hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir' + export_dynamic_flag_spec_CXX='${wl}--export-dynamic' + archive_cmds_CXX='$CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + if test "x$supports_anon_versioning" = xyes; then + archive_expsym_cmds_CXX='echo "{ global:" > $output_objdir/$libname.ver~ + cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ + echo "local: *; };" >> $output_objdir/$libname.ver~ + $CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib' + fi + ;; + *) + case `$CC -V 2>&1 | sed 5q` in + *Sun\ C*) + # Sun C++ 5.9 + no_undefined_flag_CXX=' -zdefs' + archive_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' + archive_expsym_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file ${wl}$export_symbols' + hardcode_libdir_flag_spec_CXX='-R$libdir' + whole_archive_flag_spec_CXX='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' + compiler_needs_object_CXX=yes + + # Not sure whether something based on + # $CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 + # would be better. + output_verbose_link_cmd='echo' + + # Archives containing C++ object files must be created using + # "CC -xar", where "CC" is the Sun C++ compiler. This is + # necessary to make sure instantiated templates are included + # in the archive. + old_archive_cmds_CXX='$CC -xar -o $oldlib $oldobjs' + ;; + esac + ;; + esac + ;; + + lynxos*) + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + + m88k*) + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + + mvs*) + case $cc_basename in + cxx*) + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + *) + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + esac + ;; + + netbsd*) + if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then + archive_cmds_CXX='$LD -Bshareable -o $lib $predep_objects $libobjs $deplibs $postdep_objects $linker_flags' + wlarc= + hardcode_libdir_flag_spec_CXX='-R$libdir' + hardcode_direct_CXX=yes + hardcode_shlibpath_var_CXX=no + fi + # Workaround some broken pre-1.5 toolchains + output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP conftest.$objext | $SED -e "s:-lgcc -lc -lgcc::"' + ;; + + *nto* | *qnx*) + ld_shlibs_CXX=yes + ;; + + openbsd2*) + # C++ shared libraries are fairly broken + ld_shlibs_CXX=no + ;; + + openbsd*) + if test -f /usr/libexec/ld.so; then + hardcode_direct_CXX=yes + hardcode_shlibpath_var_CXX=no + hardcode_direct_absolute_CXX=yes + archive_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib' + hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir' + if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then + archive_expsym_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file,$export_symbols -o $lib' + export_dynamic_flag_spec_CXX='${wl}-E' + whole_archive_flag_spec_CXX="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive' + fi + output_verbose_link_cmd=echo + else + ld_shlibs_CXX=no + fi + ;; + + osf3* | osf4* | osf5*) + case $cc_basename in + KCC*) + # Kuck and Associates, Inc. (KAI) C++ Compiler + + # KCC will only create a shared library if the output file + # ends with ".so" (or ".sl" for HP-UX), so rename the library + # to its proper name (with version) after linking. + archive_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo "$lib" | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib' + + hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir' + hardcode_libdir_separator_CXX=: + + # Archives containing C++ object files must be created using + # the KAI C++ compiler. + case $host in + osf3*) old_archive_cmds_CXX='$CC -Bstatic -o $oldlib $oldobjs' ;; + *) old_archive_cmds_CXX='$CC -o $oldlib $oldobjs' ;; + esac + ;; + RCC*) + # Rational C++ 2.4.1 + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + cxx*) + case $host in + osf3*) + allow_undefined_flag_CXX=' ${wl}-expect_unresolved ${wl}\*' + archive_cmds_CXX='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $soname `test -n "$verstring" && $ECHO "X${wl}-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' + hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir' + ;; + *) + allow_undefined_flag_CXX=' -expect_unresolved \*' + archive_cmds_CXX='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' + archive_expsym_cmds_CXX='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done~ + echo "-hidden">> $lib.exp~ + $CC -shared$allow_undefined_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname ${wl}-input ${wl}$lib.exp `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~ + $RM $lib.exp' + hardcode_libdir_flag_spec_CXX='-rpath $libdir' + ;; + esac + + hardcode_libdir_separator_CXX=: + + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + # + # There doesn't appear to be a way to prevent this compiler from + # explicitly linking system object files so we need to strip them + # from the output so that they don't get included in the library + # dependencies. + output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld" | $GREP -v "ld:"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed' + ;; + *) + if test "$GXX" = yes && test "$with_gnu_ld" = no; then + allow_undefined_flag_CXX=' ${wl}-expect_unresolved ${wl}\*' + case $host in + osf3*) + archive_cmds_CXX='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' + ;; + *) + archive_cmds_CXX='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' + ;; + esac + + hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir' + hardcode_libdir_separator_CXX=: + + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"' + + else + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + fi + ;; + esac + ;; + + psos*) + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + + sunos4*) + case $cc_basename in + CC*) + # Sun C++ 4.x + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + lcc*) + # Lucid + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + *) + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + esac + ;; + + solaris*) + case $cc_basename in + CC*) + # Sun C++ 4.2, 5.x and Centerline C++ + archive_cmds_need_lc_CXX=yes + no_undefined_flag_CXX=' -zdefs' + archive_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' + archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ + $CC -G${allow_undefined_flag} ${wl}-M ${wl}$lib.exp -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp' + + hardcode_libdir_flag_spec_CXX='-R$libdir' + hardcode_shlibpath_var_CXX=no + case $host_os in + solaris2.[0-5] | solaris2.[0-5].*) ;; + *) + # The compiler driver will combine and reorder linker options, + # but understands `-z linker_flag'. + # Supported since Solaris 2.6 (maybe 2.5.1?) + whole_archive_flag_spec_CXX='-z allextract$convenience -z defaultextract' + ;; + esac + link_all_deplibs_CXX=yes + + output_verbose_link_cmd='echo' + + # Archives containing C++ object files must be created using + # "CC -xar", where "CC" is the Sun C++ compiler. This is + # necessary to make sure instantiated templates are included + # in the archive. + old_archive_cmds_CXX='$CC -xar -o $oldlib $oldobjs' + ;; + gcx*) + # Green Hills C++ Compiler + archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib' + + # The C++ compiler must be used to create the archive. + old_archive_cmds_CXX='$CC $LDFLAGS -archive -o $oldlib $oldobjs' + ;; + *) + # GNU C++ compiler with Solaris linker + if test "$GXX" = yes && test "$with_gnu_ld" = no; then + no_undefined_flag_CXX=' ${wl}-z ${wl}defs' + if $CC --version | $GREP -v '^2\.7' > /dev/null; then + archive_cmds_CXX='$CC -shared -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib' + archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ + $CC -shared -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp' + + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"' + else + # g++ 2.7 appears to require `-G' NOT `-shared' on this + # platform. + archive_cmds_CXX='$CC -G -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib' + archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ + $CC -G -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp' + + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + output_verbose_link_cmd='$CC -G $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"' + fi + + hardcode_libdir_flag_spec_CXX='${wl}-R $wl$libdir' + case $host_os in + solaris2.[0-5] | solaris2.[0-5].*) ;; + *) + whole_archive_flag_spec_CXX='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract' + ;; + esac + fi + ;; + esac + ;; + + sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*) + no_undefined_flag_CXX='${wl}-z,text' + archive_cmds_need_lc_CXX=no + hardcode_shlibpath_var_CXX=no + runpath_var='LD_RUN_PATH' + + case $cc_basename in + CC*) + archive_cmds_CXX='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + archive_expsym_cmds_CXX='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + ;; + *) + archive_cmds_CXX='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + archive_expsym_cmds_CXX='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + ;; + esac + ;; + + sysv5* | sco3.2v5* | sco5v6*) + # Note: We can NOT use -z defs as we might desire, because we do not + # link with -lc, and that would cause any symbols used from libc to + # always be unresolved, which means just about no library would + # ever link correctly. If we're not using GNU ld we use -z text + # though, which does catch some bad symbols but isn't as heavy-handed + # as -z defs. + no_undefined_flag_CXX='${wl}-z,text' + allow_undefined_flag_CXX='${wl}-z,nodefs' + archive_cmds_need_lc_CXX=no + hardcode_shlibpath_var_CXX=no + hardcode_libdir_flag_spec_CXX='${wl}-R,$libdir' + hardcode_libdir_separator_CXX=':' + link_all_deplibs_CXX=yes + export_dynamic_flag_spec_CXX='${wl}-Bexport' + runpath_var='LD_RUN_PATH' + + case $cc_basename in + CC*) + archive_cmds_CXX='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + archive_expsym_cmds_CXX='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + ;; + *) + archive_cmds_CXX='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + archive_expsym_cmds_CXX='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + ;; + esac + ;; + + tandem*) + case $cc_basename in + NCC*) + # NonStop-UX NCC 3.20 + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + *) + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + esac + ;; + + vxworks*) + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + + *) + # FIXME: insert proper C++ library support + ld_shlibs_CXX=no + ;; + esac + + { $as_echo "$as_me:$LINENO: result: $ld_shlibs_CXX" >&5 +$as_echo "$ld_shlibs_CXX" >&6; } + test "$ld_shlibs_CXX" = no && can_build_shared=no + + GCC_CXX="$GXX" + LD_CXX="$LD" + + ## CAVEAT EMPTOR: + ## There is no encapsulation within the following macros, do not change + ## the running order or otherwise move them around unless you know exactly + ## what you are doing... + # Dependencies to place before and after the object being linked: +predep_objects_CXX= +postdep_objects_CXX= +predeps_CXX= +postdeps_CXX= +compiler_lib_search_path_CXX= + +cat > conftest.$ac_ext <<_LT_EOF +class Foo +{ +public: + Foo (void) { a = 0; } +private: + int a; +}; +_LT_EOF + +if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # Parse the compiler output and extract the necessary + # objects, libraries and library flags. + + # Sentinel used to keep track of whether or not we are before + # the conftest object file. + pre_test_object_deps_done=no + + for p in `eval "$output_verbose_link_cmd"`; do + case $p in + + -L* | -R* | -l*) + # Some compilers place space between "-{L,R}" and the path. + # Remove the space. + if test $p = "-L" || + test $p = "-R"; then + prev=$p + continue + else + prev= + fi + + if test "$pre_test_object_deps_done" = no; then + case $p in + -L* | -R*) + # Internal compiler library paths should come after those + # provided the user. The postdeps already come after the + # user supplied libs so there is no need to process them. + if test -z "$compiler_lib_search_path_CXX"; then + compiler_lib_search_path_CXX="${prev}${p}" + else + compiler_lib_search_path_CXX="${compiler_lib_search_path_CXX} ${prev}${p}" + fi + ;; + # The "-l" case would never come before the object being + # linked, so don't bother handling this case. + esac + else + if test -z "$postdeps_CXX"; then + postdeps_CXX="${prev}${p}" + else + postdeps_CXX="${postdeps_CXX} ${prev}${p}" + fi + fi + ;; + + *.$objext) + # This assumes that the test object file only shows up + # once in the compiler output. + if test "$p" = "conftest.$objext"; then + pre_test_object_deps_done=yes + continue + fi + + if test "$pre_test_object_deps_done" = no; then + if test -z "$predep_objects_CXX"; then + predep_objects_CXX="$p" + else + predep_objects_CXX="$predep_objects_CXX $p" + fi + else + if test -z "$postdep_objects_CXX"; then + postdep_objects_CXX="$p" + else + postdep_objects_CXX="$postdep_objects_CXX $p" + fi + fi + ;; + + *) ;; # Ignore the rest. + + esac + done + + # Clean up. + rm -f a.out a.exe +else + echo "libtool.m4: error: problem compiling CXX test program" +fi + +$RM -f confest.$objext + +# PORTME: override above test on systems where it is broken +case $host_os in +interix[3-9]*) + # Interix 3.5 installs completely hosed .la files for C++, so rather than + # hack all around it, let's just trust "g++" to DTRT. + predep_objects_CXX= + postdep_objects_CXX= + postdeps_CXX= + ;; + +linux*) + case `$CC -V 2>&1 | sed 5q` in + *Sun\ C*) + # Sun C++ 5.9 + + # The more standards-conforming stlport4 library is + # incompatible with the Cstd library. Avoid specifying + # it if it's in CXXFLAGS. Ignore libCrun as + # -library=stlport4 depends on it. + case " $CXX $CXXFLAGS " in + *" -library=stlport4 "*) + solaris_use_stlport4=yes + ;; + esac + + if test "$solaris_use_stlport4" != yes; then + postdeps_CXX='-library=Cstd -library=Crun' + fi + ;; + esac + ;; + +solaris*) + case $cc_basename in + CC*) + # The more standards-conforming stlport4 library is + # incompatible with the Cstd library. Avoid specifying + # it if it's in CXXFLAGS. Ignore libCrun as + # -library=stlport4 depends on it. + case " $CXX $CXXFLAGS " in + *" -library=stlport4 "*) + solaris_use_stlport4=yes + ;; + esac + + # Adding this requires a known-good setup of shared libraries for + # Sun compiler versions before 5.6, else PIC objects from an old + # archive will be linked into the output, leading to subtle bugs. + if test "$solaris_use_stlport4" != yes; then + postdeps_CXX='-library=Cstd -library=Crun' + fi + ;; + esac + ;; +esac + + +case " $postdeps_CXX " in +*" -lc "*) archive_cmds_need_lc_CXX=no ;; +esac + compiler_lib_search_dirs_CXX= +if test -n "${compiler_lib_search_path_CXX}"; then + compiler_lib_search_dirs_CXX=`echo " ${compiler_lib_search_path_CXX}" | ${SED} -e 's! -L! !g' -e 's!^ !!'` +fi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + lt_prog_compiler_wl_CXX= +lt_prog_compiler_pic_CXX= +lt_prog_compiler_static_CXX= + +{ $as_echo "$as_me:$LINENO: checking for $compiler option to produce PIC" >&5 +$as_echo_n "checking for $compiler option to produce PIC... " >&6; } + + # C++ specific cases for pic, static, wl, etc. + if test "$GXX" = yes; then + lt_prog_compiler_wl_CXX='-Wl,' + lt_prog_compiler_static_CXX='-static' + + case $host_os in + aix*) + # All AIX code is PIC. + if test "$host_cpu" = ia64; then + # AIX 5 now supports IA64 processor + lt_prog_compiler_static_CXX='-Bstatic' + fi + ;; + + amigaos*) + case $host_cpu in + powerpc) + # see comment about AmigaOS4 .so support + lt_prog_compiler_pic_CXX='-fPIC' + ;; + m68k) + # FIXME: we need at least 68020 code to build shared libraries, but + # adding the `-m68020' flag to GCC prevents building anything better, + # like `-m68040'. + lt_prog_compiler_pic_CXX='-m68020 -resident32 -malways-restore-a4' + ;; + esac + ;; + + beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) + # PIC is the default for these OSes. + ;; + mingw* | cygwin* | os2* | pw32* | cegcc*) + # This hack is so that the source file can tell whether it is being + # built for inclusion in a dll (and should export symbols for example). + # Although the cygwin gcc ignores -fPIC, still need this for old-style + # (--disable-auto-import) libraries + lt_prog_compiler_pic_CXX='-DDLL_EXPORT' + ;; + darwin* | rhapsody*) + # PIC is the default on this platform + # Common symbols not allowed in MH_DYLIB files + lt_prog_compiler_pic_CXX='-fno-common' + ;; + *djgpp*) + # DJGPP does not support shared libraries at all + lt_prog_compiler_pic_CXX= + ;; + interix[3-9]*) + # Interix 3.x gcc -fpic/-fPIC options generate broken code. + # Instead, we relocate shared libraries at runtime. + ;; + sysv4*MP*) + if test -d /usr/nec; then + lt_prog_compiler_pic_CXX=-Kconform_pic + fi + ;; + hpux*) + # PIC is the default for 64-bit PA HP-UX, but not for 32-bit + # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag + # sets the default TLS model and affects inlining. + case $host_cpu in + hppa*64*) + ;; + *) + lt_prog_compiler_pic_CXX='-fPIC' + ;; + esac + ;; + *qnx* | *nto*) + # QNX uses GNU C++, but need to define -shared option too, otherwise + # it will coredump. + lt_prog_compiler_pic_CXX='-fPIC -shared' + ;; + *) + lt_prog_compiler_pic_CXX='-fPIC' + ;; + esac + else + case $host_os in + aix[4-9]*) + # All AIX code is PIC. + if test "$host_cpu" = ia64; then + # AIX 5 now supports IA64 processor + lt_prog_compiler_static_CXX='-Bstatic' + else + lt_prog_compiler_static_CXX='-bnso -bI:/lib/syscalls.exp' + fi + ;; + chorus*) + case $cc_basename in + cxch68*) + # Green Hills C++ Compiler + # _LT_TAGVAR(lt_prog_compiler_static, CXX)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a" + ;; + esac + ;; + dgux*) + case $cc_basename in + ec++*) + lt_prog_compiler_pic_CXX='-KPIC' + ;; + ghcx*) + # Green Hills C++ Compiler + lt_prog_compiler_pic_CXX='-pic' + ;; + *) + ;; + esac + ;; + freebsd* | dragonfly*) + # FreeBSD uses GNU C++ + ;; + hpux9* | hpux10* | hpux11*) + case $cc_basename in + CC*) + lt_prog_compiler_wl_CXX='-Wl,' + lt_prog_compiler_static_CXX='${wl}-a ${wl}archive' + if test "$host_cpu" != ia64; then + lt_prog_compiler_pic_CXX='+Z' + fi + ;; + aCC*) + lt_prog_compiler_wl_CXX='-Wl,' + lt_prog_compiler_static_CXX='${wl}-a ${wl}archive' + case $host_cpu in + hppa*64*|ia64*) + # +Z the default + ;; + *) + lt_prog_compiler_pic_CXX='+Z' + ;; + esac + ;; + *) + ;; + esac + ;; + interix*) + # This is c89, which is MS Visual C++ (no shared libs) + # Anyone wants to do a port? + ;; + irix5* | irix6* | nonstopux*) + case $cc_basename in + CC*) + lt_prog_compiler_wl_CXX='-Wl,' + lt_prog_compiler_static_CXX='-non_shared' + # CC pic flag -KPIC is the default. + ;; + *) + ;; + esac + ;; + linux* | k*bsd*-gnu) + case $cc_basename in + KCC*) + # KAI C++ Compiler + lt_prog_compiler_wl_CXX='--backend -Wl,' + lt_prog_compiler_pic_CXX='-fPIC' + ;; + ecpc* ) + # old Intel C++ for x86_64 which still supported -KPIC. + lt_prog_compiler_wl_CXX='-Wl,' + lt_prog_compiler_pic_CXX='-KPIC' + lt_prog_compiler_static_CXX='-static' + ;; + icpc* ) + # Intel C++, used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. + lt_prog_compiler_wl_CXX='-Wl,' + lt_prog_compiler_pic_CXX='-fPIC' + lt_prog_compiler_static_CXX='-static' + ;; + pgCC* | pgcpp*) + # Portland Group C++ compiler + lt_prog_compiler_wl_CXX='-Wl,' + lt_prog_compiler_pic_CXX='-fpic' + lt_prog_compiler_static_CXX='-Bstatic' + ;; + cxx*) + # Compaq C++ + # Make sure the PIC flag is empty. It appears that all Alpha + # Linux and Compaq Tru64 Unix objects are PIC. + lt_prog_compiler_pic_CXX= + lt_prog_compiler_static_CXX='-non_shared' + ;; + xlc* | xlC*) + # IBM XL 8.0 on PPC + lt_prog_compiler_wl_CXX='-Wl,' + lt_prog_compiler_pic_CXX='-qpic' + lt_prog_compiler_static_CXX='-qstaticlink' + ;; + *) + case `$CC -V 2>&1 | sed 5q` in + *Sun\ C*) + # Sun C++ 5.9 + lt_prog_compiler_pic_CXX='-KPIC' + lt_prog_compiler_static_CXX='-Bstatic' + lt_prog_compiler_wl_CXX='-Qoption ld ' + ;; + esac + ;; + esac + ;; + lynxos*) + ;; + m88k*) + ;; + mvs*) + case $cc_basename in + cxx*) + lt_prog_compiler_pic_CXX='-W c,exportall' + ;; + *) + ;; + esac + ;; + netbsd* | netbsdelf*-gnu) + ;; + *qnx* | *nto*) + # QNX uses GNU C++, but need to define -shared option too, otherwise + # it will coredump. + lt_prog_compiler_pic_CXX='-fPIC -shared' + ;; + osf3* | osf4* | osf5*) + case $cc_basename in + KCC*) + lt_prog_compiler_wl_CXX='--backend -Wl,' + ;; + RCC*) + # Rational C++ 2.4.1 + lt_prog_compiler_pic_CXX='-pic' + ;; + cxx*) + # Digital/Compaq C++ + lt_prog_compiler_wl_CXX='-Wl,' + # Make sure the PIC flag is empty. It appears that all Alpha + # Linux and Compaq Tru64 Unix objects are PIC. + lt_prog_compiler_pic_CXX= + lt_prog_compiler_static_CXX='-non_shared' + ;; + *) + ;; + esac + ;; + psos*) + ;; + solaris*) + case $cc_basename in + CC*) + # Sun C++ 4.2, 5.x and Centerline C++ + lt_prog_compiler_pic_CXX='-KPIC' + lt_prog_compiler_static_CXX='-Bstatic' + lt_prog_compiler_wl_CXX='-Qoption ld ' + ;; + gcx*) + # Green Hills C++ Compiler + lt_prog_compiler_pic_CXX='-PIC' + ;; + *) + ;; + esac + ;; + sunos4*) + case $cc_basename in + CC*) + # Sun C++ 4.x + lt_prog_compiler_pic_CXX='-pic' + lt_prog_compiler_static_CXX='-Bstatic' + ;; + lcc*) + # Lucid + lt_prog_compiler_pic_CXX='-pic' + ;; + *) + ;; + esac + ;; + sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*) + case $cc_basename in + CC*) + lt_prog_compiler_wl_CXX='-Wl,' + lt_prog_compiler_pic_CXX='-KPIC' + lt_prog_compiler_static_CXX='-Bstatic' + ;; + esac + ;; + tandem*) + case $cc_basename in + NCC*) + # NonStop-UX NCC 3.20 + lt_prog_compiler_pic_CXX='-KPIC' + ;; + *) + ;; + esac + ;; + vxworks*) + ;; + *) + lt_prog_compiler_can_build_shared_CXX=no + ;; + esac + fi + +case $host_os in + # For platforms which do not support PIC, -DPIC is meaningless: + *djgpp*) + lt_prog_compiler_pic_CXX= + ;; + *) + lt_prog_compiler_pic_CXX="$lt_prog_compiler_pic_CXX -DPIC" + ;; +esac +{ $as_echo "$as_me:$LINENO: result: $lt_prog_compiler_pic_CXX" >&5 +$as_echo "$lt_prog_compiler_pic_CXX" >&6; } + + + +# +# Check to make sure the PIC flag actually works. +# +if test -n "$lt_prog_compiler_pic_CXX"; then + { $as_echo "$as_me:$LINENO: checking if $compiler PIC flag $lt_prog_compiler_pic_CXX works" >&5 +$as_echo_n "checking if $compiler PIC flag $lt_prog_compiler_pic_CXX works... " >&6; } +if test "${lt_cv_prog_compiler_pic_works_CXX+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_prog_compiler_pic_works_CXX=no + ac_outfile=conftest.$ac_objext + echo "$lt_simple_compile_test_code" > conftest.$ac_ext + lt_compiler_flag="$lt_prog_compiler_pic_CXX -DPIC" + # Insert the option either (1) after the last *FLAGS variable, or + # (2) before a word containing "conftest.", or (3) at the end. + # Note that $ac_compile itself does not contain backslashes and begins + # with a dollar sign (not a hyphen), so the echo should work correctly. + # The option is referenced via a variable to avoid confusing sed. + lt_compile=`echo "$ac_compile" | $SED \ + -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \ + -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \ + -e 's:$: $lt_compiler_flag:'` + (eval echo "\"\$as_me:15594: $lt_compile\"" >&5) + (eval "$lt_compile" 2>conftest.err) + ac_status=$? + cat conftest.err >&5 + echo "$as_me:15598: \$? = $ac_status" >&5 + if (exit $ac_status) && test -s "$ac_outfile"; then + # The compiler can only warn and ignore the option if not recognized + # So say no if there are warnings other than the usual output. + $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp + $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2 + if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then + lt_cv_prog_compiler_pic_works_CXX=yes + fi + fi + $RM conftest* + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_pic_works_CXX" >&5 +$as_echo "$lt_cv_prog_compiler_pic_works_CXX" >&6; } + +if test x"$lt_cv_prog_compiler_pic_works_CXX" = xyes; then + case $lt_prog_compiler_pic_CXX in + "" | " "*) ;; + *) lt_prog_compiler_pic_CXX=" $lt_prog_compiler_pic_CXX" ;; + esac +else + lt_prog_compiler_pic_CXX= + lt_prog_compiler_can_build_shared_CXX=no +fi + +fi + + + +# +# Check to make sure the static flag actually works. +# +wl=$lt_prog_compiler_wl_CXX eval lt_tmp_static_flag=\"$lt_prog_compiler_static_CXX\" +{ $as_echo "$as_me:$LINENO: checking if $compiler static flag $lt_tmp_static_flag works" >&5 +$as_echo_n "checking if $compiler static flag $lt_tmp_static_flag works... " >&6; } +if test "${lt_cv_prog_compiler_static_works_CXX+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_prog_compiler_static_works_CXX=no + save_LDFLAGS="$LDFLAGS" + LDFLAGS="$LDFLAGS $lt_tmp_static_flag" + echo "$lt_simple_link_test_code" > conftest.$ac_ext + if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then + # The linker can only warn and ignore the option if not recognized + # So say no if there are warnings + if test -s conftest.err; then + # Append any errors to the config.log. + cat conftest.err 1>&5 + $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp + $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2 + if diff conftest.exp conftest.er2 >/dev/null; then + lt_cv_prog_compiler_static_works_CXX=yes + fi + else + lt_cv_prog_compiler_static_works_CXX=yes + fi + fi + $RM -r conftest* + LDFLAGS="$save_LDFLAGS" + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_static_works_CXX" >&5 +$as_echo "$lt_cv_prog_compiler_static_works_CXX" >&6; } + +if test x"$lt_cv_prog_compiler_static_works_CXX" = xyes; then + : +else + lt_prog_compiler_static_CXX= +fi + + + + + { $as_echo "$as_me:$LINENO: checking if $compiler supports -c -o file.$ac_objext" >&5 +$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; } +if test "${lt_cv_prog_compiler_c_o_CXX+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_prog_compiler_c_o_CXX=no + $RM -r conftest 2>/dev/null + mkdir conftest + cd conftest + mkdir out + echo "$lt_simple_compile_test_code" > conftest.$ac_ext + + lt_compiler_flag="-o out/conftest2.$ac_objext" + # Insert the option either (1) after the last *FLAGS variable, or + # (2) before a word containing "conftest.", or (3) at the end. + # Note that $ac_compile itself does not contain backslashes and begins + # with a dollar sign (not a hyphen), so the echo should work correctly. + lt_compile=`echo "$ac_compile" | $SED \ + -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \ + -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \ + -e 's:$: $lt_compiler_flag:'` + (eval echo "\"\$as_me:15693: $lt_compile\"" >&5) + (eval "$lt_compile" 2>out/conftest.err) + ac_status=$? + cat out/conftest.err >&5 + echo "$as_me:15697: \$? = $ac_status" >&5 + if (exit $ac_status) && test -s out/conftest2.$ac_objext + then + # The compiler can only warn and ignore the option if not recognized + # So say no if there are warnings + $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp + $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2 + if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then + lt_cv_prog_compiler_c_o_CXX=yes + fi + fi + chmod u+w . 2>&5 + $RM conftest* + # SGI C++ compiler will create directory out/ii_files/ for + # template instantiation + test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files + $RM out/* && rmdir out + cd .. + $RM -r conftest + $RM conftest* + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_c_o_CXX" >&5 +$as_echo "$lt_cv_prog_compiler_c_o_CXX" >&6; } + + + + { $as_echo "$as_me:$LINENO: checking if $compiler supports -c -o file.$ac_objext" >&5 +$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; } +if test "${lt_cv_prog_compiler_c_o_CXX+set}" = set; then + $as_echo_n "(cached) " >&6 +else + lt_cv_prog_compiler_c_o_CXX=no + $RM -r conftest 2>/dev/null + mkdir conftest + cd conftest + mkdir out + echo "$lt_simple_compile_test_code" > conftest.$ac_ext + + lt_compiler_flag="-o out/conftest2.$ac_objext" + # Insert the option either (1) after the last *FLAGS variable, or + # (2) before a word containing "conftest.", or (3) at the end. + # Note that $ac_compile itself does not contain backslashes and begins + # with a dollar sign (not a hyphen), so the echo should work correctly. + lt_compile=`echo "$ac_compile" | $SED \ + -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \ + -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \ + -e 's:$: $lt_compiler_flag:'` + (eval echo "\"\$as_me:15745: $lt_compile\"" >&5) + (eval "$lt_compile" 2>out/conftest.err) + ac_status=$? + cat out/conftest.err >&5 + echo "$as_me:15749: \$? = $ac_status" >&5 + if (exit $ac_status) && test -s out/conftest2.$ac_objext + then + # The compiler can only warn and ignore the option if not recognized + # So say no if there are warnings + $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp + $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2 + if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then + lt_cv_prog_compiler_c_o_CXX=yes + fi + fi + chmod u+w . 2>&5 + $RM conftest* + # SGI C++ compiler will create directory out/ii_files/ for + # template instantiation + test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files + $RM out/* && rmdir out + cd .. + $RM -r conftest + $RM conftest* + +fi +{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_c_o_CXX" >&5 +$as_echo "$lt_cv_prog_compiler_c_o_CXX" >&6; } + + + + +hard_links="nottested" +if test "$lt_cv_prog_compiler_c_o_CXX" = no && test "$need_locks" != no; then + # do not overwrite the value of need_locks provided by the user + { $as_echo "$as_me:$LINENO: checking if we can lock with hard links" >&5 +$as_echo_n "checking if we can lock with hard links... 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If gcc already passes -lc + # to ld, don't add -lc before -lgcc. + { $as_echo "$as_me:$LINENO: checking whether -lc should be explicitly linked in" >&5 +$as_echo_n "checking whether -lc should be explicitly linked in... " >&6; } + $RM conftest* + echo "$lt_simple_compile_test_code" > conftest.$ac_ext + + if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 + (eval $ac_compile) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } 2>conftest.err; then + soname=conftest + lib=conftest + libobjs=conftest.$ac_objext + deplibs= + wl=$lt_prog_compiler_wl_CXX + pic_flag=$lt_prog_compiler_pic_CXX + compiler_flags=-v + linker_flags=-v + verstring= + output_objdir=. + libname=conftest + lt_save_allow_undefined_flag=$allow_undefined_flag_CXX + allow_undefined_flag_CXX= + if { (eval echo "$as_me:$LINENO: \"$archive_cmds_CXX 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1\"") >&5 + (eval $archive_cmds_CXX 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } + then + archive_cmds_need_lc_CXX=no + else + archive_cmds_need_lc_CXX=yes + fi + allow_undefined_flag_CXX=$lt_save_allow_undefined_flag + else + cat conftest.err 1>&5 + fi + $RM conftest* + { $as_echo "$as_me:$LINENO: result: $archive_cmds_need_lc_CXX" >&5 +$as_echo "$archive_cmds_need_lc_CXX" >&6; } + ;; + esac + fi + ;; +esac + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + { $as_echo "$as_me:$LINENO: checking dynamic linker characteristics" >&5 +$as_echo_n "checking dynamic linker characteristics... " >&6; } + +library_names_spec= +libname_spec='lib$name' +soname_spec= +shrext_cmds=".so" +postinstall_cmds= +postuninstall_cmds= +finish_cmds= +finish_eval= +shlibpath_var= +shlibpath_overrides_runpath=unknown +version_type=none +dynamic_linker="$host_os ld.so" +sys_lib_dlsearch_path_spec="/lib /usr/lib" +need_lib_prefix=unknown +hardcode_into_libs=no + +# when you set need_version to no, make sure it does not cause -set_version +# flags to be left without arguments +need_version=unknown + +case $host_os in +aix3*) + version_type=linux + library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a' + shlibpath_var=LIBPATH + + # AIX 3 has no versioning support, so we append a major version to the name. + soname_spec='${libname}${release}${shared_ext}$major' + ;; + +aix[4-9]*) + version_type=linux + need_lib_prefix=no + need_version=no + hardcode_into_libs=yes + if test "$host_cpu" = ia64; then + # AIX 5 supports IA64 + library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}' + shlibpath_var=LD_LIBRARY_PATH + else + # With GCC up to 2.95.x, collect2 would create an import file + # for dependence libraries. The import file would start with + # the line `#! .'. This would cause the generated library to + # depend on `.', always an invalid library. This was fixed in + # development snapshots of GCC prior to 3.0. + case $host_os in + aix4 | aix4.[01] | aix4.[01].*) + if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)' + echo ' yes ' + echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then + : + else + can_build_shared=no + fi + ;; + esac + # AIX (on Power*) has no versioning support, so currently we can not hardcode correct + # soname into executable. Probably we can add versioning support to + # collect2, so additional links can be useful in future. + if test "$aix_use_runtimelinking" = yes; then + # If using run time linking (on AIX 4.2 or later) use lib.so + # instead of lib.a to let people know that these are not + # typical AIX shared libraries. + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + else + # We preserve .a as extension for shared libraries through AIX4.2 + # and later when we are not doing run time linking. + library_names_spec='${libname}${release}.a $libname.a' + soname_spec='${libname}${release}${shared_ext}$major' + fi + shlibpath_var=LIBPATH + fi + ;; + +amigaos*) + case $host_cpu in + powerpc) + # Since July 2007 AmigaOS4 officially supports .so libraries. + # When compiling the executable, add -use-dynld -Lsobjs: to the compileline. + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + ;; + m68k) + library_names_spec='$libname.ixlibrary $libname.a' + # Create ${libname}_ixlibrary.a entries in /sys/libs. + finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done' + ;; + esac + ;; + +beos*) + library_names_spec='${libname}${shared_ext}' + dynamic_linker="$host_os ld.so" + shlibpath_var=LIBRARY_PATH + ;; + +bsdi[45]*) + version_type=linux + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir' + shlibpath_var=LD_LIBRARY_PATH + sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib" + sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib" + # the default ld.so.conf also contains /usr/contrib/lib and + # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow + # libtool to hard-code these into programs + ;; + +cygwin* | mingw* | pw32* | cegcc*) + version_type=windows + shrext_cmds=".dll" + need_version=no + need_lib_prefix=no + + case $GCC,$host_os in + yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*) + library_names_spec='$libname.dll.a' + # DLL is installed to $(libdir)/../bin by postinstall_cmds + postinstall_cmds='base_file=`basename \${file}`~ + dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~ + dldir=$destdir/`dirname \$dlpath`~ + test -d \$dldir || mkdir -p \$dldir~ + $install_prog $dir/$dlname \$dldir/$dlname~ + chmod a+x \$dldir/$dlname~ + if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then + eval '\''$striplib \$dldir/$dlname'\'' || exit \$?; + fi' + postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~ + dlpath=$dir/\$dldll~ + $RM \$dlpath' + shlibpath_overrides_runpath=yes + + case $host_os in + cygwin*) + # Cygwin DLLs use 'cyg' prefix rather than 'lib' + soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}' + sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib" + ;; + mingw* | cegcc*) + # MinGW DLLs use traditional 'lib' prefix + soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}' + sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"` + if $ECHO "$sys_lib_search_path_spec" | $GREP ';[c-zC-Z]:/' >/dev/null; then + # It is most probably a Windows format PATH printed by + # mingw gcc, but we are running on Cygwin. Gcc prints its search + # path with ; separators, and with drive letters. We can handle the + # drive letters (cygwin fileutils understands them), so leave them, + # especially as we might pass files found there to a mingw objdump, + # which wouldn't understand a cygwinified path. Ahh. + sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'` + else + sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"` + fi + ;; + pw32*) + # pw32 DLLs use 'pw' prefix rather than 'lib' + library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}' + ;; + esac + ;; + + *) + library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib' + ;; + esac + dynamic_linker='Win32 ld.exe' + # FIXME: first we should search . and the directory the executable is in + shlibpath_var=PATH + ;; + +darwin* | rhapsody*) + dynamic_linker="$host_os dyld" + version_type=darwin + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext' + soname_spec='${libname}${release}${major}$shared_ext' + shlibpath_overrides_runpath=yes + shlibpath_var=DYLD_LIBRARY_PATH + shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`' + + sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib' + ;; + +dgux*) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + ;; + +freebsd1*) + dynamic_linker=no + ;; + +freebsd* | dragonfly*) + # DragonFly does not have aout. When/if they implement a new + # versioning mechanism, adjust this. + if test -x /usr/bin/objformat; then + objformat=`/usr/bin/objformat` + else + case $host_os in + freebsd[123]*) objformat=aout ;; + *) objformat=elf ;; + esac + fi + version_type=freebsd-$objformat + case $version_type in + freebsd-elf*) + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' + need_version=no + need_lib_prefix=no + ;; + freebsd-*) + library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix' + need_version=yes + ;; + esac + shlibpath_var=LD_LIBRARY_PATH + case $host_os in + freebsd2*) + shlibpath_overrides_runpath=yes + ;; + freebsd3.[01]* | freebsdelf3.[01]*) + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + ;; + freebsd3.[2-9]* | freebsdelf3.[2-9]* | \ + freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1) + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + ;; + *) # from 4.6 on, and DragonFly + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + ;; + esac + ;; + +gnu*) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + hardcode_into_libs=yes + ;; + +hpux9* | hpux10* | hpux11*) + # Give a soname corresponding to the major version so that dld.sl refuses to + # link against other versions. + version_type=sunos + need_lib_prefix=no + need_version=no + case $host_cpu in + ia64*) + shrext_cmds='.so' + hardcode_into_libs=yes + dynamic_linker="$host_os dld.so" + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + if test "X$HPUX_IA64_MODE" = X32; then + sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib" + else + sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64" + fi + sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec + ;; + hppa*64*) + shrext_cmds='.sl' + hardcode_into_libs=yes + dynamic_linker="$host_os dld.sl" + shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH + shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64" + sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec + ;; + *) + shrext_cmds='.sl' + dynamic_linker="$host_os dld.sl" + shlibpath_var=SHLIB_PATH + shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + ;; + esac + # HP-UX runs *really* slowly unless shared libraries are mode 555. + postinstall_cmds='chmod 555 $lib' + ;; + +interix[3-9]*) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + ;; + +irix5* | irix6* | nonstopux*) + case $host_os in + nonstopux*) version_type=nonstopux ;; + *) + if test "$lt_cv_prog_gnu_ld" = yes; then + version_type=linux + else + version_type=irix + fi ;; + esac + need_lib_prefix=no + need_version=no + soname_spec='${libname}${release}${shared_ext}$major' + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}' + case $host_os in + irix5* | nonstopux*) + libsuff= shlibsuff= + ;; + *) + case $LD in # libtool.m4 will add one of these switches to LD + *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") + libsuff= shlibsuff= libmagic=32-bit;; + *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ") + libsuff=32 shlibsuff=N32 libmagic=N32;; + *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ") + libsuff=64 shlibsuff=64 libmagic=64-bit;; + *) libsuff= shlibsuff= libmagic=never-match;; + esac + ;; + esac + shlibpath_var=LD_LIBRARY${shlibsuff}_PATH + shlibpath_overrides_runpath=no + sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}" + sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}" + hardcode_into_libs=yes + ;; + +# No shared lib support for Linux oldld, aout, or coff. +linux*oldld* | linux*aout* | linux*coff*) + dynamic_linker=no + ;; + +# This must be Linux ELF. +linux* | k*bsd*-gnu) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + # Some binutils ld are patched to set DT_RUNPATH + save_LDFLAGS=$LDFLAGS + save_libdir=$libdir + eval "libdir=/foo; wl=\"$lt_prog_compiler_wl_CXX\"; \ + LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec_CXX\"" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then + shlibpath_overrides_runpath=yes +fi + +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext + LDFLAGS=$save_LDFLAGS + libdir=$save_libdir + + # This implies no fast_install, which is unacceptable. + # Some rework will be needed to allow for fast_install + # before this can be enabled. + hardcode_into_libs=yes + + # Append ld.so.conf contents to the search path + if test -f /etc/ld.so.conf; then + lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '` + sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra" + fi + + # We used to test for /lib/ld.so.1 and disable shared libraries on + # powerpc, because MkLinux only supported shared libraries with the + # GNU dynamic linker. Since this was broken with cross compilers, + # most powerpc-linux boxes support dynamic linking these days and + # people can always --disable-shared, the test was removed, and we + # assume the GNU/Linux dynamic linker is in use. + dynamic_linker='GNU/Linux ld.so' + ;; + +netbsdelf*-gnu) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + dynamic_linker='NetBSD ld.elf_so' + ;; + +netbsd*) + version_type=sunos + need_lib_prefix=no + need_version=no + if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' + finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' + dynamic_linker='NetBSD (a.out) ld.so' + else + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + dynamic_linker='NetBSD ld.elf_so' + fi + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + ;; + +newsos6) + version_type=linux + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + ;; + +*nto* | *qnx*) + version_type=qnx + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + dynamic_linker='ldqnx.so' + ;; + +openbsd*) + version_type=sunos + sys_lib_dlsearch_path_spec="/usr/lib" + need_lib_prefix=no + # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs. + case $host_os in + openbsd3.3 | openbsd3.3.*) need_version=yes ;; + *) need_version=no ;; + esac + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' + finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' + shlibpath_var=LD_LIBRARY_PATH + if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then + case $host_os in + openbsd2.[89] | openbsd2.[89].*) + shlibpath_overrides_runpath=no + ;; + *) + shlibpath_overrides_runpath=yes + ;; + esac + else + shlibpath_overrides_runpath=yes + fi + ;; + +os2*) + libname_spec='$name' + shrext_cmds=".dll" + need_lib_prefix=no + library_names_spec='$libname${shared_ext} $libname.a' + dynamic_linker='OS/2 ld.exe' + shlibpath_var=LIBPATH + ;; + +osf3* | osf4* | osf5*) + version_type=osf + need_lib_prefix=no + need_version=no + soname_spec='${libname}${release}${shared_ext}$major' + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + shlibpath_var=LD_LIBRARY_PATH + sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib" + sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec" + ;; + +rdos*) + dynamic_linker=no + ;; + +solaris*) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + # ldd complains unless libraries are executable + postinstall_cmds='chmod +x $lib' + ;; + +sunos4*) + version_type=sunos + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' + finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + if test "$with_gnu_ld" = yes; then + need_lib_prefix=no + fi + need_version=yes + ;; + +sysv4 | sysv4.3*) + version_type=linux + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + case $host_vendor in + sni) + shlibpath_overrides_runpath=no + need_lib_prefix=no + runpath_var=LD_RUN_PATH + ;; + siemens) + need_lib_prefix=no + ;; + motorola) + need_lib_prefix=no + need_version=no + shlibpath_overrides_runpath=no + sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib' + ;; + esac + ;; + +sysv4*MP*) + if test -d /usr/nec ;then + version_type=linux + library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}' + soname_spec='$libname${shared_ext}.$major' + shlibpath_var=LD_LIBRARY_PATH + fi + ;; + +sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) + version_type=freebsd-elf + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + if test "$with_gnu_ld" = yes; then + sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib' + else + sys_lib_search_path_spec='/usr/ccs/lib /usr/lib' + case $host_os in + sco3.2v5*) + sys_lib_search_path_spec="$sys_lib_search_path_spec /lib" + ;; + esac + fi + sys_lib_dlsearch_path_spec='/usr/lib' + ;; + +tpf*) + # TPF is a cross-target only. Preferred cross-host = GNU/Linux. + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + ;; + +uts4*) + version_type=linux + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + ;; + +*) + dynamic_linker=no + ;; +esac +{ $as_echo "$as_me:$LINENO: result: $dynamic_linker" >&5 +$as_echo "$dynamic_linker" >&6; } +test "$dynamic_linker" = no && can_build_shared=no + +variables_saved_for_relink="PATH $shlibpath_var $runpath_var" +if test "$GCC" = yes; then + variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH" +fi + +if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then + sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec" +fi +if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then + sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec" +fi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + { $as_echo "$as_me:$LINENO: checking how to hardcode library paths into programs" >&5 +$as_echo_n "checking how to hardcode library paths into programs... " >&6; } +hardcode_action_CXX= +if test -n "$hardcode_libdir_flag_spec_CXX" || + test -n "$runpath_var_CXX" || + test "X$hardcode_automatic_CXX" = "Xyes" ; then + + # We can hardcode non-existent directories. + if test "$hardcode_direct_CXX" != no && + # If the only mechanism to avoid hardcoding is shlibpath_var, we + # have to relink, otherwise we might link with an installed library + # when we should be linking with a yet-to-be-installed one + ## test "$_LT_TAGVAR(hardcode_shlibpath_var, CXX)" != no && + test "$hardcode_minus_L_CXX" != no; then + # Linking always hardcodes the temporary library directory. + hardcode_action_CXX=relink + else + # We can link without hardcoding, and we can hardcode nonexisting dirs. + hardcode_action_CXX=immediate + fi +else + # We cannot hardcode anything, or else we can only hardcode existing + # directories. + hardcode_action_CXX=unsupported +fi +{ $as_echo "$as_me:$LINENO: result: $hardcode_action_CXX" >&5 +$as_echo "$hardcode_action_CXX" >&6; } + +if test "$hardcode_action_CXX" = relink || + test "$inherit_rpath_CXX" = yes; then + # Fast installation is not supported + enable_fast_install=no +elif test "$shlibpath_overrides_runpath" = yes || + test "$enable_shared" = no; then + # Fast installation is not necessary + enable_fast_install=needless +fi + + + + + + + + fi # test -n "$compiler" + + CC=$lt_save_CC + LDCXX=$LD + LD=$lt_save_LD + GCC=$lt_save_GCC + with_gnu_ld=$lt_save_with_gnu_ld + lt_cv_path_LDCXX=$lt_cv_path_LD + lt_cv_path_LD=$lt_save_path_LD + lt_cv_prog_gnu_ldcxx=$lt_cv_prog_gnu_ld + lt_cv_prog_gnu_ld=$lt_save_with_gnu_ld +fi # test "$_lt_caught_CXX_error" != yes + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + +# Set CXXCPP to a command that runs the C++ preprocessor +ac_ext=cpp +ac_cpp='$CXXCPP $CPPFLAGS' +ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_cxx_compiler_gnu +{ $as_echo "$as_me:$LINENO: checking how to run the C++ preprocessor" >&5 +$as_echo_n "checking how to run the C++ preprocessor... " >&6; } +if test -z "$CXXCPP"; then + if test "${ac_cv_prog_CXXCPP+set}" = set; then + $as_echo_n "(cached) " >&6 +else + # Double quotes because CXXCPP needs to be expanded + for CXXCPP in "$CXX -E" "/lib/cpp" + do + ac_preproc_ok=false +for ac_cxx_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" || + test ! -s conftest.err + }; then + : +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Broken: fails on valid input. +continue +fi + +rm -f conftest.err conftest.$ac_ext + + # OK, works on sane cases. Now check whether nonexistent headers + # can be detected and how. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" || + test ! -s conftest.err + }; then + # Broken: success on invalid input. +continue +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Passes both tests. +ac_preproc_ok=: +break +fi + +rm -f conftest.err conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + break +fi + + done + ac_cv_prog_CXXCPP=$CXXCPP + +fi + CXXCPP=$ac_cv_prog_CXXCPP +else + ac_cv_prog_CXXCPP=$CXXCPP +fi +{ $as_echo "$as_me:$LINENO: result: $CXXCPP" >&5 +$as_echo "$CXXCPP" >&6; } +ac_preproc_ok=false +for ac_cxx_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" || + test ! -s conftest.err + }; then + : +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Broken: fails on valid input. +continue +fi + +rm -f conftest.err conftest.$ac_ext + + # OK, works on sane cases. Now check whether nonexistent headers + # can be detected and how. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" || + test ! -s conftest.err + }; then + # Broken: success on invalid input. +continue +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + # Passes both tests. +ac_preproc_ok=: +break +fi + +rm -f conftest.err conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + : +else + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: C++ preprocessor \"$CXXCPP\" fails sanity check +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: C++ preprocessor \"$CXXCPP\" fails sanity check +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + +# +# reset compiler flags to initial flags +#CXXFLAGS=$OLD_CXXFLAGS + + + + +# safety check: AC_CONFIG_SRCDIR([src/clustal.h]) + +# Let source files know in which context they are being used + +cat >>confdefs.h <<\_ACEOF +#define CLUSTALO 1 +_ACEOF + + + +cat >>confdefs.h <<_ACEOF +#define PACKAGE_CODENAME "$PACKAGE_CODENAME" +_ACEOF + + + +# Get svn revision +#AC_PATH_PROG(svnversioncommand, svnversion) +#if test "X$svnversioncommand" = "X" || test `$svnversioncommand -n '.'` = "exported"; then +#AC_DEFINE_UNQUOTED(SVN_VERSION, ["`cat saved_svn_version.txt`"], [repository svn version]) +#else +#AC_DEFINE_UNQUOTED(SVN_VERSION, ["`svnversion -n`"], [repository svn version]) +#`svnversion -n > saved_svn_version.txt` +#fi + + + + +# AW: we might need this in the future +# +case "$host_os" in +linux*) +# AC_DEFINE(LINUX,1,[This is a Linux system]) + +cat >>confdefs.h <<_ACEOF +#define LINUX 1 +_ACEOF + +# AM_CONDITIONAL(HAVE_GNU_LD, true) +# AM_CONDITIONAL(SOMEBSD, false) +# XTRA_CPPLIBS=-lstdc++ +# LIBEXT=.so + ;; +freebsd*) + +cat >>confdefs.h <<_ACEOF +#define SOMEBSD 1 +_ACEOF + +# AC_CHECK_LIB(c_r, pthread_create) +# AM_CONDITIONAL(HAVE_GNU_LD, true) +# AM_CONDITIONAL(SOMEBSD, true) +# XTRA_CPPLIBS=-lstdc++ +# LIBEXT=.so + ;; +openbsd*) + +cat >>confdefs.h <<_ACEOF +#define SOMEBSD 1 +_ACEOF + +# AC_CHECK_LIB(c_r, pthread_create) +# AM_CONDITIONAL(HAVE_GNU_LD, true) +# AM_CONDITIONAL(SOMEBSD, true) +# XTRA_CPPLIBS=-lstdc++ +# LIBEXT=.so + ;; +netbsd*) + +cat >>confdefs.h <<_ACEOF +#define SOMEBSD 1 +_ACEOF + +# AC_CHECK_LIB(c_r, pthread_create) +# AM_CONDITIONAL(HAVE_GNU_LD, true) +# AM_CONDITIONAL(SOMEBSD, true) +# XTRA_CPPLIBS=-lstdc++ +# LIBEXT=.so + ;; +*solaris*) + +cat >>confdefs.h <<_ACEOF +#define SOLARIS 1 +_ACEOF + +# AC_CHECK_LIB(resolv, res_init) +# XTRA_CPPLIBS=-lstdc++ +# AM_CONDITIONAL(HAVE_GNU_LD, false) +# AM_CONDITIONAL(SOMEBSD, false) +# CFLAGS="-D_POSIX_PTHREAD_SEMANTICS $CFLAGS" +# LIBEXT=.so + ;; +darwin*) + +cat >>confdefs.h <<_ACEOF +#define DARWIN 1 +_ACEOF + +# AM_CONDITIONAL(HAVE_GNU_LD, false) +# AM_CONDITIONAL(SOMEBSD, false) +# CFLAGS="-fno-common $CFLAGS" +# LIBEXT=.so + ;; +cygwin*) + +cat >>confdefs.h <<_ACEOF +#define CYGWIN 1 +_ACEOF + +# LDFLAGS="$LDFLAGS -no-undefined" +# AM_CONDITIONAL(SOMEBSD, false) +# AM_CONDITIONAL(HAVE_GNU_LD, false) +# LIBEXT=.dll + ;; +mingw*) + +cat >>confdefs.h <<_ACEOF +#define MINGW 1 +_ACEOF + +# AC_DEFINE_UNQUOTED(WINDOWS,1,[This is a Windows system]) +# AC_CHECK_LIB(intl, gettext) +# AC_CHECK_LIB(ws2_32, _head_libws2_32_a,,[AC_MSG_ERROR([libextractor requires Winsock2])]) +# AC_CHECK_LIB(plibc, plibc_init,,[AC_MSG_ERROR([libextractor requires PlibC])]) +# LDFLAGS="$LDFLAGS -no-undefined -Wl,--export-all-symbols" +# LIBSOLD=$LIBS +# AM_CONDITIONAL(HAVE_GNU_LD, true) +# AM_CONDITIONAL(SOMEBSD, false) +# LIBEXT=.dll + ;; +*) +# AC_MSG_RESULT(Unrecognised OS $host_os) + +cat >>confdefs.h <<_ACEOF +#define OTHEROS 1 +_ACEOF + +# AC_MSG_RESULT(otheros) +# AM_CONDITIONAL(HAVE_GNU_LD, false) +# AM_CONDITIONAL(SOMEBSD, false) +# LIBEXT=.so + ;; +esac + + + +# Checks for standard header files. +# obsolescent according to http://www.gnu.org/software/hello/manual/autoconf/Particular-Headers.html +{ $as_echo "$as_me:$LINENO: checking for ANSI C header files" >&5 +$as_echo_n "checking for ANSI C header files... " >&6; } +if test "${ac_cv_header_stdc+set}" = set; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#include +#include + +int +main () +{ + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_cv_header_stdc=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_header_stdc=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + +if test $ac_cv_header_stdc = yes; then + # SunOS 4.x string.h does not declare mem*, contrary to ANSI. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "memchr" >/dev/null 2>&1; then + : +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +_ACEOF +if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | + $EGREP "free" >/dev/null 2>&1; then + : +else + ac_cv_header_stdc=no +fi +rm -f conftest* + +fi + +if test $ac_cv_header_stdc = yes; then + # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. + if test "$cross_compiling" = yes; then + : +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include +#include +#if ((' ' & 0x0FF) == 0x020) +# define ISLOWER(c) ('a' <= (c) && (c) <= 'z') +# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) +#else +# define ISLOWER(c) \ + (('a' <= (c) && (c) <= 'i') \ + || ('j' <= (c) && (c) <= 'r') \ + || ('s' <= (c) && (c) <= 'z')) +# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) +#endif + +#define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) +int +main () +{ + int i; + for (i = 0; i < 256; i++) + if (XOR (islower (i), ISLOWER (i)) + || toupper (i) != TOUPPER (i)) + return 2; + return 0; +} +_ACEOF +rm -f conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : +else + $as_echo "$as_me: program exited with status $ac_status" >&5 +$as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +ac_cv_header_stdc=no +fi +rm -rf conftest.dSYM +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +fi + + +fi +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 +$as_echo "$ac_cv_header_stdc" >&6; } +if test $ac_cv_header_stdc = yes; then + +cat >>confdefs.h <<\_ACEOF +#define STDC_HEADERS 1 +_ACEOF + +fi + +# Guess the next one is obsolete as well then? + + + + + + + + + + + + +for ac_header in assert.h ctype.h float.h limits.h math.h memory.h stdarg.h stdio.h stdlib.h string.h time.h unistd.h +do +as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +else + # Is the header compilable? +{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5 +$as_echo_n "checking $ac_header usability... " >&6; } +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_header_compiler=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_compiler=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5 +$as_echo "$ac_header_compiler" >&6; } + +# Is the header present? +{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5 +$as_echo_n "checking $ac_header presence... " >&6; } +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include <$ac_header> +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + ac_header_preproc=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_preproc=no +fi + +rm -f conftest.err conftest.$ac_ext +{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 +$as_echo "$ac_header_preproc" >&6; } + +# So? What about this header? +case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in + yes:no: ) + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5 +$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5 +$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;} + ac_header_preproc=yes + ;; + no:yes:* ) + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5 +$as_echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5 +$as_echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5 +$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5 +$as_echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5 +$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5 +$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;} + ( cat <<\_ASBOX +## ------------------------------ ## +## Report this to clustalw@ucd.ie ## +## ------------------------------ ## +_ASBOX + ) | sed "s/^/$as_me: WARNING: /" >&2 + ;; +esac +{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + eval "$as_ac_Header=\$ac_header_preproc" +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } + +fi +as_val=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then + cat >>confdefs.h <<_ACEOF +#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +fi + +done + +# awk '/^#include *' + +# Checks for typedefs, structures, and compiler characteristics. +{ $as_echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5 +$as_echo_n "checking for an ANSI C-conforming const... " >&6; } +if test "${ac_cv_c_const+set}" = set; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +int +main () +{ +/* FIXME: Include the comments suggested by Paul. */ +#ifndef __cplusplus + /* Ultrix mips cc rejects this. */ + typedef int charset[2]; + const charset cs; + /* SunOS 4.1.1 cc rejects this. */ + char const *const *pcpcc; + char **ppc; + /* NEC SVR4.0.2 mips cc rejects this. */ + struct point {int x, y;}; + static struct point const zero = {0,0}; + /* AIX XL C 1.02.0.0 rejects this. + It does not let you subtract one const X* pointer from another in + an arm of an if-expression whose if-part is not a constant + expression */ + const char *g = "string"; + pcpcc = &g + (g ? g-g : 0); + /* HPUX 7.0 cc rejects these. */ + ++pcpcc; + ppc = (char**) pcpcc; + pcpcc = (char const *const *) ppc; + { /* SCO 3.2v4 cc rejects this. */ + char *t; + char const *s = 0 ? (char *) 0 : (char const *) 0; + + *t++ = 0; + if (s) return 0; + } + { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */ + int x[] = {25, 17}; + const int *foo = &x[0]; + ++foo; + } + { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */ + typedef const int *iptr; + iptr p = 0; + ++p; + } + { /* AIX XL C 1.02.0.0 rejects this saying + "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */ + struct s { int j; const int *ap[3]; }; + struct s *b; b->j = 5; + } + { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */ + const int foo = 10; + if (!foo) return 0; + } + return !cs[0] && !zero.x; +#endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_cv_c_const=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_c_const=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_const" >&5 +$as_echo "$ac_cv_c_const" >&6; } +if test $ac_cv_c_const = no; then + +cat >>confdefs.h <<\_ACEOF +#define const /**/ +_ACEOF + +fi + +{ $as_echo "$as_me:$LINENO: checking for size_t" >&5 +$as_echo_n "checking for size_t... " >&6; } +if test "${ac_cv_type_size_t+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_cv_type_size_t=no +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +if (sizeof (size_t)) + return 0; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +if (sizeof ((size_t))) + return 0; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + : +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_type_size_t=yes +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_type_size_t" >&5 +$as_echo "$ac_cv_type_size_t" >&6; } +if test "x$ac_cv_type_size_t" = x""yes; then + : +else + +cat >>confdefs.h <<_ACEOF +#define size_t unsigned int +_ACEOF + +fi + +{ $as_echo "$as_me:$LINENO: checking for inline" >&5 +$as_echo_n "checking for inline... " >&6; } +if test "${ac_cv_c_inline+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_cv_c_inline=no +for ac_kw in inline __inline__ __inline; do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#ifndef __cplusplus +typedef int foo_t; +static $ac_kw foo_t static_foo () {return 0; } +$ac_kw foo_t foo () {return 0; } +#endif + +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_cv_c_inline=$ac_kw +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + test "$ac_cv_c_inline" != no && break +done + +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_inline" >&5 +$as_echo "$ac_cv_c_inline" >&6; } + + +case $ac_cv_c_inline in + inline | yes) ;; + *) + case $ac_cv_c_inline in + no) ac_val=;; + *) ac_val=$ac_cv_c_inline;; + esac + cat >>confdefs.h <<_ACEOF +#ifndef __cplusplus +#define inline $ac_val +#endif +_ACEOF + ;; +esac + + +# Checks for library functions. +# AC_CHECK_FUNCS(strdup strstr strchr erand48) +# AW is there an automatic way to extract library functions used in the program? + + +# explicit libm check + +{ $as_echo "$as_me:$LINENO: checking for log in -lm" >&5 +$as_echo_n "checking for log in -lm... " >&6; } +if test "${ac_cv_lib_m_log+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lm $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char log (); +int +main () +{ +return log (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ac_cv_lib_m_log=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_m_log=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_m_log" >&5 +$as_echo "$ac_cv_lib_m_log" >&6; } +if test "x$ac_cv_lib_m_log" = x""yes; then + cat >>confdefs.h <<_ACEOF +#define HAVE_LIBM 1 +_ACEOF + + LIBS="-lm $LIBS" + +else + { { $as_echo "$as_me:$LINENO: error: Could not find libm" >&5 +$as_echo "$as_me: error: Could not find libm" >&2;} + { (exit 1); exit 1; }; } +fi + +{ $as_echo "$as_me:$LINENO: checking for log2 in -lm" >&5 +$as_echo_n "checking for log2 in -lm... " >&6; } +if test "${ac_cv_lib_m_log2+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lm $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char log2 (); +int +main () +{ +return log2 (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ac_cv_lib_m_log2=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_m_log2=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_m_log2" >&5 +$as_echo "$ac_cv_lib_m_log2" >&6; } +if test "x$ac_cv_lib_m_log2" = x""yes; then + +cat >>confdefs.h <<\_ACEOF +#define HAVE_LOG2 1 +_ACEOF + +fi + + + +# --- argtable header and library check +# +# + +for ac_header in argtable2.h +do +as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +else + # Is the header compilable? +{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5 +$as_echo_n "checking $ac_header usability... " >&6; } +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_header_compiler=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_compiler=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5 +$as_echo "$ac_header_compiler" >&6; } + +# Is the header present? +{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5 +$as_echo_n "checking $ac_header presence... " >&6; } +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include <$ac_header> +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + ac_header_preproc=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_preproc=no +fi + +rm -f conftest.err conftest.$ac_ext +{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 +$as_echo "$ac_header_preproc" >&6; } + +# So? What about this header? +case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in + yes:no: ) + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5 +$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5 +$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;} + ac_header_preproc=yes + ;; + no:yes:* ) + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5 +$as_echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5 +$as_echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5 +$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5 +$as_echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5 +$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5 +$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;} + ( cat <<\_ASBOX +## ------------------------------ ## +## Report this to clustalw@ucd.ie ## +## ------------------------------ ## +_ASBOX + ) | sed "s/^/$as_me: WARNING: /" >&2 + ;; +esac +{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + eval "$as_ac_Header=\$ac_header_preproc" +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } + +fi +as_val=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then + cat >>confdefs.h <<_ACEOF +#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 +_ACEOF + +else + { { $as_echo "$as_me:$LINENO: error: Could not find argtable2.h. Try $ ./configure CFLAGS='-Iyour-argtable2-include-path" >&5 +$as_echo "$as_me: error: Could not find argtable2.h. Try $ ./configure CFLAGS='-Iyour-argtable2-include-path" >&2;} + { (exit 1); exit 1; }; } +fi + +done + + +{ $as_echo "$as_me:$LINENO: checking for arg_parse in -largtable2" >&5 +$as_echo_n "checking for arg_parse in -largtable2... " >&6; } +if test "${ac_cv_lib_argtable2_arg_parse+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-largtable2 $LIBS" +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char arg_parse (); +int +main () +{ +return arg_parse (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ac_cv_lib_argtable2_arg_parse=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_argtable2_arg_parse=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_argtable2_arg_parse" >&5 +$as_echo "$ac_cv_lib_argtable2_arg_parse" >&6; } +if test "x$ac_cv_lib_argtable2_arg_parse" = x""yes; then + cat >>confdefs.h <<_ACEOF +#define HAVE_LIBARGTABLE2 1 +_ACEOF + + LIBS="-largtable2 $LIBS" + +else + { { $as_echo "$as_me:$LINENO: error: Could not find libargtable2. Try $ ./configure LDFLAGS=\"-Lyour-argtable2-lib-path'" >&5 +$as_echo "$as_me: error: Could not find libargtable2. Try $ ./configure LDFLAGS=\"-Lyour-argtable2-lib-path'" >&2;} + { (exit 1); exit 1; }; } +fi + + + +# enable python if requested (--with-python) +# +#AC_ARG_WITH([python], +# [AS_HELP_STRING([--with-python], +# [Enable Python Interface])], +# [with_python=$withval], +# [with_python=no]) +#if test "$with_python" = "yes"; then +# AC_MSG_CHECKING([for python-config to get compiler flags]) +# AC_CHECK_PROG(python_config, 'python-config', yes) +# if test "${python_config}" != "yes"; then +# AC_MSG_ERROR("Could not run python-config.") +# fi +# PYTHON_CFLAGS=`python-config --cflags` +# PYTHON_LDFLAGS=`python-config --ldflags` +# AC_DEFINE([PYTHON_ENABLED], [1], [define for python usage]) +#fi +#AC_SUBST(PYTHON_CFLAGS) +#AC_SUBST(PYTHON_LDFLAGS) + + +# --- SSE support +# "One instruction to do the same operation on 4 packed elements simultaneously." +# +# http://www.codeproject.com/KB/recipes/sseintro.aspx?msg=568491 +# http://www.drdobbs.com/go-parallel/blog/archives/2010/03/getting_amazing.html +# http://software.intel.com/file/1000 +# +# AC_MSG_CHECKING(for SSE in current arch/CFLAGS) +# AC_LINK_IFELSE([ +# AC_LANG_PROGRAM([[ +# #include +# __m128 testfunc(float *a, float *b) { +# return _mm_add_ps(_mm_loadu_ps(a), _mm_loadu_ps(b)); +# } +# ]])], +# [has_sse=yes], [has_sse=no] +# ) +# AC_MSG_RESULT($has_sse) +# +# AC_ARG_ENABLE([sse], +# [AS_HELP_STRING([--enable-sse], +# [Enable SSE support])], +# [has_sse="$enableval"], +# [has_sse=no]) +# +# if test x"$has_sse" = x"yes"; then +# AC_DEFINE([USE_SSE], , [Enable SSE support]) +# CFLAGS="${CFLAGS} -msse" +# fi + + +# --- openmp +# + +# =========================================================================== +# http://www.gnu.org/software/autoconf-archive/ax_openmp.html +# =========================================================================== +# +# SYNOPSIS +# +# AX_OPENMP([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]]) +# +# DESCRIPTION +# +# This macro tries to find out how to compile programs that use OpenMP a +# standard API and set of compiler directives for parallel programming +# (see http://www-unix.mcs/) +# +# On success, it sets the OPENMP_CFLAGS/OPENMP_CXXFLAGS/OPENMP_F77FLAGS +# output variable to the flag (e.g. -omp) used both to compile *and* link +# OpenMP programs in the current language. +# +# NOTE: You are assumed to not only compile your program with these flags, +# but also link it with them as well. +# +# If you want to compile everything with OpenMP, you should set: +# +# CFLAGS="$CFLAGS $OPENMP_CFLAGS" +# #OR# CXXFLAGS="$CXXFLAGS $OPENMP_CXXFLAGS" +# #OR# FFLAGS="$FFLAGS $OPENMP_FFLAGS" +# +# (depending on the selected language). +# +# The user can override the default choice by setting the corresponding +# environment variable (e.g. OPENMP_CFLAGS). +# +# ACTION-IF-FOUND is a list of shell commands to run if an OpenMP flag is +# found, and ACTION-IF-NOT-FOUND is a list of commands to run it if it is +# not found. If ACTION-IF-FOUND is not specified, the default action will +# define HAVE_OPENMP. +# +# LICENSE +# +# Copyright (c) 2008 Steven G. Johnson +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the +# Free Software Foundation, either version 3 of the License, or (at your +# option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General +# Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program. If not, see . +# +# As a special exception, the respective Autoconf Macro's copyright owner +# gives unlimited permission to copy, distribute and modify the configure +# scripts that are the output of Autoconf when processing the Macro. You +# need not follow the terms of the GNU General Public License when using +# or distributing such scripts, even though portions of the text of the +# Macro appear in them. The GNU General Public License (GPL) does govern +# all other use of the material that constitutes the Autoconf Macro. +# +# This special exception to the GPL applies to versions of the Autoconf +# Macro released by the Autoconf Archive. When you make and distribute a +# modified version of the Autoconf Macro, you may extend this special +# exception to the GPL to apply to your modified version as well. + +#serial 8 + + + +# Check whether --with-openmp was given. +if test "${with_openmp+set}" = set; then + withval=$with_openmp; +fi + +if test "x$with_openmp" = "xno"; then + : +else + + +{ $as_echo "$as_me:$LINENO: checking for OpenMP flag of C compiler" >&5 +$as_echo_n "checking for OpenMP flag of C compiler... " >&6; } +if test "${ax_cv_c_openmp+set}" = set; then + $as_echo_n "(cached) " >&6 +else + saveCFLAGS=$CFLAGS +ax_cv_c_openmp=unknown +# Flags to try: -fopenmp (gcc), -openmp (icc), -mp (SGI & PGI), +# -xopenmp (Sun), -omp (Tru64), -qsmp=omp (AIX), none +ax_openmp_flags="-fopenmp -openmp -mp -xopenmp -omp -qsmp=omp none" +if test "x$OPENMP_CFLAGS" != x; then + ax_openmp_flags="$OPENMP_CFLAGS $ax_openmp_flags" +fi +for ax_openmp_flag in $ax_openmp_flags; do + case $ax_openmp_flag in + none) CFLAGS=$saveC ;; + *) CFLAGS="$saveCFLAGS $ax_openmp_flag" ;; + esac + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char omp_set_num_threads (); +int +main () +{ +return omp_set_num_threads (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ax_cv_c_openmp=$ax_openmp_flag; break +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +done +CFLAGS=$saveCFLAGS + +fi +{ $as_echo "$as_me:$LINENO: result: $ax_cv_c_openmp" >&5 +$as_echo "$ax_cv_c_openmp" >&6; } +if test "x$ax_cv_c_openmp" = "xunknown"; then + : +else + if test "x$ax_cv_c_openmp" != "xnone"; then + OPENMP_CFLAGS=$ax_cv_c_openmp + fi + +cat >>confdefs.h <<\_ACEOF +#define HAVE_OPENMP 1 +_ACEOF + + +fi + + +fi + + +# according to http://beagle-lib.googlecode.com/svn-history/r824/trunk/configure.ac: +# "OpenMP checker only defines for C when compiling both C and C++" +OPENMP_CXXFLAGS=$OPENMP_CFLAGS + + +# version 2: enable openmp only if explicitely asked for it +#AC_ARG_ENABLE(openmp, AS_HELP_STRING([--enable-openmp], [Multi-threaded parallel version using OpenMP])) +#if test -n "${enable_openmp}" -a x"${enable_openmp}" != x"no"; then +# m4_include([m4/ax_openmp.m4]) +# AX_OPENMP(AC_DEFINE(HAVE_OPENMP, 1, [enable OpenMP support]), +# AC_MSG_ERROR([Compiler does not seem to support OpenMP])) +# AC_SUBST(OPENMP_CFLAGS) +# AC_SUBST(OPENMP_CXXFLAGS) +#fi + +# --- squid +# +# +# Extra checks for squid; see their configure, config.log, squidconf.h +# etc. For example, I'm not sure about USE_HOST_BYTESWAP_FUNCTIONS, +# SIZEOF_UNSIGNED_LONG, HAVE_STRTOUL and HAVE_STRTOULL +# +# Might not just have to set compiler flags but create use squidconf.h.in +# +# The following hopefully takes about byte ordering (big-endian...). +# My hope is that it will set WORDS_BIGENDIAN and +# USE_HOST_BYTESWAP_FUNCTIONS (as used by squid) if necessary: +# + + { $as_echo "$as_me:$LINENO: checking whether byte ordering is bigendian" >&5 +$as_echo_n "checking whether byte ordering is bigendian... " >&6; } +if test "${ac_cv_c_bigendian+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_cv_c_bigendian=unknown + # See if we're dealing with a universal compiler. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#ifndef __APPLE_CC__ + not a universal capable compiler + #endif + typedef int dummy; + +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + + # Check for potential -arch flags. It is not universal unless + # there are some -arch flags. Note that *ppc* also matches + # ppc64. This check is also rather less than ideal. + case "${CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS}" in #( + *-arch*ppc*|*-arch*i386*|*-arch*x86_64*) ac_cv_c_bigendian=universal;; + esac +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + if test $ac_cv_c_bigendian = unknown; then + # See if sys/param.h defines the BYTE_ORDER macro. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + #include + +int +main () +{ +#if ! (defined BYTE_ORDER && defined BIG_ENDIAN \ + && defined LITTLE_ENDIAN && BYTE_ORDER && BIG_ENDIAN \ + && LITTLE_ENDIAN) + bogus endian macros + #endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + # It does; now see whether it defined to BIG_ENDIAN or not. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + #include + +int +main () +{ +#if BYTE_ORDER != BIG_ENDIAN + not big endian + #endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_cv_c_bigendian=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_c_bigendian=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + fi + if test $ac_cv_c_bigendian = unknown; then + # See if defines _LITTLE_ENDIAN or _BIG_ENDIAN (e.g., Solaris). + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +int +main () +{ +#if ! (defined _LITTLE_ENDIAN || defined _BIG_ENDIAN) + bogus endian macros + #endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + # It does; now see whether it defined to _BIG_ENDIAN or not. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include + +int +main () +{ +#ifndef _BIG_ENDIAN + not big endian + #endif + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_cv_c_bigendian=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_c_bigendian=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + fi + if test $ac_cv_c_bigendian = unknown; then + # Compile a test program. + if test "$cross_compiling" = yes; then + # Try to guess by grepping values from an object file. + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +short int ascii_mm[] = + { 0x4249, 0x4765, 0x6E44, 0x6961, 0x6E53, 0x7953, 0 }; + short int ascii_ii[] = + { 0x694C, 0x5454, 0x656C, 0x6E45, 0x6944, 0x6E61, 0 }; + int use_ascii (int i) { + return ascii_mm[i] + ascii_ii[i]; + } + short int ebcdic_ii[] = + { 0x89D3, 0xE3E3, 0x8593, 0x95C5, 0x89C4, 0x9581, 0 }; + short int ebcdic_mm[] = + { 0xC2C9, 0xC785, 0x95C4, 0x8981, 0x95E2, 0xA8E2, 0 }; + int use_ebcdic (int i) { + return ebcdic_mm[i] + ebcdic_ii[i]; + } + extern int foo; + +int +main () +{ +return use_ascii (foo) == use_ebcdic (foo); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + if grep BIGenDianSyS conftest.$ac_objext >/dev/null; then + ac_cv_c_bigendian=yes + fi + if grep LiTTleEnDian conftest.$ac_objext >/dev/null ; then + if test "$ac_cv_c_bigendian" = unknown; then + ac_cv_c_bigendian=no + else + # finding both strings is unlikely to happen, but who knows? + ac_cv_c_bigendian=unknown + fi + fi +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ + + /* Are we little or big endian? From Harbison&Steele. */ + union + { + long int l; + char c[sizeof (long int)]; + } u; + u.l = 1; + return u.c[sizeof (long int) - 1] == 1; + + ; + return 0; +} +_ACEOF +rm -f conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_c_bigendian=no +else + $as_echo "$as_me: program exited with status $ac_status" >&5 +$as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +ac_cv_c_bigendian=yes +fi +rm -rf conftest.dSYM +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +fi + + + fi +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_bigendian" >&5 +$as_echo "$ac_cv_c_bigendian" >&6; } + case $ac_cv_c_bigendian in #( + yes) + { $as_echo "$as_me:$LINENO: WARNING: $PACKAGE_NAME hasn't been tested on Big-Endian machines...expecting trouble!" >&5 +$as_echo "$as_me: WARNING: $PACKAGE_NAME hasn't been tested on Big-Endian machines...expecting trouble!" >&2;};; #( + no) + ;; #( + universal) + +cat >>confdefs.h <<\_ACEOF +#define AC_APPLE_UNIVERSAL_BUILD 1 +_ACEOF + + ;; #( + *) + { { $as_echo "$as_me:$LINENO: error: unknown endianness + presetting ac_cv_c_bigendian=no (or yes) will help" >&5 +$as_echo "$as_me: error: unknown endianness + presetting ac_cv_c_bigendian=no (or yes) will help" >&2;} + { (exit 1); exit 1; }; } ;; + esac + + + + + +for ac_func in ntohs ntohl ntons ntonl +do +as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` +{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5 +$as_echo_n "checking for $ac_func... " >&6; } +if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define $ac_func to an innocuous variant, in case declares $ac_func. + For example, HP-UX 11i declares gettimeofday. */ +#define $ac_func innocuous_$ac_func + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char $ac_func (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef $ac_func + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char $ac_func (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined __stub_$ac_func || defined __stub___$ac_func +choke me +#endif + +int +main () +{ +return $ac_func (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + eval "$as_ac_var=yes" +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + eval "$as_ac_var=no" +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +fi +ac_res=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +as_val=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then + cat >>confdefs.h <<_ACEOF +#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 +_ACEOF + +fi +done + +# +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:$LINENO: checking size of unsigned short" >&5 +$as_echo_n "checking size of unsigned short... " >&6; } +if test "${ac_cv_sizeof_unsigned_short+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test "$cross_compiling" = yes; then + # Depending upon the size, compute the lo and hi bounds. +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned short))) >= 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_lo=0 ac_mid=0 + while :; do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned short))) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=$ac_mid; break +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo=`expr $ac_mid + 1` + if test $ac_lo -le $ac_mid; then + ac_lo= ac_hi= + break + fi + ac_mid=`expr 2 '*' $ac_mid + 1` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned short))) < 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=-1 ac_mid=-1 + while :; do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned short))) >= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_lo=$ac_mid; break +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_hi=`expr '(' $ac_mid ')' - 1` + if test $ac_mid -le $ac_hi; then + ac_lo= ac_hi= + break + fi + ac_mid=`expr 2 '*' $ac_mid` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo= ac_hi= +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +# Binary search between lo and hi bounds. +while test "x$ac_lo" != "x$ac_hi"; do + ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned short))) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=$ac_mid +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo=`expr '(' $ac_mid ')' + 1` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +done +case $ac_lo in +?*) ac_cv_sizeof_unsigned_short=$ac_lo;; +'') if test "$ac_cv_type_unsigned_short" = yes; then + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned short) +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute sizeof (unsigned short) +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } + else + ac_cv_sizeof_unsigned_short=0 + fi ;; +esac +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +static long int longval () { return (long int) (sizeof (unsigned short)); } +static unsigned long int ulongval () { return (long int) (sizeof (unsigned short)); } +#include +#include +int +main () +{ + + FILE *f = fopen ("conftest.val", "w"); + if (! f) + return 1; + if (((long int) (sizeof (unsigned short))) < 0) + { + long int i = longval (); + if (i != ((long int) (sizeof (unsigned short)))) + return 1; + fprintf (f, "%ld", i); + } + else + { + unsigned long int i = ulongval (); + if (i != ((long int) (sizeof (unsigned short)))) + return 1; + fprintf (f, "%lu", i); + } + /* Do not output a trailing newline, as this causes \r\n confusion + on some platforms. */ + return ferror (f) || fclose (f) != 0; + + ; + return 0; +} +_ACEOF +rm -f conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_sizeof_unsigned_short=`cat conftest.val` +else + $as_echo "$as_me: program exited with status $ac_status" >&5 +$as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +if test "$ac_cv_type_unsigned_short" = yes; then + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned short) +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute sizeof (unsigned short) +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } + else + ac_cv_sizeof_unsigned_short=0 + fi +fi +rm -rf conftest.dSYM +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +fi +rm -f conftest.val +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_sizeof_unsigned_short" >&5 +$as_echo "$ac_cv_sizeof_unsigned_short" >&6; } + + + +cat >>confdefs.h <<_ACEOF +#define SIZEOF_UNSIGNED_SHORT $ac_cv_sizeof_unsigned_short +_ACEOF + + +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:$LINENO: checking size of unsigned int" >&5 +$as_echo_n "checking size of unsigned int... " >&6; } +if test "${ac_cv_sizeof_unsigned_int+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test "$cross_compiling" = yes; then + # Depending upon the size, compute the lo and hi bounds. +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned int))) >= 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_lo=0 ac_mid=0 + while :; do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned int))) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=$ac_mid; break +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo=`expr $ac_mid + 1` + if test $ac_lo -le $ac_mid; then + ac_lo= ac_hi= + break + fi + ac_mid=`expr 2 '*' $ac_mid + 1` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned int))) < 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=-1 ac_mid=-1 + while :; do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned int))) >= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_lo=$ac_mid; break +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_hi=`expr '(' $ac_mid ')' - 1` + if test $ac_mid -le $ac_hi; then + ac_lo= ac_hi= + break + fi + ac_mid=`expr 2 '*' $ac_mid` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo= ac_hi= +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +# Binary search between lo and hi bounds. +while test "x$ac_lo" != "x$ac_hi"; do + ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned int))) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=$ac_mid +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo=`expr '(' $ac_mid ')' + 1` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +done +case $ac_lo in +?*) ac_cv_sizeof_unsigned_int=$ac_lo;; +'') if test "$ac_cv_type_unsigned_int" = yes; then + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned int) +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute sizeof (unsigned int) +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } + else + ac_cv_sizeof_unsigned_int=0 + fi ;; +esac +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +static long int longval () { return (long int) (sizeof (unsigned int)); } +static unsigned long int ulongval () { return (long int) (sizeof (unsigned int)); } +#include +#include +int +main () +{ + + FILE *f = fopen ("conftest.val", "w"); + if (! f) + return 1; + if (((long int) (sizeof (unsigned int))) < 0) + { + long int i = longval (); + if (i != ((long int) (sizeof (unsigned int)))) + return 1; + fprintf (f, "%ld", i); + } + else + { + unsigned long int i = ulongval (); + if (i != ((long int) (sizeof (unsigned int)))) + return 1; + fprintf (f, "%lu", i); + } + /* Do not output a trailing newline, as this causes \r\n confusion + on some platforms. */ + return ferror (f) || fclose (f) != 0; + + ; + return 0; +} +_ACEOF +rm -f conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_sizeof_unsigned_int=`cat conftest.val` +else + $as_echo "$as_me: program exited with status $ac_status" >&5 +$as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +if test "$ac_cv_type_unsigned_int" = yes; then + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned int) +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute sizeof (unsigned int) +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } + else + ac_cv_sizeof_unsigned_int=0 + fi +fi +rm -rf conftest.dSYM +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +fi +rm -f conftest.val +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_sizeof_unsigned_int" >&5 +$as_echo "$ac_cv_sizeof_unsigned_int" >&6; } + + + +cat >>confdefs.h <<_ACEOF +#define SIZEOF_UNSIGNED_INT $ac_cv_sizeof_unsigned_int +_ACEOF + + +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:$LINENO: checking size of unsigned long" >&5 +$as_echo_n "checking size of unsigned long... " >&6; } +if test "${ac_cv_sizeof_unsigned_long+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test "$cross_compiling" = yes; then + # Depending upon the size, compute the lo and hi bounds. +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long))) >= 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_lo=0 ac_mid=0 + while :; do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long))) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=$ac_mid; break +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo=`expr $ac_mid + 1` + if test $ac_lo -le $ac_mid; then + ac_lo= ac_hi= + break + fi + ac_mid=`expr 2 '*' $ac_mid + 1` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long))) < 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=-1 ac_mid=-1 + while :; do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long))) >= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_lo=$ac_mid; break +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_hi=`expr '(' $ac_mid ')' - 1` + if test $ac_mid -le $ac_hi; then + ac_lo= ac_hi= + break + fi + ac_mid=`expr 2 '*' $ac_mid` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo= ac_hi= +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +# Binary search between lo and hi bounds. +while test "x$ac_lo" != "x$ac_hi"; do + ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long))) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=$ac_mid +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo=`expr '(' $ac_mid ')' + 1` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +done +case $ac_lo in +?*) ac_cv_sizeof_unsigned_long=$ac_lo;; +'') if test "$ac_cv_type_unsigned_long" = yes; then + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned long) +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute sizeof (unsigned long) +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } + else + ac_cv_sizeof_unsigned_long=0 + fi ;; +esac +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +static long int longval () { return (long int) (sizeof (unsigned long)); } +static unsigned long int ulongval () { return (long int) (sizeof (unsigned long)); } +#include +#include +int +main () +{ + + FILE *f = fopen ("conftest.val", "w"); + if (! f) + return 1; + if (((long int) (sizeof (unsigned long))) < 0) + { + long int i = longval (); + if (i != ((long int) (sizeof (unsigned long)))) + return 1; + fprintf (f, "%ld", i); + } + else + { + unsigned long int i = ulongval (); + if (i != ((long int) (sizeof (unsigned long)))) + return 1; + fprintf (f, "%lu", i); + } + /* Do not output a trailing newline, as this causes \r\n confusion + on some platforms. */ + return ferror (f) || fclose (f) != 0; + + ; + return 0; +} +_ACEOF +rm -f conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_sizeof_unsigned_long=`cat conftest.val` +else + $as_echo "$as_me: program exited with status $ac_status" >&5 +$as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +if test "$ac_cv_type_unsigned_long" = yes; then + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned long) +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute sizeof (unsigned long) +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } + else + ac_cv_sizeof_unsigned_long=0 + fi +fi +rm -rf conftest.dSYM +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +fi +rm -f conftest.val +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_sizeof_unsigned_long" >&5 +$as_echo "$ac_cv_sizeof_unsigned_long" >&6; } + + + +cat >>confdefs.h <<_ACEOF +#define SIZEOF_UNSIGNED_LONG $ac_cv_sizeof_unsigned_long +_ACEOF + + +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:$LINENO: checking size of unsigned long long" >&5 +$as_echo_n "checking size of unsigned long long... " >&6; } +if test "${ac_cv_sizeof_unsigned_long_long+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test "$cross_compiling" = yes; then + # Depending upon the size, compute the lo and hi bounds. +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long long))) >= 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_lo=0 ac_mid=0 + while :; do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long long))) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=$ac_mid; break +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo=`expr $ac_mid + 1` + if test $ac_lo -le $ac_mid; then + ac_lo= ac_hi= + break + fi + ac_mid=`expr 2 '*' $ac_mid + 1` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long long))) < 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=-1 ac_mid=-1 + while :; do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long long))) >= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_lo=$ac_mid; break +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_hi=`expr '(' $ac_mid ')' - 1` + if test $ac_mid -le $ac_hi; then + ac_lo= ac_hi= + break + fi + ac_mid=`expr 2 '*' $ac_mid` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo= ac_hi= +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +# Binary search between lo and hi bounds. +while test "x$ac_lo" != "x$ac_hi"; do + ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long long))) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=$ac_mid +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo=`expr '(' $ac_mid ')' + 1` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +done +case $ac_lo in +?*) ac_cv_sizeof_unsigned_long_long=$ac_lo;; +'') if test "$ac_cv_type_unsigned_long_long" = yes; then + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned long long) +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute sizeof (unsigned long long) +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } + else + ac_cv_sizeof_unsigned_long_long=0 + fi ;; +esac +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +static long int longval () { return (long int) (sizeof (unsigned long long)); } +static unsigned long int ulongval () { return (long int) (sizeof (unsigned long long)); } +#include +#include +int +main () +{ + + FILE *f = fopen ("conftest.val", "w"); + if (! f) + return 1; + if (((long int) (sizeof (unsigned long long))) < 0) + { + long int i = longval (); + if (i != ((long int) (sizeof (unsigned long long)))) + return 1; + fprintf (f, "%ld", i); + } + else + { + unsigned long int i = ulongval (); + if (i != ((long int) (sizeof (unsigned long long)))) + return 1; + fprintf (f, "%lu", i); + } + /* Do not output a trailing newline, as this causes \r\n confusion + on some platforms. */ + return ferror (f) || fclose (f) != 0; + + ; + return 0; +} +_ACEOF +rm -f conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_sizeof_unsigned_long_long=`cat conftest.val` +else + $as_echo "$as_me: program exited with status $ac_status" >&5 +$as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +if test "$ac_cv_type_unsigned_long_long" = yes; then + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned long long) +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute sizeof (unsigned long long) +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } + else + ac_cv_sizeof_unsigned_long_long=0 + fi +fi +rm -rf conftest.dSYM +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +fi +rm -f conftest.val +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_sizeof_unsigned_long_long" >&5 +$as_echo "$ac_cv_sizeof_unsigned_long_long" >&6; } + + + +cat >>confdefs.h <<_ACEOF +#define SIZEOF_UNSIGNED_LONG_LONG $ac_cv_sizeof_unsigned_long_long +_ACEOF + + +# + + +for ac_func in stroul strtoull +do +as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` +{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5 +$as_echo_n "checking for $ac_func... " >&6; } +if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define $ac_func to an innocuous variant, in case declares $ac_func. + For example, HP-UX 11i declares gettimeofday. */ +#define $ac_func innocuous_$ac_func + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char $ac_func (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef $ac_func + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char $ac_func (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined __stub_$ac_func || defined __stub___$ac_func +choke me +#endif + +int +main () +{ +return $ac_func (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + eval "$as_ac_var=yes" +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + eval "$as_ac_var=no" +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +fi +ac_res=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +as_val=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then + cat >>confdefs.h <<_ACEOF +#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 +_ACEOF + +fi +done + + + +for ac_func in ftello fseeko +do +as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` +{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5 +$as_echo_n "checking for $ac_func... " >&6; } +if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define $ac_func to an innocuous variant, in case declares $ac_func. + For example, HP-UX 11i declares gettimeofday. */ +#define $ac_func innocuous_$ac_func + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char $ac_func (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef $ac_func + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char $ac_func (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined __stub_$ac_func || defined __stub___$ac_func +choke me +#endif + +int +main () +{ +return $ac_func (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + eval "$as_ac_var=yes" +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + eval "$as_ac_var=no" +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +fi +ac_res=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +as_val=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then + cat >>confdefs.h <<_ACEOF +#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 +_ACEOF + +fi +done + + + +for ac_func in ftello64 fseeko64 +do +as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` +{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5 +$as_echo_n "checking for $ac_func... " >&6; } +if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define $ac_func to an innocuous variant, in case declares $ac_func. + For example, HP-UX 11i declares gettimeofday. */ +#define $ac_func innocuous_$ac_func + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char $ac_func (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef $ac_func + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char $ac_func (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined __stub_$ac_func || defined __stub___$ac_func +choke me +#endif + +int +main () +{ +return $ac_func (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + eval "$as_ac_var=yes" +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + eval "$as_ac_var=no" +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +fi +ac_res=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +as_val=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then + cat >>confdefs.h <<_ACEOF +#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 +_ACEOF + +fi +done + + + +for ac_func in ftell64 fseek64 +do +as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` +{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5 +$as_echo_n "checking for $ac_func... " >&6; } +if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define $ac_func to an innocuous variant, in case declares $ac_func. + For example, HP-UX 11i declares gettimeofday. */ +#define $ac_func innocuous_$ac_func + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char $ac_func (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef $ac_func + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char $ac_func (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined __stub_$ac_func || defined __stub___$ac_func +choke me +#endif + +int +main () +{ +return $ac_func (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + eval "$as_ac_var=yes" +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + eval "$as_ac_var=no" +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +fi +ac_res=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +as_val=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then + cat >>confdefs.h <<_ACEOF +#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 +_ACEOF + +fi +done + +# +{ $as_echo "$as_me:$LINENO: checking for off_t" >&5 +$as_echo_n "checking for off_t... " >&6; } +if test "${ac_cv_type_off_t+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_cv_type_off_t=no +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +if (sizeof (off_t)) + return 0; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +if (sizeof ((off_t))) + return 0; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + : +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_type_off_t=yes +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_type_off_t" >&5 +$as_echo "$ac_cv_type_off_t" >&6; } +if test "x$ac_cv_type_off_t" = x""yes; then + : +else + +cat >>confdefs.h <<_ACEOF +#define off_t long int +_ACEOF + +fi + +# The cast to long int works around a bug in the HP C Compiler +# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects +# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'. +# This bug is HP SR number 8606223364. +{ $as_echo "$as_me:$LINENO: checking size of fpos_t" >&5 +$as_echo_n "checking size of fpos_t... " >&6; } +if test "${ac_cv_sizeof_fpos_t+set}" = set; then + $as_echo_n "(cached) " >&6 +else + if test "$cross_compiling" = yes; then + # Depending upon the size, compute the lo and hi bounds. +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (fpos_t))) >= 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_lo=0 ac_mid=0 + while :; do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (fpos_t))) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=$ac_mid; break +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo=`expr $ac_mid + 1` + if test $ac_lo -le $ac_mid; then + ac_lo= ac_hi= + break + fi + ac_mid=`expr 2 '*' $ac_mid + 1` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (fpos_t))) < 0)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=-1 ac_mid=-1 + while :; do + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (fpos_t))) >= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_lo=$ac_mid; break +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_hi=`expr '(' $ac_mid ')' - 1` + if test $ac_mid -le $ac_hi; then + ac_lo= ac_hi= + break + fi + ac_mid=`expr 2 '*' $ac_mid` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + done +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo= ac_hi= +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +# Binary search between lo and hi bounds. +while test "x$ac_lo" != "x$ac_hi"; do + ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo` + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +static int test_array [1 - 2 * !(((long int) (sizeof (fpos_t))) <= $ac_mid)]; +test_array [0] = 0 + + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_hi=$ac_mid +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_lo=`expr '(' $ac_mid ')' + 1` +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +done +case $ac_lo in +?*) ac_cv_sizeof_fpos_t=$ac_lo;; +'') if test "$ac_cv_type_fpos_t" = yes; then + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (fpos_t) +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute sizeof (fpos_t) +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } + else + ac_cv_sizeof_fpos_t=0 + fi ;; +esac +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +static long int longval () { return (long int) (sizeof (fpos_t)); } +static unsigned long int ulongval () { return (long int) (sizeof (fpos_t)); } +#include +#include +int +main () +{ + + FILE *f = fopen ("conftest.val", "w"); + if (! f) + return 1; + if (((long int) (sizeof (fpos_t))) < 0) + { + long int i = longval (); + if (i != ((long int) (sizeof (fpos_t)))) + return 1; + fprintf (f, "%ld", i); + } + else + { + unsigned long int i = ulongval (); + if (i != ((long int) (sizeof (fpos_t)))) + return 1; + fprintf (f, "%lu", i); + } + /* Do not output a trailing newline, as this causes \r\n confusion + on some platforms. */ + return ferror (f) || fclose (f) != 0; + + ; + return 0; +} +_ACEOF +rm -f conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + ac_cv_sizeof_fpos_t=`cat conftest.val` +else + $as_echo "$as_me: program exited with status $ac_status" >&5 +$as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +if test "$ac_cv_type_fpos_t" = yes; then + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (fpos_t) +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute sizeof (fpos_t) +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } + else + ac_cv_sizeof_fpos_t=0 + fi +fi +rm -rf conftest.dSYM +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +fi +rm -f conftest.val +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_sizeof_fpos_t" >&5 +$as_echo "$ac_cv_sizeof_fpos_t" >&6; } + + + +cat >>confdefs.h <<_ACEOF +#define SIZEOF_FPOS_T $ac_cv_sizeof_fpos_t +_ACEOF + + +# +# struct stat64 and stat64 test: +# version 1: +#AC_CHECK_TYPE(struct stat64, +# [AC_CHECK_FUNC([stat64], +# AC_DEFINE([HAVE_STAT64], [1], [Define if you have the stat64 function]))]) +# version 2: +#AC_MSG_CHECKING(for struct stat64) +#AC_CACHE_VAL(sc_cv_type_stat64, +#[AC_TRY_COMPILE([#include ],[struct stat64 s;], +#[sc_cv_type_stat64=yes], +#[sc_cv_type_stat64=no])]) +#if test $sc_cv_type_stat64 = yes; then +# AC_MSG_RESULT($sc_cv_type_stat64) +# AC_CHECK_FUNC([stat64], AC_DEFINE([HAVE_STAT64], [1], [Define if you have the stat64 function])) +# #AC_DEFINE(HAVE_STAT64, [1], [Define if you have the stat64 function]) +#fi +# +# +# Above fails on myosin because storage size of struct 64 is unknown: +# ssi.c:480: error: storage size of ‘s1’ isn’t known +# +# On my MacBook OS X 10.6 I get: +# ssi.c:481: warning: ‘stat64’ is deprecated (declared at /usr/include/sys/stat.h:465) +# +# So forget about it: we won't use stat64 or define HAVE_STAT64 and +# consequently do no tests here +# + + + +# Add support for the Dmalloc package. If the user runs configure with +# --with-dmalloc, then define WITH_DMALLOC and add -ldmalloc to LIBS. +{ $as_echo "$as_me:$LINENO: checking if malloc debugging is wanted" >&5 +$as_echo_n "checking if malloc debugging is wanted... " >&6; } + +# Check whether --with-dmalloc was given. +if test "${with_dmalloc+set}" = set; then + withval=$with_dmalloc; if test "$withval" = yes; then + { $as_echo "$as_me:$LINENO: result: yes" >&5 +$as_echo "yes" >&6; } + +cat >>confdefs.h <<\_ACEOF +#define WITH_DMALLOC 1 +_ACEOF + + LIBS="$LIBS -ldmalloc" + LDFLAGS="$LDFLAGS -g" +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi +else + { $as_echo "$as_me:$LINENO: result: no" >&5 +$as_echo "no" >&6; } +fi + + + + +# Check if svnversion is installed +#AC_PATH_PROG([SVNVERSION_BIN], [svnversionFIXME], [no]) +## checking if we build in a subversion WC +#wc_found="no"; +#if test "$SVNVERSION_BIN" != "no"; then +# SVNVERSION=`$SVNVERSION_BIN -n $srcdir` +# if test $SVNVERSION != "exported"; +# then +# AC_MSG_NOTICE($SVNVERSION); +# fi +#fi + + +# --- debugging +# +# +# +{ $as_echo "$as_me:$LINENO: checking whether to build with debug information" >&5 +$as_echo_n "checking whether to build with debug information... " >&6; } +# Check whether --enable-debug was given. +if test "${enable_debug+set}" = set; then + enableval=$enable_debug; debugit="$enableval" +else + debugit=no +fi + +{ $as_echo "$as_me:$LINENO: result: $debugit" >&5 +$as_echo "$debugit" >&6; } + +if test x"$debugit" = x"yes"; then + # User variables CFLAGS/CXXFLAGS are used last during compilation and + # can therefore overwrite system settings. + # + # if debugging was requested, add debugging info at the end of + # C[XX]FLAGS, which makes sure previous optimisation flags are + # overwritten (normally C[XX]FLAGS should not be modified as they + # are user variables): + # switch off assert etc + # AC_DEFINE([DEBUG],[],[Debug Mode]) + CFLAGS="${CFLAGS} -g -ansi -Wall -O0" + CXXFLAGS="${CXXFLAGS} -g -ansi -Wall -O0" +else + # switch off assert etc + +cat >>confdefs.h <<\_ACEOF +#define NDEBUG /**/ +_ACEOF + + # if no debugging is requested, we make optimisation explicit + AM_CXXFLAGS="${AM_CXXFLAGS} -O3" + AM_CFLAGS="${AM_CFLAGS} -O3" +fi + + + + + + + + +ac_config_files="$ac_config_files Makefile src/Makefile clustalo.pc Doxyfile src/clustal/Makefile src/hhalign/Makefile src/kmpp/Makefile src/squid/Makefile" + +cat >confcache <<\_ACEOF +# This file is a shell script that caches the results of configure +# tests run on this system so they can be shared between configure +# scripts and configure runs, see configure's option --config-cache. +# It is not useful on other systems. 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ac_configure_extra_args="$ac_configure_extra_args --silent" +fi + +_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +if \$ac_cs_recheck; then + set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion + shift + \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6 + CONFIG_SHELL='$SHELL' + export CONFIG_SHELL + exec "\$@" +fi + +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +exec 5>>config.log +{ + echo + sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX +## Running $as_me. ## +_ASBOX + $as_echo "$ac_log" +} >&5 + +_ACEOF +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +# +# INIT-COMMANDS +# +PACKAGE="$PACKAGE" +AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir" + + +# The HP-UX ksh and POSIX shell print the target directory to stdout +# if CDPATH is set. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + +sed_quote_subst='$sed_quote_subst' +double_quote_subst='$double_quote_subst' +delay_variable_subst='$delay_variable_subst' +macro_version='`$ECHO "X$macro_version" | $Xsed -e "$delay_single_quote_subst"`' +macro_revision='`$ECHO "X$macro_revision" | $Xsed -e "$delay_single_quote_subst"`' +enable_shared='`$ECHO "X$enable_shared" | $Xsed -e "$delay_single_quote_subst"`' +enable_static='`$ECHO "X$enable_static" | $Xsed -e "$delay_single_quote_subst"`' +pic_mode='`$ECHO "X$pic_mode" | $Xsed -e "$delay_single_quote_subst"`' +enable_fast_install='`$ECHO "X$enable_fast_install" | $Xsed -e "$delay_single_quote_subst"`' +host_alias='`$ECHO "X$host_alias" | $Xsed -e "$delay_single_quote_subst"`' +host='`$ECHO "X$host" | $Xsed -e "$delay_single_quote_subst"`' +host_os='`$ECHO "X$host_os" | $Xsed -e "$delay_single_quote_subst"`' +build_alias='`$ECHO "X$build_alias" | $Xsed -e "$delay_single_quote_subst"`' +build='`$ECHO "X$build" | $Xsed -e "$delay_single_quote_subst"`' +build_os='`$ECHO "X$build_os" | $Xsed -e "$delay_single_quote_subst"`' +SED='`$ECHO "X$SED" | $Xsed -e "$delay_single_quote_subst"`' +Xsed='`$ECHO "X$Xsed" | $Xsed -e "$delay_single_quote_subst"`' +GREP='`$ECHO "X$GREP" | $Xsed -e "$delay_single_quote_subst"`' +EGREP='`$ECHO "X$EGREP" | $Xsed -e "$delay_single_quote_subst"`' +FGREP='`$ECHO "X$FGREP" | $Xsed -e "$delay_single_quote_subst"`' +LD='`$ECHO "X$LD" | $Xsed -e "$delay_single_quote_subst"`' +NM='`$ECHO "X$NM" | $Xsed -e "$delay_single_quote_subst"`' +LN_S='`$ECHO "X$LN_S" | $Xsed -e "$delay_single_quote_subst"`' +max_cmd_len='`$ECHO "X$max_cmd_len" | $Xsed -e "$delay_single_quote_subst"`' +ac_objext='`$ECHO "X$ac_objext" | $Xsed -e "$delay_single_quote_subst"`' +exeext='`$ECHO "X$exeext" | $Xsed -e "$delay_single_quote_subst"`' +lt_unset='`$ECHO "X$lt_unset" | $Xsed -e "$delay_single_quote_subst"`' +lt_SP2NL='`$ECHO "X$lt_SP2NL" | $Xsed -e "$delay_single_quote_subst"`' +lt_NL2SP='`$ECHO "X$lt_NL2SP" | $Xsed -e "$delay_single_quote_subst"`' +reload_flag='`$ECHO "X$reload_flag" | $Xsed -e "$delay_single_quote_subst"`' +reload_cmds='`$ECHO "X$reload_cmds" | $Xsed -e "$delay_single_quote_subst"`' +OBJDUMP='`$ECHO "X$OBJDUMP" | $Xsed -e "$delay_single_quote_subst"`' +deplibs_check_method='`$ECHO "X$deplibs_check_method" | $Xsed -e "$delay_single_quote_subst"`' +file_magic_cmd='`$ECHO "X$file_magic_cmd" | $Xsed -e "$delay_single_quote_subst"`' +AR='`$ECHO "X$AR" | $Xsed -e "$delay_single_quote_subst"`' +AR_FLAGS='`$ECHO "X$AR_FLAGS" | $Xsed -e "$delay_single_quote_subst"`' +STRIP='`$ECHO "X$STRIP" | $Xsed -e "$delay_single_quote_subst"`' +RANLIB='`$ECHO "X$RANLIB" | $Xsed -e "$delay_single_quote_subst"`' +old_postinstall_cmds='`$ECHO "X$old_postinstall_cmds" | $Xsed -e "$delay_single_quote_subst"`' +old_postuninstall_cmds='`$ECHO "X$old_postuninstall_cmds" | $Xsed -e "$delay_single_quote_subst"`' +old_archive_cmds='`$ECHO "X$old_archive_cmds" | $Xsed -e "$delay_single_quote_subst"`' +CC='`$ECHO "X$CC" | $Xsed -e "$delay_single_quote_subst"`' +CFLAGS='`$ECHO "X$CFLAGS" | $Xsed -e "$delay_single_quote_subst"`' +compiler='`$ECHO "X$compiler" | $Xsed -e "$delay_single_quote_subst"`' +GCC='`$ECHO "X$GCC" | $Xsed -e "$delay_single_quote_subst"`' +lt_cv_sys_global_symbol_pipe='`$ECHO "X$lt_cv_sys_global_symbol_pipe" | $Xsed -e "$delay_single_quote_subst"`' +lt_cv_sys_global_symbol_to_cdecl='`$ECHO "X$lt_cv_sys_global_symbol_to_cdecl" | $Xsed -e "$delay_single_quote_subst"`' +lt_cv_sys_global_symbol_to_c_name_address='`$ECHO "X$lt_cv_sys_global_symbol_to_c_name_address" | $Xsed -e "$delay_single_quote_subst"`' +lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='`$ECHO "X$lt_cv_sys_global_symbol_to_c_name_address_lib_prefix" | $Xsed -e "$delay_single_quote_subst"`' +objdir='`$ECHO "X$objdir" | $Xsed -e "$delay_single_quote_subst"`' +SHELL='`$ECHO "X$SHELL" | $Xsed -e "$delay_single_quote_subst"`' +ECHO='`$ECHO "X$ECHO" | $Xsed -e "$delay_single_quote_subst"`' +MAGIC_CMD='`$ECHO "X$MAGIC_CMD" | $Xsed -e "$delay_single_quote_subst"`' +lt_prog_compiler_no_builtin_flag='`$ECHO "X$lt_prog_compiler_no_builtin_flag" | $Xsed -e "$delay_single_quote_subst"`' +lt_prog_compiler_wl='`$ECHO "X$lt_prog_compiler_wl" | $Xsed -e "$delay_single_quote_subst"`' +lt_prog_compiler_pic='`$ECHO "X$lt_prog_compiler_pic" | $Xsed -e "$delay_single_quote_subst"`' +lt_prog_compiler_static='`$ECHO "X$lt_prog_compiler_static" | $Xsed -e "$delay_single_quote_subst"`' +lt_cv_prog_compiler_c_o='`$ECHO "X$lt_cv_prog_compiler_c_o" | $Xsed -e "$delay_single_quote_subst"`' +need_locks='`$ECHO "X$need_locks" | $Xsed -e "$delay_single_quote_subst"`' +DSYMUTIL='`$ECHO "X$DSYMUTIL" | $Xsed -e "$delay_single_quote_subst"`' +NMEDIT='`$ECHO "X$NMEDIT" | $Xsed -e "$delay_single_quote_subst"`' +LIPO='`$ECHO "X$LIPO" | $Xsed -e "$delay_single_quote_subst"`' +OTOOL='`$ECHO "X$OTOOL" | $Xsed -e "$delay_single_quote_subst"`' +OTOOL64='`$ECHO "X$OTOOL64" | $Xsed -e "$delay_single_quote_subst"`' +libext='`$ECHO "X$libext" | $Xsed -e "$delay_single_quote_subst"`' +shrext_cmds='`$ECHO "X$shrext_cmds" | $Xsed -e "$delay_single_quote_subst"`' +extract_expsyms_cmds='`$ECHO "X$extract_expsyms_cmds" | $Xsed -e "$delay_single_quote_subst"`' +archive_cmds_need_lc='`$ECHO "X$archive_cmds_need_lc" | $Xsed -e "$delay_single_quote_subst"`' +enable_shared_with_static_runtimes='`$ECHO "X$enable_shared_with_static_runtimes" | $Xsed -e "$delay_single_quote_subst"`' +export_dynamic_flag_spec='`$ECHO "X$export_dynamic_flag_spec" | $Xsed -e "$delay_single_quote_subst"`' +whole_archive_flag_spec='`$ECHO "X$whole_archive_flag_spec" | $Xsed -e "$delay_single_quote_subst"`' +compiler_needs_object='`$ECHO "X$compiler_needs_object" | $Xsed -e "$delay_single_quote_subst"`' +old_archive_from_new_cmds='`$ECHO "X$old_archive_from_new_cmds" | $Xsed -e "$delay_single_quote_subst"`' +old_archive_from_expsyms_cmds='`$ECHO "X$old_archive_from_expsyms_cmds" | $Xsed -e "$delay_single_quote_subst"`' +archive_cmds='`$ECHO "X$archive_cmds" | $Xsed -e "$delay_single_quote_subst"`' +archive_expsym_cmds='`$ECHO "X$archive_expsym_cmds" | $Xsed -e "$delay_single_quote_subst"`' +module_cmds='`$ECHO "X$module_cmds" | $Xsed -e "$delay_single_quote_subst"`' +module_expsym_cmds='`$ECHO "X$module_expsym_cmds" | $Xsed -e "$delay_single_quote_subst"`' +with_gnu_ld='`$ECHO "X$with_gnu_ld" | $Xsed -e "$delay_single_quote_subst"`' +allow_undefined_flag='`$ECHO "X$allow_undefined_flag" | $Xsed -e "$delay_single_quote_subst"`' +no_undefined_flag='`$ECHO "X$no_undefined_flag" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_libdir_flag_spec='`$ECHO "X$hardcode_libdir_flag_spec" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_libdir_flag_spec_ld='`$ECHO "X$hardcode_libdir_flag_spec_ld" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_libdir_separator='`$ECHO "X$hardcode_libdir_separator" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_direct='`$ECHO "X$hardcode_direct" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_direct_absolute='`$ECHO "X$hardcode_direct_absolute" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_minus_L='`$ECHO "X$hardcode_minus_L" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_shlibpath_var='`$ECHO "X$hardcode_shlibpath_var" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_automatic='`$ECHO "X$hardcode_automatic" | $Xsed -e "$delay_single_quote_subst"`' +inherit_rpath='`$ECHO "X$inherit_rpath" | $Xsed -e "$delay_single_quote_subst"`' +link_all_deplibs='`$ECHO "X$link_all_deplibs" | $Xsed -e "$delay_single_quote_subst"`' +fix_srcfile_path='`$ECHO "X$fix_srcfile_path" | $Xsed -e "$delay_single_quote_subst"`' +always_export_symbols='`$ECHO "X$always_export_symbols" | $Xsed -e "$delay_single_quote_subst"`' +export_symbols_cmds='`$ECHO "X$export_symbols_cmds" | $Xsed -e "$delay_single_quote_subst"`' +exclude_expsyms='`$ECHO "X$exclude_expsyms" | $Xsed -e "$delay_single_quote_subst"`' +include_expsyms='`$ECHO "X$include_expsyms" | $Xsed -e "$delay_single_quote_subst"`' +prelink_cmds='`$ECHO "X$prelink_cmds" | $Xsed -e "$delay_single_quote_subst"`' +file_list_spec='`$ECHO "X$file_list_spec" | $Xsed -e "$delay_single_quote_subst"`' +variables_saved_for_relink='`$ECHO "X$variables_saved_for_relink" | $Xsed -e "$delay_single_quote_subst"`' +need_lib_prefix='`$ECHO "X$need_lib_prefix" | $Xsed -e "$delay_single_quote_subst"`' +need_version='`$ECHO "X$need_version" | $Xsed -e "$delay_single_quote_subst"`' +version_type='`$ECHO "X$version_type" | $Xsed -e "$delay_single_quote_subst"`' +runpath_var='`$ECHO "X$runpath_var" | $Xsed -e "$delay_single_quote_subst"`' +shlibpath_var='`$ECHO "X$shlibpath_var" | $Xsed -e "$delay_single_quote_subst"`' +shlibpath_overrides_runpath='`$ECHO "X$shlibpath_overrides_runpath" | $Xsed -e "$delay_single_quote_subst"`' +libname_spec='`$ECHO "X$libname_spec" | $Xsed -e "$delay_single_quote_subst"`' +library_names_spec='`$ECHO "X$library_names_spec" | $Xsed -e "$delay_single_quote_subst"`' +soname_spec='`$ECHO "X$soname_spec" | $Xsed -e "$delay_single_quote_subst"`' +postinstall_cmds='`$ECHO "X$postinstall_cmds" | $Xsed -e "$delay_single_quote_subst"`' +postuninstall_cmds='`$ECHO "X$postuninstall_cmds" | $Xsed -e "$delay_single_quote_subst"`' +finish_cmds='`$ECHO "X$finish_cmds" | $Xsed -e "$delay_single_quote_subst"`' +finish_eval='`$ECHO "X$finish_eval" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_into_libs='`$ECHO "X$hardcode_into_libs" | $Xsed -e "$delay_single_quote_subst"`' +sys_lib_search_path_spec='`$ECHO "X$sys_lib_search_path_spec" | $Xsed -e "$delay_single_quote_subst"`' +sys_lib_dlsearch_path_spec='`$ECHO "X$sys_lib_dlsearch_path_spec" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_action='`$ECHO "X$hardcode_action" | $Xsed -e "$delay_single_quote_subst"`' +enable_dlopen='`$ECHO "X$enable_dlopen" | $Xsed -e "$delay_single_quote_subst"`' +enable_dlopen_self='`$ECHO "X$enable_dlopen_self" | $Xsed -e "$delay_single_quote_subst"`' +enable_dlopen_self_static='`$ECHO "X$enable_dlopen_self_static" | $Xsed -e "$delay_single_quote_subst"`' +old_striplib='`$ECHO "X$old_striplib" | $Xsed -e "$delay_single_quote_subst"`' +striplib='`$ECHO "X$striplib" | $Xsed -e "$delay_single_quote_subst"`' +compiler_lib_search_dirs='`$ECHO "X$compiler_lib_search_dirs" | $Xsed -e "$delay_single_quote_subst"`' +predep_objects='`$ECHO "X$predep_objects" | $Xsed -e "$delay_single_quote_subst"`' +postdep_objects='`$ECHO "X$postdep_objects" | $Xsed -e "$delay_single_quote_subst"`' +predeps='`$ECHO "X$predeps" | $Xsed -e "$delay_single_quote_subst"`' +postdeps='`$ECHO "X$postdeps" | $Xsed -e "$delay_single_quote_subst"`' +compiler_lib_search_path='`$ECHO "X$compiler_lib_search_path" | $Xsed -e "$delay_single_quote_subst"`' +LD_CXX='`$ECHO "X$LD_CXX" | $Xsed -e "$delay_single_quote_subst"`' +old_archive_cmds_CXX='`$ECHO "X$old_archive_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`' +compiler_CXX='`$ECHO "X$compiler_CXX" | $Xsed -e "$delay_single_quote_subst"`' +GCC_CXX='`$ECHO "X$GCC_CXX" | $Xsed -e "$delay_single_quote_subst"`' +lt_prog_compiler_no_builtin_flag_CXX='`$ECHO "X$lt_prog_compiler_no_builtin_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`' +lt_prog_compiler_wl_CXX='`$ECHO "X$lt_prog_compiler_wl_CXX" | $Xsed -e "$delay_single_quote_subst"`' +lt_prog_compiler_pic_CXX='`$ECHO "X$lt_prog_compiler_pic_CXX" | $Xsed -e "$delay_single_quote_subst"`' +lt_prog_compiler_static_CXX='`$ECHO "X$lt_prog_compiler_static_CXX" | $Xsed -e "$delay_single_quote_subst"`' +lt_cv_prog_compiler_c_o_CXX='`$ECHO "X$lt_cv_prog_compiler_c_o_CXX" | $Xsed -e "$delay_single_quote_subst"`' +archive_cmds_need_lc_CXX='`$ECHO "X$archive_cmds_need_lc_CXX" | $Xsed -e "$delay_single_quote_subst"`' +enable_shared_with_static_runtimes_CXX='`$ECHO "X$enable_shared_with_static_runtimes_CXX" | $Xsed -e "$delay_single_quote_subst"`' +export_dynamic_flag_spec_CXX='`$ECHO "X$export_dynamic_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`' +whole_archive_flag_spec_CXX='`$ECHO "X$whole_archive_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`' +compiler_needs_object_CXX='`$ECHO "X$compiler_needs_object_CXX" | $Xsed -e "$delay_single_quote_subst"`' +old_archive_from_new_cmds_CXX='`$ECHO "X$old_archive_from_new_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`' +old_archive_from_expsyms_cmds_CXX='`$ECHO "X$old_archive_from_expsyms_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`' +archive_cmds_CXX='`$ECHO "X$archive_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`' +archive_expsym_cmds_CXX='`$ECHO "X$archive_expsym_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`' +module_cmds_CXX='`$ECHO "X$module_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`' +module_expsym_cmds_CXX='`$ECHO "X$module_expsym_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`' +with_gnu_ld_CXX='`$ECHO "X$with_gnu_ld_CXX" | $Xsed -e "$delay_single_quote_subst"`' +allow_undefined_flag_CXX='`$ECHO "X$allow_undefined_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`' +no_undefined_flag_CXX='`$ECHO "X$no_undefined_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_libdir_flag_spec_CXX='`$ECHO "X$hardcode_libdir_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_libdir_flag_spec_ld_CXX='`$ECHO "X$hardcode_libdir_flag_spec_ld_CXX" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_libdir_separator_CXX='`$ECHO "X$hardcode_libdir_separator_CXX" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_direct_CXX='`$ECHO "X$hardcode_direct_CXX" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_direct_absolute_CXX='`$ECHO "X$hardcode_direct_absolute_CXX" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_minus_L_CXX='`$ECHO "X$hardcode_minus_L_CXX" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_shlibpath_var_CXX='`$ECHO "X$hardcode_shlibpath_var_CXX" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_automatic_CXX='`$ECHO "X$hardcode_automatic_CXX" | $Xsed -e "$delay_single_quote_subst"`' +inherit_rpath_CXX='`$ECHO "X$inherit_rpath_CXX" | $Xsed -e "$delay_single_quote_subst"`' +link_all_deplibs_CXX='`$ECHO "X$link_all_deplibs_CXX" | $Xsed -e "$delay_single_quote_subst"`' +fix_srcfile_path_CXX='`$ECHO "X$fix_srcfile_path_CXX" | $Xsed -e "$delay_single_quote_subst"`' +always_export_symbols_CXX='`$ECHO "X$always_export_symbols_CXX" | $Xsed -e "$delay_single_quote_subst"`' +export_symbols_cmds_CXX='`$ECHO "X$export_symbols_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`' +exclude_expsyms_CXX='`$ECHO "X$exclude_expsyms_CXX" | $Xsed -e "$delay_single_quote_subst"`' +include_expsyms_CXX='`$ECHO "X$include_expsyms_CXX" | $Xsed -e "$delay_single_quote_subst"`' +prelink_cmds_CXX='`$ECHO "X$prelink_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`' +file_list_spec_CXX='`$ECHO "X$file_list_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`' +hardcode_action_CXX='`$ECHO "X$hardcode_action_CXX" | $Xsed -e "$delay_single_quote_subst"`' +compiler_lib_search_dirs_CXX='`$ECHO "X$compiler_lib_search_dirs_CXX" | $Xsed -e "$delay_single_quote_subst"`' +predep_objects_CXX='`$ECHO "X$predep_objects_CXX" | $Xsed -e "$delay_single_quote_subst"`' +postdep_objects_CXX='`$ECHO "X$postdep_objects_CXX" | $Xsed -e "$delay_single_quote_subst"`' +predeps_CXX='`$ECHO "X$predeps_CXX" | $Xsed -e "$delay_single_quote_subst"`' +postdeps_CXX='`$ECHO "X$postdeps_CXX" | $Xsed -e "$delay_single_quote_subst"`' +compiler_lib_search_path_CXX='`$ECHO "X$compiler_lib_search_path_CXX" | $Xsed -e "$delay_single_quote_subst"`' + +LTCC='$LTCC' +LTCFLAGS='$LTCFLAGS' +compiler='$compiler_DEFAULT' + +# Quote evaled strings. +for var in SED \ +GREP \ +EGREP \ +FGREP \ +LD \ +NM \ +LN_S \ +lt_SP2NL \ +lt_NL2SP \ +reload_flag \ +OBJDUMP \ +deplibs_check_method \ +file_magic_cmd \ +AR \ +AR_FLAGS \ +STRIP \ +RANLIB \ +CC \ +CFLAGS \ +compiler \ +lt_cv_sys_global_symbol_pipe \ +lt_cv_sys_global_symbol_to_cdecl \ +lt_cv_sys_global_symbol_to_c_name_address \ +lt_cv_sys_global_symbol_to_c_name_address_lib_prefix \ +SHELL \ +ECHO \ +lt_prog_compiler_no_builtin_flag \ +lt_prog_compiler_wl \ +lt_prog_compiler_pic \ +lt_prog_compiler_static \ +lt_cv_prog_compiler_c_o \ +need_locks \ +DSYMUTIL \ +NMEDIT \ +LIPO \ +OTOOL \ +OTOOL64 \ +shrext_cmds \ +export_dynamic_flag_spec \ +whole_archive_flag_spec \ +compiler_needs_object \ +with_gnu_ld \ +allow_undefined_flag \ +no_undefined_flag \ +hardcode_libdir_flag_spec \ +hardcode_libdir_flag_spec_ld \ +hardcode_libdir_separator \ +fix_srcfile_path \ +exclude_expsyms \ +include_expsyms \ +file_list_spec \ +variables_saved_for_relink \ +libname_spec \ +library_names_spec \ +soname_spec \ +finish_eval \ +old_striplib \ +striplib \ +compiler_lib_search_dirs \ +predep_objects \ +postdep_objects \ +predeps \ +postdeps \ +compiler_lib_search_path \ +LD_CXX \ +compiler_CXX \ +lt_prog_compiler_no_builtin_flag_CXX \ +lt_prog_compiler_wl_CXX \ +lt_prog_compiler_pic_CXX \ +lt_prog_compiler_static_CXX \ +lt_cv_prog_compiler_c_o_CXX \ +export_dynamic_flag_spec_CXX \ +whole_archive_flag_spec_CXX \ +compiler_needs_object_CXX \ +with_gnu_ld_CXX \ +allow_undefined_flag_CXX \ +no_undefined_flag_CXX \ +hardcode_libdir_flag_spec_CXX \ +hardcode_libdir_flag_spec_ld_CXX \ +hardcode_libdir_separator_CXX \ +fix_srcfile_path_CXX \ +exclude_expsyms_CXX \ +include_expsyms_CXX \ +file_list_spec_CXX \ +compiler_lib_search_dirs_CXX \ +predep_objects_CXX \ +postdep_objects_CXX \ +predeps_CXX \ +postdeps_CXX \ +compiler_lib_search_path_CXX; do + case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in + *[\\\\\\\`\\"\\\$]*) + eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$sed_quote_subst\\"\\\`\\\\\\"" + ;; + *) + eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\"" + ;; + esac +done + +# Double-quote double-evaled strings. +for var in reload_cmds \ +old_postinstall_cmds \ +old_postuninstall_cmds \ +old_archive_cmds \ +extract_expsyms_cmds \ +old_archive_from_new_cmds \ +old_archive_from_expsyms_cmds \ +archive_cmds \ +archive_expsym_cmds \ +module_cmds \ +module_expsym_cmds \ +export_symbols_cmds \ +prelink_cmds \ +postinstall_cmds \ +postuninstall_cmds \ +finish_cmds \ +sys_lib_search_path_spec \ +sys_lib_dlsearch_path_spec \ +old_archive_cmds_CXX \ +old_archive_from_new_cmds_CXX \ +old_archive_from_expsyms_cmds_CXX \ +archive_cmds_CXX \ +archive_expsym_cmds_CXX \ +module_cmds_CXX \ +module_expsym_cmds_CXX \ +export_symbols_cmds_CXX \ +prelink_cmds_CXX; do + case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in + *[\\\\\\\`\\"\\\$]*) + eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$double_quote_subst\\" -e \\"\\\$sed_quote_subst\\" -e \\"\\\$delay_variable_subst\\"\\\`\\\\\\"" + ;; + *) + eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\"" + ;; + esac +done + +# Fix-up fallback echo if it was mangled by the above quoting rules. +case \$lt_ECHO in +*'\\\$0 --fallback-echo"') lt_ECHO=\`\$ECHO "X\$lt_ECHO" | \$Xsed -e 's/\\\\\\\\\\\\\\\$0 --fallback-echo"\$/\$0 --fallback-echo"/'\` + ;; +esac + +ac_aux_dir='$ac_aux_dir' +xsi_shell='$xsi_shell' +lt_shell_append='$lt_shell_append' + +# See if we are running on zsh, and set the options which allow our +# commands through without removal of \ escapes INIT. +if test -n "\${ZSH_VERSION+set}" ; then + setopt NO_GLOB_SUBST +fi + + + PACKAGE='$PACKAGE' + VERSION='$VERSION' + TIMESTAMP='$TIMESTAMP' + RM='$RM' + ofile='$ofile' + + + + + + +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 + +# Handling of arguments. +for ac_config_target in $ac_config_targets +do + case $ac_config_target in + "src/config.h") CONFIG_HEADERS="$CONFIG_HEADERS src/config.h" ;; + "src/clustal-omega-config.h") CONFIG_COMMANDS="$CONFIG_COMMANDS src/clustal-omega-config.h" ;; + "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; + "libtool") CONFIG_COMMANDS="$CONFIG_COMMANDS libtool" ;; + "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; + "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;; + "clustalo.pc") CONFIG_FILES="$CONFIG_FILES clustalo.pc" ;; + "Doxyfile") CONFIG_FILES="$CONFIG_FILES Doxyfile" ;; + "src/clustal/Makefile") CONFIG_FILES="$CONFIG_FILES src/clustal/Makefile" ;; + "src/hhalign/Makefile") CONFIG_FILES="$CONFIG_FILES src/hhalign/Makefile" ;; + "src/kmpp/Makefile") CONFIG_FILES="$CONFIG_FILES src/kmpp/Makefile" ;; + "src/squid/Makefile") CONFIG_FILES="$CONFIG_FILES src/squid/Makefile" ;; + + *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 +$as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;} + { (exit 1); exit 1; }; };; + esac +done + + +# If the user did not use the arguments to specify the items to instantiate, +# then the envvar interface is used. Set only those that are not. +# We use the long form for the default assignment because of an extremely +# bizarre bug on SunOS 4.1.3. +if $ac_need_defaults; then + test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files + test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers + test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands +fi + +# Have a temporary directory for convenience. Make it in the build tree +# simply because there is no reason against having it here, and in addition, +# creating and moving files from /tmp can sometimes cause problems. +# Hook for its removal unless debugging. +# Note that there is a small window in which the directory will not be cleaned: +# after its creation but before its name has been assigned to `$tmp'. +$debug || +{ + tmp= + trap 'exit_status=$? + { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status +' 0 + trap '{ (exit 1); exit 1; }' 1 2 13 15 +} +# Create a (secure) tmp directory for tmp files. + +{ + tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` && + test -n "$tmp" && test -d "$tmp" +} || +{ + tmp=./conf$$-$RANDOM + (umask 077 && mkdir "$tmp") +} || +{ + $as_echo "$as_me: cannot create a temporary directory in ." >&2 + { (exit 1); exit 1; } +} + +# Set up the scripts for CONFIG_FILES section. +# No need to generate them if there are no CONFIG_FILES. +# This happens for instance with `./config.status config.h'. +if test -n "$CONFIG_FILES"; then + + +ac_cr=' ' +ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' /dev/null` +if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then + ac_cs_awk_cr='\\r' +else + ac_cs_awk_cr=$ac_cr +fi + +echo 'BEGIN {' >"$tmp/subs1.awk" && +_ACEOF + + +{ + echo "cat >conf$$subs.awk <<_ACEOF" && + echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' && + echo "_ACEOF" +} >conf$$subs.sh || + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } +ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'` +ac_delim='%!_!# ' +for ac_last_try in false false false false false :; do + . ./conf$$subs.sh || + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } + + ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X` + if test $ac_delim_n = $ac_delim_num; then + break + elif $ac_last_try; then + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } + else + ac_delim="$ac_delim!$ac_delim _$ac_delim!! " + fi +done +rm -f conf$$subs.sh + +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +cat >>"\$tmp/subs1.awk" <<\\_ACAWK && +_ACEOF +sed -n ' +h +s/^/S["/; s/!.*/"]=/ +p +g +s/^[^!]*!// +:repl +t repl +s/'"$ac_delim"'$// +t delim +:nl +h +s/\(.\{148\}\).*/\1/ +t more1 +s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/ +p +n +b repl +:more1 +s/["\\]/\\&/g; s/^/"/; s/$/"\\/ +p +g +s/.\{148\}// +t nl +:delim +h +s/\(.\{148\}\).*/\1/ +t more2 +s/["\\]/\\&/g; s/^/"/; s/$/"/ +p +b +:more2 +s/["\\]/\\&/g; s/^/"/; s/$/"\\/ +p +g +s/.\{148\}// +t delim +' >$CONFIG_STATUS || ac_write_fail=1 +rm -f conf$$subs.awk +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +_ACAWK +cat >>"\$tmp/subs1.awk" <<_ACAWK && + for (key in S) S_is_set[key] = 1 + FS = "" + +} +{ + line = $ 0 + nfields = split(line, field, "@") + substed = 0 + len = length(field[1]) + for (i = 2; i < nfields; i++) { + key = field[i] + keylen = length(key) + if (S_is_set[key]) { + value = S[key] + line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3) + len += length(value) + length(field[++i]) + substed = 1 + } else + len += 1 + keylen + } + + print line +} + +_ACAWK +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then + sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g" +else + cat +fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \ + || { { $as_echo "$as_me:$LINENO: error: could not setup config files machinery" >&5 +$as_echo "$as_me: error: could not setup config files machinery" >&2;} + { (exit 1); exit 1; }; } +_ACEOF + +# VPATH may cause trouble with some makes, so we remove $(srcdir), +# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and +# trailing colons and then remove the whole line if VPATH becomes empty +# (actually we leave an empty line to preserve line numbers). +if test "x$srcdir" = x.; then + ac_vpsub='/^[ ]*VPATH[ ]*=/{ +s/:*\$(srcdir):*/:/ +s/:*\${srcdir}:*/:/ +s/:*@srcdir@:*/:/ +s/^\([^=]*=[ ]*\):*/\1/ +s/:*$// +s/^[^=]*=[ ]*$// +}' +fi + +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +fi # test -n "$CONFIG_FILES" + +# Set up the scripts for CONFIG_HEADERS section. +# No need to generate them if there are no CONFIG_HEADERS. +# This happens for instance with `./config.status Makefile'. +if test -n "$CONFIG_HEADERS"; then +cat >"$tmp/defines.awk" <<\_ACAWK || +BEGIN { +_ACEOF + +# Transform confdefs.h into an awk script `defines.awk', embedded as +# here-document in config.status, that substitutes the proper values into +# config.h.in to produce config.h. + +# Create a delimiter string that does not exist in confdefs.h, to ease +# handling of long lines. +ac_delim='%!_!# ' +for ac_last_try in false false :; do + ac_t=`sed -n "/$ac_delim/p" confdefs.h` + if test -z "$ac_t"; then + break + elif $ac_last_try; then + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_HEADERS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_HEADERS" >&2;} + { (exit 1); exit 1; }; } + else + ac_delim="$ac_delim!$ac_delim _$ac_delim!! " + fi +done + +# For the awk script, D is an array of macro values keyed by name, +# likewise P contains macro parameters if any. Preserve backslash +# newline sequences. + +ac_word_re=[_$as_cr_Letters][_$as_cr_alnum]* +sed -n ' +s/.\{148\}/&'"$ac_delim"'/g +t rset +:rset +s/^[ ]*#[ ]*define[ ][ ]*/ / +t def +d +:def +s/\\$// +t bsnl +s/["\\]/\\&/g +s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\ +D["\1"]=" \3"/p +s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2"/p +d +:bsnl +s/["\\]/\\&/g +s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\ +D["\1"]=" \3\\\\\\n"\\/p +t cont +s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2\\\\\\n"\\/p +t cont +d +:cont +n +s/.\{148\}/&'"$ac_delim"'/g +t clear +:clear +s/\\$// +t bsnlc +s/["\\]/\\&/g; s/^/"/; s/$/"/p +d +:bsnlc +s/["\\]/\\&/g; s/^/"/; s/$/\\\\\\n"\\/p +b cont +' >$CONFIG_STATUS || ac_write_fail=1 + +cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 + for (key in D) D_is_set[key] = 1 + FS = "" +} +/^[\t ]*#[\t ]*(define|undef)[\t ]+$ac_word_re([\t (]|\$)/ { + line = \$ 0 + split(line, arg, " ") + if (arg[1] == "#") { + defundef = arg[2] + mac1 = arg[3] + } else { + defundef = substr(arg[1], 2) + mac1 = arg[2] + } + split(mac1, mac2, "(") #) + macro = mac2[1] + prefix = substr(line, 1, index(line, defundef) - 1) + if (D_is_set[macro]) { + # Preserve the white space surrounding the "#". + print prefix "define", macro P[macro] D[macro] + next + } else { + # Replace #undef with comments. This is necessary, for example, + # in the case of _POSIX_SOURCE, which is predefined and required + # on some systems where configure will not decide to define it. + if (defundef == "undef") { + print "/*", prefix defundef, macro, "*/" + next + } + } +} +{ print } +_ACAWK +_ACEOF +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 + { { $as_echo "$as_me:$LINENO: error: could not setup config headers machinery" >&5 +$as_echo "$as_me: error: could not setup config headers machinery" >&2;} + { (exit 1); exit 1; }; } +fi # test -n "$CONFIG_HEADERS" + + +eval set X " :F $CONFIG_FILES :H $CONFIG_HEADERS :C $CONFIG_COMMANDS" +shift +for ac_tag +do + case $ac_tag in + :[FHLC]) ac_mode=$ac_tag; continue;; + esac + case $ac_mode$ac_tag in + :[FHL]*:*);; + :L* | :C*:*) { { $as_echo "$as_me:$LINENO: error: invalid tag $ac_tag" >&5 +$as_echo "$as_me: error: invalid tag $ac_tag" >&2;} + { (exit 1); exit 1; }; };; + :[FH]-) ac_tag=-:-;; + :[FH]*) ac_tag=$ac_tag:$ac_tag.in;; + esac + ac_save_IFS=$IFS + IFS=: + set x $ac_tag + IFS=$ac_save_IFS + shift + ac_file=$1 + shift + + case $ac_mode in + :L) ac_source=$1;; + :[FH]) + ac_file_inputs= + for ac_f + do + case $ac_f in + -) ac_f="$tmp/stdin";; + *) # Look for the file first in the build tree, then in the source tree + # (if the path is not absolute). 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See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with GNU Libtool; see the file COPYING. If not, a copy +# can be downloaded from http://www.gnu.org/licenses/gpl.html, or +# obtained by writing to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + + +# The names of the tagged configurations supported by this script. +available_tags="CXX " + +# ### BEGIN LIBTOOL CONFIG + +# Which release of libtool.m4 was used? +macro_version=$macro_version +macro_revision=$macro_revision + +# Whether or not to build shared libraries. +build_libtool_libs=$enable_shared + +# Whether or not to build static libraries. +build_old_libs=$enable_static + +# What type of objects to build. +pic_mode=$pic_mode + +# Whether or not to optimize for fast installation. +fast_install=$enable_fast_install + +# The host system. +host_alias=$host_alias +host=$host +host_os=$host_os + +# The build system. +build_alias=$build_alias +build=$build +build_os=$build_os + +# A sed program that does not truncate output. +SED=$lt_SED + +# Sed that helps us avoid accidentally triggering echo(1) options like -n. +Xsed="\$SED -e 1s/^X//" + +# A grep program that handles long lines. +GREP=$lt_GREP + +# An ERE matcher. +EGREP=$lt_EGREP + +# A literal string matcher. +FGREP=$lt_FGREP + +# A BSD- or MS-compatible name lister. +NM=$lt_NM + +# Whether we need soft or hard links. +LN_S=$lt_LN_S + +# What is the maximum length of a command? +max_cmd_len=$max_cmd_len + +# Object file suffix (normally "o"). +objext=$ac_objext + +# Executable file suffix (normally ""). +exeext=$exeext + +# whether the shell understands "unset". +lt_unset=$lt_unset + +# turn spaces into newlines. +SP2NL=$lt_lt_SP2NL + +# turn newlines into spaces. +NL2SP=$lt_lt_NL2SP + +# How to create reloadable object files. +reload_flag=$lt_reload_flag +reload_cmds=$lt_reload_cmds + +# An object symbol dumper. +OBJDUMP=$lt_OBJDUMP + +# Method to check whether dependent libraries are shared objects. +deplibs_check_method=$lt_deplibs_check_method + +# Command to use when deplibs_check_method == "file_magic". +file_magic_cmd=$lt_file_magic_cmd + +# The archiver. +AR=$lt_AR +AR_FLAGS=$lt_AR_FLAGS + +# A symbol stripping program. +STRIP=$lt_STRIP + +# Commands used to install an old-style archive. +RANLIB=$lt_RANLIB +old_postinstall_cmds=$lt_old_postinstall_cmds +old_postuninstall_cmds=$lt_old_postuninstall_cmds + +# A C compiler. +LTCC=$lt_CC + +# LTCC compiler flags. +LTCFLAGS=$lt_CFLAGS + +# Take the output of nm and produce a listing of raw symbols and C names. +global_symbol_pipe=$lt_lt_cv_sys_global_symbol_pipe + +# Transform the output of nm in a proper C declaration. +global_symbol_to_cdecl=$lt_lt_cv_sys_global_symbol_to_cdecl + +# Transform the output of nm in a C name address pair. +global_symbol_to_c_name_address=$lt_lt_cv_sys_global_symbol_to_c_name_address + +# Transform the output of nm in a C name address pair when lib prefix is needed. +global_symbol_to_c_name_address_lib_prefix=$lt_lt_cv_sys_global_symbol_to_c_name_address_lib_prefix + +# The name of the directory that contains temporary libtool files. +objdir=$objdir + +# Shell to use when invoking shell scripts. +SHELL=$lt_SHELL + +# An echo program that does not interpret backslashes. +ECHO=$lt_ECHO + +# Used to examine libraries when file_magic_cmd begins with "file". +MAGIC_CMD=$MAGIC_CMD + +# Must we lock files when doing compilation? +need_locks=$lt_need_locks + +# Tool to manipulate archived DWARF debug symbol files on Mac OS X. +DSYMUTIL=$lt_DSYMUTIL + +# Tool to change global to local symbols on Mac OS X. +NMEDIT=$lt_NMEDIT + +# Tool to manipulate fat objects and archives on Mac OS X. +LIPO=$lt_LIPO + +# ldd/readelf like tool for Mach-O binaries on Mac OS X. +OTOOL=$lt_OTOOL + +# ldd/readelf like tool for 64 bit Mach-O binaries on Mac OS X 10.4. +OTOOL64=$lt_OTOOL64 + +# Old archive suffix (normally "a"). +libext=$libext + +# Shared library suffix (normally ".so"). +shrext_cmds=$lt_shrext_cmds + +# The commands to extract the exported symbol list from a shared archive. +extract_expsyms_cmds=$lt_extract_expsyms_cmds + +# Variables whose values should be saved in libtool wrapper scripts and +# restored at link time. +variables_saved_for_relink=$lt_variables_saved_for_relink + +# Do we need the "lib" prefix for modules? +need_lib_prefix=$need_lib_prefix + +# Do we need a version for libraries? +need_version=$need_version + +# Library versioning type. +version_type=$version_type + +# Shared library runtime path variable. +runpath_var=$runpath_var + +# Shared library path variable. +shlibpath_var=$shlibpath_var + +# Is shlibpath searched before the hard-coded library search path? +shlibpath_overrides_runpath=$shlibpath_overrides_runpath + +# Format of library name prefix. +libname_spec=$lt_libname_spec + +# List of archive names. First name is the real one, the rest are links. +# The last name is the one that the linker finds with -lNAME +library_names_spec=$lt_library_names_spec + +# The coded name of the library, if different from the real name. +soname_spec=$lt_soname_spec + +# Command to use after installation of a shared archive. +postinstall_cmds=$lt_postinstall_cmds + +# Command to use after uninstallation of a shared archive. +postuninstall_cmds=$lt_postuninstall_cmds + +# Commands used to finish a libtool library installation in a directory. +finish_cmds=$lt_finish_cmds + +# As "finish_cmds", except a single script fragment to be evaled but +# not shown. +finish_eval=$lt_finish_eval + +# Whether we should hardcode library paths into libraries. +hardcode_into_libs=$hardcode_into_libs + +# Compile-time system search path for libraries. +sys_lib_search_path_spec=$lt_sys_lib_search_path_spec + +# Run-time system search path for libraries. +sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec + +# Whether dlopen is supported. +dlopen_support=$enable_dlopen + +# Whether dlopen of programs is supported. +dlopen_self=$enable_dlopen_self + +# Whether dlopen of statically linked programs is supported. +dlopen_self_static=$enable_dlopen_self_static + +# Commands to strip libraries. +old_striplib=$lt_old_striplib +striplib=$lt_striplib + + +# The linker used to build libraries. +LD=$lt_LD + +# Commands used to build an old-style archive. +old_archive_cmds=$lt_old_archive_cmds + +# A language specific compiler. +CC=$lt_compiler + +# Is the compiler the GNU compiler? +with_gcc=$GCC + +# Compiler flag to turn off builtin functions. +no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag + +# How to pass a linker flag through the compiler. +wl=$lt_lt_prog_compiler_wl + +# Additional compiler flags for building library objects. +pic_flag=$lt_lt_prog_compiler_pic + +# Compiler flag to prevent dynamic linking. +link_static_flag=$lt_lt_prog_compiler_static + +# Does compiler simultaneously support -c and -o options? +compiler_c_o=$lt_lt_cv_prog_compiler_c_o + +# Whether or not to add -lc for building shared libraries. +build_libtool_need_lc=$archive_cmds_need_lc + +# Whether or not to disallow shared libs when runtime libs are static. +allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes + +# Compiler flag to allow reflexive dlopens. +export_dynamic_flag_spec=$lt_export_dynamic_flag_spec + +# Compiler flag to generate shared objects directly from archives. +whole_archive_flag_spec=$lt_whole_archive_flag_spec + +# Whether the compiler copes with passing no objects directly. +compiler_needs_object=$lt_compiler_needs_object + +# Create an old-style archive from a shared archive. +old_archive_from_new_cmds=$lt_old_archive_from_new_cmds + +# Create a temporary old-style archive to link instead of a shared archive. +old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds + +# Commands used to build a shared archive. +archive_cmds=$lt_archive_cmds +archive_expsym_cmds=$lt_archive_expsym_cmds + +# Commands used to build a loadable module if different from building +# a shared archive. +module_cmds=$lt_module_cmds +module_expsym_cmds=$lt_module_expsym_cmds + +# Whether we are building with GNU ld or not. +with_gnu_ld=$lt_with_gnu_ld + +# Flag that allows shared libraries with undefined symbols to be built. +allow_undefined_flag=$lt_allow_undefined_flag + +# Flag that enforces no undefined symbols. +no_undefined_flag=$lt_no_undefined_flag + +# Flag to hardcode \$libdir into a binary during linking. +# This must work even if \$libdir does not exist +hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec + +# If ld is used when linking, flag to hardcode \$libdir into a binary +# during linking. This must work even if \$libdir does not exist. +hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld + +# Whether we need a single "-rpath" flag with a separated argument. +hardcode_libdir_separator=$lt_hardcode_libdir_separator + +# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes +# DIR into the resulting binary. +hardcode_direct=$hardcode_direct + +# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes +# DIR into the resulting binary and the resulting library dependency is +# "absolute",i.e impossible to change by setting \${shlibpath_var} if the +# library is relocated. +hardcode_direct_absolute=$hardcode_direct_absolute + +# Set to "yes" if using the -LDIR flag during linking hardcodes DIR +# into the resulting binary. +hardcode_minus_L=$hardcode_minus_L + +# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR +# into the resulting binary. +hardcode_shlibpath_var=$hardcode_shlibpath_var + +# Set to "yes" if building a shared library automatically hardcodes DIR +# into the library and all subsequent libraries and executables linked +# against it. +hardcode_automatic=$hardcode_automatic + +# Set to yes if linker adds runtime paths of dependent libraries +# to runtime path list. +inherit_rpath=$inherit_rpath + +# Whether libtool must link a program against all its dependency libraries. +link_all_deplibs=$link_all_deplibs + +# Fix the shell variable \$srcfile for the compiler. +fix_srcfile_path=$lt_fix_srcfile_path + +# Set to "yes" if exported symbols are required. +always_export_symbols=$always_export_symbols + +# The commands to list exported symbols. +export_symbols_cmds=$lt_export_symbols_cmds + +# Symbols that should not be listed in the preloaded symbols. +exclude_expsyms=$lt_exclude_expsyms + +# Symbols that must always be exported. +include_expsyms=$lt_include_expsyms + +# Commands necessary for linking programs (against libraries) with templates. +prelink_cmds=$lt_prelink_cmds + +# Specify filename containing input files. +file_list_spec=$lt_file_list_spec + +# How to hardcode a shared library path into an executable. +hardcode_action=$hardcode_action + +# The directories searched by this compiler when creating a shared library. +compiler_lib_search_dirs=$lt_compiler_lib_search_dirs + +# Dependencies to place before and after the objects being linked to +# create a shared library. +predep_objects=$lt_predep_objects +postdep_objects=$lt_postdep_objects +predeps=$lt_predeps +postdeps=$lt_postdeps + +# The library search path used internally by the compiler when linking +# a shared library. +compiler_lib_search_path=$lt_compiler_lib_search_path + +# ### END LIBTOOL CONFIG + +_LT_EOF + + case $host_os in + aix3*) + cat <<\_LT_EOF >> "$cfgfile" +# AIX sometimes has problems with the GCC collect2 program. For some +# reason, if we set the COLLECT_NAMES environment variable, the problems +# vanish in a puff of smoke. +if test "X${COLLECT_NAMES+set}" != Xset; then + COLLECT_NAMES= + export COLLECT_NAMES +fi +_LT_EOF + ;; + esac + + +ltmain="$ac_aux_dir/ltmain.sh" + + + # We use sed instead of cat because bash on DJGPP gets confused if + # if finds mixed CR/LF and LF-only lines. Since sed operates in + # text mode, it properly converts lines to CR/LF. This bash problem + # is reportedly fixed, but why not run on old versions too? + sed '/^# Generated shell functions inserted here/q' "$ltmain" >> "$cfgfile" \ + || (rm -f "$cfgfile"; exit 1) + + case $xsi_shell in + yes) + cat << \_LT_EOF >> "$cfgfile" + +# func_dirname file append nondir_replacement +# Compute the dirname of FILE. If nonempty, add APPEND to the result, +# otherwise set result to NONDIR_REPLACEMENT. +func_dirname () +{ + case ${1} in + */*) func_dirname_result="${1%/*}${2}" ;; + * ) func_dirname_result="${3}" ;; + esac +} + +# func_basename file +func_basename () +{ + func_basename_result="${1##*/}" +} + +# func_dirname_and_basename file append nondir_replacement +# perform func_basename and func_dirname in a single function +# call: +# dirname: Compute the dirname of FILE. If nonempty, +# add APPEND to the result, otherwise set result +# to NONDIR_REPLACEMENT. +# value returned in "$func_dirname_result" +# basename: Compute filename of FILE. +# value retuned in "$func_basename_result" +# Implementation must be kept synchronized with func_dirname +# and func_basename. For efficiency, we do not delegate to +# those functions but instead duplicate the functionality here. +func_dirname_and_basename () +{ + case ${1} in + */*) func_dirname_result="${1%/*}${2}" ;; + * ) func_dirname_result="${3}" ;; + esac + func_basename_result="${1##*/}" +} + +# func_stripname prefix suffix name +# strip PREFIX and SUFFIX off of NAME. +# PREFIX and SUFFIX must not contain globbing or regex special +# characters, hashes, percent signs, but SUFFIX may contain a leading +# dot (in which case that matches only a dot). +func_stripname () +{ + # pdksh 5.2.14 does not do ${X%$Y} correctly if both X and Y are + # positional parameters, so assign one to ordinary parameter first. + func_stripname_result=${3} + func_stripname_result=${func_stripname_result#"${1}"} + func_stripname_result=${func_stripname_result%"${2}"} +} + +# func_opt_split +func_opt_split () +{ + func_opt_split_opt=${1%%=*} + func_opt_split_arg=${1#*=} +} + +# func_lo2o object +func_lo2o () +{ + case ${1} in + *.lo) func_lo2o_result=${1%.lo}.${objext} ;; + *) func_lo2o_result=${1} ;; + esac +} + +# func_xform libobj-or-source +func_xform () +{ + func_xform_result=${1%.*}.lo +} + +# func_arith arithmetic-term... +func_arith () +{ + func_arith_result=$(( $* )) +} + +# func_len string +# STRING may not start with a hyphen. +func_len () +{ + func_len_result=${#1} +} + +_LT_EOF + ;; + *) # Bourne compatible functions. + cat << \_LT_EOF >> "$cfgfile" + +# func_dirname file append nondir_replacement +# Compute the dirname of FILE. If nonempty, add APPEND to the result, +# otherwise set result to NONDIR_REPLACEMENT. +func_dirname () +{ + # Extract subdirectory from the argument. + func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"` + if test "X$func_dirname_result" = "X${1}"; then + func_dirname_result="${3}" + else + func_dirname_result="$func_dirname_result${2}" + fi +} + +# func_basename file +func_basename () +{ + func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"` +} + + +# func_stripname prefix suffix name +# strip PREFIX and SUFFIX off of NAME. +# PREFIX and SUFFIX must not contain globbing or regex special +# characters, hashes, percent signs, but SUFFIX may contain a leading +# dot (in which case that matches only a dot). +# func_strip_suffix prefix name +func_stripname () +{ + case ${2} in + .*) func_stripname_result=`$ECHO "X${3}" \ + | $Xsed -e "s%^${1}%%" -e "s%\\\\${2}\$%%"`;; + *) func_stripname_result=`$ECHO "X${3}" \ + | $Xsed -e "s%^${1}%%" -e "s%${2}\$%%"`;; + esac +} + +# sed scripts: +my_sed_long_opt='1s/^\(-[^=]*\)=.*/\1/;q' +my_sed_long_arg='1s/^-[^=]*=//' + +# func_opt_split +func_opt_split () +{ + func_opt_split_opt=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_opt"` + func_opt_split_arg=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_arg"` +} + +# func_lo2o object +func_lo2o () +{ + func_lo2o_result=`$ECHO "X${1}" | $Xsed -e "$lo2o"` +} + +# func_xform libobj-or-source +func_xform () +{ + func_xform_result=`$ECHO "X${1}" | $Xsed -e 's/\.[^.]*$/.lo/'` +} + +# func_arith arithmetic-term... +func_arith () +{ + func_arith_result=`expr "$@"` +} + +# func_len string +# STRING may not start with a hyphen. +func_len () +{ + func_len_result=`expr "$1" : ".*" 2>/dev/null || echo $max_cmd_len` +} + +_LT_EOF +esac + +case $lt_shell_append in + yes) + cat << \_LT_EOF >> "$cfgfile" + +# func_append var value +# Append VALUE to the end of shell variable VAR. +func_append () +{ + eval "$1+=\$2" +} +_LT_EOF + ;; + *) + cat << \_LT_EOF >> "$cfgfile" + +# func_append var value +# Append VALUE to the end of shell variable VAR. +func_append () +{ + eval "$1=\$$1\$2" +} + +_LT_EOF + ;; + esac + + + sed -n '/^# Generated shell functions inserted here/,$p' "$ltmain" >> "$cfgfile" \ + || (rm -f "$cfgfile"; exit 1) + + mv -f "$cfgfile" "$ofile" || + (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile") + chmod +x "$ofile" + + + cat <<_LT_EOF >> "$ofile" + +# ### BEGIN LIBTOOL TAG CONFIG: CXX + +# The linker used to build libraries. +LD=$lt_LD_CXX + +# Commands used to build an old-style archive. +old_archive_cmds=$lt_old_archive_cmds_CXX + +# A language specific compiler. +CC=$lt_compiler_CXX + +# Is the compiler the GNU compiler? +with_gcc=$GCC_CXX + +# Compiler flag to turn off builtin functions. +no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag_CXX + +# How to pass a linker flag through the compiler. +wl=$lt_lt_prog_compiler_wl_CXX + +# Additional compiler flags for building library objects. +pic_flag=$lt_lt_prog_compiler_pic_CXX + +# Compiler flag to prevent dynamic linking. +link_static_flag=$lt_lt_prog_compiler_static_CXX + +# Does compiler simultaneously support -c and -o options? +compiler_c_o=$lt_lt_cv_prog_compiler_c_o_CXX + +# Whether or not to add -lc for building shared libraries. +build_libtool_need_lc=$archive_cmds_need_lc_CXX + +# Whether or not to disallow shared libs when runtime libs are static. +allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes_CXX + +# Compiler flag to allow reflexive dlopens. +export_dynamic_flag_spec=$lt_export_dynamic_flag_spec_CXX + +# Compiler flag to generate shared objects directly from archives. +whole_archive_flag_spec=$lt_whole_archive_flag_spec_CXX + +# Whether the compiler copes with passing no objects directly. +compiler_needs_object=$lt_compiler_needs_object_CXX + +# Create an old-style archive from a shared archive. +old_archive_from_new_cmds=$lt_old_archive_from_new_cmds_CXX + +# Create a temporary old-style archive to link instead of a shared archive. +old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds_CXX + +# Commands used to build a shared archive. +archive_cmds=$lt_archive_cmds_CXX +archive_expsym_cmds=$lt_archive_expsym_cmds_CXX + +# Commands used to build a loadable module if different from building +# a shared archive. +module_cmds=$lt_module_cmds_CXX +module_expsym_cmds=$lt_module_expsym_cmds_CXX + +# Whether we are building with GNU ld or not. +with_gnu_ld=$lt_with_gnu_ld_CXX + +# Flag that allows shared libraries with undefined symbols to be built. +allow_undefined_flag=$lt_allow_undefined_flag_CXX + +# Flag that enforces no undefined symbols. +no_undefined_flag=$lt_no_undefined_flag_CXX + +# Flag to hardcode \$libdir into a binary during linking. +# This must work even if \$libdir does not exist +hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec_CXX + +# If ld is used when linking, flag to hardcode \$libdir into a binary +# during linking. This must work even if \$libdir does not exist. +hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld_CXX + +# Whether we need a single "-rpath" flag with a separated argument. +hardcode_libdir_separator=$lt_hardcode_libdir_separator_CXX + +# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes +# DIR into the resulting binary. +hardcode_direct=$hardcode_direct_CXX + +# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes +# DIR into the resulting binary and the resulting library dependency is +# "absolute",i.e impossible to change by setting \${shlibpath_var} if the +# library is relocated. +hardcode_direct_absolute=$hardcode_direct_absolute_CXX + +# Set to "yes" if using the -LDIR flag during linking hardcodes DIR +# into the resulting binary. +hardcode_minus_L=$hardcode_minus_L_CXX + +# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR +# into the resulting binary. +hardcode_shlibpath_var=$hardcode_shlibpath_var_CXX + +# Set to "yes" if building a shared library automatically hardcodes DIR +# into the library and all subsequent libraries and executables linked +# against it. +hardcode_automatic=$hardcode_automatic_CXX + +# Set to yes if linker adds runtime paths of dependent libraries +# to runtime path list. +inherit_rpath=$inherit_rpath_CXX + +# Whether libtool must link a program against all its dependency libraries. +link_all_deplibs=$link_all_deplibs_CXX + +# Fix the shell variable \$srcfile for the compiler. +fix_srcfile_path=$lt_fix_srcfile_path_CXX + +# Set to "yes" if exported symbols are required. +always_export_symbols=$always_export_symbols_CXX + +# The commands to list exported symbols. +export_symbols_cmds=$lt_export_symbols_cmds_CXX + +# Symbols that should not be listed in the preloaded symbols. +exclude_expsyms=$lt_exclude_expsyms_CXX + +# Symbols that must always be exported. +include_expsyms=$lt_include_expsyms_CXX + +# Commands necessary for linking programs (against libraries) with templates. +prelink_cmds=$lt_prelink_cmds_CXX + +# Specify filename containing input files. +file_list_spec=$lt_file_list_spec_CXX + +# How to hardcode a shared library path into an executable. +hardcode_action=$hardcode_action_CXX + +# The directories searched by this compiler when creating a shared library. +compiler_lib_search_dirs=$lt_compiler_lib_search_dirs_CXX + +# Dependencies to place before and after the objects being linked to +# create a shared library. +predep_objects=$lt_predep_objects_CXX +postdep_objects=$lt_postdep_objects_CXX +predeps=$lt_predeps_CXX +postdeps=$lt_postdeps_CXX + +# The library search path used internally by the compiler when linking +# a shared library. +compiler_lib_search_path=$lt_compiler_lib_search_path_CXX + +# ### END LIBTOOL TAG CONFIG: CXX +_LT_EOF + + ;; + + esac +done # for ac_tag + + +{ (exit 0); exit 0; } +_ACEOF +chmod +x $CONFIG_STATUS +ac_clean_files=$ac_clean_files_save + +test $ac_write_fail = 0 || + { { $as_echo "$as_me:$LINENO: error: write failure creating $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: write failure creating $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } + + +# configure is writing to config.log, and then calls config.status. +# config.status does its own redirection, appending to config.log. +# Unfortunately, on DOS this fails, as config.log is still kept open +# by configure, so config.status won't be able to write to it; its +# output is simply discarded. So we exec the FD to /dev/null, +# effectively closing config.log, so it can be properly (re)opened and +# appended to by config.status. When coming back to configure, we +# need to make the FD available again. +if test "$no_create" != yes; then + ac_cs_success=: + ac_config_status_args= + test "$silent" = yes && + ac_config_status_args="$ac_config_status_args --quiet" + exec 5>/dev/null + $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false + exec 5>>config.log + # Use ||, not &&, to avoid exiting from the if with $? = 1, which + # would make configure fail if this is the last instruction. + $ac_cs_success || { (exit 1); exit 1; } +fi +if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then + { $as_echo "$as_me:$LINENO: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 +$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} +fi + diff --git a/binaries/src/clustalo/configure.ac b/binaries/src/clustalo/configure.ac new file mode 100644 index 0000000..f65d9ca --- /dev/null +++ b/binaries/src/clustalo/configure.ac @@ -0,0 +1,499 @@ +# configure.ac for Clustal Omega +# +# RCS $Id: configure.ac 256 2011-06-23 13:57:28Z fabian $ + + +# release +# +#AC_INIT([Clustal Omega], [0.1.1], [clustalw@ucd.ie]) +#PACKAGE_CODENAME="OppidumLeonis" +#r238 +#AC_INIT([Clustal Omega], [0.2.0], [clustalw@ucd.ie]) +#PACKAGE_CODENAME="IbiMeVidebunt" +#r250 +#AC_INIT([Clustal Omega], [1.0.1], [clustalw@ucd.ie]) +#PACKAGE_CODENAME="DeshilHollesEamus" +#r255 +AC_INIT([Clustal Omega], [1.0.2], [clustalw@ucd.ie]) +PACKAGE_CODENAME="DeshilHollesEamus" + +# The AC_INIT macro can take any source file as an argument. It just +# checks that the file is there, which should, in turn, mean that the +# source directory is there. AC_INIT generates the following m4 +# macros, output variables and preprocessor symbols: +AC_SUBST(PACKAGE_NAME) +AC_SUBST(PACKAGE_TARNAME) +AC_SUBST(PACKAGE_VERSION) +AC_SUBST(PACKAGE_STRING) +AC_SUBST(PACKAGE_BUGREPORT) +AC_SUBST(PACKAGE_CODENAME) + +AC_MSG_NOTICE([ + + Welcome to $PACKAGE_NAME - version $PACKAGE_VERSION ($PACKAGE_CODENAME) + + +NMMMMMMMMMS= + MMMMM? :MMMMM8 + IMMMMS MMMMM, + ~MMMMN ,MMMMM + =MMMMM MMMMM + ?MMMMM +MMMMM + MMMMMS MMMMM + MMMMM MMMMM: + MMMMM MMMMM+ + MMMMM MMMMM~ + MMMMM MMMMM + MMMMMZ MMMMM + MMMMM ,MMMMZ + MMMM8 MMMM+ + MMMMS MMMM, + MMMMO MMMM + ,N SMMM MMM8 +8 + ,M7 M+ M+ :M8 + ,MMMMMMMMMMMMI MMMMMMMMMMMM8 + ,MMMMMMMMMMMM8 MMMMMMMMMMMM8 + ,MMMMMMMMMMMMN MMMMMMMMMMMM8 + + ]) +# +# Created with http://www.glassgiant.com/ascii/ and Wikipedia's Omega +# Replaced all dollars with S's. +# +# +# ,MMMMMMMMMD: MMMMM +# NMMMMMMMMMMMMMM+ SMMMM +# DMMMMMMMMMMMMMMMMMM, +MMMM +# MMMMMMMMM8ZSO8MMMMMMMM +MMMM +# MMMMM7 SMMMM +MMMM +# MMMO MM? +MMMM +# ?MMI NMIIMMMM +# MMM MMMMMMM +# MM +# MN +# MD +# MM +# MM? ,~+ISON +# =MMI MMSOMMMM +# MMMZ MMS +MMMM +# MMMM8: :NMMM +MMMM +# MMMMMMMMMDOODMMMMMMMMM +MMMM +# MMMMMMMMMMMMMMMMMMMM +MMMM +# OMMMMMMMMMMMMMMZ SMMMM +# MMMMMMMMMM+ MMMMM +# + + +# AC_MSG_NOTICE([Configuring for your system...]) + +AC_PREREQ(2.6) # 2.60 needed for AC_USE_SYSTEM_EXTENSIONS +# consider 2.64 which allows to define a URL as well + +# The AM_INIT_AUTOMAKE line adds several standard checks. +# This macro is always needed for automake +# Obsolete: It takes the program name and version number as arguments. +AM_INIT_AUTOMAKE + +# config header: provides a way for people to customise the +# configuration for their platform, via #defines. config.h.in can be +# generated automatically with the autoheader tool. However, you need +# a stamp-h file in your project to ensure that automake regenerates +# config.h from config.h.in. Type 'touch stamp-h' to add this file to +# your project. +# +AM_CONFIG_HEADER(src/config.h) + +# the following allows to install a copy config.h for libclustalo in a +# namespace like way, i.e. no name clash with your own config.h +AX_PREFIX_CONFIG_H(src/clustal-omega-config.h) + +# This macro was introduced in Autoconf 2.60. If possible, enable +# extensions to C or Posix on hosts that normally disable the +# extensions. +AC_USE_SYSTEM_EXTENSIONS + + +# for cross compilation +# +AC_CANONICAL_HOST +## AC_CANONICAL_BUILD +## AC_CANONICAL_TARGET + +# Set the @SET_MAKE@ variable=make if $(MAKE) not set +AC_PROG_MAKE_SET + +# AC_PROG_RANLIB will allow you to build code in sub-directories into +# temporary libraries, which make will then link in with the rest of +# the code. +# Rendered obsolte by LT_INIT: AC_PROG_RANLIB +#AC_PROG_LIBTOOL +LT_INIT + +# AC_PROG_INSTALL will generate an install target so that users may +# just type 'make install' to install the software. +AC_PROG_INSTALL + +# check for C++ preprocessor and compiler and the library compiler +# (might change the compiler flags) +# +# Determine a C compiler to use. If using the GNU C compiler, set +# shell variable GCC to `yes'. If output variable CFLAGS was not +# already set, set it to `-g -O2' for the GNU C compiler (`-O2' on +# systems where GCC does not accept `-g'), or `-g' for other +# compilers. +AC_PROG_CC +# Set output variable CPP to a command that runs the C preprocessor. +AC_PROG_CPP +# +# Determine a C++ compiler to use. If output variable CXXFLAGS was not +# already set, set it to `-g -O2' for the GNU C++ compiler (`-O2' on +# systems where G++ does not accept `-g'), or `-g' for other +# compilers. +AC_PROG_CXX +# Set CXXCPP to a command that runs the C++ preprocessor +AC_PROG_CXXCPP +# +# reset compiler flags to initial flags +#CXXFLAGS=$OLD_CXXFLAGS + + + + +# safety check: AC_CONFIG_SRCDIR([src/clustal.h]) + +# Let source files know in which context they are being used +AC_DEFINE([CLUSTALO], [1], + [Let all files know they are being used inside Clustal Omega]) + +AC_DEFINE_UNQUOTED(PACKAGE_CODENAME, "$PACKAGE_CODENAME", [The package code name]) + + +# Get svn revision +#AC_PATH_PROG(svnversioncommand, svnversion) +#if test "X$svnversioncommand" = "X" || test `$svnversioncommand -n '.'` = "exported"; then +#AC_DEFINE_UNQUOTED(SVN_VERSION, ["`cat saved_svn_version.txt`"], [repository svn version]) +#else +#AC_DEFINE_UNQUOTED(SVN_VERSION, ["`svnversion -n`"], [repository svn version]) +#`svnversion -n > saved_svn_version.txt` +#fi + + + + +# AW: we might need this in the future +# +case "$host_os" in +linux*) +# AC_DEFINE(LINUX,1,[This is a Linux system]) + AC_DEFINE_UNQUOTED(LINUX,1,[This is a LINUX system]) +# AM_CONDITIONAL(HAVE_GNU_LD, true) +# AM_CONDITIONAL(SOMEBSD, false) +# XTRA_CPPLIBS=-lstdc++ +# LIBEXT=.so + ;; +freebsd*) + AC_DEFINE_UNQUOTED(SOMEBSD,1,[This is a BSD system]) +# AC_CHECK_LIB(c_r, pthread_create) +# AM_CONDITIONAL(HAVE_GNU_LD, true) +# AM_CONDITIONAL(SOMEBSD, true) +# XTRA_CPPLIBS=-lstdc++ +# LIBEXT=.so + ;; +openbsd*) + AC_DEFINE_UNQUOTED(SOMEBSD,1,[This is a BSD system]) +# AC_CHECK_LIB(c_r, pthread_create) +# AM_CONDITIONAL(HAVE_GNU_LD, true) +# AM_CONDITIONAL(SOMEBSD, true) +# XTRA_CPPLIBS=-lstdc++ +# LIBEXT=.so + ;; +netbsd*) + AC_DEFINE_UNQUOTED(SOMEBSD,1,[This is a BSD system]) +# AC_CHECK_LIB(c_r, pthread_create) +# AM_CONDITIONAL(HAVE_GNU_LD, true) +# AM_CONDITIONAL(SOMEBSD, true) +# XTRA_CPPLIBS=-lstdc++ +# LIBEXT=.so + ;; +*solaris*) + AC_DEFINE_UNQUOTED(SOLARIS,1,[This is a Solaris system]) +# AC_CHECK_LIB(resolv, res_init) +# XTRA_CPPLIBS=-lstdc++ +# AM_CONDITIONAL(HAVE_GNU_LD, false) +# AM_CONDITIONAL(SOMEBSD, false) +# CFLAGS="-D_POSIX_PTHREAD_SEMANTICS $CFLAGS" +# LIBEXT=.so + ;; +darwin*) + AC_DEFINE_UNQUOTED(DARWIN,1,[This is a Darwin system]) +# AM_CONDITIONAL(HAVE_GNU_LD, false) +# AM_CONDITIONAL(SOMEBSD, false) +# CFLAGS="-fno-common $CFLAGS" +# LIBEXT=.so + ;; +cygwin*) + AC_DEFINE_UNQUOTED(CYGWIN,1,[This is a CYGWIN system]) +# LDFLAGS="$LDFLAGS -no-undefined" +# AM_CONDITIONAL(SOMEBSD, false) +# AM_CONDITIONAL(HAVE_GNU_LD, false) +# LIBEXT=.dll + ;; +mingw*) + AC_DEFINE_UNQUOTED(MINGW,1,[This is a MinGW system]) +# AC_DEFINE_UNQUOTED(WINDOWS,1,[This is a Windows system]) +# AC_CHECK_LIB(intl, gettext) +# AC_CHECK_LIB(ws2_32, _head_libws2_32_a,,[AC_MSG_ERROR([libextractor requires Winsock2])]) +# AC_CHECK_LIB(plibc, plibc_init,,[AC_MSG_ERROR([libextractor requires PlibC])]) +# LDFLAGS="$LDFLAGS -no-undefined -Wl,--export-all-symbols" +# LIBSOLD=$LIBS +# AM_CONDITIONAL(HAVE_GNU_LD, true) +# AM_CONDITIONAL(SOMEBSD, false) +# LIBEXT=.dll + ;; +*) +# AC_MSG_RESULT(Unrecognised OS $host_os) + AC_DEFINE_UNQUOTED(OTHEROS,1,[Some strange OS]) +# AC_MSG_RESULT(otheros) +# AM_CONDITIONAL(HAVE_GNU_LD, false) +# AM_CONDITIONAL(SOMEBSD, false) +# LIBEXT=.so + ;; +esac + + + +# Checks for standard header files. +# obsolescent according to http://www.gnu.org/software/hello/manual/autoconf/Particular-Headers.html +AC_HEADER_STDC +# Guess the next one is obsolete as well then? +AC_CHECK_HEADERS(assert.h ctype.h float.h limits.h math.h memory.h stdarg.h stdio.h stdlib.h string.h time.h unistd.h) +# awk '/^#include *' + +# Checks for typedefs, structures, and compiler characteristics. +AC_C_CONST +AC_TYPE_SIZE_T +AC_C_INLINE + +# Checks for library functions. +# AC_CHECK_FUNCS(strdup strstr strchr erand48) +# AW is there an automatic way to extract library functions used in the program? + + +# explicit libm check +AC_CHECK_LIB(m, log,, AC_MSG_ERROR([Could not find libm])) +AC_CHECK_LIB(m, log2, AC_DEFINE(HAVE_LOG2, 1, [Has log2()])) + + +# --- argtable header and library check +# +# +AC_CHECK_HEADERS([argtable2.h], [], + AC_MSG_ERROR([Could not find argtable2.h. Try $ ./configure CFLAGS='-Iyour-argtable2-include-path])) +AC_CHECK_LIB(argtable2, arg_parse, [], + AC_MSG_ERROR([Could not find libargtable2. Try $ ./configure LDFLAGS="-Lyour-argtable2-lib-path'])) + + +# enable python if requested (--with-python) +# +#AC_ARG_WITH([python], +# [AS_HELP_STRING([--with-python], +# [Enable Python Interface])], +# [with_python=$withval], +# [with_python=no]) +#if test "$with_python" = "yes"; then +# AC_MSG_CHECKING([for python-config to get compiler flags]) +# AC_CHECK_PROG(python_config, 'python-config', yes) +# if test "${python_config}" != "yes"; then +# AC_MSG_ERROR("Could not run python-config.") +# fi +# PYTHON_CFLAGS=`python-config --cflags` +# PYTHON_LDFLAGS=`python-config --ldflags` +# AC_DEFINE([PYTHON_ENABLED], [1], [define for python usage]) +#fi +#AC_SUBST(PYTHON_CFLAGS) +#AC_SUBST(PYTHON_LDFLAGS) + + +# --- SSE support +# "One instruction to do the same operation on 4 packed elements simultaneously." +# +# http://www.codeproject.com/KB/recipes/sseintro.aspx?msg=568491 +# http://www.drdobbs.com/go-parallel/blog/archives/2010/03/getting_amazing.html +# http://software.intel.com/file/1000 +# +# AC_MSG_CHECKING(for SSE in current arch/CFLAGS) +# AC_LINK_IFELSE([ +# AC_LANG_PROGRAM([[ +# #include +# __m128 testfunc(float *a, float *b) { +# return _mm_add_ps(_mm_loadu_ps(a), _mm_loadu_ps(b)); +# } +# ]])], +# [has_sse=yes], [has_sse=no] +# ) +# AC_MSG_RESULT($has_sse) +# +# AC_ARG_ENABLE([sse], +# [AS_HELP_STRING([--enable-sse], +# [Enable SSE support])], +# [has_sse="$enableval"], +# [has_sse=no]) +# +# if test x"$has_sse" = x"yes"; then +# AC_DEFINE([USE_SSE], , [Enable SSE support]) +# CFLAGS="${CFLAGS} -msse" +# fi + + +# --- openmp +# +AC_CONFIG_MACRO_DIR([m4]) +m4_include([m4/ax_openmp.m4]) +AC_ARG_WITH([openmp], + AS_HELP_STRING([--without-openmp], [Do not use OpenMP])) +AS_IF([test "x$with_openmp" = "xno"], + [], + [AX_OPENMP( + AC_DEFINE([HAVE_OPENMP],[1],[Defined if OpenMP should and can be used]) + )] + ) +AC_SUBST(OPENMP_CFLAGS) +# according to http://beagle-lib.googlecode.com/svn-history/r824/trunk/configure.ac: +# "OpenMP checker only defines for C when compiling both C and C++" +OPENMP_CXXFLAGS=$OPENMP_CFLAGS +AC_SUBST(OPENMP_CXXFLAGS) + +# version 2: enable openmp only if explicitely asked for it +#AC_ARG_ENABLE(openmp, AS_HELP_STRING([--enable-openmp], [Multi-threaded parallel version using OpenMP])) +#if test -n "${enable_openmp}" -a x"${enable_openmp}" != x"no"; then +# m4_include([m4/ax_openmp.m4]) +# AX_OPENMP(AC_DEFINE(HAVE_OPENMP, 1, [enable OpenMP support]), +# AC_MSG_ERROR([Compiler does not seem to support OpenMP])) +# AC_SUBST(OPENMP_CFLAGS) +# AC_SUBST(OPENMP_CXXFLAGS) +#fi + +# --- squid +# +# +# Extra checks for squid; see their configure, config.log, squidconf.h +# etc. For example, I'm not sure about USE_HOST_BYTESWAP_FUNCTIONS, +# SIZEOF_UNSIGNED_LONG, HAVE_STRTOUL and HAVE_STRTOULL +# +# Might not just have to set compiler flags but create use squidconf.h.in +# +# The following hopefully takes about byte ordering (big-endian...). +# My hope is that it will set WORDS_BIGENDIAN and +# USE_HOST_BYTESWAP_FUNCTIONS (as used by squid) if necessary: +# +AC_C_BIGENDIAN(AC_MSG_WARN([$PACKAGE_NAME hasn't been tested on Big-Endian machines...expecting trouble!])) +AC_CHECK_FUNCS([ntohs ntohl ntons ntonl]) +# +AC_CHECK_SIZEOF(unsigned short) +AC_CHECK_SIZEOF(unsigned int) +AC_CHECK_SIZEOF(unsigned long) +AC_CHECK_SIZEOF(unsigned long long) +# +AC_CHECK_FUNCS([stroul strtoull]) +AC_CHECK_FUNCS([ftello fseeko]) +AC_CHECK_FUNCS([ftello64 fseeko64]) +AC_CHECK_FUNCS([ftell64 fseek64]) +# +AC_TYPE_OFF_T +AC_CHECK_SIZEOF(fpos_t) +# +# struct stat64 and stat64 test: +# version 1: +#AC_CHECK_TYPE(struct stat64, +# [AC_CHECK_FUNC([stat64], +# AC_DEFINE([HAVE_STAT64], [1], [Define if you have the stat64 function]))]) +# version 2: +#AC_MSG_CHECKING(for struct stat64) +#AC_CACHE_VAL(sc_cv_type_stat64, +#[AC_TRY_COMPILE([#include ],[struct stat64 s;], +#[sc_cv_type_stat64=yes], +#[sc_cv_type_stat64=no])]) +#if test $sc_cv_type_stat64 = yes; then +# AC_MSG_RESULT($sc_cv_type_stat64) +# AC_CHECK_FUNC([stat64], AC_DEFINE([HAVE_STAT64], [1], [Define if you have the stat64 function])) +# #AC_DEFINE(HAVE_STAT64, [1], [Define if you have the stat64 function]) +#fi +# +# +# Above fails on myosin because storage size of struct 64 is unknown: +# ssi.c:480: error: storage size of ‘s1’ isn’t known +# +# On my MacBook OS X 10.6 I get: +# ssi.c:481: warning: ‘stat64’ is deprecated (declared at /usr/include/sys/stat.h:465) +# +# So forget about it: we won't use stat64 or define HAVE_STAT64 and +# consequently do no tests here +# + + + +# Add support for the Dmalloc package. If the user runs configure with +# --with-dmalloc, then define WITH_DMALLOC and add -ldmalloc to LIBS. +AM_WITH_DMALLOC + + +# Check if svnversion is installed +#AC_PATH_PROG([SVNVERSION_BIN], [svnversionFIXME], [no]) +## checking if we build in a subversion WC +#wc_found="no"; +#if test "$SVNVERSION_BIN" != "no"; then +# SVNVERSION=`$SVNVERSION_BIN -n $srcdir` +# if test $SVNVERSION != "exported"; +# then +# AC_MSG_NOTICE($SVNVERSION); +# fi +#fi + + +# --- debugging +# +# +# +AC_MSG_CHECKING([whether to build with debug information]) +AC_ARG_ENABLE([debug], + [AS_HELP_STRING([--enable-debug], + [Enable debugging (default=no)])], + [debugit="$enableval"], + [debugit=no]) +AC_MSG_RESULT([$debugit]) + +if test x"$debugit" = x"yes"; then + # User variables CFLAGS/CXXFLAGS are used last during compilation and + # can therefore overwrite system settings. + # + # if debugging was requested, add debugging info at the end of + # C[XX]FLAGS, which makes sure previous optimisation flags are + # overwritten (normally C[XX]FLAGS should not be modified as they + # are user variables): + # switch off assert etc + # AC_DEFINE([DEBUG],[],[Debug Mode]) + CFLAGS="${CFLAGS} -g -ansi -Wall -O0" + CXXFLAGS="${CXXFLAGS} -g -ansi -Wall -O0" +else + # switch off assert etc + AC_DEFINE([NDEBUG],[],[No-debug Mode]) + # if no debugging is requested, we make optimisation explicit + AM_CXXFLAGS="${AM_CXXFLAGS} -O3" + AM_CFLAGS="${AM_CFLAGS} -O3" +fi + + + +AC_SUBST([AM_CXXFLAGS]) +AC_SUBST([AM_CFLAGS]) +AC_SUBST([AM_LDFLAGS]) + + +AC_CONFIG_FILES(Makefile + src/Makefile + clustalo.pc + Doxyfile + src/clustal/Makefile + src/hhalign/Makefile + src/kmpp/Makefile + src/squid/Makefile) +AC_OUTPUT diff --git a/binaries/src/clustalo/depcomp b/binaries/src/clustalo/depcomp new file mode 100644 index 0000000..df8eea7 --- /dev/null +++ b/binaries/src/clustalo/depcomp @@ -0,0 +1,630 @@ +#! /bin/sh +# depcomp - compile a program generating dependencies as side-effects + +scriptversion=2009-04-28.21; # UTC + +# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free +# Software Foundation, Inc. + +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2, or (at your option) +# any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that program. + +# Originally written by Alexandre Oliva . + +case $1 in + '') + echo "$0: No command. Try \`$0 --help' for more information." 1>&2 + exit 1; + ;; + -h | --h*) + cat <<\EOF +Usage: depcomp [--help] [--version] PROGRAM [ARGS] + +Run PROGRAMS ARGS to compile a file, generating dependencies +as side-effects. + +Environment variables: + depmode Dependency tracking mode. + source Source file read by `PROGRAMS ARGS'. + object Object file output by `PROGRAMS ARGS'. + DEPDIR directory where to store dependencies. + depfile Dependency file to output. + tmpdepfile Temporary file to use when outputing dependencies. + libtool Whether libtool is used (yes/no). + +Report bugs to . +EOF + exit $? + ;; + -v | --v*) + echo "depcomp $scriptversion" + exit $? + ;; +esac + +if test -z "$depmode" || test -z "$source" || test -z "$object"; then + echo "depcomp: Variables source, object and depmode must be set" 1>&2 + exit 1 +fi + +# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po. +depfile=${depfile-`echo "$object" | + sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`} +tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`} + +rm -f "$tmpdepfile" + +# Some modes work just like other modes, but use different flags. We +# parameterize here, but still list the modes in the big case below, +# to make depend.m4 easier to write. Note that we *cannot* use a case +# here, because this file can only contain one case statement. +if test "$depmode" = hp; then + # HP compiler uses -M and no extra arg. + gccflag=-M + depmode=gcc +fi + +if test "$depmode" = dashXmstdout; then + # This is just like dashmstdout with a different argument. + dashmflag=-xM + depmode=dashmstdout +fi + +cygpath_u="cygpath -u -f -" +if test "$depmode" = msvcmsys; then + # This is just like msvisualcpp but w/o cygpath translation. + # Just convert the backslash-escaped backslashes to single forward + # slashes to satisfy depend.m4 + cygpath_u="sed s,\\\\\\\\,/,g" + depmode=msvisualcpp +fi + +case "$depmode" in +gcc3) +## gcc 3 implements dependency tracking that does exactly what +## we want. Yay! Note: for some reason libtool 1.4 doesn't like +## it if -MD -MP comes after the -MF stuff. Hmm. +## Unfortunately, FreeBSD c89 acceptance of flags depends upon +## the command line argument order; so add the flags where they +## appear in depend2.am. Note that the slowdown incurred here +## affects only configure: in makefiles, %FASTDEP% shortcuts this. + for arg + do + case $arg in + -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;; + *) set fnord "$@" "$arg" ;; + esac + shift # fnord + shift # $arg + done + "$@" + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile" + exit $stat + fi + mv "$tmpdepfile" "$depfile" + ;; + +gcc) +## There are various ways to get dependency output from gcc. Here's +## why we pick this rather obscure method: +## - Don't want to use -MD because we'd like the dependencies to end +## up in a subdir. Having to rename by hand is ugly. +## (We might end up doing this anyway to support other compilers.) +## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like +## -MM, not -M (despite what the docs say). +## - Using -M directly means running the compiler twice (even worse +## than renaming). + if test -z "$gccflag"; then + gccflag=-MD, + fi + "$@" -Wp,"$gccflag$tmpdepfile" + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile" + exit $stat + fi + rm -f "$depfile" + echo "$object : \\" > "$depfile" + alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz +## The second -e expression handles DOS-style file names with drive letters. + sed -e 's/^[^:]*: / /' \ + -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile" +## This next piece of magic avoids the `deleted header file' problem. +## The problem is that when a header file which appears in a .P file +## is deleted, the dependency causes make to die (because there is +## typically no way to rebuild the header). We avoid this by adding +## dummy dependencies for each header file. Too bad gcc doesn't do +## this for us directly. + tr ' ' ' +' < "$tmpdepfile" | +## Some versions of gcc put a space before the `:'. On the theory +## that the space means something, we add a space to the output as +## well. +## Some versions of the HPUX 10.20 sed can't process this invocation +## correctly. Breaking it into two sed invocations is a workaround. + sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +hp) + # This case exists only to let depend.m4 do its work. It works by + # looking at the text of this script. This case will never be run, + # since it is checked for above. + exit 1 + ;; + +sgi) + if test "$libtool" = yes; then + "$@" "-Wp,-MDupdate,$tmpdepfile" + else + "$@" -MDupdate "$tmpdepfile" + fi + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile" + exit $stat + fi + rm -f "$depfile" + + if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files + echo "$object : \\" > "$depfile" + + # Clip off the initial element (the dependent). Don't try to be + # clever and replace this with sed code, as IRIX sed won't handle + # lines with more than a fixed number of characters (4096 in + # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines; + # the IRIX cc adds comments like `#:fec' to the end of the + # dependency line. + tr ' ' ' +' < "$tmpdepfile" \ + | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \ + tr ' +' ' ' >> "$depfile" + echo >> "$depfile" + + # The second pass generates a dummy entry for each header file. + tr ' ' ' +' < "$tmpdepfile" \ + | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \ + >> "$depfile" + else + # The sourcefile does not contain any dependencies, so just + # store a dummy comment line, to avoid errors with the Makefile + # "include basename.Plo" scheme. + echo "#dummy" > "$depfile" + fi + rm -f "$tmpdepfile" + ;; + +aix) + # The C for AIX Compiler uses -M and outputs the dependencies + # in a .u file. In older versions, this file always lives in the + # current directory. Also, the AIX compiler puts `$object:' at the + # start of each line; $object doesn't have directory information. + # Version 6 uses the directory in both cases. + dir=`echo "$object" | sed -e 's|/[^/]*$|/|'` + test "x$dir" = "x$object" && dir= + base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'` + if test "$libtool" = yes; then + tmpdepfile1=$dir$base.u + tmpdepfile2=$base.u + tmpdepfile3=$dir.libs/$base.u + "$@" -Wc,-M + else + tmpdepfile1=$dir$base.u + tmpdepfile2=$dir$base.u + tmpdepfile3=$dir$base.u + "$@" -M + fi + stat=$? + + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" + exit $stat + fi + + for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" + do + test -f "$tmpdepfile" && break + done + if test -f "$tmpdepfile"; then + # Each line is of the form `foo.o: dependent.h'. + # Do two passes, one to just change these to + # `$object: dependent.h' and one to simply `dependent.h:'. + sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile" + # That's a tab and a space in the []. + sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile" + else + # The sourcefile does not contain any dependencies, so just + # store a dummy comment line, to avoid errors with the Makefile + # "include basename.Plo" scheme. + echo "#dummy" > "$depfile" + fi + rm -f "$tmpdepfile" + ;; + +icc) + # Intel's C compiler understands `-MD -MF file'. However on + # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c + # ICC 7.0 will fill foo.d with something like + # foo.o: sub/foo.c + # foo.o: sub/foo.h + # which is wrong. We want: + # sub/foo.o: sub/foo.c + # sub/foo.o: sub/foo.h + # sub/foo.c: + # sub/foo.h: + # ICC 7.1 will output + # foo.o: sub/foo.c sub/foo.h + # and will wrap long lines using \ : + # foo.o: sub/foo.c ... \ + # sub/foo.h ... \ + # ... + + "$@" -MD -MF "$tmpdepfile" + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile" + exit $stat + fi + rm -f "$depfile" + # Each line is of the form `foo.o: dependent.h', + # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'. + # Do two passes, one to just change these to + # `$object: dependent.h' and one to simply `dependent.h:'. + sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile" + # Some versions of the HPUX 10.20 sed can't process this invocation + # correctly. Breaking it into two sed invocations is a workaround. + sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" | + sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +hp2) + # The "hp" stanza above does not work with aCC (C++) and HP's ia64 + # compilers, which have integrated preprocessors. The correct option + # to use with these is +Maked; it writes dependencies to a file named + # 'foo.d', which lands next to the object file, wherever that + # happens to be. + # Much of this is similar to the tru64 case; see comments there. + dir=`echo "$object" | sed -e 's|/[^/]*$|/|'` + test "x$dir" = "x$object" && dir= + base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'` + if test "$libtool" = yes; then + tmpdepfile1=$dir$base.d + tmpdepfile2=$dir.libs/$base.d + "$@" -Wc,+Maked + else + tmpdepfile1=$dir$base.d + tmpdepfile2=$dir$base.d + "$@" +Maked + fi + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile1" "$tmpdepfile2" + exit $stat + fi + + for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" + do + test -f "$tmpdepfile" && break + done + if test -f "$tmpdepfile"; then + sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile" + # Add `dependent.h:' lines. + sed -ne '2,${ + s/^ *// + s/ \\*$// + s/$/:/ + p + }' "$tmpdepfile" >> "$depfile" + else + echo "#dummy" > "$depfile" + fi + rm -f "$tmpdepfile" "$tmpdepfile2" + ;; + +tru64) + # The Tru64 compiler uses -MD to generate dependencies as a side + # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'. + # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put + # dependencies in `foo.d' instead, so we check for that too. + # Subdirectories are respected. + dir=`echo "$object" | sed -e 's|/[^/]*$|/|'` + test "x$dir" = "x$object" && dir= + base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'` + + if test "$libtool" = yes; then + # With Tru64 cc, shared objects can also be used to make a + # static library. This mechanism is used in libtool 1.4 series to + # handle both shared and static libraries in a single compilation. + # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d. + # + # With libtool 1.5 this exception was removed, and libtool now + # generates 2 separate objects for the 2 libraries. These two + # compilations output dependencies in $dir.libs/$base.o.d and + # in $dir$base.o.d. We have to check for both files, because + # one of the two compilations can be disabled. We should prefer + # $dir$base.o.d over $dir.libs/$base.o.d because the latter is + # automatically cleaned when .libs/ is deleted, while ignoring + # the former would cause a distcleancheck panic. + tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4 + tmpdepfile2=$dir$base.o.d # libtool 1.5 + tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5 + tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504 + "$@" -Wc,-MD + else + tmpdepfile1=$dir$base.o.d + tmpdepfile2=$dir$base.d + tmpdepfile3=$dir$base.d + tmpdepfile4=$dir$base.d + "$@" -MD + fi + + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4" + exit $stat + fi + + for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4" + do + test -f "$tmpdepfile" && break + done + if test -f "$tmpdepfile"; then + sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile" + # That's a tab and a space in the []. + sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile" + else + echo "#dummy" > "$depfile" + fi + rm -f "$tmpdepfile" + ;; + +#nosideeffect) + # This comment above is used by automake to tell side-effect + # dependency tracking mechanisms from slower ones. + +dashmstdout) + # Important note: in order to support this mode, a compiler *must* + # always write the preprocessed file to stdout, regardless of -o. + "$@" || exit $? + + # Remove the call to Libtool. + if test "$libtool" = yes; then + while test "X$1" != 'X--mode=compile'; do + shift + done + shift + fi + + # Remove `-o $object'. + IFS=" " + for arg + do + case $arg in + -o) + shift + ;; + $object) + shift + ;; + *) + set fnord "$@" "$arg" + shift # fnord + shift # $arg + ;; + esac + done + + test -z "$dashmflag" && dashmflag=-M + # Require at least two characters before searching for `:' + # in the target name. This is to cope with DOS-style filenames: + # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise. + "$@" $dashmflag | + sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile" + rm -f "$depfile" + cat < "$tmpdepfile" > "$depfile" + tr ' ' ' +' < "$tmpdepfile" | \ +## Some versions of the HPUX 10.20 sed can't process this invocation +## correctly. Breaking it into two sed invocations is a workaround. + sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +dashXmstdout) + # This case only exists to satisfy depend.m4. It is never actually + # run, as this mode is specially recognized in the preamble. + exit 1 + ;; + +makedepend) + "$@" || exit $? + # Remove any Libtool call + if test "$libtool" = yes; then + while test "X$1" != 'X--mode=compile'; do + shift + done + shift + fi + # X makedepend + shift + cleared=no eat=no + for arg + do + case $cleared in + no) + set ""; shift + cleared=yes ;; + esac + if test $eat = yes; then + eat=no + continue + fi + case "$arg" in + -D*|-I*) + set fnord "$@" "$arg"; shift ;; + # Strip any option that makedepend may not understand. Remove + # the object too, otherwise makedepend will parse it as a source file. + -arch) + eat=yes ;; + -*|$object) + ;; + *) + set fnord "$@" "$arg"; shift ;; + esac + done + obj_suffix=`echo "$object" | sed 's/^.*\././'` + touch "$tmpdepfile" + ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@" + rm -f "$depfile" + cat < "$tmpdepfile" > "$depfile" + sed '1,2d' "$tmpdepfile" | tr ' ' ' +' | \ +## Some versions of the HPUX 10.20 sed can't process this invocation +## correctly. Breaking it into two sed invocations is a workaround. + sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" "$tmpdepfile".bak + ;; + +cpp) + # Important note: in order to support this mode, a compiler *must* + # always write the preprocessed file to stdout. + "$@" || exit $? + + # Remove the call to Libtool. + if test "$libtool" = yes; then + while test "X$1" != 'X--mode=compile'; do + shift + done + shift + fi + + # Remove `-o $object'. + IFS=" " + for arg + do + case $arg in + -o) + shift + ;; + $object) + shift + ;; + *) + set fnord "$@" "$arg" + shift # fnord + shift # $arg + ;; + esac + done + + "$@" -E | + sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \ + -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' | + sed '$ s: \\$::' > "$tmpdepfile" + rm -f "$depfile" + echo "$object : \\" > "$depfile" + cat < "$tmpdepfile" >> "$depfile" + sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +msvisualcpp) + # Important note: in order to support this mode, a compiler *must* + # always write the preprocessed file to stdout. + "$@" || exit $? + + # Remove the call to Libtool. + if test "$libtool" = yes; then + while test "X$1" != 'X--mode=compile'; do + shift + done + shift + fi + + IFS=" " + for arg + do + case "$arg" in + -o) + shift + ;; + $object) + shift + ;; + "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI") + set fnord "$@" + shift + shift + ;; + *) + set fnord "$@" "$arg" + shift + shift + ;; + esac + done + "$@" -E 2>/dev/null | + sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile" + rm -f "$depfile" + echo "$object : \\" > "$depfile" + sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" + echo " " >> "$depfile" + sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +msvcmsys) + # This case exists only to let depend.m4 do its work. It works by + # looking at the text of this script. This case will never be run, + # since it is checked for above. + exit 1 + ;; + +none) + exec "$@" + ;; + +*) + echo "Unknown depmode $depmode" 1>&2 + exit 1 + ;; +esac + +exit 0 + +# Local Variables: +# mode: shell-script +# sh-indentation: 2 +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "scriptversion=" +# time-stamp-format: "%:y-%02m-%02d.%02H" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" +# End: diff --git a/binaries/src/clustalo/install-sh b/binaries/src/clustalo/install-sh new file mode 100644 index 0000000..6781b98 --- /dev/null +++ b/binaries/src/clustalo/install-sh @@ -0,0 +1,520 @@ +#!/bin/sh +# install - install a program, script, or datafile + +scriptversion=2009-04-28.21; # UTC + +# This originates from X11R5 (mit/util/scripts/install.sh), which was +# later released in X11R6 (xc/config/util/install.sh) with the +# following copyright and license. +# +# Copyright (C) 1994 X Consortium +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to +# deal in the Software without restriction, including without limitation the +# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or +# sell copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN +# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC- +# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +# +# Except as contained in this notice, the name of the X Consortium shall not +# be used in advertising or otherwise to promote the sale, use or other deal- +# ings in this Software without prior written authorization from the X Consor- +# tium. +# +# +# FSF changes to this file are in the public domain. +# +# Calling this script install-sh is preferred over install.sh, to prevent +# `make' implicit rules from creating a file called install from it +# when there is no Makefile. +# +# This script is compatible with the BSD install script, but was written +# from scratch. + +nl=' +' +IFS=" "" $nl" + +# set DOITPROG to echo to test this script + +# Don't use :- since 4.3BSD and earlier shells don't like it. +doit=${DOITPROG-} +if test -z "$doit"; then + doit_exec=exec +else + doit_exec=$doit +fi + +# Put in absolute file names if you don't have them in your path; +# or use environment vars. + +chgrpprog=${CHGRPPROG-chgrp} +chmodprog=${CHMODPROG-chmod} +chownprog=${CHOWNPROG-chown} +cmpprog=${CMPPROG-cmp} +cpprog=${CPPROG-cp} +mkdirprog=${MKDIRPROG-mkdir} +mvprog=${MVPROG-mv} +rmprog=${RMPROG-rm} +stripprog=${STRIPPROG-strip} + +posix_glob='?' +initialize_posix_glob=' + test "$posix_glob" != "?" || { + if (set -f) 2>/dev/null; then + posix_glob= + else + posix_glob=: + fi + } +' + +posix_mkdir= + +# Desired mode of installed file. +mode=0755 + +chgrpcmd= +chmodcmd=$chmodprog +chowncmd= +mvcmd=$mvprog +rmcmd="$rmprog -f" +stripcmd= + +src= +dst= +dir_arg= +dst_arg= + +copy_on_change=false +no_target_directory= + +usage="\ +Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE + or: $0 [OPTION]... SRCFILES... DIRECTORY + or: $0 [OPTION]... -t DIRECTORY SRCFILES... + or: $0 [OPTION]... -d DIRECTORIES... + +In the 1st form, copy SRCFILE to DSTFILE. +In the 2nd and 3rd, copy all SRCFILES to DIRECTORY. +In the 4th, create DIRECTORIES. + +Options: + --help display this help and exit. + --version display version info and exit. + + -c (ignored) + -C install only if different (preserve the last data modification time) + -d create directories instead of installing files. + -g GROUP $chgrpprog installed files to GROUP. + -m MODE $chmodprog installed files to MODE. + -o USER $chownprog installed files to USER. + -s $stripprog installed files. + -t DIRECTORY install into DIRECTORY. + -T report an error if DSTFILE is a directory. + +Environment variables override the default commands: + CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG + RMPROG STRIPPROG +" + +while test $# -ne 0; do + case $1 in + -c) ;; + + -C) copy_on_change=true;; + + -d) dir_arg=true;; + + -g) chgrpcmd="$chgrpprog $2" + shift;; + + --help) echo "$usage"; exit $?;; + + -m) mode=$2 + case $mode in + *' '* | *' '* | *' +'* | *'*'* | *'?'* | *'['*) + echo "$0: invalid mode: $mode" >&2 + exit 1;; + esac + shift;; + + -o) chowncmd="$chownprog $2" + shift;; + + -s) stripcmd=$stripprog;; + + -t) dst_arg=$2 + shift;; + + -T) no_target_directory=true;; + + --version) echo "$0 $scriptversion"; exit $?;; + + --) shift + break;; + + -*) echo "$0: invalid option: $1" >&2 + exit 1;; + + *) break;; + esac + shift +done + +if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then + # When -d is used, all remaining arguments are directories to create. + # When -t is used, the destination is already specified. + # Otherwise, the last argument is the destination. Remove it from $@. + for arg + do + if test -n "$dst_arg"; then + # $@ is not empty: it contains at least $arg. + set fnord "$@" "$dst_arg" + shift # fnord + fi + shift # arg + dst_arg=$arg + done +fi + +if test $# -eq 0; then + if test -z "$dir_arg"; then + echo "$0: no input file specified." >&2 + exit 1 + fi + # It's OK to call `install-sh -d' without argument. + # This can happen when creating conditional directories. + exit 0 +fi + +if test -z "$dir_arg"; then + trap '(exit $?); exit' 1 2 13 15 + + # Set umask so as not to create temps with too-generous modes. + # However, 'strip' requires both read and write access to temps. + case $mode in + # Optimize common cases. + *644) cp_umask=133;; + *755) cp_umask=22;; + + *[0-7]) + if test -z "$stripcmd"; then + u_plus_rw= + else + u_plus_rw='% 200' + fi + cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;; + *) + if test -z "$stripcmd"; then + u_plus_rw= + else + u_plus_rw=,u+rw + fi + cp_umask=$mode$u_plus_rw;; + esac +fi + +for src +do + # Protect names starting with `-'. + case $src in + -*) src=./$src;; + esac + + if test -n "$dir_arg"; then + dst=$src + dstdir=$dst + test -d "$dstdir" + dstdir_status=$? + else + + # Waiting for this to be detected by the "$cpprog $src $dsttmp" command + # might cause directories to be created, which would be especially bad + # if $src (and thus $dsttmp) contains '*'. + if test ! -f "$src" && test ! -d "$src"; then + echo "$0: $src does not exist." >&2 + exit 1 + fi + + if test -z "$dst_arg"; then + echo "$0: no destination specified." >&2 + exit 1 + fi + + dst=$dst_arg + # Protect names starting with `-'. + case $dst in + -*) dst=./$dst;; + esac + + # If destination is a directory, append the input filename; won't work + # if double slashes aren't ignored. + if test -d "$dst"; then + if test -n "$no_target_directory"; then + echo "$0: $dst_arg: Is a directory" >&2 + exit 1 + fi + dstdir=$dst + dst=$dstdir/`basename "$src"` + dstdir_status=0 + else + # Prefer dirname, but fall back on a substitute if dirname fails. + dstdir=` + (dirname "$dst") 2>/dev/null || + expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$dst" : 'X\(//\)[^/]' \| \ + X"$dst" : 'X\(//\)$' \| \ + X"$dst" : 'X\(/\)' \| . 2>/dev/null || + echo X"$dst" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q' + ` + + test -d "$dstdir" + dstdir_status=$? + fi + fi + + obsolete_mkdir_used=false + + if test $dstdir_status != 0; then + case $posix_mkdir in + '') + # Create intermediate dirs using mode 755 as modified by the umask. + # This is like FreeBSD 'install' as of 1997-10-28. + umask=`umask` + case $stripcmd.$umask in + # Optimize common cases. + *[2367][2367]) mkdir_umask=$umask;; + .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;; + + *[0-7]) + mkdir_umask=`expr $umask + 22 \ + - $umask % 100 % 40 + $umask % 20 \ + - $umask % 10 % 4 + $umask % 2 + `;; + *) mkdir_umask=$umask,go-w;; + esac + + # With -d, create the new directory with the user-specified mode. + # Otherwise, rely on $mkdir_umask. + if test -n "$dir_arg"; then + mkdir_mode=-m$mode + else + mkdir_mode= + fi + + posix_mkdir=false + case $umask in + *[123567][0-7][0-7]) + # POSIX mkdir -p sets u+wx bits regardless of umask, which + # is incompatible with FreeBSD 'install' when (umask & 300) != 0. + ;; + *) + tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$ + trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0 + + if (umask $mkdir_umask && + exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1 + then + if test -z "$dir_arg" || { + # Check for POSIX incompatibilities with -m. + # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or + # other-writeable bit of parent directory when it shouldn't. + # FreeBSD 6.1 mkdir -m -p sets mode of existing directory. + ls_ld_tmpdir=`ls -ld "$tmpdir"` + case $ls_ld_tmpdir in + d????-?r-*) different_mode=700;; + d????-?--*) different_mode=755;; + *) false;; + esac && + $mkdirprog -m$different_mode -p -- "$tmpdir" && { + ls_ld_tmpdir_1=`ls -ld "$tmpdir"` + test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1" + } + } + then posix_mkdir=: + fi + rmdir "$tmpdir/d" "$tmpdir" + else + # Remove any dirs left behind by ancient mkdir implementations. + rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null + fi + trap '' 0;; + esac;; + esac + + if + $posix_mkdir && ( + umask $mkdir_umask && + $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir" + ) + then : + else + + # The umask is ridiculous, or mkdir does not conform to POSIX, + # or it failed possibly due to a race condition. Create the + # directory the slow way, step by step, checking for races as we go. + + case $dstdir in + /*) prefix='/';; + -*) prefix='./';; + *) prefix='';; + esac + + eval "$initialize_posix_glob" + + oIFS=$IFS + IFS=/ + $posix_glob set -f + set fnord $dstdir + shift + $posix_glob set +f + IFS=$oIFS + + prefixes= + + for d + do + test -z "$d" && continue + + prefix=$prefix$d + if test -d "$prefix"; then + prefixes= + else + if $posix_mkdir; then + (umask=$mkdir_umask && + $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break + # Don't fail if two instances are running concurrently. + test -d "$prefix" || exit 1 + else + case $prefix in + *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;; + *) qprefix=$prefix;; + esac + prefixes="$prefixes '$qprefix'" + fi + fi + prefix=$prefix/ + done + + if test -n "$prefixes"; then + # Don't fail if two instances are running concurrently. + (umask $mkdir_umask && + eval "\$doit_exec \$mkdirprog $prefixes") || + test -d "$dstdir" || exit 1 + obsolete_mkdir_used=true + fi + fi + fi + + if test -n "$dir_arg"; then + { test -z "$chowncmd" || $doit $chowncmd "$dst"; } && + { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } && + { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false || + test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1 + else + + # Make a couple of temp file names in the proper directory. + dsttmp=$dstdir/_inst.$$_ + rmtmp=$dstdir/_rm.$$_ + + # Trap to clean up those temp files at exit. + trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0 + + # Copy the file name to the temp name. + (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") && + + # and set any options; do chmod last to preserve setuid bits. + # + # If any of these fail, we abort the whole thing. If we want to + # ignore errors from any of these, just make sure not to ignore + # errors from the above "$doit $cpprog $src $dsttmp" command. + # + { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } && + { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } && + { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } && + { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } && + + # If -C, don't bother to copy if it wouldn't change the file. + if $copy_on_change && + old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` && + new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` && + + eval "$initialize_posix_glob" && + $posix_glob set -f && + set X $old && old=:$2:$4:$5:$6 && + set X $new && new=:$2:$4:$5:$6 && + $posix_glob set +f && + + test "$old" = "$new" && + $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1 + then + rm -f "$dsttmp" + else + # Rename the file to the real destination. + $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null || + + # The rename failed, perhaps because mv can't rename something else + # to itself, or perhaps because mv is so ancient that it does not + # support -f. + { + # Now remove or move aside any old file at destination location. + # We try this two ways since rm can't unlink itself on some + # systems and the destination file might be busy for other + # reasons. In this case, the final cleanup might fail but the new + # file should still install successfully. + { + test ! -f "$dst" || + $doit $rmcmd -f "$dst" 2>/dev/null || + { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null && + { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; } + } || + { echo "$0: cannot unlink or rename $dst" >&2 + (exit 1); exit 1 + } + } && + + # Now rename the file to the real destination. + $doit $mvcmd "$dsttmp" "$dst" + } + fi || exit 1 + + trap '' 0 + fi +done + +# Local variables: +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "scriptversion=" +# time-stamp-format: "%:y-%02m-%02d.%02H" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" +# End: diff --git a/binaries/src/clustalo/ltmain.sh b/binaries/src/clustalo/ltmain.sh new file mode 100644 index 0000000..b612e9a --- /dev/null +++ b/binaries/src/clustalo/ltmain.sh @@ -0,0 +1,8412 @@ +# Generated from ltmain.m4sh. + +# ltmain.sh (GNU libtool) 2.2.6 +# Written by Gordon Matzigkeit , 1996 + +# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006, 2007 2008 Free Software Foundation, Inc. +# This is free software; see the source for copying conditions. There is NO +# warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. + +# GNU Libtool is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# As a special exception to the GNU General Public License, +# if you distribute this file as part of a program or library that +# is built using GNU Libtool, you may include this file under the +# same distribution terms that you use for the rest of that program. +# +# GNU Libtool is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with GNU Libtool; see the file COPYING. If not, a copy +# can be downloaded from http://www.gnu.org/licenses/gpl.html, +# or obtained by writing to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + +# Usage: $progname [OPTION]... [MODE-ARG]... +# +# Provide generalized library-building support services. +# +# --config show all configuration variables +# --debug enable verbose shell tracing +# -n, --dry-run display commands without modifying any files +# --features display basic configuration information and exit +# --mode=MODE use operation mode MODE +# --preserve-dup-deps don't remove duplicate dependency libraries +# --quiet, --silent don't print informational messages +# --tag=TAG use configuration variables from tag TAG +# -v, --verbose print informational messages (default) +# --version print version information +# -h, --help print short or long help message +# +# MODE must be one of the following: +# +# clean remove files from the build directory +# compile compile a source file into a libtool object +# execute automatically set library path, then run a program +# finish complete the installation of libtool libraries +# install install libraries or executables +# link create a library or an executable +# uninstall remove libraries from an installed directory +# +# MODE-ARGS vary depending on the MODE. +# Try `$progname --help --mode=MODE' for a more detailed description of MODE. +# +# When reporting a bug, please describe a test case to reproduce it and +# include the following information: +# +# host-triplet: $host +# shell: $SHELL +# compiler: $LTCC +# compiler flags: $LTCFLAGS +# linker: $LD (gnu? $with_gnu_ld) +# $progname: (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1 +# automake: $automake_version +# autoconf: $autoconf_version +# +# Report bugs to . + +PROGRAM=ltmain.sh +PACKAGE=libtool +VERSION="2.2.6 Debian-2.2.6a-1ubuntu1" +TIMESTAMP="" +package_revision=1.3012 + +# Be Bourne compatible +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' + setopt NO_GLOB_SUBST +else + case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac +fi +BIN_SH=xpg4; export BIN_SH # for Tru64 +DUALCASE=1; export DUALCASE # for MKS sh + +# NLS nuisances: We save the old values to restore during execute mode. +# Only set LANG and LC_ALL to C if already set. +# These must not be set unconditionally because not all systems understand +# e.g. LANG=C (notably SCO). +lt_user_locale= +lt_safe_locale= +for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES +do + eval "if test \"\${$lt_var+set}\" = set; then + save_$lt_var=\$$lt_var + $lt_var=C + export $lt_var + lt_user_locale=\"$lt_var=\\\$save_\$lt_var; \$lt_user_locale\" + lt_safe_locale=\"$lt_var=C; \$lt_safe_locale\" + fi" +done + +$lt_unset CDPATH + + + + + +: ${CP="cp -f"} +: ${ECHO="echo"} +: ${EGREP="/bin/grep -E"} +: ${FGREP="/bin/grep -F"} +: ${GREP="/bin/grep"} +: ${LN_S="ln -s"} +: ${MAKE="make"} +: ${MKDIR="mkdir"} +: ${MV="mv -f"} +: ${RM="rm -f"} +: ${SED="/bin/sed"} +: ${SHELL="${CONFIG_SHELL-/bin/sh}"} +: ${Xsed="$SED -e 1s/^X//"} + +# Global variables: +EXIT_SUCCESS=0 +EXIT_FAILURE=1 +EXIT_MISMATCH=63 # $? = 63 is used to indicate version mismatch to missing. +EXIT_SKIP=77 # $? = 77 is used to indicate a skipped test to automake. + +exit_status=$EXIT_SUCCESS + +# Make sure IFS has a sensible default +lt_nl=' +' +IFS=" $lt_nl" + +dirname="s,/[^/]*$,," +basename="s,^.*/,," + +# func_dirname_and_basename file append nondir_replacement +# perform func_basename and func_dirname in a single function +# call: +# dirname: Compute the dirname of FILE. If nonempty, +# add APPEND to the result, otherwise set result +# to NONDIR_REPLACEMENT. +# value returned in "$func_dirname_result" +# basename: Compute filename of FILE. +# value retuned in "$func_basename_result" +# Implementation must be kept synchronized with func_dirname +# and func_basename. For efficiency, we do not delegate to +# those functions but instead duplicate the functionality here. +func_dirname_and_basename () +{ + # Extract subdirectory from the argument. + func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"` + if test "X$func_dirname_result" = "X${1}"; then + func_dirname_result="${3}" + else + func_dirname_result="$func_dirname_result${2}" + fi + func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"` +} + +# Generated shell functions inserted here. + +# Work around backward compatibility issue on IRIX 6.5. On IRIX 6.4+, sh +# is ksh but when the shell is invoked as "sh" and the current value of +# the _XPG environment variable is not equal to 1 (one), the special +# positional parameter $0, within a function call, is the name of the +# function. +progpath="$0" + +# The name of this program: +# In the unlikely event $progname began with a '-', it would play havoc with +# func_echo (imagine progname=-n), so we prepend ./ in that case: +func_dirname_and_basename "$progpath" +progname=$func_basename_result +case $progname in + -*) progname=./$progname ;; +esac + +# Make sure we have an absolute path for reexecution: +case $progpath in + [\\/]*|[A-Za-z]:\\*) ;; + *[\\/]*) + progdir=$func_dirname_result + progdir=`cd "$progdir" && pwd` + progpath="$progdir/$progname" + ;; + *) + save_IFS="$IFS" + IFS=: + for progdir in $PATH; do + IFS="$save_IFS" + test -x "$progdir/$progname" && break + done + IFS="$save_IFS" + test -n "$progdir" || progdir=`pwd` + progpath="$progdir/$progname" + ;; +esac + +# Sed substitution that helps us do robust quoting. It backslashifies +# metacharacters that are still active within double-quoted strings. +Xsed="${SED}"' -e 1s/^X//' +sed_quote_subst='s/\([`"$\\]\)/\\\1/g' + +# Same as above, but do not quote variable references. +double_quote_subst='s/\(["`\\]\)/\\\1/g' + +# Re-`\' parameter expansions in output of double_quote_subst that were +# `\'-ed in input to the same. If an odd number of `\' preceded a '$' +# in input to double_quote_subst, that '$' was protected from expansion. +# Since each input `\' is now two `\'s, look for any number of runs of +# four `\'s followed by two `\'s and then a '$'. `\' that '$'. +bs='\\' +bs2='\\\\' +bs4='\\\\\\\\' +dollar='\$' +sed_double_backslash="\ + s/$bs4/&\\ +/g + s/^$bs2$dollar/$bs&/ + s/\\([^$bs]\\)$bs2$dollar/\\1$bs2$bs$dollar/g + s/\n//g" + +# Standard options: +opt_dry_run=false +opt_help=false +opt_quiet=false +opt_verbose=false +opt_warning=: + +# func_echo arg... +# Echo program name prefixed message, along with the current mode +# name if it has been set yet. +func_echo () +{ + $ECHO "$progname${mode+: }$mode: $*" +} + +# func_verbose arg... +# Echo program name prefixed message in verbose mode only. +func_verbose () +{ + $opt_verbose && func_echo ${1+"$@"} + + # A bug in bash halts the script if the last line of a function + # fails when set -e is in force, so we need another command to + # work around that: + : +} + +# func_error arg... +# Echo program name prefixed message to standard error. +func_error () +{ + $ECHO "$progname${mode+: }$mode: "${1+"$@"} 1>&2 +} + +# func_warning arg... +# Echo program name prefixed warning message to standard error. +func_warning () +{ + $opt_warning && $ECHO "$progname${mode+: }$mode: warning: "${1+"$@"} 1>&2 + + # bash bug again: + : +} + +# func_fatal_error arg... +# Echo program name prefixed message to standard error, and exit. +func_fatal_error () +{ + func_error ${1+"$@"} + exit $EXIT_FAILURE +} + +# func_fatal_help arg... +# Echo program name prefixed message to standard error, followed by +# a help hint, and exit. +func_fatal_help () +{ + func_error ${1+"$@"} + func_fatal_error "$help" +} +help="Try \`$progname --help' for more information." ## default + + +# func_grep expression filename +# Check whether EXPRESSION matches any line of FILENAME, without output. +func_grep () +{ + $GREP "$1" "$2" >/dev/null 2>&1 +} + + +# func_mkdir_p directory-path +# Make sure the entire path to DIRECTORY-PATH is available. +func_mkdir_p () +{ + my_directory_path="$1" + my_dir_list= + + if test -n "$my_directory_path" && test "$opt_dry_run" != ":"; then + + # Protect directory names starting with `-' + case $my_directory_path in + -*) my_directory_path="./$my_directory_path" ;; + esac + + # While some portion of DIR does not yet exist... + while test ! -d "$my_directory_path"; do + # ...make a list in topmost first order. Use a colon delimited + # list incase some portion of path contains whitespace. + my_dir_list="$my_directory_path:$my_dir_list" + + # If the last portion added has no slash in it, the list is done + case $my_directory_path in */*) ;; *) break ;; esac + + # ...otherwise throw away the child directory and loop + my_directory_path=`$ECHO "X$my_directory_path" | $Xsed -e "$dirname"` + done + my_dir_list=`$ECHO "X$my_dir_list" | $Xsed -e 's,:*$,,'` + + save_mkdir_p_IFS="$IFS"; IFS=':' + for my_dir in $my_dir_list; do + IFS="$save_mkdir_p_IFS" + # mkdir can fail with a `File exist' error if two processes + # try to create one of the directories concurrently. Don't + # stop in that case! + $MKDIR "$my_dir" 2>/dev/null || : + done + IFS="$save_mkdir_p_IFS" + + # Bail out if we (or some other process) failed to create a directory. + test -d "$my_directory_path" || \ + func_fatal_error "Failed to create \`$1'" + fi +} + + +# func_mktempdir [string] +# Make a temporary directory that won't clash with other running +# libtool processes, and avoids race conditions if possible. If +# given, STRING is the basename for that directory. +func_mktempdir () +{ + my_template="${TMPDIR-/tmp}/${1-$progname}" + + if test "$opt_dry_run" = ":"; then + # Return a directory name, but don't create it in dry-run mode + my_tmpdir="${my_template}-$$" + else + + # If mktemp works, use that first and foremost + my_tmpdir=`mktemp -d "${my_template}-XXXXXXXX" 2>/dev/null` + + if test ! -d "$my_tmpdir"; then + # Failing that, at least try and use $RANDOM to avoid a race + my_tmpdir="${my_template}-${RANDOM-0}$$" + + save_mktempdir_umask=`umask` + umask 0077 + $MKDIR "$my_tmpdir" + umask $save_mktempdir_umask + fi + + # If we're not in dry-run mode, bomb out on failure + test -d "$my_tmpdir" || \ + func_fatal_error "cannot create temporary directory \`$my_tmpdir'" + fi + + $ECHO "X$my_tmpdir" | $Xsed +} + + +# func_quote_for_eval arg +# Aesthetically quote ARG to be evaled later. +# This function returns two values: FUNC_QUOTE_FOR_EVAL_RESULT +# is double-quoted, suitable for a subsequent eval, whereas +# FUNC_QUOTE_FOR_EVAL_UNQUOTED_RESULT has merely all characters +# which are still active within double quotes backslashified. +func_quote_for_eval () +{ + case $1 in + *[\\\`\"\$]*) + func_quote_for_eval_unquoted_result=`$ECHO "X$1" | $Xsed -e "$sed_quote_subst"` ;; + *) + func_quote_for_eval_unquoted_result="$1" ;; + esac + + case $func_quote_for_eval_unquoted_result in + # Double-quote args containing shell metacharacters to delay + # word splitting, command substitution and and variable + # expansion for a subsequent eval. + # Many Bourne shells cannot handle close brackets correctly + # in scan sets, so we specify it separately. + *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"") + func_quote_for_eval_result="\"$func_quote_for_eval_unquoted_result\"" + ;; + *) + func_quote_for_eval_result="$func_quote_for_eval_unquoted_result" + esac +} + + +# func_quote_for_expand arg +# Aesthetically quote ARG to be evaled later; same as above, +# but do not quote variable references. +func_quote_for_expand () +{ + case $1 in + *[\\\`\"]*) + my_arg=`$ECHO "X$1" | $Xsed \ + -e "$double_quote_subst" -e "$sed_double_backslash"` ;; + *) + my_arg="$1" ;; + esac + + case $my_arg in + # Double-quote args containing shell metacharacters to delay + # word splitting and command substitution for a subsequent eval. + # Many Bourne shells cannot handle close brackets correctly + # in scan sets, so we specify it separately. + *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"") + my_arg="\"$my_arg\"" + ;; + esac + + func_quote_for_expand_result="$my_arg" +} + + +# func_show_eval cmd [fail_exp] +# Unless opt_silent is true, then output CMD. Then, if opt_dryrun is +# not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP +# is given, then evaluate it. +func_show_eval () +{ + my_cmd="$1" + my_fail_exp="${2-:}" + + ${opt_silent-false} || { + func_quote_for_expand "$my_cmd" + eval "func_echo $func_quote_for_expand_result" + } + + if ${opt_dry_run-false}; then :; else + eval "$my_cmd" + my_status=$? + if test "$my_status" -eq 0; then :; else + eval "(exit $my_status); $my_fail_exp" + fi + fi +} + + +# func_show_eval_locale cmd [fail_exp] +# Unless opt_silent is true, then output CMD. Then, if opt_dryrun is +# not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP +# is given, then evaluate it. Use the saved locale for evaluation. +func_show_eval_locale () +{ + my_cmd="$1" + my_fail_exp="${2-:}" + + ${opt_silent-false} || { + func_quote_for_expand "$my_cmd" + eval "func_echo $func_quote_for_expand_result" + } + + if ${opt_dry_run-false}; then :; else + eval "$lt_user_locale + $my_cmd" + my_status=$? + eval "$lt_safe_locale" + if test "$my_status" -eq 0; then :; else + eval "(exit $my_status); $my_fail_exp" + fi + fi +} + + + + + +# func_version +# Echo version message to standard output and exit. +func_version () +{ + $SED -n '/^# '$PROGRAM' (GNU /,/# warranty; / { + s/^# // + s/^# *$// + s/\((C)\)[ 0-9,-]*\( [1-9][0-9]*\)/\1\2/ + p + }' < "$progpath" + exit $? +} + +# func_usage +# Echo short help message to standard output and exit. +func_usage () +{ + $SED -n '/^# Usage:/,/# -h/ { + s/^# // + s/^# *$// + s/\$progname/'$progname'/ + p + }' < "$progpath" + $ECHO + $ECHO "run \`$progname --help | more' for full usage" + exit $? +} + +# func_help +# Echo long help message to standard output and exit. +func_help () +{ + $SED -n '/^# Usage:/,/# Report bugs to/ { + s/^# // + s/^# *$// + s*\$progname*'$progname'* + s*\$host*'"$host"'* + s*\$SHELL*'"$SHELL"'* + s*\$LTCC*'"$LTCC"'* + s*\$LTCFLAGS*'"$LTCFLAGS"'* + s*\$LD*'"$LD"'* + s/\$with_gnu_ld/'"$with_gnu_ld"'/ + s/\$automake_version/'"`(automake --version) 2>/dev/null |$SED 1q`"'/ + s/\$autoconf_version/'"`(autoconf --version) 2>/dev/null |$SED 1q`"'/ + p + }' < "$progpath" + exit $? +} + +# func_missing_arg argname +# Echo program name prefixed message to standard error and set global +# exit_cmd. +func_missing_arg () +{ + func_error "missing argument for $1" + exit_cmd=exit +} + +exit_cmd=: + + + + + +# Check that we have a working $ECHO. +if test "X$1" = X--no-reexec; then + # Discard the --no-reexec flag, and continue. + shift +elif test "X$1" = X--fallback-echo; then + # Avoid inline document here, it may be left over + : +elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t'; then + # Yippee, $ECHO works! + : +else + # Restart under the correct shell, and then maybe $ECHO will work. + exec $SHELL "$progpath" --no-reexec ${1+"$@"} +fi + +if test "X$1" = X--fallback-echo; then + # used as fallback echo + shift + cat </dev/null 2>&1; then + taglist="$taglist $tagname" + + # Evaluate the configuration. Be careful to quote the path + # and the sed script, to avoid splitting on whitespace, but + # also don't use non-portable quotes within backquotes within + # quotes we have to do it in 2 steps: + extractedcf=`$SED -n -e "$sed_extractcf" < "$progpath"` + eval "$extractedcf" + else + func_error "ignoring unknown tag $tagname" + fi + ;; + esac +} + +# Parse options once, thoroughly. This comes as soon as possible in +# the script to make things like `libtool --version' happen quickly. +{ + + # Shorthand for --mode=foo, only valid as the first argument + case $1 in + clean|clea|cle|cl) + shift; set dummy --mode clean ${1+"$@"}; shift + ;; + compile|compil|compi|comp|com|co|c) + shift; set dummy --mode compile ${1+"$@"}; shift + ;; + execute|execut|execu|exec|exe|ex|e) + shift; set dummy --mode execute ${1+"$@"}; shift + ;; + finish|finis|fini|fin|fi|f) + shift; set dummy --mode finish ${1+"$@"}; shift + ;; + install|instal|insta|inst|ins|in|i) + shift; set dummy --mode install ${1+"$@"}; shift + ;; + link|lin|li|l) + shift; set dummy --mode link ${1+"$@"}; shift + ;; + uninstall|uninstal|uninsta|uninst|unins|unin|uni|un|u) + shift; set dummy --mode uninstall ${1+"$@"}; shift + ;; + esac + + # Parse non-mode specific arguments: + while test "$#" -gt 0; do + opt="$1" + shift + + case $opt in + --config) func_config ;; + + --debug) preserve_args="$preserve_args $opt" + func_echo "enabling shell trace mode" + opt_debug='set -x' + $opt_debug + ;; + + -dlopen) test "$#" -eq 0 && func_missing_arg "$opt" && break + execute_dlfiles="$execute_dlfiles $1" + shift + ;; + + --dry-run | -n) opt_dry_run=: ;; + --features) func_features ;; + --finish) mode="finish" ;; + + --mode) test "$#" -eq 0 && func_missing_arg "$opt" && break + case $1 in + # Valid mode arguments: + clean) ;; + compile) ;; + execute) ;; + finish) ;; + install) ;; + link) ;; + relink) ;; + uninstall) ;; + + # Catch anything else as an error + *) func_error "invalid argument for $opt" + exit_cmd=exit + break + ;; + esac + + mode="$1" + shift + ;; + + --preserve-dup-deps) + opt_duplicate_deps=: ;; + + --quiet|--silent) preserve_args="$preserve_args $opt" + opt_silent=: + ;; + + --verbose| -v) preserve_args="$preserve_args $opt" + opt_silent=false + ;; + + --tag) test "$#" -eq 0 && func_missing_arg "$opt" && break + preserve_args="$preserve_args $opt $1" + func_enable_tag "$1" # tagname is set here + shift + ;; + + # Separate optargs to long options: + -dlopen=*|--mode=*|--tag=*) + func_opt_split "$opt" + set dummy "$func_opt_split_opt" "$func_opt_split_arg" ${1+"$@"} + shift + ;; + + -\?|-h) func_usage ;; + --help) opt_help=: ;; + --version) func_version ;; + + -*) func_fatal_help "unrecognized option \`$opt'" ;; + + *) nonopt="$opt" + break + ;; + esac + done + + + case $host in + *cygwin* | *mingw* | *pw32* | *cegcc*) + # don't eliminate duplications in $postdeps and $predeps + opt_duplicate_compiler_generated_deps=: + ;; + *) + opt_duplicate_compiler_generated_deps=$opt_duplicate_deps + ;; + esac + + # Having warned about all mis-specified options, bail out if + # anything was wrong. + $exit_cmd $EXIT_FAILURE +} + +# func_check_version_match +# Ensure that we are using m4 macros, and libtool script from the same +# release of libtool. +func_check_version_match () +{ + if test "$package_revision" != "$macro_revision"; then + if test "$VERSION" != "$macro_version"; then + if test -z "$macro_version"; then + cat >&2 <<_LT_EOF +$progname: Version mismatch error. This is $PACKAGE $VERSION, but the +$progname: definition of this LT_INIT comes from an older release. +$progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION +$progname: and run autoconf again. +_LT_EOF + else + cat >&2 <<_LT_EOF +$progname: Version mismatch error. This is $PACKAGE $VERSION, but the +$progname: definition of this LT_INIT comes from $PACKAGE $macro_version. +$progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION +$progname: and run autoconf again. +_LT_EOF + fi + else + cat >&2 <<_LT_EOF +$progname: Version mismatch error. This is $PACKAGE $VERSION, revision $package_revision, +$progname: but the definition of this LT_INIT comes from revision $macro_revision. +$progname: You should recreate aclocal.m4 with macros from revision $package_revision +$progname: of $PACKAGE $VERSION and run autoconf again. +_LT_EOF + fi + + exit $EXIT_MISMATCH + fi +} + + +## ----------- ## +## Main. ## +## ----------- ## + +$opt_help || { + # Sanity checks first: + func_check_version_match + + if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then + func_fatal_configuration "not configured to build any kind of library" + fi + + test -z "$mode" && func_fatal_error "error: you must specify a MODE." + + + # Darwin sucks + eval std_shrext=\"$shrext_cmds\" + + + # Only execute mode is allowed to have -dlopen flags. + if test -n "$execute_dlfiles" && test "$mode" != execute; then + func_error "unrecognized option \`-dlopen'" + $ECHO "$help" 1>&2 + exit $EXIT_FAILURE + fi + + # Change the help message to a mode-specific one. + generic_help="$help" + help="Try \`$progname --help --mode=$mode' for more information." +} + + +# func_lalib_p file +# True iff FILE is a libtool `.la' library or `.lo' object file. +# This function is only a basic sanity check; it will hardly flush out +# determined imposters. +func_lalib_p () +{ + test -f "$1" && + $SED -e 4q "$1" 2>/dev/null \ + | $GREP "^# Generated by .*$PACKAGE" > /dev/null 2>&1 +} + +# func_lalib_unsafe_p file +# True iff FILE is a libtool `.la' library or `.lo' object file. +# This function implements the same check as func_lalib_p without +# resorting to external programs. To this end, it redirects stdin and +# closes it afterwards, without saving the original file descriptor. +# As a safety measure, use it only where a negative result would be +# fatal anyway. Works if `file' does not exist. +func_lalib_unsafe_p () +{ + lalib_p=no + if test -f "$1" && test -r "$1" && exec 5<&0 <"$1"; then + for lalib_p_l in 1 2 3 4 + do + read lalib_p_line + case "$lalib_p_line" in + \#\ Generated\ by\ *$PACKAGE* ) lalib_p=yes; break;; + esac + done + exec 0<&5 5<&- + fi + test "$lalib_p" = yes +} + +# func_ltwrapper_script_p file +# True iff FILE is a libtool wrapper script +# This function is only a basic sanity check; it will hardly flush out +# determined imposters. +func_ltwrapper_script_p () +{ + func_lalib_p "$1" +} + +# func_ltwrapper_executable_p file +# True iff FILE is a libtool wrapper executable +# This function is only a basic sanity check; it will hardly flush out +# determined imposters. +func_ltwrapper_executable_p () +{ + func_ltwrapper_exec_suffix= + case $1 in + *.exe) ;; + *) func_ltwrapper_exec_suffix=.exe ;; + esac + $GREP "$magic_exe" "$1$func_ltwrapper_exec_suffix" >/dev/null 2>&1 +} + +# func_ltwrapper_scriptname file +# Assumes file is an ltwrapper_executable +# uses $file to determine the appropriate filename for a +# temporary ltwrapper_script. +func_ltwrapper_scriptname () +{ + func_ltwrapper_scriptname_result="" + if func_ltwrapper_executable_p "$1"; then + func_dirname_and_basename "$1" "" "." + func_stripname '' '.exe' "$func_basename_result" + func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper" + fi +} + +# func_ltwrapper_p file +# True iff FILE is a libtool wrapper script or wrapper executable +# This function is only a basic sanity check; it will hardly flush out +# determined imposters. +func_ltwrapper_p () +{ + func_ltwrapper_script_p "$1" || func_ltwrapper_executable_p "$1" +} + + +# func_execute_cmds commands fail_cmd +# Execute tilde-delimited COMMANDS. +# If FAIL_CMD is given, eval that upon failure. +# FAIL_CMD may read-access the current command in variable CMD! +func_execute_cmds () +{ + $opt_debug + save_ifs=$IFS; IFS='~' + for cmd in $1; do + IFS=$save_ifs + eval cmd=\"$cmd\" + func_show_eval "$cmd" "${2-:}" + done + IFS=$save_ifs +} + + +# func_source file +# Source FILE, adding directory component if necessary. +# Note that it is not necessary on cygwin/mingw to append a dot to +# FILE even if both FILE and FILE.exe exist: automatic-append-.exe +# behavior happens only for exec(3), not for open(2)! Also, sourcing +# `FILE.' does not work on cygwin managed mounts. +func_source () +{ + $opt_debug + case $1 in + */* | *\\*) . "$1" ;; + *) . "./$1" ;; + esac +} + + +# func_infer_tag arg +# Infer tagged configuration to use if any are available and +# if one wasn't chosen via the "--tag" command line option. +# Only attempt this if the compiler in the base compile +# command doesn't match the default compiler. +# arg is usually of the form 'gcc ...' +func_infer_tag () +{ + $opt_debug + if test -n "$available_tags" && test -z "$tagname"; then + CC_quoted= + for arg in $CC; do + func_quote_for_eval "$arg" + CC_quoted="$CC_quoted $func_quote_for_eval_result" + done + case $@ in + # Blanks in the command may have been stripped by the calling shell, + # but not from the CC environment variable when configure was run. + " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) ;; + # Blanks at the start of $base_compile will cause this to fail + # if we don't check for them as well. + *) + for z in $available_tags; do + if $GREP "^# ### BEGIN LIBTOOL TAG CONFIG: $z$" < "$progpath" > /dev/null; then + # Evaluate the configuration. + eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$z'$/,/^# ### END LIBTOOL TAG CONFIG: '$z'$/p' < $progpath`" + CC_quoted= + for arg in $CC; do + # Double-quote args containing other shell metacharacters. + func_quote_for_eval "$arg" + CC_quoted="$CC_quoted $func_quote_for_eval_result" + done + case "$@ " in + " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) + # The compiler in the base compile command matches + # the one in the tagged configuration. + # Assume this is the tagged configuration we want. + tagname=$z + break + ;; + esac + fi + done + # If $tagname still isn't set, then no tagged configuration + # was found and let the user know that the "--tag" command + # line option must be used. + if test -z "$tagname"; then + func_echo "unable to infer tagged configuration" + func_fatal_error "specify a tag with \`--tag'" +# else +# func_verbose "using $tagname tagged configuration" + fi + ;; + esac + fi +} + + + +# func_write_libtool_object output_name pic_name nonpic_name +# Create a libtool object file (analogous to a ".la" file), +# but don't create it if we're doing a dry run. +func_write_libtool_object () +{ + write_libobj=${1} + if test "$build_libtool_libs" = yes; then + write_lobj=\'${2}\' + else + write_lobj=none + fi + + if test "$build_old_libs" = yes; then + write_oldobj=\'${3}\' + else + write_oldobj=none + fi + + $opt_dry_run || { + cat >${write_libobj}T <?"'"'"' &()|`$[]' \ + && func_warning "libobj name \`$libobj' may not contain shell special characters." + func_dirname_and_basename "$obj" "/" "" + objname="$func_basename_result" + xdir="$func_dirname_result" + lobj=${xdir}$objdir/$objname + + test -z "$base_compile" && \ + func_fatal_help "you must specify a compilation command" + + # Delete any leftover library objects. + if test "$build_old_libs" = yes; then + removelist="$obj $lobj $libobj ${libobj}T" + else + removelist="$lobj $libobj ${libobj}T" + fi + + # On Cygwin there's no "real" PIC flag so we must build both object types + case $host_os in + cygwin* | mingw* | pw32* | os2* | cegcc*) + pic_mode=default + ;; + esac + if test "$pic_mode" = no && test "$deplibs_check_method" != pass_all; then + # non-PIC code in shared libraries is not supported + pic_mode=default + fi + + # Calculate the filename of the output object if compiler does + # not support -o with -c + if test "$compiler_c_o" = no; then + output_obj=`$ECHO "X$srcfile" | $Xsed -e 's%^.*/%%' -e 's%\.[^.]*$%%'`.${objext} + lockfile="$output_obj.lock" + else + output_obj= + need_locks=no + lockfile= + fi + + # Lock this critical section if it is needed + # We use this script file to make the link, it avoids creating a new file + if test "$need_locks" = yes; then + until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do + func_echo "Waiting for $lockfile to be removed" + sleep 2 + done + elif test "$need_locks" = warn; then + if test -f "$lockfile"; then + $ECHO "\ +*** ERROR, $lockfile exists and contains: +`cat $lockfile 2>/dev/null` + +This indicates that another process is trying to use the same +temporary object file, and libtool could not work around it because +your compiler does not support \`-c' and \`-o' together. If you +repeat this compilation, it may succeed, by chance, but you had better +avoid parallel builds (make -j) in this platform, or get a better +compiler." + + $opt_dry_run || $RM $removelist + exit $EXIT_FAILURE + fi + removelist="$removelist $output_obj" + $ECHO "$srcfile" > "$lockfile" + fi + + $opt_dry_run || $RM $removelist + removelist="$removelist $lockfile" + trap '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' 1 2 15 + + if test -n "$fix_srcfile_path"; then + eval srcfile=\"$fix_srcfile_path\" + fi + func_quote_for_eval "$srcfile" + qsrcfile=$func_quote_for_eval_result + + # Only build a PIC object if we are building libtool libraries. + if test "$build_libtool_libs" = yes; then + # Without this assignment, base_compile gets emptied. + fbsd_hideous_sh_bug=$base_compile + + if test "$pic_mode" != no; then + command="$base_compile $qsrcfile $pic_flag" + else + # Don't build PIC code + command="$base_compile $qsrcfile" + fi + + func_mkdir_p "$xdir$objdir" + + if test -z "$output_obj"; then + # Place PIC objects in $objdir + command="$command -o $lobj" + fi + + func_show_eval_locale "$command" \ + 'test -n "$output_obj" && $RM $removelist; exit $EXIT_FAILURE' + + if test "$need_locks" = warn && + test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then + $ECHO "\ +*** ERROR, $lockfile contains: +`cat $lockfile 2>/dev/null` + +but it should contain: +$srcfile + +This indicates that another process is trying to use the same +temporary object file, and libtool could not work around it because +your compiler does not support \`-c' and \`-o' together. If you +repeat this compilation, it may succeed, by chance, but you had better +avoid parallel builds (make -j) in this platform, or get a better +compiler." + + $opt_dry_run || $RM $removelist + exit $EXIT_FAILURE + fi + + # Just move the object if needed, then go on to compile the next one + if test -n "$output_obj" && test "X$output_obj" != "X$lobj"; then + func_show_eval '$MV "$output_obj" "$lobj"' \ + 'error=$?; $opt_dry_run || $RM $removelist; exit $error' + fi + + # Allow error messages only from the first compilation. + if test "$suppress_opt" = yes; then + suppress_output=' >/dev/null 2>&1' + fi + fi + + # Only build a position-dependent object if we build old libraries. + if test "$build_old_libs" = yes; then + if test "$pic_mode" != yes; then + # Don't build PIC code + command="$base_compile $qsrcfile$pie_flag" + else + command="$base_compile $qsrcfile $pic_flag" + fi + if test "$compiler_c_o" = yes; then + command="$command -o $obj" + fi + + # Suppress compiler output if we already did a PIC compilation. + command="$command$suppress_output" + func_show_eval_locale "$command" \ + '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' + + if test "$need_locks" = warn && + test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then + $ECHO "\ +*** ERROR, $lockfile contains: +`cat $lockfile 2>/dev/null` + +but it should contain: +$srcfile + +This indicates that another process is trying to use the same +temporary object file, and libtool could not work around it because +your compiler does not support \`-c' and \`-o' together. If you +repeat this compilation, it may succeed, by chance, but you had better +avoid parallel builds (make -j) in this platform, or get a better +compiler." + + $opt_dry_run || $RM $removelist + exit $EXIT_FAILURE + fi + + # Just move the object if needed + if test -n "$output_obj" && test "X$output_obj" != "X$obj"; then + func_show_eval '$MV "$output_obj" "$obj"' \ + 'error=$?; $opt_dry_run || $RM $removelist; exit $error' + fi + fi + + $opt_dry_run || { + func_write_libtool_object "$libobj" "$objdir/$objname" "$objname" + + # Unlock the critical section if it was locked + if test "$need_locks" != no; then + removelist=$lockfile + $RM "$lockfile" + fi + } + + exit $EXIT_SUCCESS +} + +$opt_help || { +test "$mode" = compile && func_mode_compile ${1+"$@"} +} + +func_mode_help () +{ + # We need to display help for each of the modes. + case $mode in + "") + # Generic help is extracted from the usage comments + # at the start of this file. + func_help + ;; + + clean) + $ECHO \ +"Usage: $progname [OPTION]... --mode=clean RM [RM-OPTION]... FILE... + +Remove files from the build directory. + +RM is the name of the program to use to delete files associated with each FILE +(typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed +to RM. + +If FILE is a libtool library, object or program, all the files associated +with it are deleted. Otherwise, only FILE itself is deleted using RM." + ;; + + compile) + $ECHO \ +"Usage: $progname [OPTION]... --mode=compile COMPILE-COMMAND... SOURCEFILE + +Compile a source file into a libtool library object. + +This mode accepts the following additional options: + + -o OUTPUT-FILE set the output file name to OUTPUT-FILE + -no-suppress do not suppress compiler output for multiple passes + -prefer-pic try to building PIC objects only + -prefer-non-pic try to building non-PIC objects only + -shared do not build a \`.o' file suitable for static linking + -static only build a \`.o' file suitable for static linking + +COMPILE-COMMAND is a command to be used in creating a \`standard' object file +from the given SOURCEFILE. + +The output file name is determined by removing the directory component from +SOURCEFILE, then substituting the C source code suffix \`.c' with the +library object suffix, \`.lo'." + ;; + + execute) + $ECHO \ +"Usage: $progname [OPTION]... --mode=execute COMMAND [ARGS]... + +Automatically set library path, then run a program. + +This mode accepts the following additional options: + + -dlopen FILE add the directory containing FILE to the library path + +This mode sets the library path environment variable according to \`-dlopen' +flags. + +If any of the ARGS are libtool executable wrappers, then they are translated +into their corresponding uninstalled binary, and any of their required library +directories are added to the library path. + +Then, COMMAND is executed, with ARGS as arguments." + ;; + + finish) + $ECHO \ +"Usage: $progname [OPTION]... --mode=finish [LIBDIR]... + +Complete the installation of libtool libraries. + +Each LIBDIR is a directory that contains libtool libraries. + +The commands that this mode executes may require superuser privileges. Use +the \`--dry-run' option if you just want to see what would be executed." + ;; + + install) + $ECHO \ +"Usage: $progname [OPTION]... --mode=install INSTALL-COMMAND... + +Install executables or libraries. + +INSTALL-COMMAND is the installation command. The first component should be +either the \`install' or \`cp' program. + +The following components of INSTALL-COMMAND are treated specially: + + -inst-prefix PREFIX-DIR Use PREFIX-DIR as a staging area for installation + +The rest of the components are interpreted as arguments to that command (only +BSD-compatible install options are recognized)." + ;; + + link) + $ECHO \ +"Usage: $progname [OPTION]... --mode=link LINK-COMMAND... + +Link object files or libraries together to form another library, or to +create an executable program. + +LINK-COMMAND is a command using the C compiler that you would use to create +a program from several object files. + +The following components of LINK-COMMAND are treated specially: + + -all-static do not do any dynamic linking at all + -avoid-version do not add a version suffix if possible + -dlopen FILE \`-dlpreopen' FILE if it cannot be dlopened at runtime + -dlpreopen FILE link in FILE and add its symbols to lt_preloaded_symbols + -export-dynamic allow symbols from OUTPUT-FILE to be resolved with dlsym(3) + -export-symbols SYMFILE + try to export only the symbols listed in SYMFILE + -export-symbols-regex REGEX + try to export only the symbols matching REGEX + -LLIBDIR search LIBDIR for required installed libraries + -lNAME OUTPUT-FILE requires the installed library libNAME + -module build a library that can dlopened + -no-fast-install disable the fast-install mode + -no-install link a not-installable executable + -no-undefined declare that a library does not refer to external symbols + -o OUTPUT-FILE create OUTPUT-FILE from the specified objects + -objectlist FILE Use a list of object files found in FILE to specify objects + -precious-files-regex REGEX + don't remove output files matching REGEX + -release RELEASE specify package release information + -rpath LIBDIR the created library will eventually be installed in LIBDIR + -R[ ]LIBDIR add LIBDIR to the runtime path of programs and libraries + -shared only do dynamic linking of libtool libraries + -shrext SUFFIX override the standard shared library file extension + -static do not do any dynamic linking of uninstalled libtool libraries + -static-libtool-libs + do not do any dynamic linking of libtool libraries + -version-info CURRENT[:REVISION[:AGE]] + specify library version info [each variable defaults to 0] + -weak LIBNAME declare that the target provides the LIBNAME interface + +All other options (arguments beginning with \`-') are ignored. + +Every other argument is treated as a filename. Files ending in \`.la' are +treated as uninstalled libtool libraries, other files are standard or library +object files. + +If the OUTPUT-FILE ends in \`.la', then a libtool library is created, +only library objects (\`.lo' files) may be specified, and \`-rpath' is +required, except when creating a convenience library. + +If OUTPUT-FILE ends in \`.a' or \`.lib', then a standard library is created +using \`ar' and \`ranlib', or on Windows using \`lib'. + +If OUTPUT-FILE ends in \`.lo' or \`.${objext}', then a reloadable object file +is created, otherwise an executable program is created." + ;; + + uninstall) + $ECHO \ +"Usage: $progname [OPTION]... --mode=uninstall RM [RM-OPTION]... FILE... + +Remove libraries from an installation directory. + +RM is the name of the program to use to delete files associated with each FILE +(typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed +to RM. + +If FILE is a libtool library, all the files associated with it are deleted. +Otherwise, only FILE itself is deleted using RM." + ;; + + *) + func_fatal_help "invalid operation mode \`$mode'" + ;; + esac + + $ECHO + $ECHO "Try \`$progname --help' for more information about other modes." + + exit $? +} + + # Now that we've collected a possible --mode arg, show help if necessary + $opt_help && func_mode_help + + +# func_mode_execute arg... +func_mode_execute () +{ + $opt_debug + # The first argument is the command name. + cmd="$nonopt" + test -z "$cmd" && \ + func_fatal_help "you must specify a COMMAND" + + # Handle -dlopen flags immediately. + for file in $execute_dlfiles; do + test -f "$file" \ + || func_fatal_help "\`$file' is not a file" + + dir= + case $file in + *.la) + # Check to see that this really is a libtool archive. + func_lalib_unsafe_p "$file" \ + || func_fatal_help "\`$lib' is not a valid libtool archive" + + # Read the libtool library. + dlname= + library_names= + func_source "$file" + + # Skip this library if it cannot be dlopened. + if test -z "$dlname"; then + # Warn if it was a shared library. + test -n "$library_names" && \ + func_warning "\`$file' was not linked with \`-export-dynamic'" + continue + fi + + func_dirname "$file" "" "." + dir="$func_dirname_result" + + if test -f "$dir/$objdir/$dlname"; then + dir="$dir/$objdir" + else + if test ! -f "$dir/$dlname"; then + func_fatal_error "cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'" + fi + fi + ;; + + *.lo) + # Just add the directory containing the .lo file. + func_dirname "$file" "" "." + dir="$func_dirname_result" + ;; + + *) + func_warning "\`-dlopen' is ignored for non-libtool libraries and objects" + continue + ;; + esac + + # Get the absolute pathname. + absdir=`cd "$dir" && pwd` + test -n "$absdir" && dir="$absdir" + + # Now add the directory to shlibpath_var. + if eval "test -z \"\$$shlibpath_var\""; then + eval "$shlibpath_var=\"\$dir\"" + else + eval "$shlibpath_var=\"\$dir:\$$shlibpath_var\"" + fi + done + + # This variable tells wrapper scripts just to set shlibpath_var + # rather than running their programs. + libtool_execute_magic="$magic" + + # Check if any of the arguments is a wrapper script. + args= + for file + do + case $file in + -*) ;; + *) + # Do a test to see if this is really a libtool program. + if func_ltwrapper_script_p "$file"; then + func_source "$file" + # Transform arg to wrapped name. + file="$progdir/$program" + elif func_ltwrapper_executable_p "$file"; then + func_ltwrapper_scriptname "$file" + func_source "$func_ltwrapper_scriptname_result" + # Transform arg to wrapped name. + file="$progdir/$program" + fi + ;; + esac + # Quote arguments (to preserve shell metacharacters). + func_quote_for_eval "$file" + args="$args $func_quote_for_eval_result" + done + + if test "X$opt_dry_run" = Xfalse; then + if test -n "$shlibpath_var"; then + # Export the shlibpath_var. + eval "export $shlibpath_var" + fi + + # Restore saved environment variables + for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES + do + eval "if test \"\${save_$lt_var+set}\" = set; then + $lt_var=\$save_$lt_var; export $lt_var + else + $lt_unset $lt_var + fi" + done + + # Now prepare to actually exec the command. + exec_cmd="\$cmd$args" + else + # Display what would be done. + if test -n "$shlibpath_var"; then + eval "\$ECHO \"\$shlibpath_var=\$$shlibpath_var\"" + $ECHO "export $shlibpath_var" + fi + $ECHO "$cmd$args" + exit $EXIT_SUCCESS + fi +} + +test "$mode" = execute && func_mode_execute ${1+"$@"} + + +# func_mode_finish arg... +func_mode_finish () +{ + $opt_debug + libdirs="$nonopt" + admincmds= + + if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then + for dir + do + libdirs="$libdirs $dir" + done + + for libdir in $libdirs; do + if test -n "$finish_cmds"; then + # Do each command in the finish commands. + func_execute_cmds "$finish_cmds" 'admincmds="$admincmds +'"$cmd"'"' + fi + if test -n "$finish_eval"; then + # Do the single finish_eval. + eval cmds=\"$finish_eval\" + $opt_dry_run || eval "$cmds" || admincmds="$admincmds + $cmds" + fi + done + fi + + # Exit here if they wanted silent mode. + $opt_silent && exit $EXIT_SUCCESS + + $ECHO "X----------------------------------------------------------------------" | $Xsed + $ECHO "Libraries have been installed in:" + for libdir in $libdirs; do + $ECHO " $libdir" + done + $ECHO + $ECHO "If you ever happen to want to link against installed libraries" + $ECHO "in a given directory, LIBDIR, you must either use libtool, and" + $ECHO "specify the full pathname of the library, or use the \`-LLIBDIR'" + $ECHO "flag during linking and do at least one of the following:" + if test -n "$shlibpath_var"; then + $ECHO " - add LIBDIR to the \`$shlibpath_var' environment variable" + $ECHO " during execution" + fi + if test -n "$runpath_var"; then + $ECHO " - add LIBDIR to the \`$runpath_var' environment variable" + $ECHO " during linking" + fi + if test -n "$hardcode_libdir_flag_spec"; then + libdir=LIBDIR + eval flag=\"$hardcode_libdir_flag_spec\" + + $ECHO " - use the \`$flag' linker flag" + fi + if test -n "$admincmds"; then + $ECHO " - have your system administrator run these commands:$admincmds" + fi + if test -f /etc/ld.so.conf; then + $ECHO " - have your system administrator add LIBDIR to \`/etc/ld.so.conf'" + fi + $ECHO + + $ECHO "See any operating system documentation about shared libraries for" + case $host in + solaris2.[6789]|solaris2.1[0-9]) + $ECHO "more information, such as the ld(1), crle(1) and ld.so(8) manual" + $ECHO "pages." + ;; + *) + $ECHO "more information, such as the ld(1) and ld.so(8) manual pages." + ;; + esac + $ECHO "X----------------------------------------------------------------------" | $Xsed + exit $EXIT_SUCCESS +} + +test "$mode" = finish && func_mode_finish ${1+"$@"} + + +# func_mode_install arg... +func_mode_install () +{ + $opt_debug + # There may be an optional sh(1) argument at the beginning of + # install_prog (especially on Windows NT). + if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh || + # Allow the use of GNU shtool's install command. + $ECHO "X$nonopt" | $GREP shtool >/dev/null; then + # Aesthetically quote it. + func_quote_for_eval "$nonopt" + install_prog="$func_quote_for_eval_result " + arg=$1 + shift + else + install_prog= + arg=$nonopt + fi + + # The real first argument should be the name of the installation program. + # Aesthetically quote it. + func_quote_for_eval "$arg" + install_prog="$install_prog$func_quote_for_eval_result" + + # We need to accept at least all the BSD install flags. + dest= + files= + opts= + prev= + install_type= + isdir=no + stripme= + for arg + do + if test -n "$dest"; then + files="$files $dest" + dest=$arg + continue + fi + + case $arg in + -d) isdir=yes ;; + -f) + case " $install_prog " in + *[\\\ /]cp\ *) ;; + *) prev=$arg ;; + esac + ;; + -g | -m | -o) + prev=$arg + ;; + -s) + stripme=" -s" + continue + ;; + -*) + ;; + *) + # If the previous option needed an argument, then skip it. + if test -n "$prev"; then + prev= + else + dest=$arg + continue + fi + ;; + esac + + # Aesthetically quote the argument. + func_quote_for_eval "$arg" + install_prog="$install_prog $func_quote_for_eval_result" + done + + test -z "$install_prog" && \ + func_fatal_help "you must specify an install program" + + test -n "$prev" && \ + func_fatal_help "the \`$prev' option requires an argument" + + if test -z "$files"; then + if test -z "$dest"; then + func_fatal_help "no file or destination specified" + else + func_fatal_help "you must specify a destination" + fi + fi + + # Strip any trailing slash from the destination. + func_stripname '' '/' "$dest" + dest=$func_stripname_result + + # Check to see that the destination is a directory. + test -d "$dest" && isdir=yes + if test "$isdir" = yes; then + destdir="$dest" + destname= + else + func_dirname_and_basename "$dest" "" "." + destdir="$func_dirname_result" + destname="$func_basename_result" + + # Not a directory, so check to see that there is only one file specified. + set dummy $files; shift + test "$#" -gt 1 && \ + func_fatal_help "\`$dest' is not a directory" + fi + case $destdir in + [\\/]* | [A-Za-z]:[\\/]*) ;; + *) + for file in $files; do + case $file in + *.lo) ;; + *) + func_fatal_help "\`$destdir' must be an absolute directory name" + ;; + esac + done + ;; + esac + + # This variable tells wrapper scripts just to set variables rather + # than running their programs. + libtool_install_magic="$magic" + + staticlibs= + future_libdirs= + current_libdirs= + for file in $files; do + + # Do each installation. + case $file in + *.$libext) + # Do the static libraries later. + staticlibs="$staticlibs $file" + ;; + + *.la) + # Check to see that this really is a libtool archive. + func_lalib_unsafe_p "$file" \ + || func_fatal_help "\`$file' is not a valid libtool archive" + + library_names= + old_library= + relink_command= + func_source "$file" + + # Add the libdir to current_libdirs if it is the destination. + if test "X$destdir" = "X$libdir"; then + case "$current_libdirs " in + *" $libdir "*) ;; + *) current_libdirs="$current_libdirs $libdir" ;; + esac + else + # Note the libdir as a future libdir. + case "$future_libdirs " in + *" $libdir "*) ;; + *) future_libdirs="$future_libdirs $libdir" ;; + esac + fi + + func_dirname "$file" "/" "" + dir="$func_dirname_result" + dir="$dir$objdir" + + if test -n "$relink_command"; then + # Determine the prefix the user has applied to our future dir. + inst_prefix_dir=`$ECHO "X$destdir" | $Xsed -e "s%$libdir\$%%"` + + # Don't allow the user to place us outside of our expected + # location b/c this prevents finding dependent libraries that + # are installed to the same prefix. + # At present, this check doesn't affect windows .dll's that + # are installed into $libdir/../bin (currently, that works fine) + # but it's something to keep an eye on. + test "$inst_prefix_dir" = "$destdir" && \ + func_fatal_error "error: cannot install \`$file' to a directory not ending in $libdir" + + if test -n "$inst_prefix_dir"; then + # Stick the inst_prefix_dir data into the link command. + relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"` + else + relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%%"` + fi + + func_warning "relinking \`$file'" + func_show_eval "$relink_command" \ + 'func_fatal_error "error: relink \`$file'\'' with the above command before installing it"' + fi + + # See the names of the shared library. + set dummy $library_names; shift + if test -n "$1"; then + realname="$1" + shift + + srcname="$realname" + test -n "$relink_command" && srcname="$realname"T + + # Install the shared library and build the symlinks. + func_show_eval "$install_prog $dir/$srcname $destdir/$realname" \ + 'exit $?' + tstripme="$stripme" + case $host_os in + cygwin* | mingw* | pw32* | cegcc*) + case $realname in + *.dll.a) + tstripme="" + ;; + esac + ;; + esac + if test -n "$tstripme" && test -n "$striplib"; then + func_show_eval "$striplib $destdir/$realname" 'exit $?' + fi + + if test "$#" -gt 0; then + # Delete the old symlinks, and create new ones. + # Try `ln -sf' first, because the `ln' binary might depend on + # the symlink we replace! Solaris /bin/ln does not understand -f, + # so we also need to try rm && ln -s. + for linkname + do + test "$linkname" != "$realname" \ + && func_show_eval "(cd $destdir && { $LN_S -f $realname $linkname || { $RM $linkname && $LN_S $realname $linkname; }; })" + done + fi + + # Do each command in the postinstall commands. + lib="$destdir/$realname" + func_execute_cmds "$postinstall_cmds" 'exit $?' + fi + + # Install the pseudo-library for information purposes. + func_basename "$file" + name="$func_basename_result" + instname="$dir/$name"i + func_show_eval "$install_prog $instname $destdir/$name" 'exit $?' + + # Maybe install the static library, too. + test -n "$old_library" && staticlibs="$staticlibs $dir/$old_library" + ;; + + *.lo) + # Install (i.e. copy) a libtool object. + + # Figure out destination file name, if it wasn't already specified. + if test -n "$destname"; then + destfile="$destdir/$destname" + else + func_basename "$file" + destfile="$func_basename_result" + destfile="$destdir/$destfile" + fi + + # Deduce the name of the destination old-style object file. + case $destfile in + *.lo) + func_lo2o "$destfile" + staticdest=$func_lo2o_result + ;; + *.$objext) + staticdest="$destfile" + destfile= + ;; + *) + func_fatal_help "cannot copy a libtool object to \`$destfile'" + ;; + esac + + # Install the libtool object if requested. + test -n "$destfile" && \ + func_show_eval "$install_prog $file $destfile" 'exit $?' + + # Install the old object if enabled. + if test "$build_old_libs" = yes; then + # Deduce the name of the old-style object file. + func_lo2o "$file" + staticobj=$func_lo2o_result + func_show_eval "$install_prog \$staticobj \$staticdest" 'exit $?' + fi + exit $EXIT_SUCCESS + ;; + + *) + # Figure out destination file name, if it wasn't already specified. + if test -n "$destname"; then + destfile="$destdir/$destname" + else + func_basename "$file" + destfile="$func_basename_result" + destfile="$destdir/$destfile" + fi + + # If the file is missing, and there is a .exe on the end, strip it + # because it is most likely a libtool script we actually want to + # install + stripped_ext="" + case $file in + *.exe) + if test ! -f "$file"; then + func_stripname '' '.exe' "$file" + file=$func_stripname_result + stripped_ext=".exe" + fi + ;; + esac + + # Do a test to see if this is really a libtool program. + case $host in + *cygwin* | *mingw*) + if func_ltwrapper_executable_p "$file"; then + func_ltwrapper_scriptname "$file" + wrapper=$func_ltwrapper_scriptname_result + else + func_stripname '' '.exe' "$file" + wrapper=$func_stripname_result + fi + ;; + *) + wrapper=$file + ;; + esac + if func_ltwrapper_script_p "$wrapper"; then + notinst_deplibs= + relink_command= + + func_source "$wrapper" + + # Check the variables that should have been set. + test -z "$generated_by_libtool_version" && \ + func_fatal_error "invalid libtool wrapper script \`$wrapper'" + + finalize=yes + for lib in $notinst_deplibs; do + # Check to see that each library is installed. + libdir= + if test -f "$lib"; then + func_source "$lib" + fi + libfile="$libdir/"`$ECHO "X$lib" | $Xsed -e 's%^.*/%%g'` ### testsuite: skip nested quoting test + if test -n "$libdir" && test ! -f "$libfile"; then + func_warning "\`$lib' has not been installed in \`$libdir'" + finalize=no + fi + done + + relink_command= + func_source "$wrapper" + + outputname= + if test "$fast_install" = no && test -n "$relink_command"; then + $opt_dry_run || { + if test "$finalize" = yes; then + tmpdir=`func_mktempdir` + func_basename "$file$stripped_ext" + file="$func_basename_result" + outputname="$tmpdir/$file" + # Replace the output file specification. + relink_command=`$ECHO "X$relink_command" | $Xsed -e 's%@OUTPUT@%'"$outputname"'%g'` + + $opt_silent || { + func_quote_for_expand "$relink_command" + eval "func_echo $func_quote_for_expand_result" + } + if eval "$relink_command"; then : + else + func_error "error: relink \`$file' with the above command before installing it" + $opt_dry_run || ${RM}r "$tmpdir" + continue + fi + file="$outputname" + else + func_warning "cannot relink \`$file'" + fi + } + else + # Install the binary that we compiled earlier. + file=`$ECHO "X$file$stripped_ext" | $Xsed -e "s%\([^/]*\)$%$objdir/\1%"` + fi + fi + + # remove .exe since cygwin /usr/bin/install will append another + # one anyway + case $install_prog,$host in + */usr/bin/install*,*cygwin*) + case $file:$destfile in + *.exe:*.exe) + # this is ok + ;; + *.exe:*) + destfile=$destfile.exe + ;; + *:*.exe) + func_stripname '' '.exe' "$destfile" + destfile=$func_stripname_result + ;; + esac + ;; + esac + func_show_eval "$install_prog\$stripme \$file \$destfile" 'exit $?' + $opt_dry_run || if test -n "$outputname"; then + ${RM}r "$tmpdir" + fi + ;; + esac + done + + for file in $staticlibs; do + func_basename "$file" + name="$func_basename_result" + + # Set up the ranlib parameters. + oldlib="$destdir/$name" + + func_show_eval "$install_prog \$file \$oldlib" 'exit $?' + + if test -n "$stripme" && test -n "$old_striplib"; then + func_show_eval "$old_striplib $oldlib" 'exit $?' + fi + + # Do each command in the postinstall commands. + func_execute_cmds "$old_postinstall_cmds" 'exit $?' + done + + test -n "$future_libdirs" && \ + func_warning "remember to run \`$progname --finish$future_libdirs'" + + if test -n "$current_libdirs"; then + # Maybe just do a dry run. + $opt_dry_run && current_libdirs=" -n$current_libdirs" + exec_cmd='$SHELL $progpath $preserve_args --finish$current_libdirs' + else + exit $EXIT_SUCCESS + fi +} + +test "$mode" = install && func_mode_install ${1+"$@"} + + +# func_generate_dlsyms outputname originator pic_p +# Extract symbols from dlprefiles and create ${outputname}S.o with +# a dlpreopen symbol table. +func_generate_dlsyms () +{ + $opt_debug + my_outputname="$1" + my_originator="$2" + my_pic_p="${3-no}" + my_prefix=`$ECHO "$my_originator" | sed 's%[^a-zA-Z0-9]%_%g'` + my_dlsyms= + + if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then + if test -n "$NM" && test -n "$global_symbol_pipe"; then + my_dlsyms="${my_outputname}S.c" + else + func_error "not configured to extract global symbols from dlpreopened files" + fi + fi + + if test -n "$my_dlsyms"; then + case $my_dlsyms in + "") ;; + *.c) + # Discover the nlist of each of the dlfiles. + nlist="$output_objdir/${my_outputname}.nm" + + func_show_eval "$RM $nlist ${nlist}S ${nlist}T" + + # Parse the name list into a source file. + func_verbose "creating $output_objdir/$my_dlsyms" + + $opt_dry_run || $ECHO > "$output_objdir/$my_dlsyms" "\ +/* $my_dlsyms - symbol resolution table for \`$my_outputname' dlsym emulation. */ +/* Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION */ + +#ifdef __cplusplus +extern \"C\" { +#endif + +/* External symbol declarations for the compiler. */\ +" + + if test "$dlself" = yes; then + func_verbose "generating symbol list for \`$output'" + + $opt_dry_run || echo ': @PROGRAM@ ' > "$nlist" + + # Add our own program objects to the symbol list. + progfiles=`$ECHO "X$objs$old_deplibs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` + for progfile in $progfiles; do + func_verbose "extracting global C symbols from \`$progfile'" + $opt_dry_run || eval "$NM $progfile | $global_symbol_pipe >> '$nlist'" + done + + if test -n "$exclude_expsyms"; then + $opt_dry_run || { + eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T' + eval '$MV "$nlist"T "$nlist"' + } + fi + + if test -n "$export_symbols_regex"; then + $opt_dry_run || { + eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T' + eval '$MV "$nlist"T "$nlist"' + } + fi + + # Prepare the list of exported symbols + if test -z "$export_symbols"; then + export_symbols="$output_objdir/$outputname.exp" + $opt_dry_run || { + $RM $export_symbols + eval "${SED} -n -e '/^: @PROGRAM@ $/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"' + case $host in + *cygwin* | *mingw* | *cegcc* ) + eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' + eval 'cat "$export_symbols" >> "$output_objdir/$outputname.def"' + ;; + esac + } + else + $opt_dry_run || { + eval "${SED} -e 's/\([].[*^$]\)/\\\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$outputname.exp"' + eval '$GREP -f "$output_objdir/$outputname.exp" < "$nlist" > "$nlist"T' + eval '$MV "$nlist"T "$nlist"' + case $host in + *cygwin | *mingw* | *cegcc* ) + eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' + eval 'cat "$nlist" >> "$output_objdir/$outputname.def"' + ;; + esac + } + fi + fi + + for dlprefile in $dlprefiles; do + func_verbose "extracting global C symbols from \`$dlprefile'" + func_basename "$dlprefile" + name="$func_basename_result" + $opt_dry_run || { + eval '$ECHO ": $name " >> "$nlist"' + eval "$NM $dlprefile 2>/dev/null | $global_symbol_pipe >> '$nlist'" + } + done + + $opt_dry_run || { + # Make sure we have at least an empty file. + test -f "$nlist" || : > "$nlist" + + if test -n "$exclude_expsyms"; then + $EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T + $MV "$nlist"T "$nlist" + fi + + # Try sorting and uniquifying the output. + if $GREP -v "^: " < "$nlist" | + if sort -k 3 /dev/null 2>&1; then + sort -k 3 + else + sort +2 + fi | + uniq > "$nlist"S; then + : + else + $GREP -v "^: " < "$nlist" > "$nlist"S + fi + + if test -f "$nlist"S; then + eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$my_dlsyms"' + else + $ECHO '/* NONE */' >> "$output_objdir/$my_dlsyms" + fi + + $ECHO >> "$output_objdir/$my_dlsyms" "\ + +/* The mapping between symbol names and symbols. */ +typedef struct { + const char *name; + void *address; +} lt_dlsymlist; +" + case $host in + *cygwin* | *mingw* | *cegcc* ) + $ECHO >> "$output_objdir/$my_dlsyms" "\ +/* DATA imports from DLLs on WIN32 con't be const, because + runtime relocations are performed -- see ld's documentation + on pseudo-relocs. */" + lt_dlsym_const= ;; + *osf5*) + echo >> "$output_objdir/$my_dlsyms" "\ +/* This system does not cope well with relocations in const data */" + lt_dlsym_const= ;; + *) + lt_dlsym_const=const ;; + esac + + $ECHO >> "$output_objdir/$my_dlsyms" "\ +extern $lt_dlsym_const lt_dlsymlist +lt_${my_prefix}_LTX_preloaded_symbols[]; +$lt_dlsym_const lt_dlsymlist +lt_${my_prefix}_LTX_preloaded_symbols[] = +{\ + { \"$my_originator\", (void *) 0 }," + + case $need_lib_prefix in + no) + eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$my_dlsyms" + ;; + *) + eval "$global_symbol_to_c_name_address_lib_prefix" < "$nlist" >> "$output_objdir/$my_dlsyms" + ;; + esac + $ECHO >> "$output_objdir/$my_dlsyms" "\ + {0, (void *) 0} +}; + +/* This works around a problem in FreeBSD linker */ +#ifdef FREEBSD_WORKAROUND +static const void *lt_preloaded_setup() { + return lt_${my_prefix}_LTX_preloaded_symbols; +} +#endif + +#ifdef __cplusplus +} +#endif\ +" + } # !$opt_dry_run + + pic_flag_for_symtable= + case "$compile_command " in + *" -static "*) ;; + *) + case $host in + # compiling the symbol table file with pic_flag works around + # a FreeBSD bug that causes programs to crash when -lm is + # linked before any other PIC object. But we must not use + # pic_flag when linking with -static. The problem exists in + # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1. + *-*-freebsd2*|*-*-freebsd3.0*|*-*-freebsdelf3.0*) + pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND" ;; + *-*-hpux*) + pic_flag_for_symtable=" $pic_flag" ;; + *) + if test "X$my_pic_p" != Xno; then + pic_flag_for_symtable=" $pic_flag" + fi + ;; + esac + ;; + esac + symtab_cflags= + for arg in $LTCFLAGS; do + case $arg in + -pie | -fpie | -fPIE) ;; + *) symtab_cflags="$symtab_cflags $arg" ;; + esac + done + + # Now compile the dynamic symbol file. + func_show_eval '(cd $output_objdir && $LTCC$symtab_cflags -c$no_builtin_flag$pic_flag_for_symtable "$my_dlsyms")' 'exit $?' + + # Clean up the generated files. + func_show_eval '$RM "$output_objdir/$my_dlsyms" "$nlist" "${nlist}S" "${nlist}T"' + + # Transform the symbol file into the correct name. + symfileobj="$output_objdir/${my_outputname}S.$objext" + case $host in + *cygwin* | *mingw* | *cegcc* ) + if test -f "$output_objdir/$my_outputname.def"; then + compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` + finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` + else + compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` + finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` + fi + ;; + *) + compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` + finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` + ;; + esac + ;; + *) + func_fatal_error "unknown suffix for \`$my_dlsyms'" + ;; + esac + else + # We keep going just in case the user didn't refer to + # lt_preloaded_symbols. The linker will fail if global_symbol_pipe + # really was required. + + # Nullify the symbol file. + compile_command=`$ECHO "X$compile_command" | $Xsed -e "s% @SYMFILE@%%"` + finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s% @SYMFILE@%%"` + fi +} + +# func_win32_libid arg +# return the library type of file 'arg' +# +# Need a lot of goo to handle *both* DLLs and import libs +# Has to be a shell function in order to 'eat' the argument +# that is supplied when $file_magic_command is called. +func_win32_libid () +{ + $opt_debug + win32_libid_type="unknown" + win32_fileres=`file -L $1 2>/dev/null` + case $win32_fileres in + *ar\ archive\ import\ library*) # definitely import + win32_libid_type="x86 archive import" + ;; + *ar\ archive*) # could be an import, or static + if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null | + $EGREP 'file format pe-i386(.*architecture: i386)?' >/dev/null ; then + win32_nmres=`eval $NM -f posix -A $1 | + $SED -n -e ' + 1,100{ + / I /{ + s,.*,import, + p + q + } + }'` + case $win32_nmres in + import*) win32_libid_type="x86 archive import";; + *) win32_libid_type="x86 archive static";; + esac + fi + ;; + *DLL*) + win32_libid_type="x86 DLL" + ;; + *executable*) # but shell scripts are "executable" too... + case $win32_fileres in + *MS\ Windows\ PE\ Intel*) + win32_libid_type="x86 DLL" + ;; + esac + ;; + esac + $ECHO "$win32_libid_type" +} + + + +# func_extract_an_archive dir oldlib +func_extract_an_archive () +{ + $opt_debug + f_ex_an_ar_dir="$1"; shift + f_ex_an_ar_oldlib="$1" + func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" 'exit $?' + if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then + : + else + func_fatal_error "object name conflicts in archive: $f_ex_an_ar_dir/$f_ex_an_ar_oldlib" + fi +} + + +# func_extract_archives gentop oldlib ... +func_extract_archives () +{ + $opt_debug + my_gentop="$1"; shift + my_oldlibs=${1+"$@"} + my_oldobjs="" + my_xlib="" + my_xabs="" + my_xdir="" + + for my_xlib in $my_oldlibs; do + # Extract the objects. + case $my_xlib in + [\\/]* | [A-Za-z]:[\\/]*) my_xabs="$my_xlib" ;; + *) my_xabs=`pwd`"/$my_xlib" ;; + esac + func_basename "$my_xlib" + my_xlib="$func_basename_result" + my_xlib_u=$my_xlib + while :; do + case " $extracted_archives " in + *" $my_xlib_u "*) + func_arith $extracted_serial + 1 + extracted_serial=$func_arith_result + my_xlib_u=lt$extracted_serial-$my_xlib ;; + *) break ;; + esac + done + extracted_archives="$extracted_archives $my_xlib_u" + my_xdir="$my_gentop/$my_xlib_u" + + func_mkdir_p "$my_xdir" + + case $host in + *-darwin*) + func_verbose "Extracting $my_xabs" + # Do not bother doing anything if just a dry run + $opt_dry_run || { + darwin_orig_dir=`pwd` + cd $my_xdir || exit $? + darwin_archive=$my_xabs + darwin_curdir=`pwd` + darwin_base_archive=`basename "$darwin_archive"` + darwin_arches=`$LIPO -info "$darwin_archive" 2>/dev/null | $GREP Architectures 2>/dev/null || true` + if test -n "$darwin_arches"; then + darwin_arches=`$ECHO "$darwin_arches" | $SED -e 's/.*are://'` + darwin_arch= + func_verbose "$darwin_base_archive has multiple architectures $darwin_arches" + for darwin_arch in $darwin_arches ; do + func_mkdir_p "unfat-$$/${darwin_base_archive}-${darwin_arch}" + $LIPO -thin $darwin_arch -output "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" "${darwin_archive}" + cd "unfat-$$/${darwin_base_archive}-${darwin_arch}" + func_extract_an_archive "`pwd`" "${darwin_base_archive}" + cd "$darwin_curdir" + $RM "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" + done # $darwin_arches + ## Okay now we've a bunch of thin objects, gotta fatten them up :) + darwin_filelist=`find unfat-$$ -type f -name \*.o -print -o -name \*.lo -print | $SED -e "$basename" | sort -u` + darwin_file= + darwin_files= + for darwin_file in $darwin_filelist; do + darwin_files=`find unfat-$$ -name $darwin_file -print | $NL2SP` + $LIPO -create -output "$darwin_file" $darwin_files + done # $darwin_filelist + $RM -rf unfat-$$ + cd "$darwin_orig_dir" + else + cd $darwin_orig_dir + func_extract_an_archive "$my_xdir" "$my_xabs" + fi # $darwin_arches + } # !$opt_dry_run + ;; + *) + func_extract_an_archive "$my_xdir" "$my_xabs" + ;; + esac + my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | $NL2SP` + done + + func_extract_archives_result="$my_oldobjs" +} + + + +# func_emit_wrapper_part1 [arg=no] +# +# Emit the first part of a libtool wrapper script on stdout. +# For more information, see the description associated with +# func_emit_wrapper(), below. +func_emit_wrapper_part1 () +{ + func_emit_wrapper_part1_arg1=no + if test -n "$1" ; then + func_emit_wrapper_part1_arg1=$1 + fi + + $ECHO "\ +#! $SHELL + +# $output - temporary wrapper script for $objdir/$outputname +# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION +# +# The $output program cannot be directly executed until all the libtool +# libraries that it depends on are installed. +# +# This wrapper script should never be moved out of the build directory. +# If it is, it will not operate correctly. + +# Sed substitution that helps us do robust quoting. It backslashifies +# metacharacters that are still active within double-quoted strings. +Xsed='${SED} -e 1s/^X//' +sed_quote_subst='$sed_quote_subst' + +# Be Bourne compatible +if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which + # is contrary to our usage. Disable this feature. + alias -g '\${1+\"\$@\"}'='\"\$@\"' + setopt NO_GLOB_SUBST +else + case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac +fi +BIN_SH=xpg4; export BIN_SH # for Tru64 +DUALCASE=1; export DUALCASE # for MKS sh + +# The HP-UX ksh and POSIX shell print the target directory to stdout +# if CDPATH is set. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + +relink_command=\"$relink_command\" + +# This environment variable determines our operation mode. +if test \"\$libtool_install_magic\" = \"$magic\"; then + # install mode needs the following variables: + generated_by_libtool_version='$macro_version' + notinst_deplibs='$notinst_deplibs' +else + # When we are sourced in execute mode, \$file and \$ECHO are already set. + if test \"\$libtool_execute_magic\" != \"$magic\"; then + ECHO=\"$qecho\" + file=\"\$0\" + # Make sure echo works. + if test \"X\$1\" = X--no-reexec; then + # Discard the --no-reexec flag, and continue. + shift + elif test \"X\`{ \$ECHO '\t'; } 2>/dev/null\`\" = 'X\t'; then + # Yippee, \$ECHO works! + : + else + # Restart under the correct shell, and then maybe \$ECHO will work. + exec $SHELL \"\$0\" --no-reexec \${1+\"\$@\"} + fi + fi\ +" + $ECHO "\ + + # Find the directory that this script lives in. + thisdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*$%%'\` + test \"x\$thisdir\" = \"x\$file\" && thisdir=. + + # Follow symbolic links until we get to the real thisdir. + file=\`ls -ld \"\$file\" | ${SED} -n 's/.*-> //p'\` + while test -n \"\$file\"; do + destdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*\$%%'\` + + # If there was a directory component, then change thisdir. + if test \"x\$destdir\" != \"x\$file\"; then + case \"\$destdir\" in + [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;; + *) thisdir=\"\$thisdir/\$destdir\" ;; + esac + fi + + file=\`\$ECHO \"X\$file\" | \$Xsed -e 's%^.*/%%'\` + file=\`ls -ld \"\$thisdir/\$file\" | ${SED} -n 's/.*-> //p'\` + done +" +} +# end: func_emit_wrapper_part1 + +# func_emit_wrapper_part2 [arg=no] +# +# Emit the second part of a libtool wrapper script on stdout. +# For more information, see the description associated with +# func_emit_wrapper(), below. +func_emit_wrapper_part2 () +{ + func_emit_wrapper_part2_arg1=no + if test -n "$1" ; then + func_emit_wrapper_part2_arg1=$1 + fi + + $ECHO "\ + + # Usually 'no', except on cygwin/mingw when embedded into + # the cwrapper. + WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_part2_arg1 + if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then + # special case for '.' + if test \"\$thisdir\" = \".\"; then + thisdir=\`pwd\` + fi + # remove .libs from thisdir + case \"\$thisdir\" in + *[\\\\/]$objdir ) thisdir=\`\$ECHO \"X\$thisdir\" | \$Xsed -e 's%[\\\\/][^\\\\/]*$%%'\` ;; + $objdir ) thisdir=. ;; + esac + fi + + # Try to get the absolute directory name. + absdir=\`cd \"\$thisdir\" && pwd\` + test -n \"\$absdir\" && thisdir=\"\$absdir\" +" + + if test "$fast_install" = yes; then + $ECHO "\ + program=lt-'$outputname'$exeext + progdir=\"\$thisdir/$objdir\" + + if test ! -f \"\$progdir/\$program\" || + { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\ + test \"X\$file\" != \"X\$progdir/\$program\"; }; then + + file=\"\$\$-\$program\" + + if test ! -d \"\$progdir\"; then + $MKDIR \"\$progdir\" + else + $RM \"\$progdir/\$file\" + fi" + + $ECHO "\ + + # relink executable if necessary + if test -n \"\$relink_command\"; then + if relink_command_output=\`eval \$relink_command 2>&1\`; then : + else + $ECHO \"\$relink_command_output\" >&2 + $RM \"\$progdir/\$file\" + exit 1 + fi + fi + + $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null || + { $RM \"\$progdir/\$program\"; + $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; } + $RM \"\$progdir/\$file\" + fi" + else + $ECHO "\ + program='$outputname' + progdir=\"\$thisdir/$objdir\" +" + fi + + $ECHO "\ + + if test -f \"\$progdir/\$program\"; then" + + # Export our shlibpath_var if we have one. + if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then + $ECHO "\ + # Add our own library path to $shlibpath_var + $shlibpath_var=\"$temp_rpath\$$shlibpath_var\" + + # Some systems cannot cope with colon-terminated $shlibpath_var + # The second colon is a workaround for a bug in BeOS R4 sed + $shlibpath_var=\`\$ECHO \"X\$$shlibpath_var\" | \$Xsed -e 's/::*\$//'\` + + export $shlibpath_var +" + fi + + # fixup the dll searchpath if we need to. + if test -n "$dllsearchpath"; then + $ECHO "\ + # Add the dll search path components to the executable PATH + PATH=$dllsearchpath:\$PATH +" + fi + + $ECHO "\ + if test \"\$libtool_execute_magic\" != \"$magic\"; then + # Run the actual program with our arguments. +" + case $host in + # Backslashes separate directories on plain windows + *-*-mingw | *-*-os2* | *-cegcc*) + $ECHO "\ + exec \"\$progdir\\\\\$program\" \${1+\"\$@\"} +" + ;; + + *) + $ECHO "\ + exec \"\$progdir/\$program\" \${1+\"\$@\"} +" + ;; + esac + $ECHO "\ + \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2 + exit 1 + fi + else + # The program doesn't exist. + \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2 + \$ECHO \"This script is just a wrapper for \$program.\" 1>&2 + $ECHO \"See the $PACKAGE documentation for more information.\" 1>&2 + exit 1 + fi +fi\ +" +} +# end: func_emit_wrapper_part2 + + +# func_emit_wrapper [arg=no] +# +# Emit a libtool wrapper script on stdout. +# Don't directly open a file because we may want to +# incorporate the script contents within a cygwin/mingw +# wrapper executable. Must ONLY be called from within +# func_mode_link because it depends on a number of variables +# set therein. +# +# ARG is the value that the WRAPPER_SCRIPT_BELONGS_IN_OBJDIR +# variable will take. If 'yes', then the emitted script +# will assume that the directory in which it is stored is +# the $objdir directory. This is a cygwin/mingw-specific +# behavior. +func_emit_wrapper () +{ + func_emit_wrapper_arg1=no + if test -n "$1" ; then + func_emit_wrapper_arg1=$1 + fi + + # split this up so that func_emit_cwrapperexe_src + # can call each part independently. + func_emit_wrapper_part1 "${func_emit_wrapper_arg1}" + func_emit_wrapper_part2 "${func_emit_wrapper_arg1}" +} + + +# func_to_host_path arg +# +# Convert paths to host format when used with build tools. +# Intended for use with "native" mingw (where libtool itself +# is running under the msys shell), or in the following cross- +# build environments: +# $build $host +# mingw (msys) mingw [e.g. native] +# cygwin mingw +# *nix + wine mingw +# where wine is equipped with the `winepath' executable. +# In the native mingw case, the (msys) shell automatically +# converts paths for any non-msys applications it launches, +# but that facility isn't available from inside the cwrapper. +# Similar accommodations are necessary for $host mingw and +# $build cygwin. Calling this function does no harm for other +# $host/$build combinations not listed above. +# +# ARG is the path (on $build) that should be converted to +# the proper representation for $host. The result is stored +# in $func_to_host_path_result. +func_to_host_path () +{ + func_to_host_path_result="$1" + if test -n "$1" ; then + case $host in + *mingw* ) + lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' + case $build in + *mingw* ) # actually, msys + # awkward: cmd appends spaces to result + lt_sed_strip_trailing_spaces="s/[ ]*\$//" + func_to_host_path_tmp1=`( cmd //c echo "$1" |\ + $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""` + func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ + $SED -e "$lt_sed_naive_backslashify"` + ;; + *cygwin* ) + func_to_host_path_tmp1=`cygpath -w "$1"` + func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ + $SED -e "$lt_sed_naive_backslashify"` + ;; + * ) + # Unfortunately, winepath does not exit with a non-zero + # error code, so we are forced to check the contents of + # stdout. On the other hand, if the command is not + # found, the shell will set an exit code of 127 and print + # *an error message* to stdout. So we must check for both + # error code of zero AND non-empty stdout, which explains + # the odd construction: + func_to_host_path_tmp1=`winepath -w "$1" 2>/dev/null` + if test "$?" -eq 0 && test -n "${func_to_host_path_tmp1}"; then + func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ + $SED -e "$lt_sed_naive_backslashify"` + else + # Allow warning below. + func_to_host_path_result="" + fi + ;; + esac + if test -z "$func_to_host_path_result" ; then + func_error "Could not determine host path corresponding to" + func_error " '$1'" + func_error "Continuing, but uninstalled executables may not work." + # Fallback: + func_to_host_path_result="$1" + fi + ;; + esac + fi +} +# end: func_to_host_path + +# func_to_host_pathlist arg +# +# Convert pathlists to host format when used with build tools. +# See func_to_host_path(), above. This function supports the +# following $build/$host combinations (but does no harm for +# combinations not listed here): +# $build $host +# mingw (msys) mingw [e.g. native] +# cygwin mingw +# *nix + wine mingw +# +# Path separators are also converted from $build format to +# $host format. If ARG begins or ends with a path separator +# character, it is preserved (but converted to $host format) +# on output. +# +# ARG is a pathlist (on $build) that should be converted to +# the proper representation on $host. The result is stored +# in $func_to_host_pathlist_result. +func_to_host_pathlist () +{ + func_to_host_pathlist_result="$1" + if test -n "$1" ; then + case $host in + *mingw* ) + lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' + # Remove leading and trailing path separator characters from + # ARG. msys behavior is inconsistent here, cygpath turns them + # into '.;' and ';.', and winepath ignores them completely. + func_to_host_pathlist_tmp2="$1" + # Once set for this call, this variable should not be + # reassigned. It is used in tha fallback case. + func_to_host_pathlist_tmp1=`echo "$func_to_host_pathlist_tmp2" |\ + $SED -e 's|^:*||' -e 's|:*$||'` + case $build in + *mingw* ) # Actually, msys. + # Awkward: cmd appends spaces to result. + lt_sed_strip_trailing_spaces="s/[ ]*\$//" + func_to_host_pathlist_tmp2=`( cmd //c echo "$func_to_host_pathlist_tmp1" |\ + $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""` + func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\ + $SED -e "$lt_sed_naive_backslashify"` + ;; + *cygwin* ) + func_to_host_pathlist_tmp2=`cygpath -w -p "$func_to_host_pathlist_tmp1"` + func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\ + $SED -e "$lt_sed_naive_backslashify"` + ;; + * ) + # unfortunately, winepath doesn't convert pathlists + func_to_host_pathlist_result="" + func_to_host_pathlist_oldIFS=$IFS + IFS=: + for func_to_host_pathlist_f in $func_to_host_pathlist_tmp1 ; do + IFS=$func_to_host_pathlist_oldIFS + if test -n "$func_to_host_pathlist_f" ; then + func_to_host_path "$func_to_host_pathlist_f" + if test -n "$func_to_host_path_result" ; then + if test -z "$func_to_host_pathlist_result" ; then + func_to_host_pathlist_result="$func_to_host_path_result" + else + func_to_host_pathlist_result="$func_to_host_pathlist_result;$func_to_host_path_result" + fi + fi + fi + IFS=: + done + IFS=$func_to_host_pathlist_oldIFS + ;; + esac + if test -z "$func_to_host_pathlist_result" ; then + func_error "Could not determine the host path(s) corresponding to" + func_error " '$1'" + func_error "Continuing, but uninstalled executables may not work." + # Fallback. This may break if $1 contains DOS-style drive + # specifications. The fix is not to complicate the expression + # below, but for the user to provide a working wine installation + # with winepath so that path translation in the cross-to-mingw + # case works properly. + lt_replace_pathsep_nix_to_dos="s|:|;|g" + func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp1" |\ + $SED -e "$lt_replace_pathsep_nix_to_dos"` + fi + # Now, add the leading and trailing path separators back + case "$1" in + :* ) func_to_host_pathlist_result=";$func_to_host_pathlist_result" + ;; + esac + case "$1" in + *: ) func_to_host_pathlist_result="$func_to_host_pathlist_result;" + ;; + esac + ;; + esac + fi +} +# end: func_to_host_pathlist + +# func_emit_cwrapperexe_src +# emit the source code for a wrapper executable on stdout +# Must ONLY be called from within func_mode_link because +# it depends on a number of variable set therein. +func_emit_cwrapperexe_src () +{ + cat < +#include +#ifdef _MSC_VER +# include +# include +# include +# define setmode _setmode +#else +# include +# include +# ifdef __CYGWIN__ +# include +# define HAVE_SETENV +# ifdef __STRICT_ANSI__ +char *realpath (const char *, char *); +int putenv (char *); +int setenv (const char *, const char *, int); +# endif +# endif +#endif +#include +#include +#include +#include +#include +#include +#include +#include + +#if defined(PATH_MAX) +# define LT_PATHMAX PATH_MAX +#elif defined(MAXPATHLEN) +# define LT_PATHMAX MAXPATHLEN +#else +# define LT_PATHMAX 1024 +#endif + +#ifndef S_IXOTH +# define S_IXOTH 0 +#endif +#ifndef S_IXGRP +# define S_IXGRP 0 +#endif + +#ifdef _MSC_VER +# define S_IXUSR _S_IEXEC +# define stat _stat +# ifndef _INTPTR_T_DEFINED +# define intptr_t int +# endif +#endif + +#ifndef DIR_SEPARATOR +# define DIR_SEPARATOR '/' +# define PATH_SEPARATOR ':' +#endif + +#if defined (_WIN32) || defined (__MSDOS__) || defined (__DJGPP__) || \ + defined (__OS2__) +# define HAVE_DOS_BASED_FILE_SYSTEM +# define FOPEN_WB "wb" +# ifndef DIR_SEPARATOR_2 +# define DIR_SEPARATOR_2 '\\' +# endif +# ifndef PATH_SEPARATOR_2 +# define PATH_SEPARATOR_2 ';' +# endif +#endif + +#ifndef DIR_SEPARATOR_2 +# define IS_DIR_SEPARATOR(ch) ((ch) == DIR_SEPARATOR) +#else /* DIR_SEPARATOR_2 */ +# define IS_DIR_SEPARATOR(ch) \ + (((ch) == DIR_SEPARATOR) || ((ch) == DIR_SEPARATOR_2)) +#endif /* DIR_SEPARATOR_2 */ + +#ifndef PATH_SEPARATOR_2 +# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR) +#else /* PATH_SEPARATOR_2 */ +# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR_2) +#endif /* PATH_SEPARATOR_2 */ + +#ifdef __CYGWIN__ +# define FOPEN_WB "wb" +#endif + +#ifndef FOPEN_WB +# define FOPEN_WB "w" +#endif +#ifndef _O_BINARY +# define _O_BINARY 0 +#endif + +#define XMALLOC(type, num) ((type *) xmalloc ((num) * sizeof(type))) +#define XFREE(stale) do { \ + if (stale) { free ((void *) stale); stale = 0; } \ +} while (0) + +#undef LTWRAPPER_DEBUGPRINTF +#if defined DEBUGWRAPPER +# define LTWRAPPER_DEBUGPRINTF(args) ltwrapper_debugprintf args +static void +ltwrapper_debugprintf (const char *fmt, ...) +{ + va_list args; + va_start (args, fmt); + (void) vfprintf (stderr, fmt, args); + va_end (args); +} +#else +# define LTWRAPPER_DEBUGPRINTF(args) +#endif + +const char *program_name = NULL; + +void *xmalloc (size_t num); +char *xstrdup (const char *string); +const char *base_name (const char *name); +char *find_executable (const char *wrapper); +char *chase_symlinks (const char *pathspec); +int make_executable (const char *path); +int check_executable (const char *path); +char *strendzap (char *str, const char *pat); +void lt_fatal (const char *message, ...); +void lt_setenv (const char *name, const char *value); +char *lt_extend_str (const char *orig_value, const char *add, int to_end); +void lt_opt_process_env_set (const char *arg); +void lt_opt_process_env_prepend (const char *arg); +void lt_opt_process_env_append (const char *arg); +int lt_split_name_value (const char *arg, char** name, char** value); +void lt_update_exe_path (const char *name, const char *value); +void lt_update_lib_path (const char *name, const char *value); + +static const char *script_text_part1 = +EOF + + func_emit_wrapper_part1 yes | + $SED -e 's/\([\\"]\)/\\\1/g' \ + -e 's/^/ "/' -e 's/$/\\n"/' + echo ";" + cat <"))); + for (i = 0; i < newargc; i++) + { + LTWRAPPER_DEBUGPRINTF (("(main) newargz[%d] : %s\n", i, (newargz[i] ? newargz[i] : ""))); + } + +EOF + + case $host_os in + mingw*) + cat <<"EOF" + /* execv doesn't actually work on mingw as expected on unix */ + rval = _spawnv (_P_WAIT, lt_argv_zero, (const char * const *) newargz); + if (rval == -1) + { + /* failed to start process */ + LTWRAPPER_DEBUGPRINTF (("(main) failed to launch target \"%s\": errno = %d\n", lt_argv_zero, errno)); + return 127; + } + return rval; +EOF + ;; + *) + cat <<"EOF" + execv (lt_argv_zero, newargz); + return rval; /* =127, but avoids unused variable warning */ +EOF + ;; + esac + + cat <<"EOF" +} + +void * +xmalloc (size_t num) +{ + void *p = (void *) malloc (num); + if (!p) + lt_fatal ("Memory exhausted"); + + return p; +} + +char * +xstrdup (const char *string) +{ + return string ? strcpy ((char *) xmalloc (strlen (string) + 1), + string) : NULL; +} + +const char * +base_name (const char *name) +{ + const char *base; + +#if defined (HAVE_DOS_BASED_FILE_SYSTEM) + /* Skip over the disk name in MSDOS pathnames. */ + if (isalpha ((unsigned char) name[0]) && name[1] == ':') + name += 2; +#endif + + for (base = name; *name; name++) + if (IS_DIR_SEPARATOR (*name)) + base = name + 1; + return base; +} + +int +check_executable (const char *path) +{ + struct stat st; + + LTWRAPPER_DEBUGPRINTF (("(check_executable) : %s\n", + path ? (*path ? path : "EMPTY!") : "NULL!")); + if ((!path) || (!*path)) + return 0; + + if ((stat (path, &st) >= 0) + && (st.st_mode & (S_IXUSR | S_IXGRP | S_IXOTH))) + return 1; + else + return 0; +} + +int +make_executable (const char *path) +{ + int rval = 0; + struct stat st; + + LTWRAPPER_DEBUGPRINTF (("(make_executable) : %s\n", + path ? (*path ? path : "EMPTY!") : "NULL!")); + if ((!path) || (!*path)) + return 0; + + if (stat (path, &st) >= 0) + { + rval = chmod (path, st.st_mode | S_IXOTH | S_IXGRP | S_IXUSR); + } + return rval; +} + +/* Searches for the full path of the wrapper. Returns + newly allocated full path name if found, NULL otherwise + Does not chase symlinks, even on platforms that support them. +*/ +char * +find_executable (const char *wrapper) +{ + int has_slash = 0; + const char *p; + const char *p_next; + /* static buffer for getcwd */ + char tmp[LT_PATHMAX + 1]; + int tmp_len; + char *concat_name; + + LTWRAPPER_DEBUGPRINTF (("(find_executable) : %s\n", + wrapper ? (*wrapper ? wrapper : "EMPTY!") : "NULL!")); + + if ((wrapper == NULL) || (*wrapper == '\0')) + return NULL; + + /* Absolute path? */ +#if defined (HAVE_DOS_BASED_FILE_SYSTEM) + if (isalpha ((unsigned char) wrapper[0]) && wrapper[1] == ':') + { + concat_name = xstrdup (wrapper); + if (check_executable (concat_name)) + return concat_name; + XFREE (concat_name); + } + else + { +#endif + if (IS_DIR_SEPARATOR (wrapper[0])) + { + concat_name = xstrdup (wrapper); + if (check_executable (concat_name)) + return concat_name; + XFREE (concat_name); + } +#if defined (HAVE_DOS_BASED_FILE_SYSTEM) + } +#endif + + for (p = wrapper; *p; p++) + if (*p == '/') + { + has_slash = 1; + break; + } + if (!has_slash) + { + /* no slashes; search PATH */ + const char *path = getenv ("PATH"); + if (path != NULL) + { + for (p = path; *p; p = p_next) + { + const char *q; + size_t p_len; + for (q = p; *q; q++) + if (IS_PATH_SEPARATOR (*q)) + break; + p_len = q - p; + p_next = (*q == '\0' ? q : q + 1); + if (p_len == 0) + { + /* empty path: current directory */ + if (getcwd (tmp, LT_PATHMAX) == NULL) + lt_fatal ("getcwd failed"); + tmp_len = strlen (tmp); + concat_name = + XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); + memcpy (concat_name, tmp, tmp_len); + concat_name[tmp_len] = '/'; + strcpy (concat_name + tmp_len + 1, wrapper); + } + else + { + concat_name = + XMALLOC (char, p_len + 1 + strlen (wrapper) + 1); + memcpy (concat_name, p, p_len); + concat_name[p_len] = '/'; + strcpy (concat_name + p_len + 1, wrapper); + } + if (check_executable (concat_name)) + return concat_name; + XFREE (concat_name); + } + } + /* not found in PATH; assume curdir */ + } + /* Relative path | not found in path: prepend cwd */ + if (getcwd (tmp, LT_PATHMAX) == NULL) + lt_fatal ("getcwd failed"); + tmp_len = strlen (tmp); + concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); + memcpy (concat_name, tmp, tmp_len); + concat_name[tmp_len] = '/'; + strcpy (concat_name + tmp_len + 1, wrapper); + + if (check_executable (concat_name)) + return concat_name; + XFREE (concat_name); + return NULL; +} + +char * +chase_symlinks (const char *pathspec) +{ +#ifndef S_ISLNK + return xstrdup (pathspec); +#else + char buf[LT_PATHMAX]; + struct stat s; + char *tmp_pathspec = xstrdup (pathspec); + char *p; + int has_symlinks = 0; + while (strlen (tmp_pathspec) && !has_symlinks) + { + LTWRAPPER_DEBUGPRINTF (("checking path component for symlinks: %s\n", + tmp_pathspec)); + if (lstat (tmp_pathspec, &s) == 0) + { + if (S_ISLNK (s.st_mode) != 0) + { + has_symlinks = 1; + break; + } + + /* search backwards for last DIR_SEPARATOR */ + p = tmp_pathspec + strlen (tmp_pathspec) - 1; + while ((p > tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) + p--; + if ((p == tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) + { + /* no more DIR_SEPARATORS left */ + break; + } + *p = '\0'; + } + else + { + char *errstr = strerror (errno); + lt_fatal ("Error accessing file %s (%s)", tmp_pathspec, errstr); + } + } + XFREE (tmp_pathspec); + + if (!has_symlinks) + { + return xstrdup (pathspec); + } + + tmp_pathspec = realpath (pathspec, buf); + if (tmp_pathspec == 0) + { + lt_fatal ("Could not follow symlinks for %s", pathspec); + } + return xstrdup (tmp_pathspec); +#endif +} + +char * +strendzap (char *str, const char *pat) +{ + size_t len, patlen; + + assert (str != NULL); + assert (pat != NULL); + + len = strlen (str); + patlen = strlen (pat); + + if (patlen <= len) + { + str += len - patlen; + if (strcmp (str, pat) == 0) + *str = '\0'; + } + return str; +} + +static void +lt_error_core (int exit_status, const char *mode, + const char *message, va_list ap) +{ + fprintf (stderr, "%s: %s: ", program_name, mode); + vfprintf (stderr, message, ap); + fprintf (stderr, ".\n"); + + if (exit_status >= 0) + exit (exit_status); +} + +void +lt_fatal (const char *message, ...) +{ + va_list ap; + va_start (ap, message); + lt_error_core (EXIT_FAILURE, "FATAL", message, ap); + va_end (ap); +} + +void +lt_setenv (const char *name, const char *value) +{ + LTWRAPPER_DEBUGPRINTF (("(lt_setenv) setting '%s' to '%s'\n", + (name ? name : ""), + (value ? value : ""))); + { +#ifdef HAVE_SETENV + /* always make a copy, for consistency with !HAVE_SETENV */ + char *str = xstrdup (value); + setenv (name, str, 1); +#else + int len = strlen (name) + 1 + strlen (value) + 1; + char *str = XMALLOC (char, len); + sprintf (str, "%s=%s", name, value); + if (putenv (str) != EXIT_SUCCESS) + { + XFREE (str); + } +#endif + } +} + +char * +lt_extend_str (const char *orig_value, const char *add, int to_end) +{ + char *new_value; + if (orig_value && *orig_value) + { + int orig_value_len = strlen (orig_value); + int add_len = strlen (add); + new_value = XMALLOC (char, add_len + orig_value_len + 1); + if (to_end) + { + strcpy (new_value, orig_value); + strcpy (new_value + orig_value_len, add); + } + else + { + strcpy (new_value, add); + strcpy (new_value + add_len, orig_value); + } + } + else + { + new_value = xstrdup (add); + } + return new_value; +} + +int +lt_split_name_value (const char *arg, char** name, char** value) +{ + const char *p; + int len; + if (!arg || !*arg) + return 1; + + p = strchr (arg, (int)'='); + + if (!p) + return 1; + + *value = xstrdup (++p); + + len = strlen (arg) - strlen (*value); + *name = XMALLOC (char, len); + strncpy (*name, arg, len-1); + (*name)[len - 1] = '\0'; + + return 0; +} + +void +lt_opt_process_env_set (const char *arg) +{ + char *name = NULL; + char *value = NULL; + + if (lt_split_name_value (arg, &name, &value) != 0) + { + XFREE (name); + XFREE (value); + lt_fatal ("bad argument for %s: '%s'", env_set_opt, arg); + } + + lt_setenv (name, value); + XFREE (name); + XFREE (value); +} + +void +lt_opt_process_env_prepend (const char *arg) +{ + char *name = NULL; + char *value = NULL; + char *new_value = NULL; + + if (lt_split_name_value (arg, &name, &value) != 0) + { + XFREE (name); + XFREE (value); + lt_fatal ("bad argument for %s: '%s'", env_prepend_opt, arg); + } + + new_value = lt_extend_str (getenv (name), value, 0); + lt_setenv (name, new_value); + XFREE (new_value); + XFREE (name); + XFREE (value); +} + +void +lt_opt_process_env_append (const char *arg) +{ + char *name = NULL; + char *value = NULL; + char *new_value = NULL; + + if (lt_split_name_value (arg, &name, &value) != 0) + { + XFREE (name); + XFREE (value); + lt_fatal ("bad argument for %s: '%s'", env_append_opt, arg); + } + + new_value = lt_extend_str (getenv (name), value, 1); + lt_setenv (name, new_value); + XFREE (new_value); + XFREE (name); + XFREE (value); +} + +void +lt_update_exe_path (const char *name, const char *value) +{ + LTWRAPPER_DEBUGPRINTF (("(lt_update_exe_path) modifying '%s' by prepending '%s'\n", + (name ? name : ""), + (value ? value : ""))); + + if (name && *name && value && *value) + { + char *new_value = lt_extend_str (getenv (name), value, 0); + /* some systems can't cope with a ':'-terminated path #' */ + int len = strlen (new_value); + while (((len = strlen (new_value)) > 0) && IS_PATH_SEPARATOR (new_value[len-1])) + { + new_value[len-1] = '\0'; + } + lt_setenv (name, new_value); + XFREE (new_value); + } +} + +void +lt_update_lib_path (const char *name, const char *value) +{ + LTWRAPPER_DEBUGPRINTF (("(lt_update_lib_path) modifying '%s' by prepending '%s'\n", + (name ? name : ""), + (value ? value : ""))); + + if (name && *name && value && *value) + { + char *new_value = lt_extend_str (getenv (name), value, 0); + lt_setenv (name, new_value); + XFREE (new_value); + } +} + + +EOF +} +# end: func_emit_cwrapperexe_src + +# func_mode_link arg... +func_mode_link () +{ + $opt_debug + case $host in + *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) + # It is impossible to link a dll without this setting, and + # we shouldn't force the makefile maintainer to figure out + # which system we are compiling for in order to pass an extra + # flag for every libtool invocation. + # allow_undefined=no + + # FIXME: Unfortunately, there are problems with the above when trying + # to make a dll which has undefined symbols, in which case not + # even a static library is built. For now, we need to specify + # -no-undefined on the libtool link line when we can be certain + # that all symbols are satisfied, otherwise we get a static library. + allow_undefined=yes + ;; + *) + allow_undefined=yes + ;; + esac + libtool_args=$nonopt + base_compile="$nonopt $@" + compile_command=$nonopt + finalize_command=$nonopt + + compile_rpath= + finalize_rpath= + compile_shlibpath= + finalize_shlibpath= + convenience= + old_convenience= + deplibs= + old_deplibs= + compiler_flags= + linker_flags= + dllsearchpath= + lib_search_path=`pwd` + inst_prefix_dir= + new_inherited_linker_flags= + + avoid_version=no + dlfiles= + dlprefiles= + dlself=no + export_dynamic=no + export_symbols= + export_symbols_regex= + generated= + libobjs= + ltlibs= + module=no + no_install=no + objs= + non_pic_objects= + precious_files_regex= + prefer_static_libs=no + preload=no + prev= + prevarg= + release= + rpath= + xrpath= + perm_rpath= + temp_rpath= + thread_safe=no + vinfo= + vinfo_number=no + weak_libs= + single_module="${wl}-single_module" + func_infer_tag $base_compile + + # We need to know -static, to get the right output filenames. + for arg + do + case $arg in + -shared) + test "$build_libtool_libs" != yes && \ + func_fatal_configuration "can not build a shared library" + build_old_libs=no + break + ;; + -all-static | -static | -static-libtool-libs) + case $arg in + -all-static) + if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then + func_warning "complete static linking is impossible in this configuration" + fi + if test -n "$link_static_flag"; then + dlopen_self=$dlopen_self_static + fi + prefer_static_libs=yes + ;; + -static) + if test -z "$pic_flag" && test -n "$link_static_flag"; then + dlopen_self=$dlopen_self_static + fi + prefer_static_libs=built + ;; + -static-libtool-libs) + if test -z "$pic_flag" && test -n "$link_static_flag"; then + dlopen_self=$dlopen_self_static + fi + prefer_static_libs=yes + ;; + esac + build_libtool_libs=no + build_old_libs=yes + break + ;; + esac + done + + # See if our shared archives depend on static archives. + test -n "$old_archive_from_new_cmds" && build_old_libs=yes + + # Go through the arguments, transforming them on the way. + while test "$#" -gt 0; do + arg="$1" + shift + func_quote_for_eval "$arg" + qarg=$func_quote_for_eval_unquoted_result + func_append libtool_args " $func_quote_for_eval_result" + + # If the previous option needs an argument, assign it. + if test -n "$prev"; then + case $prev in + output) + func_append compile_command " @OUTPUT@" + func_append finalize_command " @OUTPUT@" + ;; + esac + + case $prev in + dlfiles|dlprefiles) + if test "$preload" = no; then + # Add the symbol object into the linking commands. + func_append compile_command " @SYMFILE@" + func_append finalize_command " @SYMFILE@" + preload=yes + fi + case $arg in + *.la | *.lo) ;; # We handle these cases below. + force) + if test "$dlself" = no; then + dlself=needless + export_dynamic=yes + fi + prev= + continue + ;; + self) + if test "$prev" = dlprefiles; then + dlself=yes + elif test "$prev" = dlfiles && test "$dlopen_self" != yes; then + dlself=yes + else + dlself=needless + export_dynamic=yes + fi + prev= + continue + ;; + *) + if test "$prev" = dlfiles; then + dlfiles="$dlfiles $arg" + else + dlprefiles="$dlprefiles $arg" + fi + prev= + continue + ;; + esac + ;; + expsyms) + export_symbols="$arg" + test -f "$arg" \ + || func_fatal_error "symbol file \`$arg' does not exist" + prev= + continue + ;; + expsyms_regex) + export_symbols_regex="$arg" + prev= + continue + ;; + framework) + case $host in + *-*-darwin*) + case "$deplibs " in + *" $qarg.ltframework "*) ;; + *) deplibs="$deplibs $qarg.ltframework" # this is fixed later + ;; + esac + ;; + esac + prev= + continue + ;; + inst_prefix) + inst_prefix_dir="$arg" + prev= + continue + ;; + objectlist) + if test -f "$arg"; then + save_arg=$arg + moreargs= + for fil in `cat "$save_arg"` + do +# moreargs="$moreargs $fil" + arg=$fil + # A libtool-controlled object. + + # Check to see that this really is a libtool object. + if func_lalib_unsafe_p "$arg"; then + pic_object= + non_pic_object= + + # Read the .lo file + func_source "$arg" + + if test -z "$pic_object" || + test -z "$non_pic_object" || + test "$pic_object" = none && + test "$non_pic_object" = none; then + func_fatal_error "cannot find name of object for \`$arg'" + fi + + # Extract subdirectory from the argument. + func_dirname "$arg" "/" "" + xdir="$func_dirname_result" + + if test "$pic_object" != none; then + # Prepend the subdirectory the object is found in. + pic_object="$xdir$pic_object" + + if test "$prev" = dlfiles; then + if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then + dlfiles="$dlfiles $pic_object" + prev= + continue + else + # If libtool objects are unsupported, then we need to preload. + prev=dlprefiles + fi + fi + + # CHECK ME: I think I busted this. -Ossama + if test "$prev" = dlprefiles; then + # Preload the old-style object. + dlprefiles="$dlprefiles $pic_object" + prev= + fi + + # A PIC object. + func_append libobjs " $pic_object" + arg="$pic_object" + fi + + # Non-PIC object. + if test "$non_pic_object" != none; then + # Prepend the subdirectory the object is found in. + non_pic_object="$xdir$non_pic_object" + + # A standard non-PIC object + func_append non_pic_objects " $non_pic_object" + if test -z "$pic_object" || test "$pic_object" = none ; then + arg="$non_pic_object" + fi + else + # If the PIC object exists, use it instead. + # $xdir was prepended to $pic_object above. + non_pic_object="$pic_object" + func_append non_pic_objects " $non_pic_object" + fi + else + # Only an error if not doing a dry-run. + if $opt_dry_run; then + # Extract subdirectory from the argument. + func_dirname "$arg" "/" "" + xdir="$func_dirname_result" + + func_lo2o "$arg" + pic_object=$xdir$objdir/$func_lo2o_result + non_pic_object=$xdir$func_lo2o_result + func_append libobjs " $pic_object" + func_append non_pic_objects " $non_pic_object" + else + func_fatal_error "\`$arg' is not a valid libtool object" + fi + fi + done + else + func_fatal_error "link input file \`$arg' does not exist" + fi + arg=$save_arg + prev= + continue + ;; + precious_regex) + precious_files_regex="$arg" + prev= + continue + ;; + release) + release="-$arg" + prev= + continue + ;; + rpath | xrpath) + # We need an absolute path. + case $arg in + [\\/]* | [A-Za-z]:[\\/]*) ;; + *) + func_fatal_error "only absolute run-paths are allowed" + ;; + esac + if test "$prev" = rpath; then + case "$rpath " in + *" $arg "*) ;; + *) rpath="$rpath $arg" ;; + esac + else + case "$xrpath " in + *" $arg "*) ;; + *) xrpath="$xrpath $arg" ;; + esac + fi + prev= + continue + ;; + shrext) + shrext_cmds="$arg" + prev= + continue + ;; + weak) + weak_libs="$weak_libs $arg" + prev= + continue + ;; + xcclinker) + linker_flags="$linker_flags $qarg" + compiler_flags="$compiler_flags $qarg" + prev= + func_append compile_command " $qarg" + func_append finalize_command " $qarg" + continue + ;; + xcompiler) + compiler_flags="$compiler_flags $qarg" + prev= + func_append compile_command " $qarg" + func_append finalize_command " $qarg" + continue + ;; + xlinker) + linker_flags="$linker_flags $qarg" + compiler_flags="$compiler_flags $wl$qarg" + prev= + func_append compile_command " $wl$qarg" + func_append finalize_command " $wl$qarg" + continue + ;; + *) + eval "$prev=\"\$arg\"" + prev= + continue + ;; + esac + fi # test -n "$prev" + + prevarg="$arg" + + case $arg in + -all-static) + if test -n "$link_static_flag"; then + # See comment for -static flag below, for more details. + func_append compile_command " $link_static_flag" + func_append finalize_command " $link_static_flag" + fi + continue + ;; + + -allow-undefined) + # FIXME: remove this flag sometime in the future. + func_fatal_error "\`-allow-undefined' must not be used because it is the default" + ;; + + -avoid-version) + avoid_version=yes + continue + ;; + + -dlopen) + prev=dlfiles + continue + ;; + + -dlpreopen) + prev=dlprefiles + continue + ;; + + -export-dynamic) + export_dynamic=yes + continue + ;; + + -export-symbols | -export-symbols-regex) + if test -n "$export_symbols" || test -n "$export_symbols_regex"; then + func_fatal_error "more than one -exported-symbols argument is not allowed" + fi + if test "X$arg" = "X-export-symbols"; then + prev=expsyms + else + prev=expsyms_regex + fi + continue + ;; + + -framework) + prev=framework + continue + ;; + + -inst-prefix-dir) + prev=inst_prefix + continue + ;; + + # The native IRIX linker understands -LANG:*, -LIST:* and -LNO:* + # so, if we see these flags be careful not to treat them like -L + -L[A-Z][A-Z]*:*) + case $with_gcc/$host in + no/*-*-irix* | /*-*-irix*) + func_append compile_command " $arg" + func_append finalize_command " $arg" + ;; + esac + continue + ;; + + -L*) + func_stripname '-L' '' "$arg" + dir=$func_stripname_result + if test -z "$dir"; then + if test "$#" -gt 0; then + func_fatal_error "require no space between \`-L' and \`$1'" + else + func_fatal_error "need path for \`-L' option" + fi + fi + # We need an absolute path. + case $dir in + [\\/]* | [A-Za-z]:[\\/]*) ;; + *) + absdir=`cd "$dir" && pwd` + test -z "$absdir" && \ + func_fatal_error "cannot determine absolute directory name of \`$dir'" + dir="$absdir" + ;; + esac + case "$deplibs " in + *" -L$dir "*) ;; + *) + deplibs="$deplibs -L$dir" + lib_search_path="$lib_search_path $dir" + ;; + esac + case $host in + *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) + testbindir=`$ECHO "X$dir" | $Xsed -e 's*/lib$*/bin*'` + case :$dllsearchpath: in + *":$dir:"*) ;; + ::) dllsearchpath=$dir;; + *) dllsearchpath="$dllsearchpath:$dir";; + esac + case :$dllsearchpath: in + *":$testbindir:"*) ;; + ::) dllsearchpath=$testbindir;; + *) dllsearchpath="$dllsearchpath:$testbindir";; + esac + ;; + esac + continue + ;; + + -l*) + if test "X$arg" = "X-lc" || test "X$arg" = "X-lm"; then + case $host in + *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos* | *-cegcc*) + # These systems don't actually have a C or math library (as such) + continue + ;; + *-*-os2*) + # These systems don't actually have a C library (as such) + test "X$arg" = "X-lc" && continue + ;; + *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) + # Do not include libc due to us having libc/libc_r. + test "X$arg" = "X-lc" && continue + ;; + *-*-rhapsody* | *-*-darwin1.[012]) + # Rhapsody C and math libraries are in the System framework + deplibs="$deplibs System.ltframework" + continue + ;; + *-*-sco3.2v5* | *-*-sco5v6*) + # Causes problems with __ctype + test "X$arg" = "X-lc" && continue + ;; + *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*) + # Compiler inserts libc in the correct place for threads to work + test "X$arg" = "X-lc" && continue + ;; + esac + elif test "X$arg" = "X-lc_r"; then + case $host in + *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) + # Do not include libc_r directly, use -pthread flag. + continue + ;; + esac + fi + deplibs="$deplibs $arg" + continue + ;; + + -module) + module=yes + continue + ;; + + # Tru64 UNIX uses -model [arg] to determine the layout of C++ + # classes, name mangling, and exception handling. + # Darwin uses the -arch flag to determine output architecture. + -model|-arch|-isysroot) + compiler_flags="$compiler_flags $arg" + func_append compile_command " $arg" + func_append finalize_command " $arg" + prev=xcompiler + continue + ;; + + -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads) + compiler_flags="$compiler_flags $arg" + func_append compile_command " $arg" + func_append finalize_command " $arg" + case "$new_inherited_linker_flags " in + *" $arg "*) ;; + * ) new_inherited_linker_flags="$new_inherited_linker_flags $arg" ;; + esac + continue + ;; + + -multi_module) + single_module="${wl}-multi_module" + continue + ;; + + -no-fast-install) + fast_install=no + continue + ;; + + -no-install) + case $host in + *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-darwin* | *-cegcc*) + # The PATH hackery in wrapper scripts is required on Windows + # and Darwin in order for the loader to find any dlls it needs. + func_warning "\`-no-install' is ignored for $host" + func_warning "assuming \`-no-fast-install' instead" + fast_install=no + ;; + *) no_install=yes ;; + esac + continue + ;; + + -no-undefined) + allow_undefined=no + continue + ;; + + -objectlist) + prev=objectlist + continue + ;; + + -o) prev=output ;; + + -precious-files-regex) + prev=precious_regex + continue + ;; + + -release) + prev=release + continue + ;; + + -rpath) + prev=rpath + continue + ;; + + -R) + prev=xrpath + continue + ;; + + -R*) + func_stripname '-R' '' "$arg" + dir=$func_stripname_result + # We need an absolute path. + case $dir in + [\\/]* | [A-Za-z]:[\\/]*) ;; + *) + func_fatal_error "only absolute run-paths are allowed" + ;; + esac + case "$xrpath " in + *" $dir "*) ;; + *) xrpath="$xrpath $dir" ;; + esac + continue + ;; + + -shared) + # The effects of -shared are defined in a previous loop. + continue + ;; + + -shrext) + prev=shrext + continue + ;; + + -static | -static-libtool-libs) + # The effects of -static are defined in a previous loop. + # We used to do the same as -all-static on platforms that + # didn't have a PIC flag, but the assumption that the effects + # would be equivalent was wrong. It would break on at least + # Digital Unix and AIX. + continue + ;; + + -thread-safe) + thread_safe=yes + continue + ;; + + -version-info) + prev=vinfo + continue + ;; + + -version-number) + prev=vinfo + vinfo_number=yes + continue + ;; + + -weak) + prev=weak + continue + ;; + + -Wc,*) + func_stripname '-Wc,' '' "$arg" + args=$func_stripname_result + arg= + save_ifs="$IFS"; IFS=',' + for flag in $args; do + IFS="$save_ifs" + func_quote_for_eval "$flag" + arg="$arg $wl$func_quote_for_eval_result" + compiler_flags="$compiler_flags $func_quote_for_eval_result" + done + IFS="$save_ifs" + func_stripname ' ' '' "$arg" + arg=$func_stripname_result + ;; + + -Wl,*) + func_stripname '-Wl,' '' "$arg" + args=$func_stripname_result + arg= + save_ifs="$IFS"; IFS=',' + for flag in $args; do + IFS="$save_ifs" + func_quote_for_eval "$flag" + arg="$arg $wl$func_quote_for_eval_result" + compiler_flags="$compiler_flags $wl$func_quote_for_eval_result" + linker_flags="$linker_flags $func_quote_for_eval_result" + done + IFS="$save_ifs" + func_stripname ' ' '' "$arg" + arg=$func_stripname_result + ;; + + -Xcompiler) + prev=xcompiler + continue + ;; + + -Xlinker) + prev=xlinker + continue + ;; + + -XCClinker) + prev=xcclinker + continue + ;; + + # -msg_* for osf cc + -msg_*) + func_quote_for_eval "$arg" + arg="$func_quote_for_eval_result" + ;; + + # -64, -mips[0-9] enable 64-bit mode on the SGI compiler + # -r[0-9][0-9]* specifies the processor on the SGI compiler + # -xarch=*, -xtarget=* enable 64-bit mode on the Sun compiler + # +DA*, +DD* enable 64-bit mode on the HP compiler + # -q* pass through compiler args for the IBM compiler + # -m*, -t[45]*, -txscale* pass through architecture-specific + # compiler args for GCC + # -F/path gives path to uninstalled frameworks, gcc on darwin + # -p, -pg, --coverage, -fprofile-* pass through profiling flag for GCC + # @file GCC response files + -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \ + -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*) + func_quote_for_eval "$arg" + arg="$func_quote_for_eval_result" + func_append compile_command " $arg" + func_append finalize_command " $arg" + compiler_flags="$compiler_flags $arg" + continue + ;; + + # Some other compiler flag. + -* | +*) + func_quote_for_eval "$arg" + arg="$func_quote_for_eval_result" + ;; + + *.$objext) + # A standard object. + objs="$objs $arg" + ;; + + *.lo) + # A libtool-controlled object. + + # Check to see that this really is a libtool object. + if func_lalib_unsafe_p "$arg"; then + pic_object= + non_pic_object= + + # Read the .lo file + func_source "$arg" + + if test -z "$pic_object" || + test -z "$non_pic_object" || + test "$pic_object" = none && + test "$non_pic_object" = none; then + func_fatal_error "cannot find name of object for \`$arg'" + fi + + # Extract subdirectory from the argument. + func_dirname "$arg" "/" "" + xdir="$func_dirname_result" + + if test "$pic_object" != none; then + # Prepend the subdirectory the object is found in. + pic_object="$xdir$pic_object" + + if test "$prev" = dlfiles; then + if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then + dlfiles="$dlfiles $pic_object" + prev= + continue + else + # If libtool objects are unsupported, then we need to preload. + prev=dlprefiles + fi + fi + + # CHECK ME: I think I busted this. -Ossama + if test "$prev" = dlprefiles; then + # Preload the old-style object. + dlprefiles="$dlprefiles $pic_object" + prev= + fi + + # A PIC object. + func_append libobjs " $pic_object" + arg="$pic_object" + fi + + # Non-PIC object. + if test "$non_pic_object" != none; then + # Prepend the subdirectory the object is found in. + non_pic_object="$xdir$non_pic_object" + + # A standard non-PIC object + func_append non_pic_objects " $non_pic_object" + if test -z "$pic_object" || test "$pic_object" = none ; then + arg="$non_pic_object" + fi + else + # If the PIC object exists, use it instead. + # $xdir was prepended to $pic_object above. + non_pic_object="$pic_object" + func_append non_pic_objects " $non_pic_object" + fi + else + # Only an error if not doing a dry-run. + if $opt_dry_run; then + # Extract subdirectory from the argument. + func_dirname "$arg" "/" "" + xdir="$func_dirname_result" + + func_lo2o "$arg" + pic_object=$xdir$objdir/$func_lo2o_result + non_pic_object=$xdir$func_lo2o_result + func_append libobjs " $pic_object" + func_append non_pic_objects " $non_pic_object" + else + func_fatal_error "\`$arg' is not a valid libtool object" + fi + fi + ;; + + *.$libext) + # An archive. + deplibs="$deplibs $arg" + old_deplibs="$old_deplibs $arg" + continue + ;; + + *.la) + # A libtool-controlled library. + + if test "$prev" = dlfiles; then + # This library was specified with -dlopen. + dlfiles="$dlfiles $arg" + prev= + elif test "$prev" = dlprefiles; then + # The library was specified with -dlpreopen. + dlprefiles="$dlprefiles $arg" + prev= + else + deplibs="$deplibs $arg" + fi + continue + ;; + + # Some other compiler argument. + *) + # Unknown arguments in both finalize_command and compile_command need + # to be aesthetically quoted because they are evaled later. + func_quote_for_eval "$arg" + arg="$func_quote_for_eval_result" + ;; + esac # arg + + # Now actually substitute the argument into the commands. + if test -n "$arg"; then + func_append compile_command " $arg" + func_append finalize_command " $arg" + fi + done # argument parsing loop + + test -n "$prev" && \ + func_fatal_help "the \`$prevarg' option requires an argument" + + if test "$export_dynamic" = yes && test -n "$export_dynamic_flag_spec"; then + eval arg=\"$export_dynamic_flag_spec\" + func_append compile_command " $arg" + func_append finalize_command " $arg" + fi + + oldlibs= + # calculate the name of the file, without its directory + func_basename "$output" + outputname="$func_basename_result" + libobjs_save="$libobjs" + + if test -n "$shlibpath_var"; then + # get the directories listed in $shlibpath_var + eval shlib_search_path=\`\$ECHO \"X\${$shlibpath_var}\" \| \$Xsed -e \'s/:/ /g\'\` + else + shlib_search_path= + fi + eval sys_lib_search_path=\"$sys_lib_search_path_spec\" + eval sys_lib_dlsearch_path=\"$sys_lib_dlsearch_path_spec\" + + func_dirname "$output" "/" "" + output_objdir="$func_dirname_result$objdir" + # Create the object directory. + func_mkdir_p "$output_objdir" + + # Determine the type of output + case $output in + "") + func_fatal_help "you must specify an output file" + ;; + *.$libext) linkmode=oldlib ;; + *.lo | *.$objext) linkmode=obj ;; + *.la) linkmode=lib ;; + *) linkmode=prog ;; # Anything else should be a program. + esac + + specialdeplibs= + + libs= + # Find all interdependent deplibs by searching for libraries + # that are linked more than once (e.g. -la -lb -la) + for deplib in $deplibs; do + if $opt_duplicate_deps ; then + case "$libs " in + *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; + esac + fi + libs="$libs $deplib" + done + + if test "$linkmode" = lib; then + libs="$predeps $libs $compiler_lib_search_path $postdeps" + + # Compute libraries that are listed more than once in $predeps + # $postdeps and mark them as special (i.e., whose duplicates are + # not to be eliminated). + pre_post_deps= + if $opt_duplicate_compiler_generated_deps; then + for pre_post_dep in $predeps $postdeps; do + case "$pre_post_deps " in + *" $pre_post_dep "*) specialdeplibs="$specialdeplibs $pre_post_deps" ;; + esac + pre_post_deps="$pre_post_deps $pre_post_dep" + done + fi + pre_post_deps= + fi + + deplibs= + newdependency_libs= + newlib_search_path= + need_relink=no # whether we're linking any uninstalled libtool libraries + notinst_deplibs= # not-installed libtool libraries + notinst_path= # paths that contain not-installed libtool libraries + + case $linkmode in + lib) + passes="conv dlpreopen link" + for file in $dlfiles $dlprefiles; do + case $file in + *.la) ;; + *) + func_fatal_help "libraries can \`-dlopen' only libtool libraries: $file" + ;; + esac + done + ;; + prog) + compile_deplibs= + finalize_deplibs= + alldeplibs=no + newdlfiles= + newdlprefiles= + passes="conv scan dlopen dlpreopen link" + ;; + *) passes="conv" + ;; + esac + + for pass in $passes; do + # The preopen pass in lib mode reverses $deplibs; put it back here + # so that -L comes before libs that need it for instance... + if test "$linkmode,$pass" = "lib,link"; then + ## FIXME: Find the place where the list is rebuilt in the wrong + ## order, and fix it there properly + tmp_deplibs= + for deplib in $deplibs; do + tmp_deplibs="$deplib $tmp_deplibs" + done + deplibs="$tmp_deplibs" + fi + + if test "$linkmode,$pass" = "lib,link" || + test "$linkmode,$pass" = "prog,scan"; then + libs="$deplibs" + deplibs= + fi + if test "$linkmode" = prog; then + case $pass in + dlopen) libs="$dlfiles" ;; + dlpreopen) libs="$dlprefiles" ;; + link) + libs="$deplibs %DEPLIBS%" + test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs" + ;; + esac + fi + if test "$linkmode,$pass" = "lib,dlpreopen"; then + # Collect and forward deplibs of preopened libtool libs + for lib in $dlprefiles; do + # Ignore non-libtool-libs + dependency_libs= + case $lib in + *.la) func_source "$lib" ;; + esac + + # Collect preopened libtool deplibs, except any this library + # has declared as weak libs + for deplib in $dependency_libs; do + deplib_base=`$ECHO "X$deplib" | $Xsed -e "$basename"` + case " $weak_libs " in + *" $deplib_base "*) ;; + *) deplibs="$deplibs $deplib" ;; + esac + done + done + libs="$dlprefiles" + fi + if test "$pass" = dlopen; then + # Collect dlpreopened libraries + save_deplibs="$deplibs" + deplibs= + fi + + for deplib in $libs; do + lib= + found=no + case $deplib in + -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads) + if test "$linkmode,$pass" = "prog,link"; then + compile_deplibs="$deplib $compile_deplibs" + finalize_deplibs="$deplib $finalize_deplibs" + else + compiler_flags="$compiler_flags $deplib" + if test "$linkmode" = lib ; then + case "$new_inherited_linker_flags " in + *" $deplib "*) ;; + * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;; + esac + fi + fi + continue + ;; + -l*) + if test "$linkmode" != lib && test "$linkmode" != prog; then + func_warning "\`-l' is ignored for archives/objects" + continue + fi + func_stripname '-l' '' "$deplib" + name=$func_stripname_result + if test "$linkmode" = lib; then + searchdirs="$newlib_search_path $lib_search_path $compiler_lib_search_dirs $sys_lib_search_path $shlib_search_path" + else + searchdirs="$newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path" + fi + for searchdir in $searchdirs; do + for search_ext in .la $std_shrext .so .a; do + # Search the libtool library + lib="$searchdir/lib${name}${search_ext}" + if test -f "$lib"; then + if test "$search_ext" = ".la"; then + found=yes + else + found=no + fi + break 2 + fi + done + done + if test "$found" != yes; then + # deplib doesn't seem to be a libtool library + if test "$linkmode,$pass" = "prog,link"; then + compile_deplibs="$deplib $compile_deplibs" + finalize_deplibs="$deplib $finalize_deplibs" + else + deplibs="$deplib $deplibs" + test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" + fi + continue + else # deplib is a libtool library + # If $allow_libtool_libs_with_static_runtimes && $deplib is a stdlib, + # We need to do some special things here, and not later. + if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then + case " $predeps $postdeps " in + *" $deplib "*) + if func_lalib_p "$lib"; then + library_names= + old_library= + func_source "$lib" + for l in $old_library $library_names; do + ll="$l" + done + if test "X$ll" = "X$old_library" ; then # only static version available + found=no + func_dirname "$lib" "" "." + ladir="$func_dirname_result" + lib=$ladir/$old_library + if test "$linkmode,$pass" = "prog,link"; then + compile_deplibs="$deplib $compile_deplibs" + finalize_deplibs="$deplib $finalize_deplibs" + else + deplibs="$deplib $deplibs" + test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" + fi + continue + fi + fi + ;; + *) ;; + esac + fi + fi + ;; # -l + *.ltframework) + if test "$linkmode,$pass" = "prog,link"; then + compile_deplibs="$deplib $compile_deplibs" + finalize_deplibs="$deplib $finalize_deplibs" + else + deplibs="$deplib $deplibs" + if test "$linkmode" = lib ; then + case "$new_inherited_linker_flags " in + *" $deplib "*) ;; + * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;; + esac + fi + fi + continue + ;; + -L*) + case $linkmode in + lib) + deplibs="$deplib $deplibs" + test "$pass" = conv && continue + newdependency_libs="$deplib $newdependency_libs" + func_stripname '-L' '' "$deplib" + newlib_search_path="$newlib_search_path $func_stripname_result" + ;; + prog) + if test "$pass" = conv; then + deplibs="$deplib $deplibs" + continue + fi + if test "$pass" = scan; then + deplibs="$deplib $deplibs" + else + compile_deplibs="$deplib $compile_deplibs" + finalize_deplibs="$deplib $finalize_deplibs" + fi + func_stripname '-L' '' "$deplib" + newlib_search_path="$newlib_search_path $func_stripname_result" + ;; + *) + func_warning "\`-L' is ignored for archives/objects" + ;; + esac # linkmode + continue + ;; # -L + -R*) + if test "$pass" = link; then + func_stripname '-R' '' "$deplib" + dir=$func_stripname_result + # Make sure the xrpath contains only unique directories. + case "$xrpath " in + *" $dir "*) ;; + *) xrpath="$xrpath $dir" ;; + esac + fi + deplibs="$deplib $deplibs" + continue + ;; + *.la) lib="$deplib" ;; + *.$libext) + if test "$pass" = conv; then + deplibs="$deplib $deplibs" + continue + fi + case $linkmode in + lib) + # Linking convenience modules into shared libraries is allowed, + # but linking other static libraries is non-portable. + case " $dlpreconveniencelibs " in + *" $deplib "*) ;; + *) + valid_a_lib=no + case $deplibs_check_method in + match_pattern*) + set dummy $deplibs_check_method; shift + match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` + if eval "\$ECHO \"X$deplib\"" 2>/dev/null | $Xsed -e 10q \ + | $EGREP "$match_pattern_regex" > /dev/null; then + valid_a_lib=yes + fi + ;; + pass_all) + valid_a_lib=yes + ;; + esac + if test "$valid_a_lib" != yes; then + $ECHO + $ECHO "*** Warning: Trying to link with static lib archive $deplib." + $ECHO "*** I have the capability to make that library automatically link in when" + $ECHO "*** you link to this library. But I can only do this if you have a" + $ECHO "*** shared version of the library, which you do not appear to have" + $ECHO "*** because the file extensions .$libext of this argument makes me believe" + $ECHO "*** that it is just a static archive that I should not use here." + else + $ECHO + $ECHO "*** Warning: Linking the shared library $output against the" + $ECHO "*** static library $deplib is not portable!" + deplibs="$deplib $deplibs" + fi + ;; + esac + continue + ;; + prog) + if test "$pass" != link; then + deplibs="$deplib $deplibs" + else + compile_deplibs="$deplib $compile_deplibs" + finalize_deplibs="$deplib $finalize_deplibs" + fi + continue + ;; + esac # linkmode + ;; # *.$libext + *.lo | *.$objext) + if test "$pass" = conv; then + deplibs="$deplib $deplibs" + elif test "$linkmode" = prog; then + if test "$pass" = dlpreopen || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then + # If there is no dlopen support or we're linking statically, + # we need to preload. + newdlprefiles="$newdlprefiles $deplib" + compile_deplibs="$deplib $compile_deplibs" + finalize_deplibs="$deplib $finalize_deplibs" + else + newdlfiles="$newdlfiles $deplib" + fi + fi + continue + ;; + %DEPLIBS%) + alldeplibs=yes + continue + ;; + esac # case $deplib + + if test "$found" = yes || test -f "$lib"; then : + else + func_fatal_error "cannot find the library \`$lib' or unhandled argument \`$deplib'" + fi + + # Check to see that this really is a libtool archive. + func_lalib_unsafe_p "$lib" \ + || func_fatal_error "\`$lib' is not a valid libtool archive" + + func_dirname "$lib" "" "." + ladir="$func_dirname_result" + + dlname= + dlopen= + dlpreopen= + libdir= + library_names= + old_library= + inherited_linker_flags= + # If the library was installed with an old release of libtool, + # it will not redefine variables installed, or shouldnotlink + installed=yes + shouldnotlink=no + avoidtemprpath= + + + # Read the .la file + func_source "$lib" + + # Convert "-framework foo" to "foo.ltframework" + if test -n "$inherited_linker_flags"; then + tmp_inherited_linker_flags=`$ECHO "X$inherited_linker_flags" | $Xsed -e 's/-framework \([^ $]*\)/\1.ltframework/g'` + for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do + case " $new_inherited_linker_flags " in + *" $tmp_inherited_linker_flag "*) ;; + *) new_inherited_linker_flags="$new_inherited_linker_flags $tmp_inherited_linker_flag";; + esac + done + fi + dependency_libs=`$ECHO "X $dependency_libs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` + if test "$linkmode,$pass" = "lib,link" || + test "$linkmode,$pass" = "prog,scan" || + { test "$linkmode" != prog && test "$linkmode" != lib; }; then + test -n "$dlopen" && dlfiles="$dlfiles $dlopen" + test -n "$dlpreopen" && dlprefiles="$dlprefiles $dlpreopen" + fi + + if test "$pass" = conv; then + # Only check for convenience libraries + deplibs="$lib $deplibs" + if test -z "$libdir"; then + if test -z "$old_library"; then + func_fatal_error "cannot find name of link library for \`$lib'" + fi + # It is a libtool convenience library, so add in its objects. + convenience="$convenience $ladir/$objdir/$old_library" + old_convenience="$old_convenience $ladir/$objdir/$old_library" + elif test "$linkmode" != prog && test "$linkmode" != lib; then + func_fatal_error "\`$lib' is not a convenience library" + fi + tmp_libs= + for deplib in $dependency_libs; do + deplibs="$deplib $deplibs" + if $opt_duplicate_deps ; then + case "$tmp_libs " in + *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; + esac + fi + tmp_libs="$tmp_libs $deplib" + done + continue + fi # $pass = conv + + + # Get the name of the library we link against. + linklib= + for l in $old_library $library_names; do + linklib="$l" + done + if test -z "$linklib"; then + func_fatal_error "cannot find name of link library for \`$lib'" + fi + + # This library was specified with -dlopen. + if test "$pass" = dlopen; then + if test -z "$libdir"; then + func_fatal_error "cannot -dlopen a convenience library: \`$lib'" + fi + if test -z "$dlname" || + test "$dlopen_support" != yes || + test "$build_libtool_libs" = no; then + # If there is no dlname, no dlopen support or we're linking + # statically, we need to preload. We also need to preload any + # dependent libraries so libltdl's deplib preloader doesn't + # bomb out in the load deplibs phase. + dlprefiles="$dlprefiles $lib $dependency_libs" + else + newdlfiles="$newdlfiles $lib" + fi + continue + fi # $pass = dlopen + + # We need an absolute path. + case $ladir in + [\\/]* | [A-Za-z]:[\\/]*) abs_ladir="$ladir" ;; + *) + abs_ladir=`cd "$ladir" && pwd` + if test -z "$abs_ladir"; then + func_warning "cannot determine absolute directory name of \`$ladir'" + func_warning "passing it literally to the linker, although it might fail" + abs_ladir="$ladir" + fi + ;; + esac + func_basename "$lib" + laname="$func_basename_result" + + # Find the relevant object directory and library name. + if test "X$installed" = Xyes; then + if test ! -f "$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then + func_warning "library \`$lib' was moved." + dir="$ladir" + absdir="$abs_ladir" + libdir="$abs_ladir" + else + dir="$libdir" + absdir="$libdir" + fi + test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes + else + if test ! -f "$ladir/$objdir/$linklib" && test -f "$abs_ladir/$linklib"; then + dir="$ladir" + absdir="$abs_ladir" + # Remove this search path later + notinst_path="$notinst_path $abs_ladir" + else + dir="$ladir/$objdir" + absdir="$abs_ladir/$objdir" + # Remove this search path later + notinst_path="$notinst_path $abs_ladir" + fi + fi # $installed = yes + func_stripname 'lib' '.la' "$laname" + name=$func_stripname_result + + # This library was specified with -dlpreopen. + if test "$pass" = dlpreopen; then + if test -z "$libdir" && test "$linkmode" = prog; then + func_fatal_error "only libraries may -dlpreopen a convenience library: \`$lib'" + fi + # Prefer using a static library (so that no silly _DYNAMIC symbols + # are required to link). + if test -n "$old_library"; then + newdlprefiles="$newdlprefiles $dir/$old_library" + # Keep a list of preopened convenience libraries to check + # that they are being used correctly in the link pass. + test -z "$libdir" && \ + dlpreconveniencelibs="$dlpreconveniencelibs $dir/$old_library" + # Otherwise, use the dlname, so that lt_dlopen finds it. + elif test -n "$dlname"; then + newdlprefiles="$newdlprefiles $dir/$dlname" + else + newdlprefiles="$newdlprefiles $dir/$linklib" + fi + fi # $pass = dlpreopen + + if test -z "$libdir"; then + # Link the convenience library + if test "$linkmode" = lib; then + deplibs="$dir/$old_library $deplibs" + elif test "$linkmode,$pass" = "prog,link"; then + compile_deplibs="$dir/$old_library $compile_deplibs" + finalize_deplibs="$dir/$old_library $finalize_deplibs" + else + deplibs="$lib $deplibs" # used for prog,scan pass + fi + continue + fi + + + if test "$linkmode" = prog && test "$pass" != link; then + newlib_search_path="$newlib_search_path $ladir" + deplibs="$lib $deplibs" + + linkalldeplibs=no + if test "$link_all_deplibs" != no || test -z "$library_names" || + test "$build_libtool_libs" = no; then + linkalldeplibs=yes + fi + + tmp_libs= + for deplib in $dependency_libs; do + case $deplib in + -L*) func_stripname '-L' '' "$deplib" + newlib_search_path="$newlib_search_path $func_stripname_result" + ;; + esac + # Need to link against all dependency_libs? + if test "$linkalldeplibs" = yes; then + deplibs="$deplib $deplibs" + else + # Need to hardcode shared library paths + # or/and link against static libraries + newdependency_libs="$deplib $newdependency_libs" + fi + if $opt_duplicate_deps ; then + case "$tmp_libs " in + *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; + esac + fi + tmp_libs="$tmp_libs $deplib" + done # for deplib + continue + fi # $linkmode = prog... + + if test "$linkmode,$pass" = "prog,link"; then + if test -n "$library_names" && + { { test "$prefer_static_libs" = no || + test "$prefer_static_libs,$installed" = "built,yes"; } || + test -z "$old_library"; }; then + # We need to hardcode the library path + if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then + # Make sure the rpath contains only unique directories. + case "$temp_rpath:" in + *"$absdir:"*) ;; + *) temp_rpath="$temp_rpath$absdir:" ;; + esac + fi + + # Hardcode the library path. + # Skip directories that are in the system default run-time + # search path. + case " $sys_lib_dlsearch_path " in + *" $absdir "*) ;; + *) + case "$compile_rpath " in + *" $absdir "*) ;; + *) compile_rpath="$compile_rpath $absdir" + esac + ;; + esac + case " $sys_lib_dlsearch_path " in + *" $libdir "*) ;; + *) + case "$finalize_rpath " in + *" $libdir "*) ;; + *) finalize_rpath="$finalize_rpath $libdir" + esac + ;; + esac + fi # $linkmode,$pass = prog,link... + + if test "$alldeplibs" = yes && + { test "$deplibs_check_method" = pass_all || + { test "$build_libtool_libs" = yes && + test -n "$library_names"; }; }; then + # We only need to search for static libraries + continue + fi + fi + + link_static=no # Whether the deplib will be linked statically + use_static_libs=$prefer_static_libs + if test "$use_static_libs" = built && test "$installed" = yes; then + use_static_libs=no + fi + if test -n "$library_names" && + { test "$use_static_libs" = no || test -z "$old_library"; }; then + case $host in + *cygwin* | *mingw* | *cegcc*) + # No point in relinking DLLs because paths are not encoded + notinst_deplibs="$notinst_deplibs $lib" + need_relink=no + ;; + *) + if test "$installed" = no; then + notinst_deplibs="$notinst_deplibs $lib" + need_relink=yes + fi + ;; + esac + # This is a shared library + + # Warn about portability, can't link against -module's on some + # systems (darwin). Don't bleat about dlopened modules though! + dlopenmodule="" + for dlpremoduletest in $dlprefiles; do + if test "X$dlpremoduletest" = "X$lib"; then + dlopenmodule="$dlpremoduletest" + break + fi + done + if test -z "$dlopenmodule" && test "$shouldnotlink" = yes && test "$pass" = link; then + $ECHO + if test "$linkmode" = prog; then + $ECHO "*** Warning: Linking the executable $output against the loadable module" + else + $ECHO "*** Warning: Linking the shared library $output against the loadable module" + fi + $ECHO "*** $linklib is not portable!" + fi + if test "$linkmode" = lib && + test "$hardcode_into_libs" = yes; then + # Hardcode the library path. + # Skip directories that are in the system default run-time + # search path. + case " $sys_lib_dlsearch_path " in + *" $absdir "*) ;; + *) + case "$compile_rpath " in + *" $absdir "*) ;; + *) compile_rpath="$compile_rpath $absdir" + esac + ;; + esac + case " $sys_lib_dlsearch_path " in + *" $libdir "*) ;; + *) + case "$finalize_rpath " in + *" $libdir "*) ;; + *) finalize_rpath="$finalize_rpath $libdir" + esac + ;; + esac + fi + + if test -n "$old_archive_from_expsyms_cmds"; then + # figure out the soname + set dummy $library_names + shift + realname="$1" + shift + libname=`eval "\\$ECHO \"$libname_spec\""` + # use dlname if we got it. it's perfectly good, no? + if test -n "$dlname"; then + soname="$dlname" + elif test -n "$soname_spec"; then + # bleh windows + case $host in + *cygwin* | mingw* | *cegcc*) + func_arith $current - $age + major=$func_arith_result + versuffix="-$major" + ;; + esac + eval soname=\"$soname_spec\" + else + soname="$realname" + fi + + # Make a new name for the extract_expsyms_cmds to use + soroot="$soname" + func_basename "$soroot" + soname="$func_basename_result" + func_stripname 'lib' '.dll' "$soname" + newlib=libimp-$func_stripname_result.a + + # If the library has no export list, then create one now + if test -f "$output_objdir/$soname-def"; then : + else + func_verbose "extracting exported symbol list from \`$soname'" + func_execute_cmds "$extract_expsyms_cmds" 'exit $?' + fi + + # Create $newlib + if test -f "$output_objdir/$newlib"; then :; else + func_verbose "generating import library for \`$soname'" + func_execute_cmds "$old_archive_from_expsyms_cmds" 'exit $?' + fi + # make sure the library variables are pointing to the new library + dir=$output_objdir + linklib=$newlib + fi # test -n "$old_archive_from_expsyms_cmds" + + if test "$linkmode" = prog || test "$mode" != relink; then + add_shlibpath= + add_dir= + add= + lib_linked=yes + case $hardcode_action in + immediate | unsupported) + if test "$hardcode_direct" = no; then + add="$dir/$linklib" + case $host in + *-*-sco3.2v5.0.[024]*) add_dir="-L$dir" ;; + *-*-sysv4*uw2*) add_dir="-L$dir" ;; + *-*-sysv5OpenUNIX* | *-*-sysv5UnixWare7.[01].[10]* | \ + *-*-unixware7*) add_dir="-L$dir" ;; + *-*-darwin* ) + # if the lib is a (non-dlopened) module then we can not + # link against it, someone is ignoring the earlier warnings + if /usr/bin/file -L $add 2> /dev/null | + $GREP ": [^:]* bundle" >/dev/null ; then + if test "X$dlopenmodule" != "X$lib"; then + $ECHO "*** Warning: lib $linklib is a module, not a shared library" + if test -z "$old_library" ; then + $ECHO + $ECHO "*** And there doesn't seem to be a static archive available" + $ECHO "*** The link will probably fail, sorry" + else + add="$dir/$old_library" + fi + elif test -n "$old_library"; then + add="$dir/$old_library" + fi + fi + esac + elif test "$hardcode_minus_L" = no; then + case $host in + *-*-sunos*) add_shlibpath="$dir" ;; + esac + add_dir="-L$dir" + add="-l$name" + elif test "$hardcode_shlibpath_var" = no; then + add_shlibpath="$dir" + add="-l$name" + else + lib_linked=no + fi + ;; + relink) + if test "$hardcode_direct" = yes && + test "$hardcode_direct_absolute" = no; then + add="$dir/$linklib" + elif test "$hardcode_minus_L" = yes; then + add_dir="-L$dir" + # Try looking first in the location we're being installed to. + if test -n "$inst_prefix_dir"; then + case $libdir in + [\\/]*) + add_dir="$add_dir -L$inst_prefix_dir$libdir" + ;; + esac + fi + add="-l$name" + elif test "$hardcode_shlibpath_var" = yes; then + add_shlibpath="$dir" + add="-l$name" + else + lib_linked=no + fi + ;; + *) lib_linked=no ;; + esac + + if test "$lib_linked" != yes; then + func_fatal_configuration "unsupported hardcode properties" + fi + + if test -n "$add_shlibpath"; then + case :$compile_shlibpath: in + *":$add_shlibpath:"*) ;; + *) compile_shlibpath="$compile_shlibpath$add_shlibpath:" ;; + esac + fi + if test "$linkmode" = prog; then + test -n "$add_dir" && compile_deplibs="$add_dir $compile_deplibs" + test -n "$add" && compile_deplibs="$add $compile_deplibs" + else + test -n "$add_dir" && deplibs="$add_dir $deplibs" + test -n "$add" && deplibs="$add $deplibs" + if test "$hardcode_direct" != yes && + test "$hardcode_minus_L" != yes && + test "$hardcode_shlibpath_var" = yes; then + case :$finalize_shlibpath: in + *":$libdir:"*) ;; + *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;; + esac + fi + fi + fi + + if test "$linkmode" = prog || test "$mode" = relink; then + add_shlibpath= + add_dir= + add= + # Finalize command for both is simple: just hardcode it. + if test "$hardcode_direct" = yes && + test "$hardcode_direct_absolute" = no; then + add="$libdir/$linklib" + elif test "$hardcode_minus_L" = yes; then + add_dir="-L$libdir" + add="-l$name" + elif test "$hardcode_shlibpath_var" = yes; then + case :$finalize_shlibpath: in + *":$libdir:"*) ;; + *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;; + esac + add="-l$name" + elif test "$hardcode_automatic" = yes; then + if test -n "$inst_prefix_dir" && + test -f "$inst_prefix_dir$libdir/$linklib" ; then + add="$inst_prefix_dir$libdir/$linklib" + else + add="$libdir/$linklib" + fi + else + # We cannot seem to hardcode it, guess we'll fake it. + add_dir="-L$libdir" + # Try looking first in the location we're being installed to. + if test -n "$inst_prefix_dir"; then + case $libdir in + [\\/]*) + add_dir="$add_dir -L$inst_prefix_dir$libdir" + ;; + esac + fi + add="-l$name" + fi + + if test "$linkmode" = prog; then + test -n "$add_dir" && finalize_deplibs="$add_dir $finalize_deplibs" + test -n "$add" && finalize_deplibs="$add $finalize_deplibs" + else + test -n "$add_dir" && deplibs="$add_dir $deplibs" + test -n "$add" && deplibs="$add $deplibs" + fi + fi + elif test "$linkmode" = prog; then + # Here we assume that one of hardcode_direct or hardcode_minus_L + # is not unsupported. This is valid on all known static and + # shared platforms. + if test "$hardcode_direct" != unsupported; then + test -n "$old_library" && linklib="$old_library" + compile_deplibs="$dir/$linklib $compile_deplibs" + finalize_deplibs="$dir/$linklib $finalize_deplibs" + else + compile_deplibs="-l$name -L$dir $compile_deplibs" + finalize_deplibs="-l$name -L$dir $finalize_deplibs" + fi + elif test "$build_libtool_libs" = yes; then + # Not a shared library + if test "$deplibs_check_method" != pass_all; then + # We're trying link a shared library against a static one + # but the system doesn't support it. + + # Just print a warning and add the library to dependency_libs so + # that the program can be linked against the static library. + $ECHO + $ECHO "*** Warning: This system can not link to static lib archive $lib." + $ECHO "*** I have the capability to make that library automatically link in when" + $ECHO "*** you link to this library. But I can only do this if you have a" + $ECHO "*** shared version of the library, which you do not appear to have." + if test "$module" = yes; then + $ECHO "*** But as you try to build a module library, libtool will still create " + $ECHO "*** a static module, that should work as long as the dlopening application" + $ECHO "*** is linked with the -dlopen flag to resolve symbols at runtime." + if test -z "$global_symbol_pipe"; then + $ECHO + $ECHO "*** However, this would only work if libtool was able to extract symbol" + $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could" + $ECHO "*** not find such a program. So, this module is probably useless." + $ECHO "*** \`nm' from GNU binutils and a full rebuild may help." + fi + if test "$build_old_libs" = no; then + build_libtool_libs=module + build_old_libs=yes + else + build_libtool_libs=no + fi + fi + else + deplibs="$dir/$old_library $deplibs" + link_static=yes + fi + fi # link shared/static library? + + if test "$linkmode" = lib; then + if test -n "$dependency_libs" && + { test "$hardcode_into_libs" != yes || + test "$build_old_libs" = yes || + test "$link_static" = yes; }; then + # Extract -R from dependency_libs + temp_deplibs= + for libdir in $dependency_libs; do + case $libdir in + -R*) func_stripname '-R' '' "$libdir" + temp_xrpath=$func_stripname_result + case " $xrpath " in + *" $temp_xrpath "*) ;; + *) xrpath="$xrpath $temp_xrpath";; + esac;; + *) temp_deplibs="$temp_deplibs $libdir";; + esac + done + dependency_libs="$temp_deplibs" + fi + + newlib_search_path="$newlib_search_path $absdir" + # Link against this library + test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs" + # ... and its dependency_libs + tmp_libs= + for deplib in $dependency_libs; do + newdependency_libs="$deplib $newdependency_libs" + if $opt_duplicate_deps ; then + case "$tmp_libs " in + *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; + esac + fi + tmp_libs="$tmp_libs $deplib" + done + + if test "$link_all_deplibs" != no; then + # Add the search paths of all dependency libraries + for deplib in $dependency_libs; do + case $deplib in + -L*) path="$deplib" ;; + *.la) + func_dirname "$deplib" "" "." + dir="$func_dirname_result" + # We need an absolute path. + case $dir in + [\\/]* | [A-Za-z]:[\\/]*) absdir="$dir" ;; + *) + absdir=`cd "$dir" && pwd` + if test -z "$absdir"; then + func_warning "cannot determine absolute directory name of \`$dir'" + absdir="$dir" + fi + ;; + esac + if $GREP "^installed=no" $deplib > /dev/null; then + case $host in + *-*-darwin*) + depdepl= + eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib` + if test -n "$deplibrary_names" ; then + for tmp in $deplibrary_names ; do + depdepl=$tmp + done + if test -f "$absdir/$objdir/$depdepl" ; then + depdepl="$absdir/$objdir/$depdepl" + darwin_install_name=`${OTOOL} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` + if test -z "$darwin_install_name"; then + darwin_install_name=`${OTOOL64} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` + fi + compiler_flags="$compiler_flags ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}" + linker_flags="$linker_flags -dylib_file ${darwin_install_name}:${depdepl}" + path= + fi + fi + ;; + *) + path="-L$absdir/$objdir" + ;; + esac + else + eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib` + test -z "$libdir" && \ + func_fatal_error "\`$deplib' is not a valid libtool archive" + test "$absdir" != "$libdir" && \ + func_warning "\`$deplib' seems to be moved" + + path="-L$absdir" + fi + ;; + esac + case " $deplibs " in + *" $path "*) ;; + *) deplibs="$path $deplibs" ;; + esac + done + fi # link_all_deplibs != no + fi # linkmode = lib + done # for deplib in $libs + if test "$pass" = link; then + if test "$linkmode" = "prog"; then + compile_deplibs="$new_inherited_linker_flags $compile_deplibs" + finalize_deplibs="$new_inherited_linker_flags $finalize_deplibs" + else + compiler_flags="$compiler_flags "`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` + fi + fi + dependency_libs="$newdependency_libs" + if test "$pass" = dlpreopen; then + # Link the dlpreopened libraries before other libraries + for deplib in $save_deplibs; do + deplibs="$deplib $deplibs" + done + fi + if test "$pass" != dlopen; then + if test "$pass" != conv; then + # Make sure lib_search_path contains only unique directories. + lib_search_path= + for dir in $newlib_search_path; do + case "$lib_search_path " in + *" $dir "*) ;; + *) lib_search_path="$lib_search_path $dir" ;; + esac + done + newlib_search_path= + fi + + if test "$linkmode,$pass" != "prog,link"; then + vars="deplibs" + else + vars="compile_deplibs finalize_deplibs" + fi + for var in $vars dependency_libs; do + # Add libraries to $var in reverse order + eval tmp_libs=\"\$$var\" + new_libs= + for deplib in $tmp_libs; do + # FIXME: Pedantically, this is the right thing to do, so + # that some nasty dependency loop isn't accidentally + # broken: + #new_libs="$deplib $new_libs" + # Pragmatically, this seems to cause very few problems in + # practice: + case $deplib in + -L*) new_libs="$deplib $new_libs" ;; + -R*) ;; + *) + # And here is the reason: when a library appears more + # than once as an explicit dependence of a library, or + # is implicitly linked in more than once by the + # compiler, it is considered special, and multiple + # occurrences thereof are not removed. Compare this + # with having the same library being listed as a + # dependency of multiple other libraries: in this case, + # we know (pedantically, we assume) the library does not + # need to be listed more than once, so we keep only the + # last copy. This is not always right, but it is rare + # enough that we require users that really mean to play + # such unportable linking tricks to link the library + # using -Wl,-lname, so that libtool does not consider it + # for duplicate removal. + case " $specialdeplibs " in + *" $deplib "*) new_libs="$deplib $new_libs" ;; + *) + case " $new_libs " in + *" $deplib "*) ;; + *) new_libs="$deplib $new_libs" ;; + esac + ;; + esac + ;; + esac + done + tmp_libs= + for deplib in $new_libs; do + case $deplib in + -L*) + case " $tmp_libs " in + *" $deplib "*) ;; + *) tmp_libs="$tmp_libs $deplib" ;; + esac + ;; + *) tmp_libs="$tmp_libs $deplib" ;; + esac + done + eval $var=\"$tmp_libs\" + done # for var + fi + # Last step: remove runtime libs from dependency_libs + # (they stay in deplibs) + tmp_libs= + for i in $dependency_libs ; do + case " $predeps $postdeps $compiler_lib_search_path " in + *" $i "*) + i="" + ;; + esac + if test -n "$i" ; then + tmp_libs="$tmp_libs $i" + fi + done + dependency_libs=$tmp_libs + done # for pass + if test "$linkmode" = prog; then + dlfiles="$newdlfiles" + fi + if test "$linkmode" = prog || test "$linkmode" = lib; then + dlprefiles="$newdlprefiles" + fi + + case $linkmode in + oldlib) + if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then + func_warning "\`-dlopen' is ignored for archives" + fi + + case " $deplibs" in + *\ -l* | *\ -L*) + func_warning "\`-l' and \`-L' are ignored for archives" ;; + esac + + test -n "$rpath" && \ + func_warning "\`-rpath' is ignored for archives" + + test -n "$xrpath" && \ + func_warning "\`-R' is ignored for archives" + + test -n "$vinfo" && \ + func_warning "\`-version-info/-version-number' is ignored for archives" + + test -n "$release" && \ + func_warning "\`-release' is ignored for archives" + + test -n "$export_symbols$export_symbols_regex" && \ + func_warning "\`-export-symbols' is ignored for archives" + + # Now set the variables for building old libraries. + build_libtool_libs=no + oldlibs="$output" + objs="$objs$old_deplibs" + ;; + + lib) + # Make sure we only generate libraries of the form `libNAME.la'. + case $outputname in + lib*) + func_stripname 'lib' '.la' "$outputname" + name=$func_stripname_result + eval shared_ext=\"$shrext_cmds\" + eval libname=\"$libname_spec\" + ;; + *) + test "$module" = no && \ + func_fatal_help "libtool library \`$output' must begin with \`lib'" + + if test "$need_lib_prefix" != no; then + # Add the "lib" prefix for modules if required + func_stripname '' '.la' "$outputname" + name=$func_stripname_result + eval shared_ext=\"$shrext_cmds\" + eval libname=\"$libname_spec\" + else + func_stripname '' '.la' "$outputname" + libname=$func_stripname_result + fi + ;; + esac + + if test -n "$objs"; then + if test "$deplibs_check_method" != pass_all; then + func_fatal_error "cannot build libtool library \`$output' from non-libtool objects on this host:$objs" + else + $ECHO + $ECHO "*** Warning: Linking the shared library $output against the non-libtool" + $ECHO "*** objects $objs is not portable!" + libobjs="$libobjs $objs" + fi + fi + + test "$dlself" != no && \ + func_warning "\`-dlopen self' is ignored for libtool libraries" + + set dummy $rpath + shift + test "$#" -gt 1 && \ + func_warning "ignoring multiple \`-rpath's for a libtool library" + + install_libdir="$1" + + oldlibs= + if test -z "$rpath"; then + if test "$build_libtool_libs" = yes; then + # Building a libtool convenience library. + # Some compilers have problems with a `.al' extension so + # convenience libraries should have the same extension an + # archive normally would. + oldlibs="$output_objdir/$libname.$libext $oldlibs" + build_libtool_libs=convenience + build_old_libs=yes + fi + + test -n "$vinfo" && \ + func_warning "\`-version-info/-version-number' is ignored for convenience libraries" + + test -n "$release" && \ + func_warning "\`-release' is ignored for convenience libraries" + else + + # Parse the version information argument. + save_ifs="$IFS"; IFS=':' + set dummy $vinfo 0 0 0 + shift + IFS="$save_ifs" + + test -n "$7" && \ + func_fatal_help "too many parameters to \`-version-info'" + + # convert absolute version numbers to libtool ages + # this retains compatibility with .la files and attempts + # to make the code below a bit more comprehensible + + case $vinfo_number in + yes) + number_major="$1" + number_minor="$2" + number_revision="$3" + # + # There are really only two kinds -- those that + # use the current revision as the major version + # and those that subtract age and use age as + # a minor version. But, then there is irix + # which has an extra 1 added just for fun + # + case $version_type in + darwin|linux|osf|windows|none) + func_arith $number_major + $number_minor + current=$func_arith_result + age="$number_minor" + revision="$number_revision" + ;; + freebsd-aout|freebsd-elf|sunos) + current="$number_major" + revision="$number_minor" + age="0" + ;; + irix|nonstopux) + func_arith $number_major + $number_minor + current=$func_arith_result + age="$number_minor" + revision="$number_minor" + lt_irix_increment=no + ;; + *) + func_fatal_configuration "$modename: unknown library version type \`$version_type'" + ;; + esac + ;; + no) + current="$1" + revision="$2" + age="$3" + ;; + esac + + # Check that each of the things are valid numbers. + case $current in + 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; + *) + func_error "CURRENT \`$current' must be a nonnegative integer" + func_fatal_error "\`$vinfo' is not valid version information" + ;; + esac + + case $revision in + 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; + *) + func_error "REVISION \`$revision' must be a nonnegative integer" + func_fatal_error "\`$vinfo' is not valid version information" + ;; + esac + + case $age in + 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; + *) + func_error "AGE \`$age' must be a nonnegative integer" + func_fatal_error "\`$vinfo' is not valid version information" + ;; + esac + + if test "$age" -gt "$current"; then + func_error "AGE \`$age' is greater than the current interface number \`$current'" + func_fatal_error "\`$vinfo' is not valid version information" + fi + + # Calculate the version variables. + major= + versuffix= + verstring= + case $version_type in + none) ;; + + darwin) + # Like Linux, but with the current version available in + # verstring for coding it into the library header + func_arith $current - $age + major=.$func_arith_result + versuffix="$major.$age.$revision" + # Darwin ld doesn't like 0 for these options... + func_arith $current + 1 + minor_current=$func_arith_result + xlcverstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision" + verstring="-compatibility_version $minor_current -current_version $minor_current.$revision" + ;; + + freebsd-aout) + major=".$current" + versuffix=".$current.$revision"; + ;; + + freebsd-elf) + major=".$current" + versuffix=".$current" + ;; + + irix | nonstopux) + if test "X$lt_irix_increment" = "Xno"; then + func_arith $current - $age + else + func_arith $current - $age + 1 + fi + major=$func_arith_result + + case $version_type in + nonstopux) verstring_prefix=nonstopux ;; + *) verstring_prefix=sgi ;; + esac + verstring="$verstring_prefix$major.$revision" + + # Add in all the interfaces that we are compatible with. + loop=$revision + while test "$loop" -ne 0; do + func_arith $revision - $loop + iface=$func_arith_result + func_arith $loop - 1 + loop=$func_arith_result + verstring="$verstring_prefix$major.$iface:$verstring" + done + + # Before this point, $major must not contain `.'. + major=.$major + versuffix="$major.$revision" + ;; + + linux) + func_arith $current - $age + major=.$func_arith_result + versuffix="$major.$age.$revision" + ;; + + osf) + func_arith $current - $age + major=.$func_arith_result + versuffix=".$current.$age.$revision" + verstring="$current.$age.$revision" + + # Add in all the interfaces that we are compatible with. + loop=$age + while test "$loop" -ne 0; do + func_arith $current - $loop + iface=$func_arith_result + func_arith $loop - 1 + loop=$func_arith_result + verstring="$verstring:${iface}.0" + done + + # Make executables depend on our current version. + verstring="$verstring:${current}.0" + ;; + + qnx) + major=".$current" + versuffix=".$current" + ;; + + sunos) + major=".$current" + versuffix=".$current.$revision" + ;; + + windows) + # Use '-' rather than '.', since we only want one + # extension on DOS 8.3 filesystems. + func_arith $current - $age + major=$func_arith_result + versuffix="-$major" + ;; + + *) + func_fatal_configuration "unknown library version type \`$version_type'" + ;; + esac + + # Clear the version info if we defaulted, and they specified a release. + if test -z "$vinfo" && test -n "$release"; then + major= + case $version_type in + darwin) + # we can't check for "0.0" in archive_cmds due to quoting + # problems, so we reset it completely + verstring= + ;; + *) + verstring="0.0" + ;; + esac + if test "$need_version" = no; then + versuffix= + else + versuffix=".0.0" + fi + fi + + # Remove version info from name if versioning should be avoided + if test "$avoid_version" = yes && test "$need_version" = no; then + major= + versuffix= + verstring="" + fi + + # Check to see if the archive will have undefined symbols. + if test "$allow_undefined" = yes; then + if test "$allow_undefined_flag" = unsupported; then + func_warning "undefined symbols not allowed in $host shared libraries" + build_libtool_libs=no + build_old_libs=yes + fi + else + # Don't allow undefined symbols. + allow_undefined_flag="$no_undefined_flag" + fi + + fi + + func_generate_dlsyms "$libname" "$libname" "yes" + libobjs="$libobjs $symfileobj" + test "X$libobjs" = "X " && libobjs= + + if test "$mode" != relink; then + # Remove our outputs, but don't remove object files since they + # may have been created when compiling PIC objects. + removelist= + tempremovelist=`$ECHO "$output_objdir/*"` + for p in $tempremovelist; do + case $p in + *.$objext | *.gcno) + ;; + $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*) + if test "X$precious_files_regex" != "X"; then + if $ECHO "$p" | $EGREP -e "$precious_files_regex" >/dev/null 2>&1 + then + continue + fi + fi + removelist="$removelist $p" + ;; + *) ;; + esac + done + test -n "$removelist" && \ + func_show_eval "${RM}r \$removelist" + fi + + # Now set the variables for building old libraries. + if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then + oldlibs="$oldlibs $output_objdir/$libname.$libext" + + # Transform .lo files to .o files. + oldobjs="$objs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}'$/d' -e "$lo2o" | $NL2SP` + fi + + # Eliminate all temporary directories. + #for path in $notinst_path; do + # lib_search_path=`$ECHO "X$lib_search_path " | $Xsed -e "s% $path % %g"` + # deplibs=`$ECHO "X$deplibs " | $Xsed -e "s% -L$path % %g"` + # dependency_libs=`$ECHO "X$dependency_libs " | $Xsed -e "s% -L$path % %g"` + #done + + if test -n "$xrpath"; then + # If the user specified any rpath flags, then add them. + temp_xrpath= + for libdir in $xrpath; do + temp_xrpath="$temp_xrpath -R$libdir" + case "$finalize_rpath " in + *" $libdir "*) ;; + *) finalize_rpath="$finalize_rpath $libdir" ;; + esac + done + if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then + dependency_libs="$temp_xrpath $dependency_libs" + fi + fi + + # Make sure dlfiles contains only unique files that won't be dlpreopened + old_dlfiles="$dlfiles" + dlfiles= + for lib in $old_dlfiles; do + case " $dlprefiles $dlfiles " in + *" $lib "*) ;; + *) dlfiles="$dlfiles $lib" ;; + esac + done + + # Make sure dlprefiles contains only unique files + old_dlprefiles="$dlprefiles" + dlprefiles= + for lib in $old_dlprefiles; do + case "$dlprefiles " in + *" $lib "*) ;; + *) dlprefiles="$dlprefiles $lib" ;; + esac + done + + if test "$build_libtool_libs" = yes; then + if test -n "$rpath"; then + case $host in + *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc*) + # these systems don't actually have a c library (as such)! + ;; + *-*-rhapsody* | *-*-darwin1.[012]) + # Rhapsody C library is in the System framework + deplibs="$deplibs System.ltframework" + ;; + *-*-netbsd*) + # Don't link with libc until the a.out ld.so is fixed. + ;; + *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) + # Do not include libc due to us having libc/libc_r. + ;; + *-*-sco3.2v5* | *-*-sco5v6*) + # Causes problems with __ctype + ;; + *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*) + # Compiler inserts libc in the correct place for threads to work + ;; + *) + # Add libc to deplibs on all other systems if necessary. + if test "$build_libtool_need_lc" = "yes"; then + deplibs="$deplibs -lc" + fi + ;; + esac + fi + + # Transform deplibs into only deplibs that can be linked in shared. + name_save=$name + libname_save=$libname + release_save=$release + versuffix_save=$versuffix + major_save=$major + # I'm not sure if I'm treating the release correctly. I think + # release should show up in the -l (ie -lgmp5) so we don't want to + # add it in twice. Is that correct? + release="" + versuffix="" + major="" + newdeplibs= + droppeddeps=no + case $deplibs_check_method in + pass_all) + # Don't check for shared/static. Everything works. + # This might be a little naive. We might want to check + # whether the library exists or not. But this is on + # osf3 & osf4 and I'm not really sure... Just + # implementing what was already the behavior. + newdeplibs=$deplibs + ;; + test_compile) + # This code stresses the "libraries are programs" paradigm to its + # limits. Maybe even breaks it. We compile a program, linking it + # against the deplibs as a proxy for the library. Then we can check + # whether they linked in statically or dynamically with ldd. + $opt_dry_run || $RM conftest.c + cat > conftest.c </dev/null` + for potent_lib in $potential_libs; do + # Follow soft links. + if ls -lLd "$potent_lib" 2>/dev/null | + $GREP " -> " >/dev/null; then + continue + fi + # The statement above tries to avoid entering an + # endless loop below, in case of cyclic links. + # We might still enter an endless loop, since a link + # loop can be closed while we follow links, + # but so what? + potlib="$potent_lib" + while test -h "$potlib" 2>/dev/null; do + potliblink=`ls -ld $potlib | ${SED} 's/.* -> //'` + case $potliblink in + [\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";; + *) potlib=`$ECHO "X$potlib" | $Xsed -e 's,[^/]*$,,'`"$potliblink";; + esac + done + if eval $file_magic_cmd \"\$potlib\" 2>/dev/null | + $SED -e 10q | + $EGREP "$file_magic_regex" > /dev/null; then + newdeplibs="$newdeplibs $a_deplib" + a_deplib="" + break 2 + fi + done + done + fi + if test -n "$a_deplib" ; then + droppeddeps=yes + $ECHO + $ECHO "*** Warning: linker path does not have real file for library $a_deplib." + $ECHO "*** I have the capability to make that library automatically link in when" + $ECHO "*** you link to this library. But I can only do this if you have a" + $ECHO "*** shared version of the library, which you do not appear to have" + $ECHO "*** because I did check the linker path looking for a file starting" + if test -z "$potlib" ; then + $ECHO "*** with $libname but no candidates were found. (...for file magic test)" + else + $ECHO "*** with $libname and none of the candidates passed a file format test" + $ECHO "*** using a file magic. Last file checked: $potlib" + fi + fi + ;; + *) + # Add a -L argument. + newdeplibs="$newdeplibs $a_deplib" + ;; + esac + done # Gone through all deplibs. + ;; + match_pattern*) + set dummy $deplibs_check_method; shift + match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` + for a_deplib in $deplibs; do + case $a_deplib in + -l*) + func_stripname -l '' "$a_deplib" + name=$func_stripname_result + if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then + case " $predeps $postdeps " in + *" $a_deplib "*) + newdeplibs="$newdeplibs $a_deplib" + a_deplib="" + ;; + esac + fi + if test -n "$a_deplib" ; then + libname=`eval "\\$ECHO \"$libname_spec\""` + for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do + potential_libs=`ls $i/$libname[.-]* 2>/dev/null` + for potent_lib in $potential_libs; do + potlib="$potent_lib" # see symlink-check above in file_magic test + if eval "\$ECHO \"X$potent_lib\"" 2>/dev/null | $Xsed -e 10q | \ + $EGREP "$match_pattern_regex" > /dev/null; then + newdeplibs="$newdeplibs $a_deplib" + a_deplib="" + break 2 + fi + done + done + fi + if test -n "$a_deplib" ; then + droppeddeps=yes + $ECHO + $ECHO "*** Warning: linker path does not have real file for library $a_deplib." + $ECHO "*** I have the capability to make that library automatically link in when" + $ECHO "*** you link to this library. But I can only do this if you have a" + $ECHO "*** shared version of the library, which you do not appear to have" + $ECHO "*** because I did check the linker path looking for a file starting" + if test -z "$potlib" ; then + $ECHO "*** with $libname but no candidates were found. (...for regex pattern test)" + else + $ECHO "*** with $libname and none of the candidates passed a file format test" + $ECHO "*** using a regex pattern. Last file checked: $potlib" + fi + fi + ;; + *) + # Add a -L argument. + newdeplibs="$newdeplibs $a_deplib" + ;; + esac + done # Gone through all deplibs. + ;; + none | unknown | *) + newdeplibs="" + tmp_deplibs=`$ECHO "X $deplibs" | $Xsed \ + -e 's/ -lc$//' -e 's/ -[LR][^ ]*//g'` + if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then + for i in $predeps $postdeps ; do + # can't use Xsed below, because $i might contain '/' + tmp_deplibs=`$ECHO "X $tmp_deplibs" | $Xsed -e "s,$i,,"` + done + fi + if $ECHO "X $tmp_deplibs" | $Xsed -e 's/[ ]//g' | + $GREP . >/dev/null; then + $ECHO + if test "X$deplibs_check_method" = "Xnone"; then + $ECHO "*** Warning: inter-library dependencies are not supported in this platform." + else + $ECHO "*** Warning: inter-library dependencies are not known to be supported." + fi + $ECHO "*** All declared inter-library dependencies are being dropped." + droppeddeps=yes + fi + ;; + esac + versuffix=$versuffix_save + major=$major_save + release=$release_save + libname=$libname_save + name=$name_save + + case $host in + *-*-rhapsody* | *-*-darwin1.[012]) + # On Rhapsody replace the C library with the System framework + newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's/ -lc / System.ltframework /'` + ;; + esac + + if test "$droppeddeps" = yes; then + if test "$module" = yes; then + $ECHO + $ECHO "*** Warning: libtool could not satisfy all declared inter-library" + $ECHO "*** dependencies of module $libname. Therefore, libtool will create" + $ECHO "*** a static module, that should work as long as the dlopening" + $ECHO "*** application is linked with the -dlopen flag." + if test -z "$global_symbol_pipe"; then + $ECHO + $ECHO "*** However, this would only work if libtool was able to extract symbol" + $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could" + $ECHO "*** not find such a program. So, this module is probably useless." + $ECHO "*** \`nm' from GNU binutils and a full rebuild may help." + fi + if test "$build_old_libs" = no; then + oldlibs="$output_objdir/$libname.$libext" + build_libtool_libs=module + build_old_libs=yes + else + build_libtool_libs=no + fi + else + $ECHO "*** The inter-library dependencies that have been dropped here will be" + $ECHO "*** automatically added whenever a program is linked with this library" + $ECHO "*** or is declared to -dlopen it." + + if test "$allow_undefined" = no; then + $ECHO + $ECHO "*** Since this library must not contain undefined symbols," + $ECHO "*** because either the platform does not support them or" + $ECHO "*** it was explicitly requested with -no-undefined," + $ECHO "*** libtool will only create a static version of it." + if test "$build_old_libs" = no; then + oldlibs="$output_objdir/$libname.$libext" + build_libtool_libs=module + build_old_libs=yes + else + build_libtool_libs=no + fi + fi + fi + fi + # Done checking deplibs! + deplibs=$newdeplibs + fi + # Time to change all our "foo.ltframework" stuff back to "-framework foo" + case $host in + *-*-darwin*) + newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` + new_inherited_linker_flags=`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` + deplibs=`$ECHO "X $deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` + ;; + esac + + # move library search paths that coincide with paths to not yet + # installed libraries to the beginning of the library search list + new_libs= + for path in $notinst_path; do + case " $new_libs " in + *" -L$path/$objdir "*) ;; + *) + case " $deplibs " in + *" -L$path/$objdir "*) + new_libs="$new_libs -L$path/$objdir" ;; + esac + ;; + esac + done + for deplib in $deplibs; do + case $deplib in + -L*) + case " $new_libs " in + *" $deplib "*) ;; + *) new_libs="$new_libs $deplib" ;; + esac + ;; + *) new_libs="$new_libs $deplib" ;; + esac + done + deplibs="$new_libs" + + # All the library-specific variables (install_libdir is set above). + library_names= + old_library= + dlname= + + # Test again, we may have decided not to build it any more + if test "$build_libtool_libs" = yes; then + if test "$hardcode_into_libs" = yes; then + # Hardcode the library paths + hardcode_libdirs= + dep_rpath= + rpath="$finalize_rpath" + test "$mode" != relink && rpath="$compile_rpath$rpath" + for libdir in $rpath; do + if test -n "$hardcode_libdir_flag_spec"; then + if test -n "$hardcode_libdir_separator"; then + if test -z "$hardcode_libdirs"; then + hardcode_libdirs="$libdir" + else + # Just accumulate the unique libdirs. + case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in + *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) + ;; + *) + hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" + ;; + esac + fi + else + eval flag=\"$hardcode_libdir_flag_spec\" + dep_rpath="$dep_rpath $flag" + fi + elif test -n "$runpath_var"; then + case "$perm_rpath " in + *" $libdir "*) ;; + *) perm_rpath="$perm_rpath $libdir" ;; + esac + fi + done + # Substitute the hardcoded libdirs into the rpath. + if test -n "$hardcode_libdir_separator" && + test -n "$hardcode_libdirs"; then + libdir="$hardcode_libdirs" + if test -n "$hardcode_libdir_flag_spec_ld"; then + eval dep_rpath=\"$hardcode_libdir_flag_spec_ld\" + else + eval dep_rpath=\"$hardcode_libdir_flag_spec\" + fi + fi + if test -n "$runpath_var" && test -n "$perm_rpath"; then + # We should set the runpath_var. + rpath= + for dir in $perm_rpath; do + rpath="$rpath$dir:" + done + eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var" + fi + test -n "$dep_rpath" && deplibs="$dep_rpath $deplibs" + fi + + shlibpath="$finalize_shlibpath" + test "$mode" != relink && shlibpath="$compile_shlibpath$shlibpath" + if test -n "$shlibpath"; then + eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var" + fi + + # Get the real and link names of the library. + eval shared_ext=\"$shrext_cmds\" + eval library_names=\"$library_names_spec\" + set dummy $library_names + shift + realname="$1" + shift + + if test -n "$soname_spec"; then + eval soname=\"$soname_spec\" + else + soname="$realname" + fi + if test -z "$dlname"; then + dlname=$soname + fi + + lib="$output_objdir/$realname" + linknames= + for link + do + linknames="$linknames $link" + done + + # Use standard objects if they are pic + test -z "$pic_flag" && libobjs=`$ECHO "X$libobjs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` + test "X$libobjs" = "X " && libobjs= + + delfiles= + if test -n "$export_symbols" && test -n "$include_expsyms"; then + $opt_dry_run || cp "$export_symbols" "$output_objdir/$libname.uexp" + export_symbols="$output_objdir/$libname.uexp" + delfiles="$delfiles $export_symbols" + fi + + orig_export_symbols= + case $host_os in + cygwin* | mingw* | cegcc*) + if test -n "$export_symbols" && test -z "$export_symbols_regex"; then + # exporting using user supplied symfile + if test "x`$SED 1q $export_symbols`" != xEXPORTS; then + # and it's NOT already a .def file. Must figure out + # which of the given symbols are data symbols and tag + # them as such. So, trigger use of export_symbols_cmds. + # export_symbols gets reassigned inside the "prepare + # the list of exported symbols" if statement, so the + # include_expsyms logic still works. + orig_export_symbols="$export_symbols" + export_symbols= + always_export_symbols=yes + fi + fi + ;; + esac + + # Prepare the list of exported symbols + if test -z "$export_symbols"; then + if test "$always_export_symbols" = yes || test -n "$export_symbols_regex"; then + func_verbose "generating symbol list for \`$libname.la'" + export_symbols="$output_objdir/$libname.exp" + $opt_dry_run || $RM $export_symbols + cmds=$export_symbols_cmds + save_ifs="$IFS"; IFS='~' + for cmd in $cmds; do + IFS="$save_ifs" + eval cmd=\"$cmd\" + func_len " $cmd" + len=$func_len_result + if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then + func_show_eval "$cmd" 'exit $?' + skipped_export=false + else + # The command line is too long to execute in one step. + func_verbose "using reloadable object file for export list..." + skipped_export=: + # Break out early, otherwise skipped_export may be + # set to false by a later but shorter cmd. + break + fi + done + IFS="$save_ifs" + if test -n "$export_symbols_regex" && test "X$skipped_export" != "X:"; then + func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' + func_show_eval '$MV "${export_symbols}T" "$export_symbols"' + fi + fi + fi + + if test -n "$export_symbols" && test -n "$include_expsyms"; then + tmp_export_symbols="$export_symbols" + test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" + $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"' + fi + + if test "X$skipped_export" != "X:" && test -n "$orig_export_symbols"; then + # The given exports_symbols file has to be filtered, so filter it. + func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" + # FIXME: $output_objdir/$libname.filter potentially contains lots of + # 's' commands which not all seds can handle. GNU sed should be fine + # though. Also, the filter scales superlinearly with the number of + # global variables. join(1) would be nice here, but unfortunately + # isn't a blessed tool. + $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter + delfiles="$delfiles $export_symbols $output_objdir/$libname.filter" + export_symbols=$output_objdir/$libname.def + $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols + fi + + tmp_deplibs= + for test_deplib in $deplibs; do + case " $convenience " in + *" $test_deplib "*) ;; + *) + tmp_deplibs="$tmp_deplibs $test_deplib" + ;; + esac + done + deplibs="$tmp_deplibs" + + if test -n "$convenience"; then + if test -n "$whole_archive_flag_spec" && + test "$compiler_needs_object" = yes && + test -z "$libobjs"; then + # extract the archives, so we have objects to list. + # TODO: could optimize this to just extract one archive. + whole_archive_flag_spec= + fi + if test -n "$whole_archive_flag_spec"; then + save_libobjs=$libobjs + eval libobjs=\"\$libobjs $whole_archive_flag_spec\" + test "X$libobjs" = "X " && libobjs= + else + gentop="$output_objdir/${outputname}x" + generated="$generated $gentop" + + func_extract_archives $gentop $convenience + libobjs="$libobjs $func_extract_archives_result" + test "X$libobjs" = "X " && libobjs= + fi + fi + + if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then + eval flag=\"$thread_safe_flag_spec\" + linker_flags="$linker_flags $flag" + fi + + # Make a backup of the uninstalled library when relinking + if test "$mode" = relink; then + $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}U && $MV $realname ${realname}U)' || exit $? + fi + + # Do each of the archive commands. + if test "$module" = yes && test -n "$module_cmds" ; then + if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then + eval test_cmds=\"$module_expsym_cmds\" + cmds=$module_expsym_cmds + else + eval test_cmds=\"$module_cmds\" + cmds=$module_cmds + fi + else + if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then + eval test_cmds=\"$archive_expsym_cmds\" + cmds=$archive_expsym_cmds + else + eval test_cmds=\"$archive_cmds\" + cmds=$archive_cmds + fi + fi + + if test "X$skipped_export" != "X:" && + func_len " $test_cmds" && + len=$func_len_result && + test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then + : + else + # The command line is too long to link in one step, link piecewise + # or, if using GNU ld and skipped_export is not :, use a linker + # script. + + # Save the value of $output and $libobjs because we want to + # use them later. If we have whole_archive_flag_spec, we + # want to use save_libobjs as it was before + # whole_archive_flag_spec was expanded, because we can't + # assume the linker understands whole_archive_flag_spec. + # This may have to be revisited, in case too many + # convenience libraries get linked in and end up exceeding + # the spec. + if test -z "$convenience" || test -z "$whole_archive_flag_spec"; then + save_libobjs=$libobjs + fi + save_output=$output + output_la=`$ECHO "X$output" | $Xsed -e "$basename"` + + # Clear the reloadable object creation command queue and + # initialize k to one. + test_cmds= + concat_cmds= + objlist= + last_robj= + k=1 + + if test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "$with_gnu_ld" = yes; then + output=${output_objdir}/${output_la}.lnkscript + func_verbose "creating GNU ld script: $output" + $ECHO 'INPUT (' > $output + for obj in $save_libobjs + do + $ECHO "$obj" >> $output + done + $ECHO ')' >> $output + delfiles="$delfiles $output" + elif test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "X$file_list_spec" != X; then + output=${output_objdir}/${output_la}.lnk + func_verbose "creating linker input file list: $output" + : > $output + set x $save_libobjs + shift + firstobj= + if test "$compiler_needs_object" = yes; then + firstobj="$1 " + shift + fi + for obj + do + $ECHO "$obj" >> $output + done + delfiles="$delfiles $output" + output=$firstobj\"$file_list_spec$output\" + else + if test -n "$save_libobjs"; then + func_verbose "creating reloadable object files..." + output=$output_objdir/$output_la-${k}.$objext + eval test_cmds=\"$reload_cmds\" + func_len " $test_cmds" + len0=$func_len_result + len=$len0 + + # Loop over the list of objects to be linked. + for obj in $save_libobjs + do + func_len " $obj" + func_arith $len + $func_len_result + len=$func_arith_result + if test "X$objlist" = X || + test "$len" -lt "$max_cmd_len"; then + func_append objlist " $obj" + else + # The command $test_cmds is almost too long, add a + # command to the queue. + if test "$k" -eq 1 ; then + # The first file doesn't have a previous command to add. + eval concat_cmds=\"$reload_cmds $objlist $last_robj\" + else + # All subsequent reloadable object files will link in + # the last one created. + eval concat_cmds=\"\$concat_cmds~$reload_cmds $objlist $last_robj~\$RM $last_robj\" + fi + last_robj=$output_objdir/$output_la-${k}.$objext + func_arith $k + 1 + k=$func_arith_result + output=$output_objdir/$output_la-${k}.$objext + objlist=$obj + func_len " $last_robj" + func_arith $len0 + $func_len_result + len=$func_arith_result + fi + done + # Handle the remaining objects by creating one last + # reloadable object file. All subsequent reloadable object + # files will link in the last one created. + test -z "$concat_cmds" || concat_cmds=$concat_cmds~ + eval concat_cmds=\"\${concat_cmds}$reload_cmds $objlist $last_robj\" + if test -n "$last_robj"; then + eval concat_cmds=\"\${concat_cmds}~\$RM $last_robj\" + fi + delfiles="$delfiles $output" + + else + output= + fi + + if ${skipped_export-false}; then + func_verbose "generating symbol list for \`$libname.la'" + export_symbols="$output_objdir/$libname.exp" + $opt_dry_run || $RM $export_symbols + libobjs=$output + # Append the command to create the export file. + test -z "$concat_cmds" || concat_cmds=$concat_cmds~ + eval concat_cmds=\"\$concat_cmds$export_symbols_cmds\" + if test -n "$last_robj"; then + eval concat_cmds=\"\$concat_cmds~\$RM $last_robj\" + fi + fi + + test -n "$save_libobjs" && + func_verbose "creating a temporary reloadable object file: $output" + + # Loop through the commands generated above and execute them. + save_ifs="$IFS"; IFS='~' + for cmd in $concat_cmds; do + IFS="$save_ifs" + $opt_silent || { + func_quote_for_expand "$cmd" + eval "func_echo $func_quote_for_expand_result" + } + $opt_dry_run || eval "$cmd" || { + lt_exit=$? + + # Restore the uninstalled library and exit + if test "$mode" = relink; then + ( cd "$output_objdir" && \ + $RM "${realname}T" && \ + $MV "${realname}U" "$realname" ) + fi + + exit $lt_exit + } + done + IFS="$save_ifs" + + if test -n "$export_symbols_regex" && ${skipped_export-false}; then + func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' + func_show_eval '$MV "${export_symbols}T" "$export_symbols"' + fi + fi + + if ${skipped_export-false}; then + if test -n "$export_symbols" && test -n "$include_expsyms"; then + tmp_export_symbols="$export_symbols" + test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" + $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"' + fi + + if test -n "$orig_export_symbols"; then + # The given exports_symbols file has to be filtered, so filter it. + func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" + # FIXME: $output_objdir/$libname.filter potentially contains lots of + # 's' commands which not all seds can handle. GNU sed should be fine + # though. Also, the filter scales superlinearly with the number of + # global variables. join(1) would be nice here, but unfortunately + # isn't a blessed tool. + $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter + delfiles="$delfiles $export_symbols $output_objdir/$libname.filter" + export_symbols=$output_objdir/$libname.def + $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols + fi + fi + + libobjs=$output + # Restore the value of output. + output=$save_output + + if test -n "$convenience" && test -n "$whole_archive_flag_spec"; then + eval libobjs=\"\$libobjs $whole_archive_flag_spec\" + test "X$libobjs" = "X " && libobjs= + fi + # Expand the library linking commands again to reset the + # value of $libobjs for piecewise linking. + + # Do each of the archive commands. + if test "$module" = yes && test -n "$module_cmds" ; then + if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then + cmds=$module_expsym_cmds + else + cmds=$module_cmds + fi + else + if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then + cmds=$archive_expsym_cmds + else + cmds=$archive_cmds + fi + fi + fi + + if test -n "$delfiles"; then + # Append the command to remove temporary files to $cmds. + eval cmds=\"\$cmds~\$RM $delfiles\" + fi + + # Add any objects from preloaded convenience libraries + if test -n "$dlprefiles"; then + gentop="$output_objdir/${outputname}x" + generated="$generated $gentop" + + func_extract_archives $gentop $dlprefiles + libobjs="$libobjs $func_extract_archives_result" + test "X$libobjs" = "X " && libobjs= + fi + + save_ifs="$IFS"; IFS='~' + for cmd in $cmds; do + IFS="$save_ifs" + eval cmd=\"$cmd\" + $opt_silent || { + func_quote_for_expand "$cmd" + eval "func_echo $func_quote_for_expand_result" + } + $opt_dry_run || eval "$cmd" || { + lt_exit=$? + + # Restore the uninstalled library and exit + if test "$mode" = relink; then + ( cd "$output_objdir" && \ + $RM "${realname}T" && \ + $MV "${realname}U" "$realname" ) + fi + + exit $lt_exit + } + done + IFS="$save_ifs" + + # Restore the uninstalled library and exit + if test "$mode" = relink; then + $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}T && $MV $realname ${realname}T && $MV ${realname}U $realname)' || exit $? + + if test -n "$convenience"; then + if test -z "$whole_archive_flag_spec"; then + func_show_eval '${RM}r "$gentop"' + fi + fi + + exit $EXIT_SUCCESS + fi + + # Create links to the real library. + for linkname in $linknames; do + if test "$realname" != "$linkname"; then + func_show_eval '(cd "$output_objdir" && $RM "$linkname" && $LN_S "$realname" "$linkname")' 'exit $?' + fi + done + + # If -module or -export-dynamic was specified, set the dlname. + if test "$module" = yes || test "$export_dynamic" = yes; then + # On all known operating systems, these are identical. + dlname="$soname" + fi + fi + ;; + + obj) + if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then + func_warning "\`-dlopen' is ignored for objects" + fi + + case " $deplibs" in + *\ -l* | *\ -L*) + func_warning "\`-l' and \`-L' are ignored for objects" ;; + esac + + test -n "$rpath" && \ + func_warning "\`-rpath' is ignored for objects" + + test -n "$xrpath" && \ + func_warning "\`-R' is ignored for objects" + + test -n "$vinfo" && \ + func_warning "\`-version-info' is ignored for objects" + + test -n "$release" && \ + func_warning "\`-release' is ignored for objects" + + case $output in + *.lo) + test -n "$objs$old_deplibs" && \ + func_fatal_error "cannot build library object \`$output' from non-libtool objects" + + libobj=$output + func_lo2o "$libobj" + obj=$func_lo2o_result + ;; + *) + libobj= + obj="$output" + ;; + esac + + # Delete the old objects. + $opt_dry_run || $RM $obj $libobj + + # Objects from convenience libraries. This assumes + # single-version convenience libraries. Whenever we create + # different ones for PIC/non-PIC, this we'll have to duplicate + # the extraction. + reload_conv_objs= + gentop= + # reload_cmds runs $LD directly, so let us get rid of + # -Wl from whole_archive_flag_spec and hope we can get by with + # turning comma into space.. + wl= + + if test -n "$convenience"; then + if test -n "$whole_archive_flag_spec"; then + eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\" + reload_conv_objs=$reload_objs\ `$ECHO "X$tmp_whole_archive_flags" | $Xsed -e 's|,| |g'` + else + gentop="$output_objdir/${obj}x" + generated="$generated $gentop" + + func_extract_archives $gentop $convenience + reload_conv_objs="$reload_objs $func_extract_archives_result" + fi + fi + + # Create the old-style object. + reload_objs="$objs$old_deplibs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}$'/d' -e '/\.lib$/d' -e "$lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test + + output="$obj" + func_execute_cmds "$reload_cmds" 'exit $?' + + # Exit if we aren't doing a library object file. + if test -z "$libobj"; then + if test -n "$gentop"; then + func_show_eval '${RM}r "$gentop"' + fi + + exit $EXIT_SUCCESS + fi + + if test "$build_libtool_libs" != yes; then + if test -n "$gentop"; then + func_show_eval '${RM}r "$gentop"' + fi + + # Create an invalid libtool object if no PIC, so that we don't + # accidentally link it into a program. + # $show "echo timestamp > $libobj" + # $opt_dry_run || eval "echo timestamp > $libobj" || exit $? + exit $EXIT_SUCCESS + fi + + if test -n "$pic_flag" || test "$pic_mode" != default; then + # Only do commands if we really have different PIC objects. + reload_objs="$libobjs $reload_conv_objs" + output="$libobj" + func_execute_cmds "$reload_cmds" 'exit $?' + fi + + if test -n "$gentop"; then + func_show_eval '${RM}r "$gentop"' + fi + + exit $EXIT_SUCCESS + ;; + + prog) + case $host in + *cygwin*) func_stripname '' '.exe' "$output" + output=$func_stripname_result.exe;; + esac + test -n "$vinfo" && \ + func_warning "\`-version-info' is ignored for programs" + + test -n "$release" && \ + func_warning "\`-release' is ignored for programs" + + test "$preload" = yes \ + && test "$dlopen_support" = unknown \ + && test "$dlopen_self" = unknown \ + && test "$dlopen_self_static" = unknown && \ + func_warning "\`LT_INIT([dlopen])' not used. Assuming no dlopen support." + + case $host in + *-*-rhapsody* | *-*-darwin1.[012]) + # On Rhapsody replace the C library is the System framework + compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'` + finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'` + ;; + esac + + case $host in + *-*-darwin*) + # Don't allow lazy linking, it breaks C++ global constructors + # But is supposedly fixed on 10.4 or later (yay!). + if test "$tagname" = CXX ; then + case ${MACOSX_DEPLOYMENT_TARGET-10.0} in + 10.[0123]) + compile_command="$compile_command ${wl}-bind_at_load" + finalize_command="$finalize_command ${wl}-bind_at_load" + ;; + esac + fi + # Time to change all our "foo.ltframework" stuff back to "-framework foo" + compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` + finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` + ;; + esac + + + # move library search paths that coincide with paths to not yet + # installed libraries to the beginning of the library search list + new_libs= + for path in $notinst_path; do + case " $new_libs " in + *" -L$path/$objdir "*) ;; + *) + case " $compile_deplibs " in + *" -L$path/$objdir "*) + new_libs="$new_libs -L$path/$objdir" ;; + esac + ;; + esac + done + for deplib in $compile_deplibs; do + case $deplib in + -L*) + case " $new_libs " in + *" $deplib "*) ;; + *) new_libs="$new_libs $deplib" ;; + esac + ;; + *) new_libs="$new_libs $deplib" ;; + esac + done + compile_deplibs="$new_libs" + + + compile_command="$compile_command $compile_deplibs" + finalize_command="$finalize_command $finalize_deplibs" + + if test -n "$rpath$xrpath"; then + # If the user specified any rpath flags, then add them. + for libdir in $rpath $xrpath; do + # This is the magic to use -rpath. + case "$finalize_rpath " in + *" $libdir "*) ;; + *) finalize_rpath="$finalize_rpath $libdir" ;; + esac + done + fi + + # Now hardcode the library paths + rpath= + hardcode_libdirs= + for libdir in $compile_rpath $finalize_rpath; do + if test -n "$hardcode_libdir_flag_spec"; then + if test -n "$hardcode_libdir_separator"; then + if test -z "$hardcode_libdirs"; then + hardcode_libdirs="$libdir" + else + # Just accumulate the unique libdirs. + case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in + *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) + ;; + *) + hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" + ;; + esac + fi + else + eval flag=\"$hardcode_libdir_flag_spec\" + rpath="$rpath $flag" + fi + elif test -n "$runpath_var"; then + case "$perm_rpath " in + *" $libdir "*) ;; + *) perm_rpath="$perm_rpath $libdir" ;; + esac + fi + case $host in + *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) + testbindir=`${ECHO} "$libdir" | ${SED} -e 's*/lib$*/bin*'` + case :$dllsearchpath: in + *":$libdir:"*) ;; + ::) dllsearchpath=$libdir;; + *) dllsearchpath="$dllsearchpath:$libdir";; + esac + case :$dllsearchpath: in + *":$testbindir:"*) ;; + ::) dllsearchpath=$testbindir;; + *) dllsearchpath="$dllsearchpath:$testbindir";; + esac + ;; + esac + done + # Substitute the hardcoded libdirs into the rpath. + if test -n "$hardcode_libdir_separator" && + test -n "$hardcode_libdirs"; then + libdir="$hardcode_libdirs" + eval rpath=\" $hardcode_libdir_flag_spec\" + fi + compile_rpath="$rpath" + + rpath= + hardcode_libdirs= + for libdir in $finalize_rpath; do + if test -n "$hardcode_libdir_flag_spec"; then + if test -n "$hardcode_libdir_separator"; then + if test -z "$hardcode_libdirs"; then + hardcode_libdirs="$libdir" + else + # Just accumulate the unique libdirs. + case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in + *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) + ;; + *) + hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" + ;; + esac + fi + else + eval flag=\"$hardcode_libdir_flag_spec\" + rpath="$rpath $flag" + fi + elif test -n "$runpath_var"; then + case "$finalize_perm_rpath " in + *" $libdir "*) ;; + *) finalize_perm_rpath="$finalize_perm_rpath $libdir" ;; + esac + fi + done + # Substitute the hardcoded libdirs into the rpath. + if test -n "$hardcode_libdir_separator" && + test -n "$hardcode_libdirs"; then + libdir="$hardcode_libdirs" + eval rpath=\" $hardcode_libdir_flag_spec\" + fi + finalize_rpath="$rpath" + + if test -n "$libobjs" && test "$build_old_libs" = yes; then + # Transform all the library objects into standard objects. + compile_command=`$ECHO "X$compile_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` + finalize_command=`$ECHO "X$finalize_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` + fi + + func_generate_dlsyms "$outputname" "@PROGRAM@" "no" + + # template prelinking step + if test -n "$prelink_cmds"; then + func_execute_cmds "$prelink_cmds" 'exit $?' + fi + + wrappers_required=yes + case $host in + *cygwin* | *mingw* ) + if test "$build_libtool_libs" != yes; then + wrappers_required=no + fi + ;; + *cegcc) + # Disable wrappers for cegcc, we are cross compiling anyway. + wrappers_required=no + ;; + *) + if test "$need_relink" = no || test "$build_libtool_libs" != yes; then + wrappers_required=no + fi + ;; + esac + if test "$wrappers_required" = no; then + # Replace the output file specification. + compile_command=`$ECHO "X$compile_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'` + link_command="$compile_command$compile_rpath" + + # We have no uninstalled library dependencies, so finalize right now. + exit_status=0 + func_show_eval "$link_command" 'exit_status=$?' + + # Delete the generated files. + if test -f "$output_objdir/${outputname}S.${objext}"; then + func_show_eval '$RM "$output_objdir/${outputname}S.${objext}"' + fi + + exit $exit_status + fi + + if test -n "$compile_shlibpath$finalize_shlibpath"; then + compile_command="$shlibpath_var=\"$compile_shlibpath$finalize_shlibpath\$$shlibpath_var\" $compile_command" + fi + if test -n "$finalize_shlibpath"; then + finalize_command="$shlibpath_var=\"$finalize_shlibpath\$$shlibpath_var\" $finalize_command" + fi + + compile_var= + finalize_var= + if test -n "$runpath_var"; then + if test -n "$perm_rpath"; then + # We should set the runpath_var. + rpath= + for dir in $perm_rpath; do + rpath="$rpath$dir:" + done + compile_var="$runpath_var=\"$rpath\$$runpath_var\" " + fi + if test -n "$finalize_perm_rpath"; then + # We should set the runpath_var. + rpath= + for dir in $finalize_perm_rpath; do + rpath="$rpath$dir:" + done + finalize_var="$runpath_var=\"$rpath\$$runpath_var\" " + fi + fi + + if test "$no_install" = yes; then + # We don't need to create a wrapper script. + link_command="$compile_var$compile_command$compile_rpath" + # Replace the output file specification. + link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'` + # Delete the old output file. + $opt_dry_run || $RM $output + # Link the executable and exit + func_show_eval "$link_command" 'exit $?' + exit $EXIT_SUCCESS + fi + + if test "$hardcode_action" = relink; then + # Fast installation is not supported + link_command="$compile_var$compile_command$compile_rpath" + relink_command="$finalize_var$finalize_command$finalize_rpath" + + func_warning "this platform does not like uninstalled shared libraries" + func_warning "\`$output' will be relinked during installation" + else + if test "$fast_install" != no; then + link_command="$finalize_var$compile_command$finalize_rpath" + if test "$fast_install" = yes; then + relink_command=`$ECHO "X$compile_var$compile_command$compile_rpath" | $Xsed -e 's%@OUTPUT@%\$progdir/\$file%g'` + else + # fast_install is set to needless + relink_command= + fi + else + link_command="$compile_var$compile_command$compile_rpath" + relink_command="$finalize_var$finalize_command$finalize_rpath" + fi + fi + + # Replace the output file specification. + link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'` + + # Delete the old output files. + $opt_dry_run || $RM $output $output_objdir/$outputname $output_objdir/lt-$outputname + + func_show_eval "$link_command" 'exit $?' + + # Now create the wrapper script. + func_verbose "creating $output" + + # Quote the relink command for shipping. + if test -n "$relink_command"; then + # Preserve any variables that may affect compiler behavior + for var in $variables_saved_for_relink; do + if eval test -z \"\${$var+set}\"; then + relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command" + elif eval var_value=\$$var; test -z "$var_value"; then + relink_command="$var=; export $var; $relink_command" + else + func_quote_for_eval "$var_value" + relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command" + fi + done + relink_command="(cd `pwd`; $relink_command)" + relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"` + fi + + # Quote $ECHO for shipping. + if test "X$ECHO" = "X$SHELL $progpath --fallback-echo"; then + case $progpath in + [\\/]* | [A-Za-z]:[\\/]*) qecho="$SHELL $progpath --fallback-echo";; + *) qecho="$SHELL `pwd`/$progpath --fallback-echo";; + esac + qecho=`$ECHO "X$qecho" | $Xsed -e "$sed_quote_subst"` + else + qecho=`$ECHO "X$ECHO" | $Xsed -e "$sed_quote_subst"` + fi + + # Only actually do things if not in dry run mode. + $opt_dry_run || { + # win32 will think the script is a binary if it has + # a .exe suffix, so we strip it off here. + case $output in + *.exe) func_stripname '' '.exe' "$output" + output=$func_stripname_result ;; + esac + # test for cygwin because mv fails w/o .exe extensions + case $host in + *cygwin*) + exeext=.exe + func_stripname '' '.exe' "$outputname" + outputname=$func_stripname_result ;; + *) exeext= ;; + esac + case $host in + *cygwin* | *mingw* ) + func_dirname_and_basename "$output" "" "." + output_name=$func_basename_result + output_path=$func_dirname_result + cwrappersource="$output_path/$objdir/lt-$output_name.c" + cwrapper="$output_path/$output_name.exe" + $RM $cwrappersource $cwrapper + trap "$RM $cwrappersource $cwrapper; exit $EXIT_FAILURE" 1 2 15 + + func_emit_cwrapperexe_src > $cwrappersource + + # The wrapper executable is built using the $host compiler, + # because it contains $host paths and files. If cross- + # compiling, it, like the target executable, must be + # executed on the $host or under an emulation environment. + $opt_dry_run || { + $LTCC $LTCFLAGS -o $cwrapper $cwrappersource + $STRIP $cwrapper + } + + # Now, create the wrapper script for func_source use: + func_ltwrapper_scriptname $cwrapper + $RM $func_ltwrapper_scriptname_result + trap "$RM $func_ltwrapper_scriptname_result; exit $EXIT_FAILURE" 1 2 15 + $opt_dry_run || { + # note: this script will not be executed, so do not chmod. + if test "x$build" = "x$host" ; then + $cwrapper --lt-dump-script > $func_ltwrapper_scriptname_result + else + func_emit_wrapper no > $func_ltwrapper_scriptname_result + fi + } + ;; + * ) + $RM $output + trap "$RM $output; exit $EXIT_FAILURE" 1 2 15 + + func_emit_wrapper no > $output + chmod +x $output + ;; + esac + } + exit $EXIT_SUCCESS + ;; + esac + + # See if we need to build an old-fashioned archive. + for oldlib in $oldlibs; do + + if test "$build_libtool_libs" = convenience; then + oldobjs="$libobjs_save $symfileobj" + addlibs="$convenience" + build_libtool_libs=no + else + if test "$build_libtool_libs" = module; then + oldobjs="$libobjs_save" + build_libtool_libs=no + else + oldobjs="$old_deplibs $non_pic_objects" + if test "$preload" = yes && test -f "$symfileobj"; then + oldobjs="$oldobjs $symfileobj" + fi + fi + addlibs="$old_convenience" + fi + + if test -n "$addlibs"; then + gentop="$output_objdir/${outputname}x" + generated="$generated $gentop" + + func_extract_archives $gentop $addlibs + oldobjs="$oldobjs $func_extract_archives_result" + fi + + # Do each command in the archive commands. + if test -n "$old_archive_from_new_cmds" && test "$build_libtool_libs" = yes; then + cmds=$old_archive_from_new_cmds + else + + # Add any objects from preloaded convenience libraries + if test -n "$dlprefiles"; then + gentop="$output_objdir/${outputname}x" + generated="$generated $gentop" + + func_extract_archives $gentop $dlprefiles + oldobjs="$oldobjs $func_extract_archives_result" + fi + + # POSIX demands no paths to be encoded in archives. We have + # to avoid creating archives with duplicate basenames if we + # might have to extract them afterwards, e.g., when creating a + # static archive out of a convenience library, or when linking + # the entirety of a libtool archive into another (currently + # not supported by libtool). + if (for obj in $oldobjs + do + func_basename "$obj" + $ECHO "$func_basename_result" + done | sort | sort -uc >/dev/null 2>&1); then + : + else + $ECHO "copying selected object files to avoid basename conflicts..." + gentop="$output_objdir/${outputname}x" + generated="$generated $gentop" + func_mkdir_p "$gentop" + save_oldobjs=$oldobjs + oldobjs= + counter=1 + for obj in $save_oldobjs + do + func_basename "$obj" + objbase="$func_basename_result" + case " $oldobjs " in + " ") oldobjs=$obj ;; + *[\ /]"$objbase "*) + while :; do + # Make sure we don't pick an alternate name that also + # overlaps. + newobj=lt$counter-$objbase + func_arith $counter + 1 + counter=$func_arith_result + case " $oldobjs " in + *[\ /]"$newobj "*) ;; + *) if test ! -f "$gentop/$newobj"; then break; fi ;; + esac + done + func_show_eval "ln $obj $gentop/$newobj || cp $obj $gentop/$newobj" + oldobjs="$oldobjs $gentop/$newobj" + ;; + *) oldobjs="$oldobjs $obj" ;; + esac + done + fi + eval cmds=\"$old_archive_cmds\" + + func_len " $cmds" + len=$func_len_result + if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then + cmds=$old_archive_cmds + else + # the command line is too long to link in one step, link in parts + func_verbose "using piecewise archive linking..." + save_RANLIB=$RANLIB + RANLIB=: + objlist= + concat_cmds= + save_oldobjs=$oldobjs + oldobjs= + # Is there a better way of finding the last object in the list? + for obj in $save_oldobjs + do + last_oldobj=$obj + done + eval test_cmds=\"$old_archive_cmds\" + func_len " $test_cmds" + len0=$func_len_result + len=$len0 + for obj in $save_oldobjs + do + func_len " $obj" + func_arith $len + $func_len_result + len=$func_arith_result + func_append objlist " $obj" + if test "$len" -lt "$max_cmd_len"; then + : + else + # the above command should be used before it gets too long + oldobjs=$objlist + if test "$obj" = "$last_oldobj" ; then + RANLIB=$save_RANLIB + fi + test -z "$concat_cmds" || concat_cmds=$concat_cmds~ + eval concat_cmds=\"\${concat_cmds}$old_archive_cmds\" + objlist= + len=$len0 + fi + done + RANLIB=$save_RANLIB + oldobjs=$objlist + if test "X$oldobjs" = "X" ; then + eval cmds=\"\$concat_cmds\" + else + eval cmds=\"\$concat_cmds~\$old_archive_cmds\" + fi + fi + fi + func_execute_cmds "$cmds" 'exit $?' + done + + test -n "$generated" && \ + func_show_eval "${RM}r$generated" + + # Now create the libtool archive. + case $output in + *.la) + old_library= + test "$build_old_libs" = yes && old_library="$libname.$libext" + func_verbose "creating $output" + + # Preserve any variables that may affect compiler behavior + for var in $variables_saved_for_relink; do + if eval test -z \"\${$var+set}\"; then + relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command" + elif eval var_value=\$$var; test -z "$var_value"; then + relink_command="$var=; export $var; $relink_command" + else + func_quote_for_eval "$var_value" + relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command" + fi + done + # Quote the link command for shipping. + relink_command="(cd `pwd`; $SHELL $progpath $preserve_args --mode=relink $libtool_args @inst_prefix_dir@)" + relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"` + if test "$hardcode_automatic" = yes ; then + relink_command= + fi + + # Only create the output if not a dry run. + $opt_dry_run || { + for installed in no yes; do + if test "$installed" = yes; then + if test -z "$install_libdir"; then + break + fi + output="$output_objdir/$outputname"i + # Replace all uninstalled libtool libraries with the installed ones + newdependency_libs= + for deplib in $dependency_libs; do + case $deplib in + *.la) + func_basename "$deplib" + name="$func_basename_result" + eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib` + test -z "$libdir" && \ + func_fatal_error "\`$deplib' is not a valid libtool archive" + newdependency_libs="$newdependency_libs $libdir/$name" + ;; + *) newdependency_libs="$newdependency_libs $deplib" ;; + esac + done + dependency_libs="$newdependency_libs" + newdlfiles= + + for lib in $dlfiles; do + case $lib in + *.la) + func_basename "$lib" + name="$func_basename_result" + eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib` + test -z "$libdir" && \ + func_fatal_error "\`$lib' is not a valid libtool archive" + newdlfiles="$newdlfiles $libdir/$name" + ;; + *) newdlfiles="$newdlfiles $lib" ;; + esac + done + dlfiles="$newdlfiles" + newdlprefiles= + for lib in $dlprefiles; do + case $lib in + *.la) + # Only pass preopened files to the pseudo-archive (for + # eventual linking with the app. that links it) if we + # didn't already link the preopened objects directly into + # the library: + func_basename "$lib" + name="$func_basename_result" + eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib` + test -z "$libdir" && \ + func_fatal_error "\`$lib' is not a valid libtool archive" + newdlprefiles="$newdlprefiles $libdir/$name" + ;; + esac + done + dlprefiles="$newdlprefiles" + else + newdlfiles= + for lib in $dlfiles; do + case $lib in + [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;; + *) abs=`pwd`"/$lib" ;; + esac + newdlfiles="$newdlfiles $abs" + done + dlfiles="$newdlfiles" + newdlprefiles= + for lib in $dlprefiles; do + case $lib in + [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;; + *) abs=`pwd`"/$lib" ;; + esac + newdlprefiles="$newdlprefiles $abs" + done + dlprefiles="$newdlprefiles" + fi + $RM $output + # place dlname in correct position for cygwin + tdlname=$dlname + case $host,$output,$installed,$module,$dlname in + *cygwin*,*lai,yes,no,*.dll | *mingw*,*lai,yes,no,*.dll | *cegcc*,*lai,yes,no,*.dll) tdlname=../bin/$dlname ;; + esac + $ECHO > $output "\ +# $outputname - a libtool library file +# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION +# +# Please DO NOT delete this file! +# It is necessary for linking the library. + +# The name that we can dlopen(3). +dlname='$tdlname' + +# Names of this library. +library_names='$library_names' + +# The name of the static archive. +old_library='$old_library' + +# Linker flags that can not go in dependency_libs. +inherited_linker_flags='$new_inherited_linker_flags' + +# Libraries that this one depends upon. +dependency_libs='$dependency_libs' + +# Names of additional weak libraries provided by this library +weak_library_names='$weak_libs' + +# Version information for $libname. +current=$current +age=$age +revision=$revision + +# Is this an already installed library? +installed=$installed + +# Should we warn about portability when linking against -modules? +shouldnotlink=$module + +# Files to dlopen/dlpreopen +dlopen='$dlfiles' +dlpreopen='$dlprefiles' + +# Directory that this library needs to be installed in: +libdir='$install_libdir'" + if test "$installed" = no && test "$need_relink" = yes; then + $ECHO >> $output "\ +relink_command=\"$relink_command\"" + fi + done + } + + # Do a symbolic link so that the libtool archive can be found in + # LD_LIBRARY_PATH before the program is installed. + func_show_eval '( cd "$output_objdir" && $RM "$outputname" && $LN_S "../$outputname" "$outputname" )' 'exit $?' + ;; + esac + exit $EXIT_SUCCESS +} + +{ test "$mode" = link || test "$mode" = relink; } && + func_mode_link ${1+"$@"} + + +# func_mode_uninstall arg... +func_mode_uninstall () +{ + $opt_debug + RM="$nonopt" + files= + rmforce= + exit_status=0 + + # This variable tells wrapper scripts just to set variables rather + # than running their programs. + libtool_install_magic="$magic" + + for arg + do + case $arg in + -f) RM="$RM $arg"; rmforce=yes ;; + -*) RM="$RM $arg" ;; + *) files="$files $arg" ;; + esac + done + + test -z "$RM" && \ + func_fatal_help "you must specify an RM program" + + rmdirs= + + origobjdir="$objdir" + for file in $files; do + func_dirname "$file" "" "." + dir="$func_dirname_result" + if test "X$dir" = X.; then + objdir="$origobjdir" + else + objdir="$dir/$origobjdir" + fi + func_basename "$file" + name="$func_basename_result" + test "$mode" = uninstall && objdir="$dir" + + # Remember objdir for removal later, being careful to avoid duplicates + if test "$mode" = clean; then + case " $rmdirs " in + *" $objdir "*) ;; + *) rmdirs="$rmdirs $objdir" ;; + esac + fi + + # Don't error if the file doesn't exist and rm -f was used. + if { test -L "$file"; } >/dev/null 2>&1 || + { test -h "$file"; } >/dev/null 2>&1 || + test -f "$file"; then + : + elif test -d "$file"; then + exit_status=1 + continue + elif test "$rmforce" = yes; then + continue + fi + + rmfiles="$file" + + case $name in + *.la) + # Possibly a libtool archive, so verify it. + if func_lalib_p "$file"; then + func_source $dir/$name + + # Delete the libtool libraries and symlinks. + for n in $library_names; do + rmfiles="$rmfiles $objdir/$n" + done + test -n "$old_library" && rmfiles="$rmfiles $objdir/$old_library" + + case "$mode" in + clean) + case " $library_names " in + # " " in the beginning catches empty $dlname + *" $dlname "*) ;; + *) rmfiles="$rmfiles $objdir/$dlname" ;; + esac + test -n "$libdir" && rmfiles="$rmfiles $objdir/$name $objdir/${name}i" + ;; + uninstall) + if test -n "$library_names"; then + # Do each command in the postuninstall commands. + func_execute_cmds "$postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1' + fi + + if test -n "$old_library"; then + # Do each command in the old_postuninstall commands. + func_execute_cmds "$old_postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1' + fi + # FIXME: should reinstall the best remaining shared library. + ;; + esac + fi + ;; + + *.lo) + # Possibly a libtool object, so verify it. + if func_lalib_p "$file"; then + + # Read the .lo file + func_source $dir/$name + + # Add PIC object to the list of files to remove. + if test -n "$pic_object" && + test "$pic_object" != none; then + rmfiles="$rmfiles $dir/$pic_object" + fi + + # Add non-PIC object to the list of files to remove. + if test -n "$non_pic_object" && + test "$non_pic_object" != none; then + rmfiles="$rmfiles $dir/$non_pic_object" + fi + fi + ;; + + *) + if test "$mode" = clean ; then + noexename=$name + case $file in + *.exe) + func_stripname '' '.exe' "$file" + file=$func_stripname_result + func_stripname '' '.exe' "$name" + noexename=$func_stripname_result + # $file with .exe has already been added to rmfiles, + # add $file without .exe + rmfiles="$rmfiles $file" + ;; + esac + # Do a test to see if this is a libtool program. + if func_ltwrapper_p "$file"; then + if func_ltwrapper_executable_p "$file"; then + func_ltwrapper_scriptname "$file" + relink_command= + func_source $func_ltwrapper_scriptname_result + rmfiles="$rmfiles $func_ltwrapper_scriptname_result" + else + relink_command= + func_source $dir/$noexename + fi + + # note $name still contains .exe if it was in $file originally + # as does the version of $file that was added into $rmfiles + rmfiles="$rmfiles $objdir/$name $objdir/${name}S.${objext}" + if test "$fast_install" = yes && test -n "$relink_command"; then + rmfiles="$rmfiles $objdir/lt-$name" + fi + if test "X$noexename" != "X$name" ; then + rmfiles="$rmfiles $objdir/lt-${noexename}.c" + fi + fi + fi + ;; + esac + func_show_eval "$RM $rmfiles" 'exit_status=1' + done + objdir="$origobjdir" + + # Try to remove the ${objdir}s in the directories where we deleted files + for dir in $rmdirs; do + if test -d "$dir"; then + func_show_eval "rmdir $dir >/dev/null 2>&1" + fi + done + + exit $exit_status +} + +{ test "$mode" = uninstall || test "$mode" = clean; } && + func_mode_uninstall ${1+"$@"} + +test -z "$mode" && { + help="$generic_help" + func_fatal_help "you must specify a MODE" +} + +test -z "$exec_cmd" && \ + func_fatal_help "invalid operation mode \`$mode'" + +if test -n "$exec_cmd"; then + eval exec "$exec_cmd" + exit $EXIT_FAILURE +fi + +exit $exit_status + + +# The TAGs below are defined such that we never get into a situation +# in which we disable both kinds of libraries. Given conflicting +# choices, we go for a static library, that is the most portable, +# since we can't tell whether shared libraries were disabled because +# the user asked for that or because the platform doesn't support +# them. This is particularly important on AIX, because we don't +# support having both static and shared libraries enabled at the same +# time on that platform, so we default to a shared-only configuration. +# If a disable-shared tag is given, we'll fallback to a static-only +# configuration. But we'll never go from static-only to shared-only. + +# ### BEGIN LIBTOOL TAG CONFIG: disable-shared +build_libtool_libs=no +build_old_libs=yes +# ### END LIBTOOL TAG CONFIG: disable-shared + +# ### BEGIN LIBTOOL TAG CONFIG: disable-static +build_old_libs=`case $build_libtool_libs in yes) echo no;; *) echo yes;; esac` +# ### END LIBTOOL TAG CONFIG: disable-static + +# Local Variables: +# mode:shell-script +# sh-indentation:2 +# End: +# vi:sw=2 + diff --git a/binaries/src/clustalo/m4/ax_openmp.m4 b/binaries/src/clustalo/m4/ax_openmp.m4 new file mode 100644 index 0000000..7ea794b --- /dev/null +++ b/binaries/src/clustalo/m4/ax_openmp.m4 @@ -0,0 +1,99 @@ +# =========================================================================== +# http://www.gnu.org/software/autoconf-archive/ax_openmp.html +# =========================================================================== +# +# SYNOPSIS +# +# AX_OPENMP([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]]) +# +# DESCRIPTION +# +# This macro tries to find out how to compile programs that use OpenMP a +# standard API and set of compiler directives for parallel programming +# (see http://www-unix.mcs/) +# +# On success, it sets the OPENMP_CFLAGS/OPENMP_CXXFLAGS/OPENMP_F77FLAGS +# output variable to the flag (e.g. -omp) used both to compile *and* link +# OpenMP programs in the current language. +# +# NOTE: You are assumed to not only compile your program with these flags, +# but also link it with them as well. +# +# If you want to compile everything with OpenMP, you should set: +# +# CFLAGS="$CFLAGS $OPENMP_CFLAGS" +# #OR# CXXFLAGS="$CXXFLAGS $OPENMP_CXXFLAGS" +# #OR# FFLAGS="$FFLAGS $OPENMP_FFLAGS" +# +# (depending on the selected language). +# +# The user can override the default choice by setting the corresponding +# environment variable (e.g. OPENMP_CFLAGS). +# +# ACTION-IF-FOUND is a list of shell commands to run if an OpenMP flag is +# found, and ACTION-IF-NOT-FOUND is a list of commands to run it if it is +# not found. If ACTION-IF-FOUND is not specified, the default action will +# define HAVE_OPENMP. +# +# LICENSE +# +# Copyright (c) 2008 Steven G. Johnson +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the +# Free Software Foundation, either version 3 of the License, or (at your +# option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General +# Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program. If not, see . +# +# As a special exception, the respective Autoconf Macro's copyright owner +# gives unlimited permission to copy, distribute and modify the configure +# scripts that are the output of Autoconf when processing the Macro. You +# need not follow the terms of the GNU General Public License when using +# or distributing such scripts, even though portions of the text of the +# Macro appear in them. The GNU General Public License (GPL) does govern +# all other use of the material that constitutes the Autoconf Macro. +# +# This special exception to the GPL applies to versions of the Autoconf +# Macro released by the Autoconf Archive. When you make and distribute a +# modified version of the Autoconf Macro, you may extend this special +# exception to the GPL to apply to your modified version as well. + +#serial 8 + +AC_DEFUN([AX_OPENMP], [ +AC_PREREQ(2.59) dnl for _AC_LANG_PREFIX + +AC_CACHE_CHECK([for OpenMP flag of _AC_LANG compiler], ax_cv_[]_AC_LANG_ABBREV[]_openmp, [save[]_AC_LANG_PREFIX[]FLAGS=$[]_AC_LANG_PREFIX[]FLAGS +ax_cv_[]_AC_LANG_ABBREV[]_openmp=unknown +# Flags to try: -fopenmp (gcc), -openmp (icc), -mp (SGI & PGI), +# -xopenmp (Sun), -omp (Tru64), -qsmp=omp (AIX), none +ax_openmp_flags="-fopenmp -openmp -mp -xopenmp -omp -qsmp=omp none" +if test "x$OPENMP_[]_AC_LANG_PREFIX[]FLAGS" != x; then + ax_openmp_flags="$OPENMP_[]_AC_LANG_PREFIX[]FLAGS $ax_openmp_flags" +fi +for ax_openmp_flag in $ax_openmp_flags; do + case $ax_openmp_flag in + none) []_AC_LANG_PREFIX[]FLAGS=$save[]_AC_LANG_PREFIX[] ;; + *) []_AC_LANG_PREFIX[]FLAGS="$save[]_AC_LANG_PREFIX[]FLAGS $ax_openmp_flag" ;; + esac + AC_TRY_LINK_FUNC(omp_set_num_threads, + [ax_cv_[]_AC_LANG_ABBREV[]_openmp=$ax_openmp_flag; break]) +done +[]_AC_LANG_PREFIX[]FLAGS=$save[]_AC_LANG_PREFIX[]FLAGS +]) +if test "x$ax_cv_[]_AC_LANG_ABBREV[]_openmp" = "xunknown"; then + m4_default([$2],:) +else + if test "x$ax_cv_[]_AC_LANG_ABBREV[]_openmp" != "xnone"; then + OPENMP_[]_AC_LANG_PREFIX[]FLAGS=$ax_cv_[]_AC_LANG_ABBREV[]_openmp + fi + m4_default([$1], [AC_DEFINE(HAVE_OPENMP,1,[Define if OpenMP is enabled])]) +fi +])dnl AX_OPENMP diff --git a/binaries/src/clustalo/m4/ax_prefix_config_h.m4 b/binaries/src/clustalo/m4/ax_prefix_config_h.m4 new file mode 100644 index 0000000..43a3906 --- /dev/null +++ b/binaries/src/clustalo/m4/ax_prefix_config_h.m4 @@ -0,0 +1,209 @@ +# =========================================================================== +# http://www.gnu.org/software/autoconf-archive/ax_prefix_config_h.html +# =========================================================================== +# +# SYNOPSIS +# +# AX_PREFIX_CONFIG_H [(OUTPUT-HEADER [,PREFIX [,ORIG-HEADER]])] +# +# DESCRIPTION +# +# This is a new variant from ac_prefix_config_ this one will use a +# lowercase-prefix if the config-define was starting with a +# lowercase-char, e.g. "#define const", "#define restrict", or "#define +# off_t", (and this one can live in another directory, e.g. +# testpkg/config.h therefore I decided to move the output-header to be the +# first arg) +# +# takes the usual config.h generated header file; looks for each of the +# generated "#define SOMEDEF" lines, and prefixes the defined name (ie. +# makes it "#define PREFIX_SOMEDEF". The result is written to the output +# config.header file. The PREFIX is converted to uppercase for the +# conversions. +# +# Defaults: +# +# OUTPUT-HEADER = $PACKAGE-config.h +# PREFIX = $PACKAGE +# ORIG-HEADER, from AM_CONFIG_HEADER(config.h) +# +# Your configure.ac script should contain both macros in this order, and +# unlike the earlier variations of this prefix-macro it is okay to place +# the AX_PREFIX_CONFIG_H call before the AC_OUTPUT invokation. +# +# Example: +# +# AC_INIT(config.h.in) # config.h.in as created by "autoheader" +# AM_INIT_AUTOMAKE(testpkg, 0.1.1) # makes #undef VERSION and PACKAGE +# AM_CONFIG_HEADER(config.h) # prep config.h from config.h.in +# AX_PREFIX_CONFIG_H(mylib/_config.h) # prep mylib/_config.h from it.. +# AC_MEMORY_H # makes "#undef NEED_MEMORY_H" +# AC_C_CONST_H # makes "#undef const" +# AC_OUTPUT(Makefile) # creates the "config.h" now +# # and also mylib/_config.h +# +# if the argument to AX_PREFIX_CONFIG_H would have been omitted then the +# default outputfile would have been called simply "testpkg-config.h", but +# even under the name "mylib/_config.h" it contains prefix-defines like +# +# #ifndef TESTPKG_VERSION +# #define TESTPKG_VERSION "0.1.1" +# #endif +# #ifndef TESTPKG_NEED_MEMORY_H +# #define TESTPKG_NEED_MEMORY_H 1 +# #endif +# #ifndef _testpkg_const +# #define _testpkg_const _const +# #endif +# +# and this "mylib/_config.h" can be installed along with other +# header-files, which is most convenient when creating a shared library +# (that has some headers) where some functionality is dependent on the +# OS-features detected at compile-time. No need to invent some +# "mylib-confdefs.h.in" manually. :-) +# +# Note that some AC_DEFINEs that end up in the config.h file are actually +# self-referential - e.g. AC_C_INLINE, AC_C_CONST, and the AC_TYPE_OFF_T +# say that they "will define inline|const|off_t if the system does not do +# it by itself". You might want to clean up about these - consider an +# extra mylib/conf.h that reads something like: +# +# #include +# #ifndef _testpkg_const +# #define _testpkg_const const +# #endif +# +# and then start using _testpkg_const in the header files. That is also a +# good thing to differentiate whether some library-user has starting to +# take up with a different compiler, so perhaps it could read something +# like this: +# +# #ifdef _MSC_VER +# #include +# #else +# #include +# #endif +# #ifndef _testpkg_const +# #define _testpkg_const const +# #endif +# +# LICENSE +# +# Copyright (c) 2008 Guido U. Draheim +# Copyright (c) 2008 Marten Svantesson +# Copyright (c) 2008 Gerald Point +# +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the +# Free Software Foundation; either version 3 of the License, or (at your +# option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General +# Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program. If not, see . +# +# As a special exception, the respective Autoconf Macro's copyright owner +# gives unlimited permission to copy, distribute and modify the configure +# scripts that are the output of Autoconf when processing the Macro. You +# need not follow the terms of the GNU General Public License when using +# or distributing such scripts, even though portions of the text of the +# Macro appear in them. The GNU General Public License (GPL) does govern +# all other use of the material that constitutes the Autoconf Macro. +# +# This special exception to the GPL applies to versions of the Autoconf +# Macro released by the Autoconf Archive. When you make and distribute a +# modified version of the Autoconf Macro, you may extend this special +# exception to the GPL to apply to your modified version as well. + +#serial 11 + +AC_DEFUN([AX_PREFIX_CONFIG_H],[dnl +AC_PREREQ([2.62]) +AC_BEFORE([AC_CONFIG_HEADERS],[$0])dnl +AC_CONFIG_COMMANDS([ifelse($1,,$PACKAGE-config.h,$1)],[dnl +AS_VAR_PUSHDEF([_OUT],[ac_prefix_conf_OUT])dnl +AS_VAR_PUSHDEF([_DEF],[ac_prefix_conf_DEF])dnl +AS_VAR_PUSHDEF([_PKG],[ac_prefix_conf_PKG])dnl +AS_VAR_PUSHDEF([_LOW],[ac_prefix_conf_LOW])dnl +AS_VAR_PUSHDEF([_UPP],[ac_prefix_conf_UPP])dnl +AS_VAR_PUSHDEF([_INP],[ac_prefix_conf_INP])dnl +m4_pushdef([_script],[conftest.prefix])dnl +m4_pushdef([_symbol],[m4_cr_Letters[]m4_cr_digits[]_])dnl +_OUT=`echo ifelse($1, , $PACKAGE-config.h, $1)` +_DEF=`echo _$_OUT | sed -e "y:m4_cr_letters:m4_cr_LETTERS[]:" -e "s/@<:@^m4_cr_Letters@:>@/_/g"` +_PKG=`echo ifelse($2, , $PACKAGE, $2)` +_LOW=`echo _$_PKG | sed -e "y:m4_cr_LETTERS-:m4_cr_letters[]_:"` +_UPP=`echo $_PKG | sed -e "y:m4_cr_letters-:m4_cr_LETTERS[]_:" -e "/^@<:@m4_cr_digits@:>@/s/^/_/"` +_INP=`echo "ifelse($3,,,$3)" | sed -e 's/ *//'` +if test ".$_INP" = "."; then + for ac_file in : $CONFIG_HEADERS; do test "_$ac_file" = _: && continue + case "$ac_file" in + *.h) _INP=$ac_file ;; + *) + esac + test ".$_INP" != "." && break + done +fi +if test ".$_INP" = "."; then + case "$_OUT" in + */*) _INP=`basename "$_OUT"` + ;; + *-*) _INP=`echo "$_OUT" | sed -e "s/@<:@_symbol@:>@*-//"` + ;; + *) _INP=config.h + ;; + esac +fi +if test -z "$_PKG" ; then + AC_MSG_ERROR([no prefix for _PREFIX_PKG_CONFIG_H]) +else + if test ! -f "$_INP" ; then if test -f "$srcdir/$_INP" ; then + _INP="$srcdir/$_INP" + fi fi + AC_MSG_NOTICE(creating $_OUT - prefix $_UPP for $_INP defines) + if test -f $_INP ; then + AS_ECHO(["s/^@%:@undef *\\(@<:@m4_cr_LETTERS[]_@:>@\\)/@%:@undef $_UPP""_\\1/"]) > _script + AS_ECHO(["s/^@%:@undef *\\(@<:@m4_cr_letters@:>@\\)/@%:@undef $_LOW""_\\1/"]) >> _script + AS_ECHO(["s/^@%:@def[]ine *\\(@<:@m4_cr_LETTERS[]_@:>@@<:@_symbol@:>@*\\)\\(.*\\)/@%:@ifndef $_UPP""_\\1\\"]) >> _script + AS_ECHO(["@%:@def[]ine $_UPP""_\\1\\2\\"]) >> _script + AS_ECHO(["@%:@endif/"]) >> _script + AS_ECHO(["s/^@%:@def[]ine *\\(@<:@m4_cr_letters@:>@@<:@_symbol@:>@*\\)\\(.*\\)/@%:@ifndef $_LOW""_\\1\\"]) >> _script + AS_ECHO(["@%:@define $_LOW""_\\1\\2\\"]) >> _script + AS_ECHO(["@%:@endif/"]) >> _script + # now executing _script on _DEF input to create _OUT output file + echo "@%:@ifndef $_DEF" >$tmp/pconfig.h + echo "@%:@def[]ine $_DEF 1" >>$tmp/pconfig.h + echo ' ' >>$tmp/pconfig.h + echo /'*' $_OUT. Generated automatically at end of configure. '*'/ >>$tmp/pconfig.h + + sed -f _script $_INP >>$tmp/pconfig.h + echo ' ' >>$tmp/pconfig.h + echo '/* once:' $_DEF '*/' >>$tmp/pconfig.h + echo "@%:@endif" >>$tmp/pconfig.h + if cmp -s $_OUT $tmp/pconfig.h 2>/dev/null; then + AC_MSG_NOTICE([$_OUT is unchanged]) + else + ac_dir=`AS_DIRNAME(["$_OUT"])` + AS_MKDIR_P(["$ac_dir"]) + rm -f "$_OUT" + mv $tmp/pconfig.h "$_OUT" + fi + cp _script _configs.sed + else + AC_MSG_ERROR([input file $_INP does not exist - skip generating $_OUT]) + fi + rm -f conftest.* +fi +m4_popdef([_symbol])dnl +m4_popdef([_script])dnl +AS_VAR_POPDEF([_INP])dnl +AS_VAR_POPDEF([_UPP])dnl +AS_VAR_POPDEF([_LOW])dnl +AS_VAR_POPDEF([_PKG])dnl +AS_VAR_POPDEF([_DEF])dnl +AS_VAR_POPDEF([_OUT])dnl +],[PACKAGE="$PACKAGE"])]) diff --git a/binaries/src/clustalo/m4/libtool.m4 b/binaries/src/clustalo/m4/libtool.m4 new file mode 100644 index 0000000..2ca1c1f --- /dev/null +++ b/binaries/src/clustalo/m4/libtool.m4 @@ -0,0 +1,7373 @@ +# libtool.m4 - Configure libtool for the host system. -*-Autoconf-*- +# +# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, +# 2006, 2007, 2008 Free Software Foundation, Inc. +# Written by Gordon Matzigkeit, 1996 +# +# This file is free software; the Free Software Foundation gives +# unlimited permission to copy and/or distribute it, with or without +# modifications, as long as this notice is preserved. + +m4_define([_LT_COPYING], [dnl +# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, +# 2006, 2007, 2008 Free Software Foundation, Inc. +# Written by Gordon Matzigkeit, 1996 +# +# This file is part of GNU Libtool. +# +# GNU Libtool is free software; you can redistribute it and/or +# modify it under the terms of the GNU General Public License as +# published by the Free Software Foundation; either version 2 of +# the License, or (at your option) any later version. +# +# As a special exception to the GNU General Public License, +# if you distribute this file as part of a program or library that +# is built using GNU Libtool, you may include this file under the +# same distribution terms that you use for the rest of that program. +# +# GNU Libtool is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with GNU Libtool; see the file COPYING. If not, a copy +# can be downloaded from http://www.gnu.org/licenses/gpl.html, or +# obtained by writing to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +]) + +# serial 56 LT_INIT + + +# LT_PREREQ(VERSION) +# ------------------ +# Complain and exit if this libtool version is less that VERSION. +m4_defun([LT_PREREQ], +[m4_if(m4_version_compare(m4_defn([LT_PACKAGE_VERSION]), [$1]), -1, + [m4_default([$3], + [m4_fatal([Libtool version $1 or higher is required], + 63)])], + [$2])]) + + +# _LT_CHECK_BUILDDIR +# ------------------ +# Complain if the absolute build directory name contains unusual characters +m4_defun([_LT_CHECK_BUILDDIR], +[case `pwd` in + *\ * | *\ *) + AC_MSG_WARN([Libtool does not cope well with whitespace in `pwd`]) ;; +esac +]) + + +# LT_INIT([OPTIONS]) +# ------------------ +AC_DEFUN([LT_INIT], +[AC_PREREQ([2.58])dnl We use AC_INCLUDES_DEFAULT +AC_BEFORE([$0], [LT_LANG])dnl +AC_BEFORE([$0], [LT_OUTPUT])dnl +AC_BEFORE([$0], [LTDL_INIT])dnl +m4_require([_LT_CHECK_BUILDDIR])dnl + +dnl Autoconf doesn't catch unexpanded LT_ macros by default: +m4_pattern_forbid([^_?LT_[A-Z_]+$])dnl +m4_pattern_allow([^(_LT_EOF|LT_DLGLOBAL|LT_DLLAZY_OR_NOW|LT_MULTI_MODULE)$])dnl +dnl aclocal doesn't pull ltoptions.m4, ltsugar.m4, or ltversion.m4 +dnl unless we require an AC_DEFUNed macro: +AC_REQUIRE([LTOPTIONS_VERSION])dnl +AC_REQUIRE([LTSUGAR_VERSION])dnl +AC_REQUIRE([LTVERSION_VERSION])dnl +AC_REQUIRE([LTOBSOLETE_VERSION])dnl +m4_require([_LT_PROG_LTMAIN])dnl + +dnl Parse OPTIONS +_LT_SET_OPTIONS([$0], [$1]) + +# This can be used to rebuild libtool when needed +LIBTOOL_DEPS="$ltmain" + +# Always use our own libtool. +LIBTOOL='$(SHELL) $(top_builddir)/libtool' +AC_SUBST(LIBTOOL)dnl + +_LT_SETUP + +# Only expand once: +m4_define([LT_INIT]) +])# LT_INIT + +# Old names: +AU_ALIAS([AC_PROG_LIBTOOL], [LT_INIT]) +AU_ALIAS([AM_PROG_LIBTOOL], [LT_INIT]) +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AC_PROG_LIBTOOL], []) +dnl AC_DEFUN([AM_PROG_LIBTOOL], []) + + +# _LT_CC_BASENAME(CC) +# ------------------- +# Calculate cc_basename. Skip known compiler wrappers and cross-prefix. +m4_defun([_LT_CC_BASENAME], +[for cc_temp in $1""; do + case $cc_temp in + compile | *[[\\/]]compile | ccache | *[[\\/]]ccache ) ;; + distcc | *[[\\/]]distcc | purify | *[[\\/]]purify ) ;; + \-*) ;; + *) break;; + esac +done +cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"` +]) + + +# _LT_FILEUTILS_DEFAULTS +# ---------------------- +# It is okay to use these file commands and assume they have been set +# sensibly after `m4_require([_LT_FILEUTILS_DEFAULTS])'. +m4_defun([_LT_FILEUTILS_DEFAULTS], +[: ${CP="cp -f"} +: ${MV="mv -f"} +: ${RM="rm -f"} +])# _LT_FILEUTILS_DEFAULTS + + +# _LT_SETUP +# --------- +m4_defun([_LT_SETUP], +[AC_REQUIRE([AC_CANONICAL_HOST])dnl +AC_REQUIRE([AC_CANONICAL_BUILD])dnl +_LT_DECL([], [host_alias], [0], [The host system])dnl +_LT_DECL([], [host], [0])dnl +_LT_DECL([], [host_os], [0])dnl +dnl +_LT_DECL([], [build_alias], [0], [The build system])dnl +_LT_DECL([], [build], [0])dnl +_LT_DECL([], [build_os], [0])dnl +dnl +AC_REQUIRE([AC_PROG_CC])dnl +AC_REQUIRE([LT_PATH_LD])dnl +AC_REQUIRE([LT_PATH_NM])dnl +dnl +AC_REQUIRE([AC_PROG_LN_S])dnl +test -z "$LN_S" && LN_S="ln -s" +_LT_DECL([], [LN_S], [1], [Whether we need soft or hard links])dnl +dnl +AC_REQUIRE([LT_CMD_MAX_LEN])dnl +_LT_DECL([objext], [ac_objext], [0], [Object file suffix (normally "o")])dnl +_LT_DECL([], [exeext], [0], [Executable file suffix (normally "")])dnl +dnl +m4_require([_LT_FILEUTILS_DEFAULTS])dnl +m4_require([_LT_CHECK_SHELL_FEATURES])dnl +m4_require([_LT_CMD_RELOAD])dnl +m4_require([_LT_CHECK_MAGIC_METHOD])dnl +m4_require([_LT_CMD_OLD_ARCHIVE])dnl +m4_require([_LT_CMD_GLOBAL_SYMBOLS])dnl + +_LT_CONFIG_LIBTOOL_INIT([ +# See if we are running on zsh, and set the options which allow our +# commands through without removal of \ escapes INIT. +if test -n "\${ZSH_VERSION+set}" ; then + setopt NO_GLOB_SUBST +fi +]) +if test -n "${ZSH_VERSION+set}" ; then + setopt NO_GLOB_SUBST +fi + +_LT_CHECK_OBJDIR + +m4_require([_LT_TAG_COMPILER])dnl +_LT_PROG_ECHO_BACKSLASH + +case $host_os in +aix3*) + # AIX sometimes has problems with the GCC collect2 program. For some + # reason, if we set the COLLECT_NAMES environment variable, the problems + # vanish in a puff of smoke. + if test "X${COLLECT_NAMES+set}" != Xset; then + COLLECT_NAMES= + export COLLECT_NAMES + fi + ;; +esac + +# Sed substitution that helps us do robust quoting. It backslashifies +# metacharacters that are still active within double-quoted strings. +sed_quote_subst='s/\([["`$\\]]\)/\\\1/g' + +# Same as above, but do not quote variable references. +double_quote_subst='s/\([["`\\]]\)/\\\1/g' + +# Sed substitution to delay expansion of an escaped shell variable in a +# double_quote_subst'ed string. +delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g' + +# Sed substitution to delay expansion of an escaped single quote. +delay_single_quote_subst='s/'\''/'\'\\\\\\\'\''/g' + +# Sed substitution to avoid accidental globbing in evaled expressions +no_glob_subst='s/\*/\\\*/g' + +# Global variables: +ofile=libtool +can_build_shared=yes + +# All known linkers require a `.a' archive for static linking (except MSVC, +# which needs '.lib'). +libext=a + +with_gnu_ld="$lt_cv_prog_gnu_ld" + +old_CC="$CC" +old_CFLAGS="$CFLAGS" + +# Set sane defaults for various variables +test -z "$CC" && CC=cc +test -z "$LTCC" && LTCC=$CC +test -z "$LTCFLAGS" && LTCFLAGS=$CFLAGS +test -z "$LD" && LD=ld +test -z "$ac_objext" && ac_objext=o + +_LT_CC_BASENAME([$compiler]) + +# Only perform the check for file, if the check method requires it +test -z "$MAGIC_CMD" && MAGIC_CMD=file +case $deplibs_check_method in +file_magic*) + if test "$file_magic_cmd" = '$MAGIC_CMD'; then + _LT_PATH_MAGIC + fi + ;; +esac + +# Use C for the default configuration in the libtool script +LT_SUPPORTED_TAG([CC]) +_LT_LANG_C_CONFIG +_LT_LANG_DEFAULT_CONFIG +_LT_CONFIG_COMMANDS +])# _LT_SETUP + + +# _LT_PROG_LTMAIN +# --------------- +# Note that this code is called both from `configure', and `config.status' +# now that we use AC_CONFIG_COMMANDS to generate libtool. Notably, +# `config.status' has no value for ac_aux_dir unless we are using Automake, +# so we pass a copy along to make sure it has a sensible value anyway. +m4_defun([_LT_PROG_LTMAIN], +[m4_ifdef([AC_REQUIRE_AUX_FILE], [AC_REQUIRE_AUX_FILE([ltmain.sh])])dnl +_LT_CONFIG_LIBTOOL_INIT([ac_aux_dir='$ac_aux_dir']) +ltmain="$ac_aux_dir/ltmain.sh" +])# _LT_PROG_LTMAIN + + +## ------------------------------------- ## +## Accumulate code for creating libtool. ## +## ------------------------------------- ## + +# So that we can recreate a full libtool script including additional +# tags, we accumulate the chunks of code to send to AC_CONFIG_COMMANDS +# in macros and then make a single call at the end using the `libtool' +# label. + + +# _LT_CONFIG_LIBTOOL_INIT([INIT-COMMANDS]) +# ---------------------------------------- +# Register INIT-COMMANDS to be passed to AC_CONFIG_COMMANDS later. +m4_define([_LT_CONFIG_LIBTOOL_INIT], +[m4_ifval([$1], + [m4_append([_LT_OUTPUT_LIBTOOL_INIT], + [$1 +])])]) + +# Initialize. +m4_define([_LT_OUTPUT_LIBTOOL_INIT]) + + +# _LT_CONFIG_LIBTOOL([COMMANDS]) +# ------------------------------ +# Register COMMANDS to be passed to AC_CONFIG_COMMANDS later. +m4_define([_LT_CONFIG_LIBTOOL], +[m4_ifval([$1], + [m4_append([_LT_OUTPUT_LIBTOOL_COMMANDS], + [$1 +])])]) + +# Initialize. +m4_define([_LT_OUTPUT_LIBTOOL_COMMANDS]) + + +# _LT_CONFIG_SAVE_COMMANDS([COMMANDS], [INIT_COMMANDS]) +# ----------------------------------------------------- +m4_defun([_LT_CONFIG_SAVE_COMMANDS], +[_LT_CONFIG_LIBTOOL([$1]) +_LT_CONFIG_LIBTOOL_INIT([$2]) +]) + + +# _LT_FORMAT_COMMENT([COMMENT]) +# ----------------------------- +# Add leading comment marks to the start of each line, and a trailing +# full-stop to the whole comment if one is not present already. +m4_define([_LT_FORMAT_COMMENT], +[m4_ifval([$1], [ +m4_bpatsubst([m4_bpatsubst([$1], [^ *], [# ])], + [['`$\]], [\\\&])]m4_bmatch([$1], [[!?.]$], [], [.]) +)]) + + + +## ------------------------ ## +## FIXME: Eliminate VARNAME ## +## ------------------------ ## + + +# _LT_DECL([CONFIGNAME], VARNAME, VALUE, [DESCRIPTION], [IS-TAGGED?]) +# ------------------------------------------------------------------- +# CONFIGNAME is the name given to the value in the libtool script. +# VARNAME is the (base) name used in the configure script. +# VALUE may be 0, 1 or 2 for a computed quote escaped value based on +# VARNAME. Any other value will be used directly. +m4_define([_LT_DECL], +[lt_if_append_uniq([lt_decl_varnames], [$2], [, ], + [lt_dict_add_subkey([lt_decl_dict], [$2], [libtool_name], + [m4_ifval([$1], [$1], [$2])]) + lt_dict_add_subkey([lt_decl_dict], [$2], [value], [$3]) + m4_ifval([$4], + [lt_dict_add_subkey([lt_decl_dict], [$2], [description], [$4])]) + lt_dict_add_subkey([lt_decl_dict], [$2], + [tagged?], [m4_ifval([$5], [yes], [no])])]) +]) + + +# _LT_TAGDECL([CONFIGNAME], VARNAME, VALUE, [DESCRIPTION]) +# -------------------------------------------------------- +m4_define([_LT_TAGDECL], [_LT_DECL([$1], [$2], [$3], [$4], [yes])]) + + +# lt_decl_tag_varnames([SEPARATOR], [VARNAME1...]) +# ------------------------------------------------ +m4_define([lt_decl_tag_varnames], +[_lt_decl_filter([tagged?], [yes], $@)]) + + +# _lt_decl_filter(SUBKEY, VALUE, [SEPARATOR], [VARNAME1..]) +# --------------------------------------------------------- +m4_define([_lt_decl_filter], +[m4_case([$#], + [0], [m4_fatal([$0: too few arguments: $#])], + [1], [m4_fatal([$0: too few arguments: $#: $1])], + [2], [lt_dict_filter([lt_decl_dict], [$1], [$2], [], lt_decl_varnames)], + [3], [lt_dict_filter([lt_decl_dict], [$1], [$2], [$3], lt_decl_varnames)], + [lt_dict_filter([lt_decl_dict], $@)])[]dnl +]) + + +# lt_decl_quote_varnames([SEPARATOR], [VARNAME1...]) +# -------------------------------------------------- +m4_define([lt_decl_quote_varnames], +[_lt_decl_filter([value], [1], $@)]) + + +# lt_decl_dquote_varnames([SEPARATOR], [VARNAME1...]) +# --------------------------------------------------- +m4_define([lt_decl_dquote_varnames], +[_lt_decl_filter([value], [2], $@)]) + + +# lt_decl_varnames_tagged([SEPARATOR], [VARNAME1...]) +# --------------------------------------------------- +m4_define([lt_decl_varnames_tagged], +[m4_assert([$# <= 2])dnl +_$0(m4_quote(m4_default([$1], [[, ]])), + m4_ifval([$2], [[$2]], [m4_dquote(lt_decl_tag_varnames)]), + m4_split(m4_normalize(m4_quote(_LT_TAGS)), [ ]))]) +m4_define([_lt_decl_varnames_tagged], +[m4_ifval([$3], [lt_combine([$1], [$2], [_], $3)])]) + + +# lt_decl_all_varnames([SEPARATOR], [VARNAME1...]) +# ------------------------------------------------ +m4_define([lt_decl_all_varnames], +[_$0(m4_quote(m4_default([$1], [[, ]])), + m4_if([$2], [], + m4_quote(lt_decl_varnames), + m4_quote(m4_shift($@))))[]dnl +]) +m4_define([_lt_decl_all_varnames], +[lt_join($@, lt_decl_varnames_tagged([$1], + lt_decl_tag_varnames([[, ]], m4_shift($@))))dnl +]) + + +# _LT_CONFIG_STATUS_DECLARE([VARNAME]) +# ------------------------------------ +# Quote a variable value, and forward it to `config.status' so that its +# declaration there will have the same value as in `configure'. VARNAME +# must have a single quote delimited value for this to work. +m4_define([_LT_CONFIG_STATUS_DECLARE], +[$1='`$ECHO "X$][$1" | $Xsed -e "$delay_single_quote_subst"`']) + + +# _LT_CONFIG_STATUS_DECLARATIONS +# ------------------------------ +# We delimit libtool config variables with single quotes, so when +# we write them to config.status, we have to be sure to quote all +# embedded single quotes properly. In configure, this macro expands +# each variable declared with _LT_DECL (and _LT_TAGDECL) into: +# +# ='`$ECHO "X$" | $Xsed -e "$delay_single_quote_subst"`' +m4_defun([_LT_CONFIG_STATUS_DECLARATIONS], +[m4_foreach([_lt_var], m4_quote(lt_decl_all_varnames), + [m4_n([_LT_CONFIG_STATUS_DECLARE(_lt_var)])])]) + + +# _LT_LIBTOOL_TAGS +# ---------------- +# Output comment and list of tags supported by the script +m4_defun([_LT_LIBTOOL_TAGS], +[_LT_FORMAT_COMMENT([The names of the tagged configurations supported by this script])dnl +available_tags="_LT_TAGS"dnl +]) + + +# _LT_LIBTOOL_DECLARE(VARNAME, [TAG]) +# ----------------------------------- +# Extract the dictionary values for VARNAME (optionally with TAG) and +# expand to a commented shell variable setting: +# +# # Some comment about what VAR is for. +# visible_name=$lt_internal_name +m4_define([_LT_LIBTOOL_DECLARE], +[_LT_FORMAT_COMMENT(m4_quote(lt_dict_fetch([lt_decl_dict], [$1], + [description])))[]dnl +m4_pushdef([_libtool_name], + m4_quote(lt_dict_fetch([lt_decl_dict], [$1], [libtool_name])))[]dnl +m4_case(m4_quote(lt_dict_fetch([lt_decl_dict], [$1], [value])), + [0], [_libtool_name=[$]$1], + [1], [_libtool_name=$lt_[]$1], + [2], [_libtool_name=$lt_[]$1], + [_libtool_name=lt_dict_fetch([lt_decl_dict], [$1], [value])])[]dnl +m4_ifval([$2], [_$2])[]m4_popdef([_libtool_name])[]dnl +]) + + +# _LT_LIBTOOL_CONFIG_VARS +# ----------------------- +# Produce commented declarations of non-tagged libtool config variables +# suitable for insertion in the LIBTOOL CONFIG section of the `libtool' +# script. Tagged libtool config variables (even for the LIBTOOL CONFIG +# section) are produced by _LT_LIBTOOL_TAG_VARS. +m4_defun([_LT_LIBTOOL_CONFIG_VARS], +[m4_foreach([_lt_var], + m4_quote(_lt_decl_filter([tagged?], [no], [], lt_decl_varnames)), + [m4_n([_LT_LIBTOOL_DECLARE(_lt_var)])])]) + + +# _LT_LIBTOOL_TAG_VARS(TAG) +# ------------------------- +m4_define([_LT_LIBTOOL_TAG_VARS], +[m4_foreach([_lt_var], m4_quote(lt_decl_tag_varnames), + [m4_n([_LT_LIBTOOL_DECLARE(_lt_var, [$1])])])]) + + +# _LT_TAGVAR(VARNAME, [TAGNAME]) +# ------------------------------ +m4_define([_LT_TAGVAR], [m4_ifval([$2], [$1_$2], [$1])]) + + +# _LT_CONFIG_COMMANDS +# ------------------- +# Send accumulated output to $CONFIG_STATUS. Thanks to the lists of +# variables for single and double quote escaping we saved from calls +# to _LT_DECL, we can put quote escaped variables declarations +# into `config.status', and then the shell code to quote escape them in +# for loops in `config.status'. Finally, any additional code accumulated +# from calls to _LT_CONFIG_LIBTOOL_INIT is expanded. +m4_defun([_LT_CONFIG_COMMANDS], +[AC_PROVIDE_IFELSE([LT_OUTPUT], + dnl If the libtool generation code has been placed in $CONFIG_LT, + dnl instead of duplicating it all over again into config.status, + dnl then we will have config.status run $CONFIG_LT later, so it + dnl needs to know what name is stored there: + [AC_CONFIG_COMMANDS([libtool], + [$SHELL $CONFIG_LT || AS_EXIT(1)], [CONFIG_LT='$CONFIG_LT'])], + dnl If the libtool generation code is destined for config.status, + dnl expand the accumulated commands and init code now: + [AC_CONFIG_COMMANDS([libtool], + [_LT_OUTPUT_LIBTOOL_COMMANDS], [_LT_OUTPUT_LIBTOOL_COMMANDS_INIT])]) +])#_LT_CONFIG_COMMANDS + + +# Initialize. +m4_define([_LT_OUTPUT_LIBTOOL_COMMANDS_INIT], +[ + +# The HP-UX ksh and POSIX shell print the target directory to stdout +# if CDPATH is set. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + +sed_quote_subst='$sed_quote_subst' +double_quote_subst='$double_quote_subst' +delay_variable_subst='$delay_variable_subst' +_LT_CONFIG_STATUS_DECLARATIONS +LTCC='$LTCC' +LTCFLAGS='$LTCFLAGS' +compiler='$compiler_DEFAULT' + +# Quote evaled strings. +for var in lt_decl_all_varnames([[ \ +]], lt_decl_quote_varnames); do + case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in + *[[\\\\\\\`\\"\\\$]]*) + eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$sed_quote_subst\\"\\\`\\\\\\"" + ;; + *) + eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\"" + ;; + esac +done + +# Double-quote double-evaled strings. +for var in lt_decl_all_varnames([[ \ +]], lt_decl_dquote_varnames); do + case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in + *[[\\\\\\\`\\"\\\$]]*) + eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$double_quote_subst\\" -e \\"\\\$sed_quote_subst\\" -e \\"\\\$delay_variable_subst\\"\\\`\\\\\\"" + ;; + *) + eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\"" + ;; + esac +done + +# Fix-up fallback echo if it was mangled by the above quoting rules. +case \$lt_ECHO in +*'\\\[$]0 --fallback-echo"')dnl " + lt_ECHO=\`\$ECHO "X\$lt_ECHO" | \$Xsed -e 's/\\\\\\\\\\\\\\\[$]0 --fallback-echo"\[$]/\[$]0 --fallback-echo"/'\` + ;; +esac + +_LT_OUTPUT_LIBTOOL_INIT +]) + + +# LT_OUTPUT +# --------- +# This macro allows early generation of the libtool script (before +# AC_OUTPUT is called), incase it is used in configure for compilation +# tests. +AC_DEFUN([LT_OUTPUT], +[: ${CONFIG_LT=./config.lt} +AC_MSG_NOTICE([creating $CONFIG_LT]) +cat >"$CONFIG_LT" <<_LTEOF +#! $SHELL +# Generated by $as_me. +# Run this file to recreate a libtool stub with the current configuration. + +lt_cl_silent=false +SHELL=\${CONFIG_SHELL-$SHELL} +_LTEOF + +cat >>"$CONFIG_LT" <<\_LTEOF +AS_SHELL_SANITIZE +_AS_PREPARE + +exec AS_MESSAGE_FD>&1 +exec AS_MESSAGE_LOG_FD>>config.log +{ + echo + AS_BOX([Running $as_me.]) +} >&AS_MESSAGE_LOG_FD + +lt_cl_help="\ +\`$as_me' creates a local libtool stub from the current configuration, +for use in further configure time tests before the real libtool is +generated. + +Usage: $[0] [[OPTIONS]] + + -h, --help print this help, then exit + -V, --version print version number, then exit + -q, --quiet do not print progress messages + -d, --debug don't remove temporary files + +Report bugs to ." + +lt_cl_version="\ +m4_ifset([AC_PACKAGE_NAME], [AC_PACKAGE_NAME ])config.lt[]dnl +m4_ifset([AC_PACKAGE_VERSION], [ AC_PACKAGE_VERSION]) +configured by $[0], generated by m4_PACKAGE_STRING. + +Copyright (C) 2008 Free Software Foundation, Inc. +This config.lt script is free software; the Free Software Foundation +gives unlimited permision to copy, distribute and modify it." + +while test $[#] != 0 +do + case $[1] in + --version | --v* | -V ) + echo "$lt_cl_version"; exit 0 ;; + --help | --h* | -h ) + echo "$lt_cl_help"; exit 0 ;; + --debug | --d* | -d ) + debug=: ;; + --quiet | --q* | --silent | --s* | -q ) + lt_cl_silent=: ;; + + -*) AC_MSG_ERROR([unrecognized option: $[1] +Try \`$[0] --help' for more information.]) ;; + + *) AC_MSG_ERROR([unrecognized argument: $[1] +Try \`$[0] --help' for more information.]) ;; + esac + shift +done + +if $lt_cl_silent; then + exec AS_MESSAGE_FD>/dev/null +fi +_LTEOF + +cat >>"$CONFIG_LT" <<_LTEOF +_LT_OUTPUT_LIBTOOL_COMMANDS_INIT +_LTEOF + +cat >>"$CONFIG_LT" <<\_LTEOF +AC_MSG_NOTICE([creating $ofile]) +_LT_OUTPUT_LIBTOOL_COMMANDS +AS_EXIT(0) +_LTEOF +chmod +x "$CONFIG_LT" + +# configure is writing to config.log, but config.lt does its own redirection, +# appending to config.log, which fails on DOS, as config.log is still kept +# open by configure. Here we exec the FD to /dev/null, effectively closing +# config.log, so it can be properly (re)opened and appended to by config.lt. +if test "$no_create" != yes; then + lt_cl_success=: + test "$silent" = yes && + lt_config_lt_args="$lt_config_lt_args --quiet" + exec AS_MESSAGE_LOG_FD>/dev/null + $SHELL "$CONFIG_LT" $lt_config_lt_args || lt_cl_success=false + exec AS_MESSAGE_LOG_FD>>config.log + $lt_cl_success || AS_EXIT(1) +fi +])# LT_OUTPUT + + +# _LT_CONFIG(TAG) +# --------------- +# If TAG is the built-in tag, create an initial libtool script with a +# default configuration from the untagged config vars. Otherwise add code +# to config.status for appending the configuration named by TAG from the +# matching tagged config vars. +m4_defun([_LT_CONFIG], +[m4_require([_LT_FILEUTILS_DEFAULTS])dnl +_LT_CONFIG_SAVE_COMMANDS([ + m4_define([_LT_TAG], m4_if([$1], [], [C], [$1]))dnl + m4_if(_LT_TAG, [C], [ + # See if we are running on zsh, and set the options which allow our + # commands through without removal of \ escapes. + if test -n "${ZSH_VERSION+set}" ; then + setopt NO_GLOB_SUBST + fi + + cfgfile="${ofile}T" + trap "$RM \"$cfgfile\"; exit 1" 1 2 15 + $RM "$cfgfile" + + cat <<_LT_EOF >> "$cfgfile" +#! $SHELL + +# `$ECHO "$ofile" | sed 's%^.*/%%'` - Provide generalized library-building support services. +# Generated automatically by $as_me ($PACKAGE$TIMESTAMP) $VERSION +# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`: +# NOTE: Changes made to this file will be lost: look at ltmain.sh. +# +_LT_COPYING +_LT_LIBTOOL_TAGS + +# ### BEGIN LIBTOOL CONFIG +_LT_LIBTOOL_CONFIG_VARS +_LT_LIBTOOL_TAG_VARS +# ### END LIBTOOL CONFIG + +_LT_EOF + + case $host_os in + aix3*) + cat <<\_LT_EOF >> "$cfgfile" +# AIX sometimes has problems with the GCC collect2 program. For some +# reason, if we set the COLLECT_NAMES environment variable, the problems +# vanish in a puff of smoke. +if test "X${COLLECT_NAMES+set}" != Xset; then + COLLECT_NAMES= + export COLLECT_NAMES +fi +_LT_EOF + ;; + esac + + _LT_PROG_LTMAIN + + # We use sed instead of cat because bash on DJGPP gets confused if + # if finds mixed CR/LF and LF-only lines. Since sed operates in + # text mode, it properly converts lines to CR/LF. This bash problem + # is reportedly fixed, but why not run on old versions too? + sed '/^# Generated shell functions inserted here/q' "$ltmain" >> "$cfgfile" \ + || (rm -f "$cfgfile"; exit 1) + + _LT_PROG_XSI_SHELLFNS + + sed -n '/^# Generated shell functions inserted here/,$p' "$ltmain" >> "$cfgfile" \ + || (rm -f "$cfgfile"; exit 1) + + mv -f "$cfgfile" "$ofile" || + (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile") + chmod +x "$ofile" +], +[cat <<_LT_EOF >> "$ofile" + +dnl Unfortunately we have to use $1 here, since _LT_TAG is not expanded +dnl in a comment (ie after a #). +# ### BEGIN LIBTOOL TAG CONFIG: $1 +_LT_LIBTOOL_TAG_VARS(_LT_TAG) +# ### END LIBTOOL TAG CONFIG: $1 +_LT_EOF +])dnl /m4_if +], +[m4_if([$1], [], [ + PACKAGE='$PACKAGE' + VERSION='$VERSION' + TIMESTAMP='$TIMESTAMP' + RM='$RM' + ofile='$ofile'], []) +])dnl /_LT_CONFIG_SAVE_COMMANDS +])# _LT_CONFIG + + +# LT_SUPPORTED_TAG(TAG) +# --------------------- +# Trace this macro to discover what tags are supported by the libtool +# --tag option, using: +# autoconf --trace 'LT_SUPPORTED_TAG:$1' +AC_DEFUN([LT_SUPPORTED_TAG], []) + + +# C support is built-in for now +m4_define([_LT_LANG_C_enabled], []) +m4_define([_LT_TAGS], []) + + +# LT_LANG(LANG) +# ------------- +# Enable libtool support for the given language if not already enabled. +AC_DEFUN([LT_LANG], +[AC_BEFORE([$0], [LT_OUTPUT])dnl +m4_case([$1], + [C], [_LT_LANG(C)], + [C++], [_LT_LANG(CXX)], + [Java], [_LT_LANG(GCJ)], + [Fortran 77], [_LT_LANG(F77)], + [Fortran], [_LT_LANG(FC)], + [Windows Resource], [_LT_LANG(RC)], + [m4_ifdef([_LT_LANG_]$1[_CONFIG], + [_LT_LANG($1)], + [m4_fatal([$0: unsupported language: "$1"])])])dnl +])# LT_LANG + + +# _LT_LANG(LANGNAME) +# ------------------ +m4_defun([_LT_LANG], +[m4_ifdef([_LT_LANG_]$1[_enabled], [], + [LT_SUPPORTED_TAG([$1])dnl + m4_append([_LT_TAGS], [$1 ])dnl + m4_define([_LT_LANG_]$1[_enabled], [])dnl + _LT_LANG_$1_CONFIG($1)])dnl +])# _LT_LANG + + +# _LT_LANG_DEFAULT_CONFIG +# ----------------------- +m4_defun([_LT_LANG_DEFAULT_CONFIG], +[AC_PROVIDE_IFELSE([AC_PROG_CXX], + [LT_LANG(CXX)], + [m4_define([AC_PROG_CXX], defn([AC_PROG_CXX])[LT_LANG(CXX)])]) + +AC_PROVIDE_IFELSE([AC_PROG_F77], + [LT_LANG(F77)], + [m4_define([AC_PROG_F77], defn([AC_PROG_F77])[LT_LANG(F77)])]) + +AC_PROVIDE_IFELSE([AC_PROG_FC], + [LT_LANG(FC)], + [m4_define([AC_PROG_FC], defn([AC_PROG_FC])[LT_LANG(FC)])]) + +dnl The call to [A][M_PROG_GCJ] is quoted like that to stop aclocal +dnl pulling things in needlessly. +AC_PROVIDE_IFELSE([AC_PROG_GCJ], + [LT_LANG(GCJ)], + [AC_PROVIDE_IFELSE([A][M_PROG_GCJ], + [LT_LANG(GCJ)], + [AC_PROVIDE_IFELSE([LT_PROG_GCJ], + [LT_LANG(GCJ)], + [m4_ifdef([AC_PROG_GCJ], + [m4_define([AC_PROG_GCJ], defn([AC_PROG_GCJ])[LT_LANG(GCJ)])]) + m4_ifdef([A][M_PROG_GCJ], + [m4_define([A][M_PROG_GCJ], defn([A][M_PROG_GCJ])[LT_LANG(GCJ)])]) + m4_ifdef([LT_PROG_GCJ], + [m4_define([LT_PROG_GCJ], defn([LT_PROG_GCJ])[LT_LANG(GCJ)])])])])]) + +AC_PROVIDE_IFELSE([LT_PROG_RC], + [LT_LANG(RC)], + [m4_define([LT_PROG_RC], defn([LT_PROG_RC])[LT_LANG(RC)])]) +])# _LT_LANG_DEFAULT_CONFIG + +# Obsolete macros: +AU_DEFUN([AC_LIBTOOL_CXX], [LT_LANG(C++)]) +AU_DEFUN([AC_LIBTOOL_F77], [LT_LANG(Fortran 77)]) +AU_DEFUN([AC_LIBTOOL_FC], [LT_LANG(Fortran)]) +AU_DEFUN([AC_LIBTOOL_GCJ], [LT_LANG(Java)]) +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AC_LIBTOOL_CXX], []) +dnl AC_DEFUN([AC_LIBTOOL_F77], []) +dnl AC_DEFUN([AC_LIBTOOL_FC], []) +dnl AC_DEFUN([AC_LIBTOOL_GCJ], []) + + +# _LT_TAG_COMPILER +# ---------------- +m4_defun([_LT_TAG_COMPILER], +[AC_REQUIRE([AC_PROG_CC])dnl + +_LT_DECL([LTCC], [CC], [1], [A C compiler])dnl +_LT_DECL([LTCFLAGS], [CFLAGS], [1], [LTCC compiler flags])dnl +_LT_TAGDECL([CC], [compiler], [1], [A language specific compiler])dnl +_LT_TAGDECL([with_gcc], [GCC], [0], [Is the compiler the GNU compiler?])dnl + +# If no C compiler was specified, use CC. +LTCC=${LTCC-"$CC"} + +# If no C compiler flags were specified, use CFLAGS. +LTCFLAGS=${LTCFLAGS-"$CFLAGS"} + +# Allow CC to be a program name with arguments. +compiler=$CC +])# _LT_TAG_COMPILER + + +# _LT_COMPILER_BOILERPLATE +# ------------------------ +# Check for compiler boilerplate output or warnings with +# the simple compiler test code. +m4_defun([_LT_COMPILER_BOILERPLATE], +[m4_require([_LT_DECL_SED])dnl +ac_outfile=conftest.$ac_objext +echo "$lt_simple_compile_test_code" >conftest.$ac_ext +eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err +_lt_compiler_boilerplate=`cat conftest.err` +$RM conftest* +])# _LT_COMPILER_BOILERPLATE + + +# _LT_LINKER_BOILERPLATE +# ---------------------- +# Check for linker boilerplate output or warnings with +# the simple link test code. +m4_defun([_LT_LINKER_BOILERPLATE], +[m4_require([_LT_DECL_SED])dnl +ac_outfile=conftest.$ac_objext +echo "$lt_simple_link_test_code" >conftest.$ac_ext +eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err +_lt_linker_boilerplate=`cat conftest.err` +$RM -r conftest* +])# _LT_LINKER_BOILERPLATE + +# _LT_REQUIRED_DARWIN_CHECKS +# ------------------------- +m4_defun_once([_LT_REQUIRED_DARWIN_CHECKS],[ + case $host_os in + rhapsody* | darwin*) + AC_CHECK_TOOL([DSYMUTIL], [dsymutil], [:]) + AC_CHECK_TOOL([NMEDIT], [nmedit], [:]) + AC_CHECK_TOOL([LIPO], [lipo], [:]) + AC_CHECK_TOOL([OTOOL], [otool], [:]) + AC_CHECK_TOOL([OTOOL64], [otool64], [:]) + _LT_DECL([], [DSYMUTIL], [1], + [Tool to manipulate archived DWARF debug symbol files on Mac OS X]) + _LT_DECL([], [NMEDIT], [1], + [Tool to change global to local symbols on Mac OS X]) + _LT_DECL([], [LIPO], [1], + [Tool to manipulate fat objects and archives on Mac OS X]) + _LT_DECL([], [OTOOL], [1], + [ldd/readelf like tool for Mach-O binaries on Mac OS X]) + _LT_DECL([], [OTOOL64], [1], + [ldd/readelf like tool for 64 bit Mach-O binaries on Mac OS X 10.4]) + + AC_CACHE_CHECK([for -single_module linker flag],[lt_cv_apple_cc_single_mod], + [lt_cv_apple_cc_single_mod=no + if test -z "${LT_MULTI_MODULE}"; then + # By default we will add the -single_module flag. You can override + # by either setting the environment variable LT_MULTI_MODULE + # non-empty at configure time, or by adding -multi_module to the + # link flags. + rm -rf libconftest.dylib* + echo "int foo(void){return 1;}" > conftest.c + echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ +-dynamiclib -Wl,-single_module conftest.c" >&AS_MESSAGE_LOG_FD + $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ + -dynamiclib -Wl,-single_module conftest.c 2>conftest.err + _lt_result=$? + if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then + lt_cv_apple_cc_single_mod=yes + else + cat conftest.err >&AS_MESSAGE_LOG_FD + fi + rm -rf libconftest.dylib* + rm -f conftest.* + fi]) + AC_CACHE_CHECK([for -exported_symbols_list linker flag], + [lt_cv_ld_exported_symbols_list], + [lt_cv_ld_exported_symbols_list=no + save_LDFLAGS=$LDFLAGS + echo "_main" > conftest.sym + LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym" + AC_LINK_IFELSE([AC_LANG_PROGRAM([],[])], + [lt_cv_ld_exported_symbols_list=yes], + [lt_cv_ld_exported_symbols_list=no]) + LDFLAGS="$save_LDFLAGS" + ]) + case $host_os in + rhapsody* | darwin1.[[012]]) + _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;; + darwin1.*) + _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; + darwin*) # darwin 5.x on + # if running on 10.5 or later, the deployment target defaults + # to the OS version, if on x86, and 10.4, the deployment + # target defaults to 10.4. Don't you love it? + case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in + 10.0,*86*-darwin8*|10.0,*-darwin[[91]]*) + _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; + 10.[[012]]*) + _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; + 10.*) + _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; + esac + ;; + esac + if test "$lt_cv_apple_cc_single_mod" = "yes"; then + _lt_dar_single_mod='$single_module' + fi + if test "$lt_cv_ld_exported_symbols_list" = "yes"; then + _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym' + else + _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}' + fi + if test "$DSYMUTIL" != ":"; then + _lt_dsymutil='~$DSYMUTIL $lib || :' + else + _lt_dsymutil= + fi + ;; + esac +]) + + +# _LT_DARWIN_LINKER_FEATURES +# -------------------------- +# Checks for linker and compiler features on darwin +m4_defun([_LT_DARWIN_LINKER_FEATURES], +[ + m4_require([_LT_REQUIRED_DARWIN_CHECKS]) + _LT_TAGVAR(archive_cmds_need_lc, $1)=no + _LT_TAGVAR(hardcode_direct, $1)=no + _LT_TAGVAR(hardcode_automatic, $1)=yes + _LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported + _LT_TAGVAR(whole_archive_flag_spec, $1)='' + _LT_TAGVAR(link_all_deplibs, $1)=yes + _LT_TAGVAR(allow_undefined_flag, $1)="$_lt_dar_allow_undefined" + case $cc_basename in + ifort*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then + output_verbose_link_cmd=echo + _LT_TAGVAR(archive_cmds, $1)="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}" + _LT_TAGVAR(module_cmds, $1)="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}" + _LT_TAGVAR(archive_expsym_cmds, $1)="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}" + _LT_TAGVAR(module_expsym_cmds, $1)="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}" + m4_if([$1], [CXX], +[ if test "$lt_cv_apple_cc_single_mod" != "yes"; then + _LT_TAGVAR(archive_cmds, $1)="\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dsymutil}" + _LT_TAGVAR(archive_expsym_cmds, $1)="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dar_export_syms}${_lt_dsymutil}" + fi +],[]) + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi +]) + +# _LT_SYS_MODULE_PATH_AIX +# ----------------------- +# Links a minimal program and checks the executable +# for the system default hardcoded library path. In most cases, +# this is /usr/lib:/lib, but when the MPI compilers are used +# the location of the communication and MPI libs are included too. +# If we don't find anything, use the default library path according +# to the aix ld manual. +m4_defun([_LT_SYS_MODULE_PATH_AIX], +[m4_require([_LT_DECL_SED])dnl +AC_LINK_IFELSE(AC_LANG_PROGRAM,[ +lt_aix_libpath_sed=' + /Import File Strings/,/^$/ { + /^0/ { + s/^0 *\(.*\)$/\1/ + p + } + }' +aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` +# Check for a 64-bit object if we didn't find anything. +if test -z "$aix_libpath"; then + aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` +fi],[]) +if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi +])# _LT_SYS_MODULE_PATH_AIX + + +# _LT_SHELL_INIT(ARG) +# ------------------- +m4_define([_LT_SHELL_INIT], +[ifdef([AC_DIVERSION_NOTICE], + [AC_DIVERT_PUSH(AC_DIVERSION_NOTICE)], + [AC_DIVERT_PUSH(NOTICE)]) +$1 +AC_DIVERT_POP +])# _LT_SHELL_INIT + + +# _LT_PROG_ECHO_BACKSLASH +# ----------------------- +# Add some code to the start of the generated configure script which +# will find an echo command which doesn't interpret backslashes. +m4_defun([_LT_PROG_ECHO_BACKSLASH], +[_LT_SHELL_INIT([ +# Check that we are running under the correct shell. +SHELL=${CONFIG_SHELL-/bin/sh} + +case X$lt_ECHO in +X*--fallback-echo) + # Remove one level of quotation (which was required for Make). + ECHO=`echo "$lt_ECHO" | sed 's,\\\\\[$]\\[$]0,'[$]0','` + ;; +esac + +ECHO=${lt_ECHO-echo} +if test "X[$]1" = X--no-reexec; then + # Discard the --no-reexec flag, and continue. + shift +elif test "X[$]1" = X--fallback-echo; then + # Avoid inline document here, it may be left over + : +elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' ; then + # Yippee, $ECHO works! + : +else + # Restart under the correct shell. + exec $SHELL "[$]0" --no-reexec ${1+"[$]@"} +fi + +if test "X[$]1" = X--fallback-echo; then + # used as fallback echo + shift + cat <<_LT_EOF +[$]* +_LT_EOF + exit 0 +fi + +# The HP-UX ksh and POSIX shell print the target directory to stdout +# if CDPATH is set. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + +if test -z "$lt_ECHO"; then + if test "X${echo_test_string+set}" != Xset; then + # find a string as large as possible, as long as the shell can cope with it + for cmd in 'sed 50q "[$]0"' 'sed 20q "[$]0"' 'sed 10q "[$]0"' 'sed 2q "[$]0"' 'echo test'; do + # expected sizes: less than 2Kb, 1Kb, 512 bytes, 16 bytes, ... + if { echo_test_string=`eval $cmd`; } 2>/dev/null && + { test "X$echo_test_string" = "X$echo_test_string"; } 2>/dev/null + then + break + fi + done + fi + + if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' && + echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` && + test "X$echo_testing_string" = "X$echo_test_string"; then + : + else + # The Solaris, AIX, and Digital Unix default echo programs unquote + # backslashes. This makes it impossible to quote backslashes using + # echo "$something" | sed 's/\\/\\\\/g' + # + # So, first we look for a working echo in the user's PATH. + + lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR + for dir in $PATH /usr/ucb; do + IFS="$lt_save_ifs" + if (test -f $dir/echo || test -f $dir/echo$ac_exeext) && + test "X`($dir/echo '\t') 2>/dev/null`" = 'X\t' && + echo_testing_string=`($dir/echo "$echo_test_string") 2>/dev/null` && + test "X$echo_testing_string" = "X$echo_test_string"; then + ECHO="$dir/echo" + break + fi + done + IFS="$lt_save_ifs" + + if test "X$ECHO" = Xecho; then + # We didn't find a better echo, so look for alternatives. + if test "X`{ print -r '\t'; } 2>/dev/null`" = 'X\t' && + echo_testing_string=`{ print -r "$echo_test_string"; } 2>/dev/null` && + test "X$echo_testing_string" = "X$echo_test_string"; then + # This shell has a builtin print -r that does the trick. + ECHO='print -r' + elif { test -f /bin/ksh || test -f /bin/ksh$ac_exeext; } && + test "X$CONFIG_SHELL" != X/bin/ksh; then + # If we have ksh, try running configure again with it. + ORIGINAL_CONFIG_SHELL=${CONFIG_SHELL-/bin/sh} + export ORIGINAL_CONFIG_SHELL + CONFIG_SHELL=/bin/ksh + export CONFIG_SHELL + exec $CONFIG_SHELL "[$]0" --no-reexec ${1+"[$]@"} + else + # Try using printf. + ECHO='printf %s\n' + if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' && + echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` && + test "X$echo_testing_string" = "X$echo_test_string"; then + # Cool, printf works + : + elif echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` && + test "X$echo_testing_string" = 'X\t' && + echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` && + test "X$echo_testing_string" = "X$echo_test_string"; then + CONFIG_SHELL=$ORIGINAL_CONFIG_SHELL + export CONFIG_SHELL + SHELL="$CONFIG_SHELL" + export SHELL + ECHO="$CONFIG_SHELL [$]0 --fallback-echo" + elif echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` && + test "X$echo_testing_string" = 'X\t' && + echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` && + test "X$echo_testing_string" = "X$echo_test_string"; then + ECHO="$CONFIG_SHELL [$]0 --fallback-echo" + else + # maybe with a smaller string... + prev=: + + for cmd in 'echo test' 'sed 2q "[$]0"' 'sed 10q "[$]0"' 'sed 20q "[$]0"' 'sed 50q "[$]0"'; do + if { test "X$echo_test_string" = "X`eval $cmd`"; } 2>/dev/null + then + break + fi + prev="$cmd" + done + + if test "$prev" != 'sed 50q "[$]0"'; then + echo_test_string=`eval $prev` + export echo_test_string + exec ${ORIGINAL_CONFIG_SHELL-${CONFIG_SHELL-/bin/sh}} "[$]0" ${1+"[$]@"} + else + # Oops. We lost completely, so just stick with echo. + ECHO=echo + fi + fi + fi + fi + fi +fi + +# Copy echo and quote the copy suitably for passing to libtool from +# the Makefile, instead of quoting the original, which is used later. +lt_ECHO=$ECHO +if test "X$lt_ECHO" = "X$CONFIG_SHELL [$]0 --fallback-echo"; then + lt_ECHO="$CONFIG_SHELL \\\$\[$]0 --fallback-echo" +fi + +AC_SUBST(lt_ECHO) +]) +_LT_DECL([], [SHELL], [1], [Shell to use when invoking shell scripts]) +_LT_DECL([], [ECHO], [1], + [An echo program that does not interpret backslashes]) +])# _LT_PROG_ECHO_BACKSLASH + + +# _LT_ENABLE_LOCK +# --------------- +m4_defun([_LT_ENABLE_LOCK], +[AC_ARG_ENABLE([libtool-lock], + [AS_HELP_STRING([--disable-libtool-lock], + [avoid locking (might break parallel builds)])]) +test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes + +# Some flags need to be propagated to the compiler or linker for good +# libtool support. +case $host in +ia64-*-hpux*) + # Find out which ABI we are using. + echo 'int i;' > conftest.$ac_ext + if AC_TRY_EVAL(ac_compile); then + case `/usr/bin/file conftest.$ac_objext` in + *ELF-32*) + HPUX_IA64_MODE="32" + ;; + *ELF-64*) + HPUX_IA64_MODE="64" + ;; + esac + fi + rm -rf conftest* + ;; +*-*-irix6*) + # Find out which ABI we are using. + echo '[#]line __oline__ "configure"' > conftest.$ac_ext + if AC_TRY_EVAL(ac_compile); then + if test "$lt_cv_prog_gnu_ld" = yes; then + case `/usr/bin/file conftest.$ac_objext` in + *32-bit*) + LD="${LD-ld} -melf32bsmip" + ;; + *N32*) + LD="${LD-ld} -melf32bmipn32" + ;; + *64-bit*) + LD="${LD-ld} -melf64bmip" + ;; + esac + else + case `/usr/bin/file conftest.$ac_objext` in + *32-bit*) + LD="${LD-ld} -32" + ;; + *N32*) + LD="${LD-ld} -n32" + ;; + *64-bit*) + LD="${LD-ld} -64" + ;; + esac + fi + fi + rm -rf conftest* + ;; + +x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \ +s390*-*linux*|s390*-*tpf*|sparc*-*linux*) + # Find out which ABI we are using. + echo 'int i;' > conftest.$ac_ext + if AC_TRY_EVAL(ac_compile); then + case `/usr/bin/file conftest.o` in + *32-bit*) + case $host in + x86_64-*kfreebsd*-gnu) + LD="${LD-ld} -m elf_i386_fbsd" + ;; + x86_64-*linux*) + LD="${LD-ld} -m elf_i386" + ;; + ppc64-*linux*|powerpc64-*linux*) + LD="${LD-ld} -m elf32ppclinux" + ;; + s390x-*linux*) + LD="${LD-ld} -m elf_s390" + ;; + sparc64-*linux*) + LD="${LD-ld} -m elf32_sparc" + ;; + esac + ;; + *64-bit*) + case $host in + x86_64-*kfreebsd*-gnu) + LD="${LD-ld} -m elf_x86_64_fbsd" + ;; + x86_64-*linux*) + LD="${LD-ld} -m elf_x86_64" + ;; + ppc*-*linux*|powerpc*-*linux*) + LD="${LD-ld} -m elf64ppc" + ;; + s390*-*linux*|s390*-*tpf*) + LD="${LD-ld} -m elf64_s390" + ;; + sparc*-*linux*) + LD="${LD-ld} -m elf64_sparc" + ;; + esac + ;; + esac + fi + rm -rf conftest* + ;; + +*-*-sco3.2v5*) + # On SCO OpenServer 5, we need -belf to get full-featured binaries. + SAVE_CFLAGS="$CFLAGS" + CFLAGS="$CFLAGS -belf" + AC_CACHE_CHECK([whether the C compiler needs -belf], lt_cv_cc_needs_belf, + [AC_LANG_PUSH(C) + AC_LINK_IFELSE([AC_LANG_PROGRAM([[]],[[]])],[lt_cv_cc_needs_belf=yes],[lt_cv_cc_needs_belf=no]) + AC_LANG_POP]) + if test x"$lt_cv_cc_needs_belf" != x"yes"; then + # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf + CFLAGS="$SAVE_CFLAGS" + fi + ;; +sparc*-*solaris*) + # Find out which ABI we are using. + echo 'int i;' > conftest.$ac_ext + if AC_TRY_EVAL(ac_compile); then + case `/usr/bin/file conftest.o` in + *64-bit*) + case $lt_cv_prog_gnu_ld in + yes*) LD="${LD-ld} -m elf64_sparc" ;; + *) + if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then + LD="${LD-ld} -64" + fi + ;; + esac + ;; + esac + fi + rm -rf conftest* + ;; +esac + +need_locks="$enable_libtool_lock" +])# _LT_ENABLE_LOCK + + +# _LT_CMD_OLD_ARCHIVE +# ------------------- +m4_defun([_LT_CMD_OLD_ARCHIVE], +[AC_CHECK_TOOL(AR, ar, false) +test -z "$AR" && AR=ar +test -z "$AR_FLAGS" && AR_FLAGS=cru +_LT_DECL([], [AR], [1], [The archiver]) +_LT_DECL([], [AR_FLAGS], [1]) + +AC_CHECK_TOOL(STRIP, strip, :) +test -z "$STRIP" && STRIP=: +_LT_DECL([], [STRIP], [1], [A symbol stripping program]) + +AC_CHECK_TOOL(RANLIB, ranlib, :) +test -z "$RANLIB" && RANLIB=: +_LT_DECL([], [RANLIB], [1], + [Commands used to install an old-style archive]) + +# Determine commands to create old-style static archives. +old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs' +old_postinstall_cmds='chmod 644 $oldlib' +old_postuninstall_cmds= + +if test -n "$RANLIB"; then + case $host_os in + openbsd*) + old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib" + ;; + *) + old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib" + ;; + esac + old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib" +fi +_LT_DECL([], [old_postinstall_cmds], [2]) +_LT_DECL([], [old_postuninstall_cmds], [2]) +_LT_TAGDECL([], [old_archive_cmds], [2], + [Commands used to build an old-style archive]) +])# _LT_CMD_OLD_ARCHIVE + + +# _LT_COMPILER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS, +# [OUTPUT-FILE], [ACTION-SUCCESS], [ACTION-FAILURE]) +# ---------------------------------------------------------------- +# Check whether the given compiler option works +AC_DEFUN([_LT_COMPILER_OPTION], +[m4_require([_LT_FILEUTILS_DEFAULTS])dnl +m4_require([_LT_DECL_SED])dnl +AC_CACHE_CHECK([$1], [$2], + [$2=no + m4_if([$4], , [ac_outfile=conftest.$ac_objext], [ac_outfile=$4]) + echo "$lt_simple_compile_test_code" > conftest.$ac_ext + lt_compiler_flag="$3" + # Insert the option either (1) after the last *FLAGS variable, or + # (2) before a word containing "conftest.", or (3) at the end. + # Note that $ac_compile itself does not contain backslashes and begins + # with a dollar sign (not a hyphen), so the echo should work correctly. + # The option is referenced via a variable to avoid confusing sed. + lt_compile=`echo "$ac_compile" | $SED \ + -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \ + -e 's: [[^ ]]*conftest\.: $lt_compiler_flag&:; t' \ + -e 's:$: $lt_compiler_flag:'` + (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&AS_MESSAGE_LOG_FD) + (eval "$lt_compile" 2>conftest.err) + ac_status=$? + cat conftest.err >&AS_MESSAGE_LOG_FD + echo "$as_me:__oline__: \$? = $ac_status" >&AS_MESSAGE_LOG_FD + if (exit $ac_status) && test -s "$ac_outfile"; then + # The compiler can only warn and ignore the option if not recognized + # So say no if there are warnings other than the usual output. + $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp + $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2 + if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then + $2=yes + fi + fi + $RM conftest* +]) + +if test x"[$]$2" = xyes; then + m4_if([$5], , :, [$5]) +else + m4_if([$6], , :, [$6]) +fi +])# _LT_COMPILER_OPTION + +# Old name: +AU_ALIAS([AC_LIBTOOL_COMPILER_OPTION], [_LT_COMPILER_OPTION]) +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AC_LIBTOOL_COMPILER_OPTION], []) + + +# _LT_LINKER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS, +# [ACTION-SUCCESS], [ACTION-FAILURE]) +# ---------------------------------------------------- +# Check whether the given linker option works +AC_DEFUN([_LT_LINKER_OPTION], +[m4_require([_LT_FILEUTILS_DEFAULTS])dnl +m4_require([_LT_DECL_SED])dnl +AC_CACHE_CHECK([$1], [$2], + [$2=no + save_LDFLAGS="$LDFLAGS" + LDFLAGS="$LDFLAGS $3" + echo "$lt_simple_link_test_code" > conftest.$ac_ext + if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then + # The linker can only warn and ignore the option if not recognized + # So say no if there are warnings + if test -s conftest.err; then + # Append any errors to the config.log. + cat conftest.err 1>&AS_MESSAGE_LOG_FD + $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp + $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2 + if diff conftest.exp conftest.er2 >/dev/null; then + $2=yes + fi + else + $2=yes + fi + fi + $RM -r conftest* + LDFLAGS="$save_LDFLAGS" +]) + +if test x"[$]$2" = xyes; then + m4_if([$4], , :, [$4]) +else + m4_if([$5], , :, [$5]) +fi +])# _LT_LINKER_OPTION + +# Old name: +AU_ALIAS([AC_LIBTOOL_LINKER_OPTION], [_LT_LINKER_OPTION]) +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AC_LIBTOOL_LINKER_OPTION], []) + + +# LT_CMD_MAX_LEN +#--------------- +AC_DEFUN([LT_CMD_MAX_LEN], +[AC_REQUIRE([AC_CANONICAL_HOST])dnl +# find the maximum length of command line arguments +AC_MSG_CHECKING([the maximum length of command line arguments]) +AC_CACHE_VAL([lt_cv_sys_max_cmd_len], [dnl + i=0 + teststring="ABCD" + + case $build_os in + msdosdjgpp*) + # On DJGPP, this test can blow up pretty badly due to problems in libc + # (any single argument exceeding 2000 bytes causes a buffer overrun + # during glob expansion). Even if it were fixed, the result of this + # check would be larger than it should be. + lt_cv_sys_max_cmd_len=12288; # 12K is about right + ;; + + gnu*) + # Under GNU Hurd, this test is not required because there is + # no limit to the length of command line arguments. + # Libtool will interpret -1 as no limit whatsoever + lt_cv_sys_max_cmd_len=-1; + ;; + + cygwin* | mingw* | cegcc*) + # On Win9x/ME, this test blows up -- it succeeds, but takes + # about 5 minutes as the teststring grows exponentially. + # Worse, since 9x/ME are not pre-emptively multitasking, + # you end up with a "frozen" computer, even though with patience + # the test eventually succeeds (with a max line length of 256k). + # Instead, let's just punt: use the minimum linelength reported by + # all of the supported platforms: 8192 (on NT/2K/XP). + lt_cv_sys_max_cmd_len=8192; + ;; + + amigaos*) + # On AmigaOS with pdksh, this test takes hours, literally. + # So we just punt and use a minimum line length of 8192. + lt_cv_sys_max_cmd_len=8192; + ;; + + netbsd* | freebsd* | openbsd* | darwin* | dragonfly*) + # This has been around since 386BSD, at least. Likely further. + if test -x /sbin/sysctl; then + lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax` + elif test -x /usr/sbin/sysctl; then + lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax` + else + lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs + fi + # And add a safety zone + lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` + lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` + ;; + + interix*) + # We know the value 262144 and hardcode it with a safety zone (like BSD) + lt_cv_sys_max_cmd_len=196608 + ;; + + osf*) + # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure + # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not + # nice to cause kernel panics so lets avoid the loop below. + # First set a reasonable default. + lt_cv_sys_max_cmd_len=16384 + # + if test -x /sbin/sysconfig; then + case `/sbin/sysconfig -q proc exec_disable_arg_limit` in + *1*) lt_cv_sys_max_cmd_len=-1 ;; + esac + fi + ;; + sco3.2v5*) + lt_cv_sys_max_cmd_len=102400 + ;; + sysv5* | sco5v6* | sysv4.2uw2*) + kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null` + if test -n "$kargmax"; then + lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[[ ]]//'` + else + lt_cv_sys_max_cmd_len=32768 + fi + ;; + *) + lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null` + if test -n "$lt_cv_sys_max_cmd_len"; then + lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` + lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` + else + # Make teststring a little bigger before we do anything with it. + # a 1K string should be a reasonable start. + for i in 1 2 3 4 5 6 7 8 ; do + teststring=$teststring$teststring + done + SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}} + # If test is not a shell built-in, we'll probably end up computing a + # maximum length that is only half of the actual maximum length, but + # we can't tell. + while { test "X"`$SHELL [$]0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \ + = "XX$teststring$teststring"; } >/dev/null 2>&1 && + test $i != 17 # 1/2 MB should be enough + do + i=`expr $i + 1` + teststring=$teststring$teststring + done + # Only check the string length outside the loop. + lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1` + teststring= + # Add a significant safety factor because C++ compilers can tack on + # massive amounts of additional arguments before passing them to the + # linker. It appears as though 1/2 is a usable value. + lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2` + fi + ;; + esac +]) +if test -n $lt_cv_sys_max_cmd_len ; then + AC_MSG_RESULT($lt_cv_sys_max_cmd_len) +else + AC_MSG_RESULT(none) +fi +max_cmd_len=$lt_cv_sys_max_cmd_len +_LT_DECL([], [max_cmd_len], [0], + [What is the maximum length of a command?]) +])# LT_CMD_MAX_LEN + +# Old name: +AU_ALIAS([AC_LIBTOOL_SYS_MAX_CMD_LEN], [LT_CMD_MAX_LEN]) +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AC_LIBTOOL_SYS_MAX_CMD_LEN], []) + + +# _LT_HEADER_DLFCN +# ---------------- +m4_defun([_LT_HEADER_DLFCN], +[AC_CHECK_HEADERS([dlfcn.h], [], [], [AC_INCLUDES_DEFAULT])dnl +])# _LT_HEADER_DLFCN + + +# _LT_TRY_DLOPEN_SELF (ACTION-IF-TRUE, ACTION-IF-TRUE-W-USCORE, +# ACTION-IF-FALSE, ACTION-IF-CROSS-COMPILING) +# ---------------------------------------------------------------- +m4_defun([_LT_TRY_DLOPEN_SELF], +[m4_require([_LT_HEADER_DLFCN])dnl +if test "$cross_compiling" = yes; then : + [$4] +else + lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2 + lt_status=$lt_dlunknown + cat > conftest.$ac_ext <<_LT_EOF +[#line __oline__ "configure" +#include "confdefs.h" + +#if HAVE_DLFCN_H +#include +#endif + +#include + +#ifdef RTLD_GLOBAL +# define LT_DLGLOBAL RTLD_GLOBAL +#else +# ifdef DL_GLOBAL +# define LT_DLGLOBAL DL_GLOBAL +# else +# define LT_DLGLOBAL 0 +# endif +#endif + +/* We may have to define LT_DLLAZY_OR_NOW in the command line if we + find out it does not work in some platform. */ +#ifndef LT_DLLAZY_OR_NOW +# ifdef RTLD_LAZY +# define LT_DLLAZY_OR_NOW RTLD_LAZY +# else +# ifdef DL_LAZY +# define LT_DLLAZY_OR_NOW DL_LAZY +# else +# ifdef RTLD_NOW +# define LT_DLLAZY_OR_NOW RTLD_NOW +# else +# ifdef DL_NOW +# define LT_DLLAZY_OR_NOW DL_NOW +# else +# define LT_DLLAZY_OR_NOW 0 +# endif +# endif +# endif +# endif +#endif + +void fnord() { int i=42;} +int main () +{ + void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW); + int status = $lt_dlunknown; + + if (self) + { + if (dlsym (self,"fnord")) status = $lt_dlno_uscore; + else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore; + /* dlclose (self); */ + } + else + puts (dlerror ()); + + return status; +}] +_LT_EOF + if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext} 2>/dev/null; then + (./conftest; exit; ) >&AS_MESSAGE_LOG_FD 2>/dev/null + lt_status=$? + case x$lt_status in + x$lt_dlno_uscore) $1 ;; + x$lt_dlneed_uscore) $2 ;; + x$lt_dlunknown|x*) $3 ;; + esac + else : + # compilation failed + $3 + fi +fi +rm -fr conftest* +])# _LT_TRY_DLOPEN_SELF + + +# LT_SYS_DLOPEN_SELF +# ------------------ +AC_DEFUN([LT_SYS_DLOPEN_SELF], +[m4_require([_LT_HEADER_DLFCN])dnl +if test "x$enable_dlopen" != xyes; then + enable_dlopen=unknown + enable_dlopen_self=unknown + enable_dlopen_self_static=unknown +else + lt_cv_dlopen=no + lt_cv_dlopen_libs= + + case $host_os in + beos*) + lt_cv_dlopen="load_add_on" + lt_cv_dlopen_libs= + lt_cv_dlopen_self=yes + ;; + + mingw* | pw32* | cegcc*) + lt_cv_dlopen="LoadLibrary" + lt_cv_dlopen_libs= + ;; + + cygwin*) + lt_cv_dlopen="dlopen" + lt_cv_dlopen_libs= + ;; + + darwin*) + # if libdl is installed we need to link against it + AC_CHECK_LIB([dl], [dlopen], + [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"],[ + lt_cv_dlopen="dyld" + lt_cv_dlopen_libs= + lt_cv_dlopen_self=yes + ]) + ;; + + *) + AC_CHECK_FUNC([shl_load], + [lt_cv_dlopen="shl_load"], + [AC_CHECK_LIB([dld], [shl_load], + [lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld"], + [AC_CHECK_FUNC([dlopen], + [lt_cv_dlopen="dlopen"], + [AC_CHECK_LIB([dl], [dlopen], + [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"], + [AC_CHECK_LIB([svld], [dlopen], + [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld"], + [AC_CHECK_LIB([dld], [dld_link], + [lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld"]) + ]) + ]) + ]) + ]) + ]) + ;; + esac + + if test "x$lt_cv_dlopen" != xno; then + enable_dlopen=yes + else + enable_dlopen=no + fi + + case $lt_cv_dlopen in + dlopen) + save_CPPFLAGS="$CPPFLAGS" + test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H" + + save_LDFLAGS="$LDFLAGS" + wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\" + + save_LIBS="$LIBS" + LIBS="$lt_cv_dlopen_libs $LIBS" + + AC_CACHE_CHECK([whether a program can dlopen itself], + lt_cv_dlopen_self, [dnl + _LT_TRY_DLOPEN_SELF( + lt_cv_dlopen_self=yes, lt_cv_dlopen_self=yes, + lt_cv_dlopen_self=no, lt_cv_dlopen_self=cross) + ]) + + if test "x$lt_cv_dlopen_self" = xyes; then + wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\" + AC_CACHE_CHECK([whether a statically linked program can dlopen itself], + lt_cv_dlopen_self_static, [dnl + _LT_TRY_DLOPEN_SELF( + lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=yes, + lt_cv_dlopen_self_static=no, lt_cv_dlopen_self_static=cross) + ]) + fi + + CPPFLAGS="$save_CPPFLAGS" + LDFLAGS="$save_LDFLAGS" + LIBS="$save_LIBS" + ;; + esac + + case $lt_cv_dlopen_self in + yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;; + *) enable_dlopen_self=unknown ;; + esac + + case $lt_cv_dlopen_self_static in + yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;; + *) enable_dlopen_self_static=unknown ;; + esac +fi +_LT_DECL([dlopen_support], [enable_dlopen], [0], + [Whether dlopen is supported]) +_LT_DECL([dlopen_self], [enable_dlopen_self], [0], + [Whether dlopen of programs is supported]) +_LT_DECL([dlopen_self_static], [enable_dlopen_self_static], [0], + [Whether dlopen of statically linked programs is supported]) +])# LT_SYS_DLOPEN_SELF + +# Old name: +AU_ALIAS([AC_LIBTOOL_DLOPEN_SELF], [LT_SYS_DLOPEN_SELF]) +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AC_LIBTOOL_DLOPEN_SELF], []) + + +# _LT_COMPILER_C_O([TAGNAME]) +# --------------------------- +# Check to see if options -c and -o are simultaneously supported by compiler. +# This macro does not hard code the compiler like AC_PROG_CC_C_O. +m4_defun([_LT_COMPILER_C_O], +[m4_require([_LT_DECL_SED])dnl +m4_require([_LT_FILEUTILS_DEFAULTS])dnl +m4_require([_LT_TAG_COMPILER])dnl +AC_CACHE_CHECK([if $compiler supports -c -o file.$ac_objext], + [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)], + [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=no + $RM -r conftest 2>/dev/null + mkdir conftest + cd conftest + mkdir out + echo "$lt_simple_compile_test_code" > conftest.$ac_ext + + lt_compiler_flag="-o out/conftest2.$ac_objext" + # Insert the option either (1) after the last *FLAGS variable, or + # (2) before a word containing "conftest.", or (3) at the end. + # Note that $ac_compile itself does not contain backslashes and begins + # with a dollar sign (not a hyphen), so the echo should work correctly. + lt_compile=`echo "$ac_compile" | $SED \ + -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \ + -e 's: [[^ ]]*conftest\.: $lt_compiler_flag&:; t' \ + -e 's:$: $lt_compiler_flag:'` + (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&AS_MESSAGE_LOG_FD) + (eval "$lt_compile" 2>out/conftest.err) + ac_status=$? + cat out/conftest.err >&AS_MESSAGE_LOG_FD + echo "$as_me:__oline__: \$? = $ac_status" >&AS_MESSAGE_LOG_FD + if (exit $ac_status) && test -s out/conftest2.$ac_objext + then + # The compiler can only warn and ignore the option if not recognized + # So say no if there are warnings + $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp + $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2 + if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then + _LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=yes + fi + fi + chmod u+w . 2>&AS_MESSAGE_LOG_FD + $RM conftest* + # SGI C++ compiler will create directory out/ii_files/ for + # template instantiation + test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files + $RM out/* && rmdir out + cd .. + $RM -r conftest + $RM conftest* +]) +_LT_TAGDECL([compiler_c_o], [lt_cv_prog_compiler_c_o], [1], + [Does compiler simultaneously support -c and -o options?]) +])# _LT_COMPILER_C_O + + +# _LT_COMPILER_FILE_LOCKS([TAGNAME]) +# ---------------------------------- +# Check to see if we can do hard links to lock some files if needed +m4_defun([_LT_COMPILER_FILE_LOCKS], +[m4_require([_LT_ENABLE_LOCK])dnl +m4_require([_LT_FILEUTILS_DEFAULTS])dnl +_LT_COMPILER_C_O([$1]) + +hard_links="nottested" +if test "$_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)" = no && test "$need_locks" != no; then + # do not overwrite the value of need_locks provided by the user + AC_MSG_CHECKING([if we can lock with hard links]) + hard_links=yes + $RM conftest* + ln conftest.a conftest.b 2>/dev/null && hard_links=no + touch conftest.a + ln conftest.a conftest.b 2>&5 || hard_links=no + ln conftest.a conftest.b 2>/dev/null && hard_links=no + AC_MSG_RESULT([$hard_links]) + if test "$hard_links" = no; then + AC_MSG_WARN([`$CC' does not support `-c -o', so `make -j' may be unsafe]) + need_locks=warn + fi +else + need_locks=no +fi +_LT_DECL([], [need_locks], [1], [Must we lock files when doing compilation?]) +])# _LT_COMPILER_FILE_LOCKS + + +# _LT_CHECK_OBJDIR +# ---------------- +m4_defun([_LT_CHECK_OBJDIR], +[AC_CACHE_CHECK([for objdir], [lt_cv_objdir], +[rm -f .libs 2>/dev/null +mkdir .libs 2>/dev/null +if test -d .libs; then + lt_cv_objdir=.libs +else + # MS-DOS does not allow filenames that begin with a dot. + lt_cv_objdir=_libs +fi +rmdir .libs 2>/dev/null]) +objdir=$lt_cv_objdir +_LT_DECL([], [objdir], [0], + [The name of the directory that contains temporary libtool files])dnl +m4_pattern_allow([LT_OBJDIR])dnl +AC_DEFINE_UNQUOTED(LT_OBJDIR, "$lt_cv_objdir/", + [Define to the sub-directory in which libtool stores uninstalled libraries.]) +])# _LT_CHECK_OBJDIR + + +# _LT_LINKER_HARDCODE_LIBPATH([TAGNAME]) +# -------------------------------------- +# Check hardcoding attributes. +m4_defun([_LT_LINKER_HARDCODE_LIBPATH], +[AC_MSG_CHECKING([how to hardcode library paths into programs]) +_LT_TAGVAR(hardcode_action, $1)= +if test -n "$_LT_TAGVAR(hardcode_libdir_flag_spec, $1)" || + test -n "$_LT_TAGVAR(runpath_var, $1)" || + test "X$_LT_TAGVAR(hardcode_automatic, $1)" = "Xyes" ; then + + # We can hardcode non-existent directories. + if test "$_LT_TAGVAR(hardcode_direct, $1)" != no && + # If the only mechanism to avoid hardcoding is shlibpath_var, we + # have to relink, otherwise we might link with an installed library + # when we should be linking with a yet-to-be-installed one + ## test "$_LT_TAGVAR(hardcode_shlibpath_var, $1)" != no && + test "$_LT_TAGVAR(hardcode_minus_L, $1)" != no; then + # Linking always hardcodes the temporary library directory. + _LT_TAGVAR(hardcode_action, $1)=relink + else + # We can link without hardcoding, and we can hardcode nonexisting dirs. + _LT_TAGVAR(hardcode_action, $1)=immediate + fi +else + # We cannot hardcode anything, or else we can only hardcode existing + # directories. + _LT_TAGVAR(hardcode_action, $1)=unsupported +fi +AC_MSG_RESULT([$_LT_TAGVAR(hardcode_action, $1)]) + +if test "$_LT_TAGVAR(hardcode_action, $1)" = relink || + test "$_LT_TAGVAR(inherit_rpath, $1)" = yes; then + # Fast installation is not supported + enable_fast_install=no +elif test "$shlibpath_overrides_runpath" = yes || + test "$enable_shared" = no; then + # Fast installation is not necessary + enable_fast_install=needless +fi +_LT_TAGDECL([], [hardcode_action], [0], + [How to hardcode a shared library path into an executable]) +])# _LT_LINKER_HARDCODE_LIBPATH + + +# _LT_CMD_STRIPLIB +# ---------------- +m4_defun([_LT_CMD_STRIPLIB], +[m4_require([_LT_DECL_EGREP]) +striplib= +old_striplib= +AC_MSG_CHECKING([whether stripping libraries is possible]) +if test -n "$STRIP" && $STRIP -V 2>&1 | $GREP "GNU strip" >/dev/null; then + test -z "$old_striplib" && old_striplib="$STRIP --strip-debug" + test -z "$striplib" && striplib="$STRIP --strip-unneeded" + AC_MSG_RESULT([yes]) +else +# FIXME - insert some real tests, host_os isn't really good enough + case $host_os in + darwin*) + if test -n "$STRIP" ; then + striplib="$STRIP -x" + old_striplib="$STRIP -S" + AC_MSG_RESULT([yes]) + else + AC_MSG_RESULT([no]) + fi + ;; + *) + AC_MSG_RESULT([no]) + ;; + esac +fi +_LT_DECL([], [old_striplib], [1], [Commands to strip libraries]) +_LT_DECL([], [striplib], [1]) +])# _LT_CMD_STRIPLIB + + +# _LT_SYS_DYNAMIC_LINKER([TAG]) +# ----------------------------- +# PORTME Fill in your ld.so characteristics +m4_defun([_LT_SYS_DYNAMIC_LINKER], +[AC_REQUIRE([AC_CANONICAL_HOST])dnl +m4_require([_LT_DECL_EGREP])dnl +m4_require([_LT_FILEUTILS_DEFAULTS])dnl +m4_require([_LT_DECL_OBJDUMP])dnl +m4_require([_LT_DECL_SED])dnl +AC_MSG_CHECKING([dynamic linker characteristics]) +m4_if([$1], + [], [ +if test "$GCC" = yes; then + case $host_os in + darwin*) lt_awk_arg="/^libraries:/,/LR/" ;; + *) lt_awk_arg="/^libraries:/" ;; + esac + lt_search_path_spec=`$CC -print-search-dirs | awk $lt_awk_arg | $SED -e "s/^libraries://" -e "s,=/,/,g"` + if $ECHO "$lt_search_path_spec" | $GREP ';' >/dev/null ; then + # if the path contains ";" then we assume it to be the separator + # otherwise default to the standard path separator (i.e. ":") - it is + # assumed that no part of a normal pathname contains ";" but that should + # okay in the real world where ";" in dirpaths is itself problematic. + lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e 's/;/ /g'` + else + lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"` + fi + # Ok, now we have the path, separated by spaces, we can step through it + # and add multilib dir if necessary. + lt_tmp_lt_search_path_spec= + lt_multi_os_dir=`$CC $CPPFLAGS $CFLAGS $LDFLAGS -print-multi-os-directory 2>/dev/null` + for lt_sys_path in $lt_search_path_spec; do + if test -d "$lt_sys_path/$lt_multi_os_dir"; then + lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path/$lt_multi_os_dir" + else + test -d "$lt_sys_path" && \ + lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path" + fi + done + lt_search_path_spec=`$ECHO $lt_tmp_lt_search_path_spec | awk ' +BEGIN {RS=" "; FS="/|\n";} { + lt_foo=""; + lt_count=0; + for (lt_i = NF; lt_i > 0; lt_i--) { + if ($lt_i != "" && $lt_i != ".") { + if ($lt_i == "..") { + lt_count++; + } else { + if (lt_count == 0) { + lt_foo="/" $lt_i lt_foo; + } else { + lt_count--; + } + } + } + } + if (lt_foo != "") { lt_freq[[lt_foo]]++; } + if (lt_freq[[lt_foo]] == 1) { print lt_foo; } +}'` + sys_lib_search_path_spec=`$ECHO $lt_search_path_spec` +else + sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib" +fi]) +library_names_spec= +libname_spec='lib$name' +soname_spec= +shrext_cmds=".so" +postinstall_cmds= +postuninstall_cmds= +finish_cmds= +finish_eval= +shlibpath_var= +shlibpath_overrides_runpath=unknown +version_type=none +dynamic_linker="$host_os ld.so" +sys_lib_dlsearch_path_spec="/lib /usr/lib" +need_lib_prefix=unknown +hardcode_into_libs=no + +# when you set need_version to no, make sure it does not cause -set_version +# flags to be left without arguments +need_version=unknown + +case $host_os in +aix3*) + version_type=linux + library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a' + shlibpath_var=LIBPATH + + # AIX 3 has no versioning support, so we append a major version to the name. + soname_spec='${libname}${release}${shared_ext}$major' + ;; + +aix[[4-9]]*) + version_type=linux + need_lib_prefix=no + need_version=no + hardcode_into_libs=yes + if test "$host_cpu" = ia64; then + # AIX 5 supports IA64 + library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}' + shlibpath_var=LD_LIBRARY_PATH + else + # With GCC up to 2.95.x, collect2 would create an import file + # for dependence libraries. The import file would start with + # the line `#! .'. This would cause the generated library to + # depend on `.', always an invalid library. This was fixed in + # development snapshots of GCC prior to 3.0. + case $host_os in + aix4 | aix4.[[01]] | aix4.[[01]].*) + if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)' + echo ' yes ' + echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then + : + else + can_build_shared=no + fi + ;; + esac + # AIX (on Power*) has no versioning support, so currently we can not hardcode correct + # soname into executable. Probably we can add versioning support to + # collect2, so additional links can be useful in future. + if test "$aix_use_runtimelinking" = yes; then + # If using run time linking (on AIX 4.2 or later) use lib.so + # instead of lib.a to let people know that these are not + # typical AIX shared libraries. + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + else + # We preserve .a as extension for shared libraries through AIX4.2 + # and later when we are not doing run time linking. + library_names_spec='${libname}${release}.a $libname.a' + soname_spec='${libname}${release}${shared_ext}$major' + fi + shlibpath_var=LIBPATH + fi + ;; + +amigaos*) + case $host_cpu in + powerpc) + # Since July 2007 AmigaOS4 officially supports .so libraries. + # When compiling the executable, add -use-dynld -Lsobjs: to the compileline. + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + ;; + m68k) + library_names_spec='$libname.ixlibrary $libname.a' + # Create ${libname}_ixlibrary.a entries in /sys/libs. + finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([[^/]]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done' + ;; + esac + ;; + +beos*) + library_names_spec='${libname}${shared_ext}' + dynamic_linker="$host_os ld.so" + shlibpath_var=LIBRARY_PATH + ;; + +bsdi[[45]]*) + version_type=linux + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir' + shlibpath_var=LD_LIBRARY_PATH + sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib" + sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib" + # the default ld.so.conf also contains /usr/contrib/lib and + # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow + # libtool to hard-code these into programs + ;; + +cygwin* | mingw* | pw32* | cegcc*) + version_type=windows + shrext_cmds=".dll" + need_version=no + need_lib_prefix=no + + case $GCC,$host_os in + yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*) + library_names_spec='$libname.dll.a' + # DLL is installed to $(libdir)/../bin by postinstall_cmds + postinstall_cmds='base_file=`basename \${file}`~ + dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~ + dldir=$destdir/`dirname \$dlpath`~ + test -d \$dldir || mkdir -p \$dldir~ + $install_prog $dir/$dlname \$dldir/$dlname~ + chmod a+x \$dldir/$dlname~ + if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then + eval '\''$striplib \$dldir/$dlname'\'' || exit \$?; + fi' + postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~ + dlpath=$dir/\$dldll~ + $RM \$dlpath' + shlibpath_overrides_runpath=yes + + case $host_os in + cygwin*) + # Cygwin DLLs use 'cyg' prefix rather than 'lib' + soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}' + sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib" + ;; + mingw* | cegcc*) + # MinGW DLLs use traditional 'lib' prefix + soname_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}' + sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"` + if $ECHO "$sys_lib_search_path_spec" | [$GREP ';[c-zC-Z]:/' >/dev/null]; then + # It is most probably a Windows format PATH printed by + # mingw gcc, but we are running on Cygwin. Gcc prints its search + # path with ; separators, and with drive letters. We can handle the + # drive letters (cygwin fileutils understands them), so leave them, + # especially as we might pass files found there to a mingw objdump, + # which wouldn't understand a cygwinified path. Ahh. + sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'` + else + sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"` + fi + ;; + pw32*) + # pw32 DLLs use 'pw' prefix rather than 'lib' + library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}' + ;; + esac + ;; + + *) + library_names_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext} $libname.lib' + ;; + esac + dynamic_linker='Win32 ld.exe' + # FIXME: first we should search . and the directory the executable is in + shlibpath_var=PATH + ;; + +darwin* | rhapsody*) + dynamic_linker="$host_os dyld" + version_type=darwin + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext' + soname_spec='${libname}${release}${major}$shared_ext' + shlibpath_overrides_runpath=yes + shlibpath_var=DYLD_LIBRARY_PATH + shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`' +m4_if([$1], [],[ + sys_lib_search_path_spec="$sys_lib_search_path_spec /usr/local/lib"]) + sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib' + ;; + +dgux*) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + ;; + +freebsd1*) + dynamic_linker=no + ;; + +freebsd* | dragonfly*) + # DragonFly does not have aout. When/if they implement a new + # versioning mechanism, adjust this. + if test -x /usr/bin/objformat; then + objformat=`/usr/bin/objformat` + else + case $host_os in + freebsd[[123]]*) objformat=aout ;; + *) objformat=elf ;; + esac + fi + version_type=freebsd-$objformat + case $version_type in + freebsd-elf*) + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' + need_version=no + need_lib_prefix=no + ;; + freebsd-*) + library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix' + need_version=yes + ;; + esac + shlibpath_var=LD_LIBRARY_PATH + case $host_os in + freebsd2*) + shlibpath_overrides_runpath=yes + ;; + freebsd3.[[01]]* | freebsdelf3.[[01]]*) + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + ;; + freebsd3.[[2-9]]* | freebsdelf3.[[2-9]]* | \ + freebsd4.[[0-5]] | freebsdelf4.[[0-5]] | freebsd4.1.1 | freebsdelf4.1.1) + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + ;; + *) # from 4.6 on, and DragonFly + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + ;; + esac + ;; + +gnu*) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + hardcode_into_libs=yes + ;; + +hpux9* | hpux10* | hpux11*) + # Give a soname corresponding to the major version so that dld.sl refuses to + # link against other versions. + version_type=sunos + need_lib_prefix=no + need_version=no + case $host_cpu in + ia64*) + shrext_cmds='.so' + hardcode_into_libs=yes + dynamic_linker="$host_os dld.so" + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + if test "X$HPUX_IA64_MODE" = X32; then + sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib" + else + sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64" + fi + sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec + ;; + hppa*64*) + shrext_cmds='.sl' + hardcode_into_libs=yes + dynamic_linker="$host_os dld.sl" + shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH + shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64" + sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec + ;; + *) + shrext_cmds='.sl' + dynamic_linker="$host_os dld.sl" + shlibpath_var=SHLIB_PATH + shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + ;; + esac + # HP-UX runs *really* slowly unless shared libraries are mode 555. + postinstall_cmds='chmod 555 $lib' + ;; + +interix[[3-9]]*) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + ;; + +irix5* | irix6* | nonstopux*) + case $host_os in + nonstopux*) version_type=nonstopux ;; + *) + if test "$lt_cv_prog_gnu_ld" = yes; then + version_type=linux + else + version_type=irix + fi ;; + esac + need_lib_prefix=no + need_version=no + soname_spec='${libname}${release}${shared_ext}$major' + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}' + case $host_os in + irix5* | nonstopux*) + libsuff= shlibsuff= + ;; + *) + case $LD in # libtool.m4 will add one of these switches to LD + *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") + libsuff= shlibsuff= libmagic=32-bit;; + *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ") + libsuff=32 shlibsuff=N32 libmagic=N32;; + *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ") + libsuff=64 shlibsuff=64 libmagic=64-bit;; + *) libsuff= shlibsuff= libmagic=never-match;; + esac + ;; + esac + shlibpath_var=LD_LIBRARY${shlibsuff}_PATH + shlibpath_overrides_runpath=no + sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}" + sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}" + hardcode_into_libs=yes + ;; + +# No shared lib support for Linux oldld, aout, or coff. +linux*oldld* | linux*aout* | linux*coff*) + dynamic_linker=no + ;; + +# This must be Linux ELF. +linux* | k*bsd*-gnu) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + # Some binutils ld are patched to set DT_RUNPATH + save_LDFLAGS=$LDFLAGS + save_libdir=$libdir + eval "libdir=/foo; wl=\"$_LT_TAGVAR(lt_prog_compiler_wl, $1)\"; \ + LDFLAGS=\"\$LDFLAGS $_LT_TAGVAR(hardcode_libdir_flag_spec, $1)\"" + AC_LINK_IFELSE([AC_LANG_PROGRAM([],[])], + [AS_IF([ ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null], + [shlibpath_overrides_runpath=yes])]) + LDFLAGS=$save_LDFLAGS + libdir=$save_libdir + + # This implies no fast_install, which is unacceptable. + # Some rework will be needed to allow for fast_install + # before this can be enabled. + hardcode_into_libs=yes + + # Append ld.so.conf contents to the search path + if test -f /etc/ld.so.conf; then + lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '` + sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra" + fi + + # We used to test for /lib/ld.so.1 and disable shared libraries on + # powerpc, because MkLinux only supported shared libraries with the + # GNU dynamic linker. Since this was broken with cross compilers, + # most powerpc-linux boxes support dynamic linking these days and + # people can always --disable-shared, the test was removed, and we + # assume the GNU/Linux dynamic linker is in use. + dynamic_linker='GNU/Linux ld.so' + ;; + +netbsdelf*-gnu) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + dynamic_linker='NetBSD ld.elf_so' + ;; + +netbsd*) + version_type=sunos + need_lib_prefix=no + need_version=no + if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' + finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' + dynamic_linker='NetBSD (a.out) ld.so' + else + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + dynamic_linker='NetBSD ld.elf_so' + fi + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + ;; + +newsos6) + version_type=linux + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + ;; + +*nto* | *qnx*) + version_type=qnx + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + dynamic_linker='ldqnx.so' + ;; + +openbsd*) + version_type=sunos + sys_lib_dlsearch_path_spec="/usr/lib" + need_lib_prefix=no + # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs. + case $host_os in + openbsd3.3 | openbsd3.3.*) need_version=yes ;; + *) need_version=no ;; + esac + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' + finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' + shlibpath_var=LD_LIBRARY_PATH + if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then + case $host_os in + openbsd2.[[89]] | openbsd2.[[89]].*) + shlibpath_overrides_runpath=no + ;; + *) + shlibpath_overrides_runpath=yes + ;; + esac + else + shlibpath_overrides_runpath=yes + fi + ;; + +os2*) + libname_spec='$name' + shrext_cmds=".dll" + need_lib_prefix=no + library_names_spec='$libname${shared_ext} $libname.a' + dynamic_linker='OS/2 ld.exe' + shlibpath_var=LIBPATH + ;; + +osf3* | osf4* | osf5*) + version_type=osf + need_lib_prefix=no + need_version=no + soname_spec='${libname}${release}${shared_ext}$major' + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + shlibpath_var=LD_LIBRARY_PATH + sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib" + sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec" + ;; + +rdos*) + dynamic_linker=no + ;; + +solaris*) + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + # ldd complains unless libraries are executable + postinstall_cmds='chmod +x $lib' + ;; + +sunos4*) + version_type=sunos + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' + finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + if test "$with_gnu_ld" = yes; then + need_lib_prefix=no + fi + need_version=yes + ;; + +sysv4 | sysv4.3*) + version_type=linux + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + case $host_vendor in + sni) + shlibpath_overrides_runpath=no + need_lib_prefix=no + runpath_var=LD_RUN_PATH + ;; + siemens) + need_lib_prefix=no + ;; + motorola) + need_lib_prefix=no + need_version=no + shlibpath_overrides_runpath=no + sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib' + ;; + esac + ;; + +sysv4*MP*) + if test -d /usr/nec ;then + version_type=linux + library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}' + soname_spec='$libname${shared_ext}.$major' + shlibpath_var=LD_LIBRARY_PATH + fi + ;; + +sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) + version_type=freebsd-elf + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=yes + hardcode_into_libs=yes + if test "$with_gnu_ld" = yes; then + sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib' + else + sys_lib_search_path_spec='/usr/ccs/lib /usr/lib' + case $host_os in + sco3.2v5*) + sys_lib_search_path_spec="$sys_lib_search_path_spec /lib" + ;; + esac + fi + sys_lib_dlsearch_path_spec='/usr/lib' + ;; + +tpf*) + # TPF is a cross-target only. Preferred cross-host = GNU/Linux. + version_type=linux + need_lib_prefix=no + need_version=no + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + shlibpath_var=LD_LIBRARY_PATH + shlibpath_overrides_runpath=no + hardcode_into_libs=yes + ;; + +uts4*) + version_type=linux + library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' + soname_spec='${libname}${release}${shared_ext}$major' + shlibpath_var=LD_LIBRARY_PATH + ;; + +*) + dynamic_linker=no + ;; +esac +AC_MSG_RESULT([$dynamic_linker]) +test "$dynamic_linker" = no && can_build_shared=no + +variables_saved_for_relink="PATH $shlibpath_var $runpath_var" +if test "$GCC" = yes; then + variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH" +fi + +if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then + sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec" +fi +if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then + sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec" +fi + +_LT_DECL([], [variables_saved_for_relink], [1], + [Variables whose values should be saved in libtool wrapper scripts and + restored at link time]) +_LT_DECL([], [need_lib_prefix], [0], + [Do we need the "lib" prefix for modules?]) +_LT_DECL([], [need_version], [0], [Do we need a version for libraries?]) +_LT_DECL([], [version_type], [0], [Library versioning type]) +_LT_DECL([], [runpath_var], [0], [Shared library runtime path variable]) +_LT_DECL([], [shlibpath_var], [0],[Shared library path variable]) +_LT_DECL([], [shlibpath_overrides_runpath], [0], + [Is shlibpath searched before the hard-coded library search path?]) +_LT_DECL([], [libname_spec], [1], [Format of library name prefix]) +_LT_DECL([], [library_names_spec], [1], + [[List of archive names. First name is the real one, the rest are links. + The last name is the one that the linker finds with -lNAME]]) +_LT_DECL([], [soname_spec], [1], + [[The coded name of the library, if different from the real name]]) +_LT_DECL([], [postinstall_cmds], [2], + [Command to use after installation of a shared archive]) +_LT_DECL([], [postuninstall_cmds], [2], + [Command to use after uninstallation of a shared archive]) +_LT_DECL([], [finish_cmds], [2], + [Commands used to finish a libtool library installation in a directory]) +_LT_DECL([], [finish_eval], [1], + [[As "finish_cmds", except a single script fragment to be evaled but + not shown]]) +_LT_DECL([], [hardcode_into_libs], [0], + [Whether we should hardcode library paths into libraries]) +_LT_DECL([], [sys_lib_search_path_spec], [2], + [Compile-time system search path for libraries]) +_LT_DECL([], [sys_lib_dlsearch_path_spec], [2], + [Run-time system search path for libraries]) +])# _LT_SYS_DYNAMIC_LINKER + + +# _LT_PATH_TOOL_PREFIX(TOOL) +# -------------------------- +# find a file program which can recognize shared library +AC_DEFUN([_LT_PATH_TOOL_PREFIX], +[m4_require([_LT_DECL_EGREP])dnl +AC_MSG_CHECKING([for $1]) +AC_CACHE_VAL(lt_cv_path_MAGIC_CMD, +[case $MAGIC_CMD in +[[\\/*] | ?:[\\/]*]) + lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path. + ;; +*) + lt_save_MAGIC_CMD="$MAGIC_CMD" + lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR +dnl $ac_dummy forces splitting on constant user-supplied paths. +dnl POSIX.2 word splitting is done only on the output of word expansions, +dnl not every word. This closes a longstanding sh security hole. + ac_dummy="m4_if([$2], , $PATH, [$2])" + for ac_dir in $ac_dummy; do + IFS="$lt_save_ifs" + test -z "$ac_dir" && ac_dir=. + if test -f $ac_dir/$1; then + lt_cv_path_MAGIC_CMD="$ac_dir/$1" + if test -n "$file_magic_test_file"; then + case $deplibs_check_method in + "file_magic "*) + file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"` + MAGIC_CMD="$lt_cv_path_MAGIC_CMD" + if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null | + $EGREP "$file_magic_regex" > /dev/null; then + : + else + cat <<_LT_EOF 1>&2 + +*** Warning: the command libtool uses to detect shared libraries, +*** $file_magic_cmd, produces output that libtool cannot recognize. +*** The result is that libtool may fail to recognize shared libraries +*** as such. This will affect the creation of libtool libraries that +*** depend on shared libraries, but programs linked with such libtool +*** libraries will work regardless of this problem. Nevertheless, you +*** may want to report the problem to your system manager and/or to +*** bug-libtool@gnu.org + +_LT_EOF + fi ;; + esac + fi + break + fi + done + IFS="$lt_save_ifs" + MAGIC_CMD="$lt_save_MAGIC_CMD" + ;; +esac]) +MAGIC_CMD="$lt_cv_path_MAGIC_CMD" +if test -n "$MAGIC_CMD"; then + AC_MSG_RESULT($MAGIC_CMD) +else + AC_MSG_RESULT(no) +fi +_LT_DECL([], [MAGIC_CMD], [0], + [Used to examine libraries when file_magic_cmd begins with "file"])dnl +])# _LT_PATH_TOOL_PREFIX + +# Old name: +AU_ALIAS([AC_PATH_TOOL_PREFIX], [_LT_PATH_TOOL_PREFIX]) +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AC_PATH_TOOL_PREFIX], []) + + +# _LT_PATH_MAGIC +# -------------- +# find a file program which can recognize a shared library +m4_defun([_LT_PATH_MAGIC], +[_LT_PATH_TOOL_PREFIX(${ac_tool_prefix}file, /usr/bin$PATH_SEPARATOR$PATH) +if test -z "$lt_cv_path_MAGIC_CMD"; then + if test -n "$ac_tool_prefix"; then + _LT_PATH_TOOL_PREFIX(file, /usr/bin$PATH_SEPARATOR$PATH) + else + MAGIC_CMD=: + fi +fi +])# _LT_PATH_MAGIC + + +# LT_PATH_LD +# ---------- +# find the pathname to the GNU or non-GNU linker +AC_DEFUN([LT_PATH_LD], +[AC_REQUIRE([AC_PROG_CC])dnl +AC_REQUIRE([AC_CANONICAL_HOST])dnl +AC_REQUIRE([AC_CANONICAL_BUILD])dnl +m4_require([_LT_DECL_SED])dnl +m4_require([_LT_DECL_EGREP])dnl + +AC_ARG_WITH([gnu-ld], + [AS_HELP_STRING([--with-gnu-ld], + [assume the C compiler uses GNU ld @<:@default=no@:>@])], + [test "$withval" = no || with_gnu_ld=yes], + [with_gnu_ld=no])dnl + +ac_prog=ld +if test "$GCC" = yes; then + # Check if gcc -print-prog-name=ld gives a path. + AC_MSG_CHECKING([for ld used by $CC]) + case $host in + *-*-mingw*) + # gcc leaves a trailing carriage return which upsets mingw + ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;; + *) + ac_prog=`($CC -print-prog-name=ld) 2>&5` ;; + esac + case $ac_prog in + # Accept absolute paths. + [[\\/]]* | ?:[[\\/]]*) + re_direlt='/[[^/]][[^/]]*/\.\./' + # Canonicalize the pathname of ld + ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'` + while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do + ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"` + done + test -z "$LD" && LD="$ac_prog" + ;; + "") + # If it fails, then pretend we aren't using GCC. + ac_prog=ld + ;; + *) + # If it is relative, then search for the first ld in PATH. + with_gnu_ld=unknown + ;; + esac +elif test "$with_gnu_ld" = yes; then + AC_MSG_CHECKING([for GNU ld]) +else + AC_MSG_CHECKING([for non-GNU ld]) +fi +AC_CACHE_VAL(lt_cv_path_LD, +[if test -z "$LD"; then + lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR + for ac_dir in $PATH; do + IFS="$lt_save_ifs" + test -z "$ac_dir" && ac_dir=. + if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then + lt_cv_path_LD="$ac_dir/$ac_prog" + # Check to see if the program is GNU ld. I'd rather use --version, + # but apparently some variants of GNU ld only accept -v. + # Break only if it was the GNU/non-GNU ld that we prefer. + case `"$lt_cv_path_LD" -v 2>&1 &1 /dev/null 2>&1; then + lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' + lt_cv_file_magic_cmd='func_win32_libid' + else + lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?' + lt_cv_file_magic_cmd='$OBJDUMP -f' + fi + ;; + +cegcc) + # use the weaker test based on 'objdump'. See mingw*. + lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?' + lt_cv_file_magic_cmd='$OBJDUMP -f' + ;; + +darwin* | rhapsody*) + lt_cv_deplibs_check_method=pass_all + ;; + +freebsd* | dragonfly*) + if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then + case $host_cpu in + i*86 ) + # Not sure whether the presence of OpenBSD here was a mistake. + # Let's accept both of them until this is cleared up. + lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[[3-9]]86 (compact )?demand paged shared library' + lt_cv_file_magic_cmd=/usr/bin/file + lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*` + ;; + esac + else + lt_cv_deplibs_check_method=pass_all + fi + ;; + +gnu*) + lt_cv_deplibs_check_method=pass_all + ;; + +hpux10.20* | hpux11*) + lt_cv_file_magic_cmd=/usr/bin/file + case $host_cpu in + ia64*) + lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|ELF-[[0-9]][[0-9]]) shared object file - IA64' + lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so + ;; + hppa*64*) + [lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]'] + lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl + ;; + *) + lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|PA-RISC[[0-9]].[[0-9]]) shared library' + lt_cv_file_magic_test_file=/usr/lib/libc.sl + ;; + esac + ;; + +interix[[3-9]]*) + # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here + lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|\.a)$' + ;; + +irix5* | irix6* | nonstopux*) + case $LD in + *-32|*"-32 ") libmagic=32-bit;; + *-n32|*"-n32 ") libmagic=N32;; + *-64|*"-64 ") libmagic=64-bit;; + *) libmagic=never-match;; + esac + lt_cv_deplibs_check_method=pass_all + ;; + +# This must be Linux ELF. +linux* | k*bsd*-gnu) + lt_cv_deplibs_check_method=pass_all + ;; + +netbsd* | netbsdelf*-gnu) + if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then + lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$' + else + lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|_pic\.a)$' + fi + ;; + +newos6*) + lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (executable|dynamic lib)' + lt_cv_file_magic_cmd=/usr/bin/file + lt_cv_file_magic_test_file=/usr/lib/libnls.so + ;; + +*nto* | *qnx*) + lt_cv_deplibs_check_method=pass_all + ;; + +openbsd*) + if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then + lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|\.so|_pic\.a)$' + else + lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$' + fi + ;; + +osf3* | osf4* | osf5*) + lt_cv_deplibs_check_method=pass_all + ;; + +rdos*) + lt_cv_deplibs_check_method=pass_all + ;; + +solaris*) + lt_cv_deplibs_check_method=pass_all + ;; + +sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) + lt_cv_deplibs_check_method=pass_all + ;; + +sysv4 | sysv4.3*) + case $host_vendor in + motorola) + lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib) M[[0-9]][[0-9]]* Version [[0-9]]' + lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` + ;; + ncr) + lt_cv_deplibs_check_method=pass_all + ;; + sequent) + lt_cv_file_magic_cmd='/bin/file' + lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB (shared object|dynamic lib )' + ;; + sni) + lt_cv_file_magic_cmd='/bin/file' + lt_cv_deplibs_check_method="file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB dynamic lib" + lt_cv_file_magic_test_file=/lib/libc.so + ;; + siemens) + lt_cv_deplibs_check_method=pass_all + ;; + pc) + lt_cv_deplibs_check_method=pass_all + ;; + esac + ;; + +tpf*) + lt_cv_deplibs_check_method=pass_all + ;; +esac +]) +file_magic_cmd=$lt_cv_file_magic_cmd +deplibs_check_method=$lt_cv_deplibs_check_method +test -z "$deplibs_check_method" && deplibs_check_method=unknown + +_LT_DECL([], [deplibs_check_method], [1], + [Method to check whether dependent libraries are shared objects]) +_LT_DECL([], [file_magic_cmd], [1], + [Command to use when deplibs_check_method == "file_magic"]) +])# _LT_CHECK_MAGIC_METHOD + + +# LT_PATH_NM +# ---------- +# find the pathname to a BSD- or MS-compatible name lister +AC_DEFUN([LT_PATH_NM], +[AC_REQUIRE([AC_PROG_CC])dnl +AC_CACHE_CHECK([for BSD- or MS-compatible name lister (nm)], lt_cv_path_NM, +[if test -n "$NM"; then + # Let the user override the test. + lt_cv_path_NM="$NM" +else + lt_nm_to_check="${ac_tool_prefix}nm" + if test -n "$ac_tool_prefix" && test "$build" = "$host"; then + lt_nm_to_check="$lt_nm_to_check nm" + fi + for lt_tmp_nm in $lt_nm_to_check; do + lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR + for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do + IFS="$lt_save_ifs" + test -z "$ac_dir" && ac_dir=. + tmp_nm="$ac_dir/$lt_tmp_nm" + if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then + # Check to see if the nm accepts a BSD-compat flag. + # Adding the `sed 1q' prevents false positives on HP-UX, which says: + # nm: unknown option "B" ignored + # Tru64's nm complains that /dev/null is an invalid object file + case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in + */dev/null* | *'Invalid file or object type'*) + lt_cv_path_NM="$tmp_nm -B" + break + ;; + *) + case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in + */dev/null*) + lt_cv_path_NM="$tmp_nm -p" + break + ;; + *) + lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but + continue # so that we can try to find one that supports BSD flags + ;; + esac + ;; + esac + fi + done + IFS="$lt_save_ifs" + done + : ${lt_cv_path_NM=no} +fi]) +if test "$lt_cv_path_NM" != "no"; then + NM="$lt_cv_path_NM" +else + # Didn't find any BSD compatible name lister, look for dumpbin. + AC_CHECK_TOOLS(DUMPBIN, ["dumpbin -symbols" "link -dump -symbols"], :) + AC_SUBST([DUMPBIN]) + if test "$DUMPBIN" != ":"; then + NM="$DUMPBIN" + fi +fi +test -z "$NM" && NM=nm +AC_SUBST([NM]) +_LT_DECL([], [NM], [1], [A BSD- or MS-compatible name lister])dnl + +AC_CACHE_CHECK([the name lister ($NM) interface], [lt_cv_nm_interface], + [lt_cv_nm_interface="BSD nm" + echo "int some_variable = 0;" > conftest.$ac_ext + (eval echo "\"\$as_me:__oline__: $ac_compile\"" >&AS_MESSAGE_LOG_FD) + (eval "$ac_compile" 2>conftest.err) + cat conftest.err >&AS_MESSAGE_LOG_FD + (eval echo "\"\$as_me:__oline__: $NM \\\"conftest.$ac_objext\\\"\"" >&AS_MESSAGE_LOG_FD) + (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out) + cat conftest.err >&AS_MESSAGE_LOG_FD + (eval echo "\"\$as_me:__oline__: output\"" >&AS_MESSAGE_LOG_FD) + cat conftest.out >&AS_MESSAGE_LOG_FD + if $GREP 'External.*some_variable' conftest.out > /dev/null; then + lt_cv_nm_interface="MS dumpbin" + fi + rm -f conftest*]) +])# LT_PATH_NM + +# Old names: +AU_ALIAS([AM_PROG_NM], [LT_PATH_NM]) +AU_ALIAS([AC_PROG_NM], [LT_PATH_NM]) +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AM_PROG_NM], []) +dnl AC_DEFUN([AC_PROG_NM], []) + + +# LT_LIB_M +# -------- +# check for math library +AC_DEFUN([LT_LIB_M], +[AC_REQUIRE([AC_CANONICAL_HOST])dnl +LIBM= +case $host in +*-*-beos* | *-*-cygwin* | *-*-pw32* | *-*-darwin*) + # These system don't have libm, or don't need it + ;; +*-ncr-sysv4.3*) + AC_CHECK_LIB(mw, _mwvalidcheckl, LIBM="-lmw") + AC_CHECK_LIB(m, cos, LIBM="$LIBM -lm") + ;; +*) + AC_CHECK_LIB(m, cos, LIBM="-lm") + ;; +esac +AC_SUBST([LIBM]) +])# LT_LIB_M + +# Old name: +AU_ALIAS([AC_CHECK_LIBM], [LT_LIB_M]) +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AC_CHECK_LIBM], []) + + +# _LT_COMPILER_NO_RTTI([TAGNAME]) +# ------------------------------- +m4_defun([_LT_COMPILER_NO_RTTI], +[m4_require([_LT_TAG_COMPILER])dnl + +_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)= + +if test "$GCC" = yes; then + _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin' + + _LT_COMPILER_OPTION([if $compiler supports -fno-rtti -fno-exceptions], + lt_cv_prog_compiler_rtti_exceptions, + [-fno-rtti -fno-exceptions], [], + [_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)="$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) -fno-rtti -fno-exceptions"]) +fi +_LT_TAGDECL([no_builtin_flag], [lt_prog_compiler_no_builtin_flag], [1], + [Compiler flag to turn off builtin functions]) +])# _LT_COMPILER_NO_RTTI + + +# _LT_CMD_GLOBAL_SYMBOLS +# ---------------------- +m4_defun([_LT_CMD_GLOBAL_SYMBOLS], +[AC_REQUIRE([AC_CANONICAL_HOST])dnl +AC_REQUIRE([AC_PROG_CC])dnl +AC_REQUIRE([LT_PATH_NM])dnl +AC_REQUIRE([LT_PATH_LD])dnl +m4_require([_LT_DECL_SED])dnl +m4_require([_LT_DECL_EGREP])dnl +m4_require([_LT_TAG_COMPILER])dnl + +# Check for command to grab the raw symbol name followed by C symbol from nm. +AC_MSG_CHECKING([command to parse $NM output from $compiler object]) +AC_CACHE_VAL([lt_cv_sys_global_symbol_pipe], +[ +# These are sane defaults that work on at least a few old systems. +# [They come from Ultrix. What could be older than Ultrix?!! ;)] + +# Character class describing NM global symbol codes. +symcode='[[BCDEGRST]]' + +# Regexp to match symbols that can be accessed directly from C. +sympat='\([[_A-Za-z]][[_A-Za-z0-9]]*\)' + +# Define system-specific variables. +case $host_os in +aix*) + symcode='[[BCDT]]' + ;; +cygwin* | mingw* | pw32* | cegcc*) + symcode='[[ABCDGISTW]]' + ;; +hpux*) + if test "$host_cpu" = ia64; then + symcode='[[ABCDEGRST]]' + fi + ;; +irix* | nonstopux*) + symcode='[[BCDEGRST]]' + ;; +osf*) + symcode='[[BCDEGQRST]]' + ;; +solaris*) + symcode='[[BDRT]]' + ;; +sco3.2v5*) + symcode='[[DT]]' + ;; +sysv4.2uw2*) + symcode='[[DT]]' + ;; +sysv5* | sco5v6* | unixware* | OpenUNIX*) + symcode='[[ABDT]]' + ;; +sysv4) + symcode='[[DFNSTU]]' + ;; +esac + +# If we're using GNU nm, then use its standard symbol codes. +case `$NM -V 2>&1` in +*GNU* | *'with BFD'*) + symcode='[[ABCDGIRSTW]]' ;; +esac + +# Transform an extracted symbol line into a proper C declaration. +# Some systems (esp. on ia64) link data and code symbols differently, +# so use this general approach. +lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" + +# Transform an extracted symbol line into symbol name and symbol address +lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p'" +lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \(lib[[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"lib\2\", (void *) \&\2},/p'" + +# Handle CRLF in mingw tool chain +opt_cr= +case $build_os in +mingw*) + opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp + ;; +esac + +# Try without a prefix underscore, then with it. +for ac_symprfx in "" "_"; do + + # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. + symxfrm="\\1 $ac_symprfx\\2 \\2" + + # Write the raw and C identifiers. + if test "$lt_cv_nm_interface" = "MS dumpbin"; then + # Fake it for dumpbin and say T for any non-static function + # and D for any global variable. + # Also find C++ and __fastcall symbols from MSVC++, + # which start with @ or ?. + lt_cv_sys_global_symbol_pipe="$AWK ['"\ +" {last_section=section; section=\$ 3};"\ +" /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ +" \$ 0!~/External *\|/{next};"\ +" / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ +" {if(hide[section]) next};"\ +" {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ +" {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ +" s[1]~/^[@?]/{print s[1], s[1]; next};"\ +" s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ +" ' prfx=^$ac_symprfx]" + else + lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[[ ]]\($symcode$symcode*\)[[ ]][[ ]]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" + fi + + # Check to see that the pipe works correctly. + pipe_works=no + + rm -f conftest* + cat > conftest.$ac_ext <<_LT_EOF +#ifdef __cplusplus +extern "C" { +#endif +char nm_test_var; +void nm_test_func(void); +void nm_test_func(void){} +#ifdef __cplusplus +} +#endif +int main(){nm_test_var='a';nm_test_func();return(0);} +_LT_EOF + + if AC_TRY_EVAL(ac_compile); then + # Now try to grab the symbols. + nlist=conftest.nm + if AC_TRY_EVAL(NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) && test -s "$nlist"; then + # Try sorting and uniquifying the output. + if sort "$nlist" | uniq > "$nlist"T; then + mv -f "$nlist"T "$nlist" + else + rm -f "$nlist"T + fi + + # Make sure that we snagged all the symbols we need. + if $GREP ' nm_test_var$' "$nlist" >/dev/null; then + if $GREP ' nm_test_func$' "$nlist" >/dev/null; then + cat <<_LT_EOF > conftest.$ac_ext +#ifdef __cplusplus +extern "C" { +#endif + +_LT_EOF + # Now generate the symbol file. + eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' + + cat <<_LT_EOF >> conftest.$ac_ext + +/* The mapping between symbol names and symbols. */ +const struct { + const char *name; + void *address; +} +lt__PROGRAM__LTX_preloaded_symbols[[]] = +{ + { "@PROGRAM@", (void *) 0 }, +_LT_EOF + $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext + cat <<\_LT_EOF >> conftest.$ac_ext + {0, (void *) 0} +}; + +/* This works around a problem in FreeBSD linker */ +#ifdef FREEBSD_WORKAROUND +static const void *lt_preloaded_setup() { + return lt__PROGRAM__LTX_preloaded_symbols; +} +#endif + +#ifdef __cplusplus +} +#endif +_LT_EOF + # Now try linking the two files. + mv conftest.$ac_objext conftstm.$ac_objext + lt_save_LIBS="$LIBS" + lt_save_CFLAGS="$CFLAGS" + LIBS="conftstm.$ac_objext" + CFLAGS="$CFLAGS$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)" + if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then + pipe_works=yes + fi + LIBS="$lt_save_LIBS" + CFLAGS="$lt_save_CFLAGS" + else + echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD + fi + else + echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD + fi + else + echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD + fi + else + echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD + cat conftest.$ac_ext >&5 + fi + rm -rf conftest* conftst* + + # Do not use the global_symbol_pipe unless it works. + if test "$pipe_works" = yes; then + break + else + lt_cv_sys_global_symbol_pipe= + fi +done +]) +if test -z "$lt_cv_sys_global_symbol_pipe"; then + lt_cv_sys_global_symbol_to_cdecl= +fi +if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then + AC_MSG_RESULT(failed) +else + AC_MSG_RESULT(ok) +fi + +_LT_DECL([global_symbol_pipe], [lt_cv_sys_global_symbol_pipe], [1], + [Take the output of nm and produce a listing of raw symbols and C names]) +_LT_DECL([global_symbol_to_cdecl], [lt_cv_sys_global_symbol_to_cdecl], [1], + [Transform the output of nm in a proper C declaration]) +_LT_DECL([global_symbol_to_c_name_address], + [lt_cv_sys_global_symbol_to_c_name_address], [1], + [Transform the output of nm in a C name address pair]) +_LT_DECL([global_symbol_to_c_name_address_lib_prefix], + [lt_cv_sys_global_symbol_to_c_name_address_lib_prefix], [1], + [Transform the output of nm in a C name address pair when lib prefix is needed]) +]) # _LT_CMD_GLOBAL_SYMBOLS + + +# _LT_COMPILER_PIC([TAGNAME]) +# --------------------------- +m4_defun([_LT_COMPILER_PIC], +[m4_require([_LT_TAG_COMPILER])dnl +_LT_TAGVAR(lt_prog_compiler_wl, $1)= +_LT_TAGVAR(lt_prog_compiler_pic, $1)= +_LT_TAGVAR(lt_prog_compiler_static, $1)= + +AC_MSG_CHECKING([for $compiler option to produce PIC]) +m4_if([$1], [CXX], [ + # C++ specific cases for pic, static, wl, etc. + if test "$GXX" = yes; then + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' + + case $host_os in + aix*) + # All AIX code is PIC. + if test "$host_cpu" = ia64; then + # AIX 5 now supports IA64 processor + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + fi + ;; + + amigaos*) + case $host_cpu in + powerpc) + # see comment about AmigaOS4 .so support + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' + ;; + m68k) + # FIXME: we need at least 68020 code to build shared libraries, but + # adding the `-m68020' flag to GCC prevents building anything better, + # like `-m68040'. + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' + ;; + esac + ;; + + beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) + # PIC is the default for these OSes. + ;; + mingw* | cygwin* | os2* | pw32* | cegcc*) + # This hack is so that the source file can tell whether it is being + # built for inclusion in a dll (and should export symbols for example). + # Although the cygwin gcc ignores -fPIC, still need this for old-style + # (--disable-auto-import) libraries + m4_if([$1], [GCJ], [], + [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) + ;; + darwin* | rhapsody*) + # PIC is the default on this platform + # Common symbols not allowed in MH_DYLIB files + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' + ;; + *djgpp*) + # DJGPP does not support shared libraries at all + _LT_TAGVAR(lt_prog_compiler_pic, $1)= + ;; + interix[[3-9]]*) + # Interix 3.x gcc -fpic/-fPIC options generate broken code. + # Instead, we relocate shared libraries at runtime. + ;; + sysv4*MP*) + if test -d /usr/nec; then + _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic + fi + ;; + hpux*) + # PIC is the default for 64-bit PA HP-UX, but not for 32-bit + # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag + # sets the default TLS model and affects inlining. + case $host_cpu in + hppa*64*) + ;; + *) + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' + ;; + esac + ;; + *qnx* | *nto*) + # QNX uses GNU C++, but need to define -shared option too, otherwise + # it will coredump. + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' + ;; + *) + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' + ;; + esac + else + case $host_os in + aix[[4-9]]*) + # All AIX code is PIC. + if test "$host_cpu" = ia64; then + # AIX 5 now supports IA64 processor + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + else + _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' + fi + ;; + chorus*) + case $cc_basename in + cxch68*) + # Green Hills C++ Compiler + # _LT_TAGVAR(lt_prog_compiler_static, $1)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a" + ;; + esac + ;; + dgux*) + case $cc_basename in + ec++*) + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' + ;; + ghcx*) + # Green Hills C++ Compiler + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' + ;; + *) + ;; + esac + ;; + freebsd* | dragonfly*) + # FreeBSD uses GNU C++ + ;; + hpux9* | hpux10* | hpux11*) + case $cc_basename in + CC*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' + if test "$host_cpu" != ia64; then + _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' + fi + ;; + aCC*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' + case $host_cpu in + hppa*64*|ia64*) + # +Z the default + ;; + *) + _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' + ;; + esac + ;; + *) + ;; + esac + ;; + interix*) + # This is c89, which is MS Visual C++ (no shared libs) + # Anyone wants to do a port? + ;; + irix5* | irix6* | nonstopux*) + case $cc_basename in + CC*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' + # CC pic flag -KPIC is the default. + ;; + *) + ;; + esac + ;; + linux* | k*bsd*-gnu) + case $cc_basename in + KCC*) + # KAI C++ Compiler + _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' + ;; + ecpc* ) + # old Intel C++ for x86_64 which still supported -KPIC. + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' + ;; + icpc* ) + # Intel C++, used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' + ;; + pgCC* | pgcpp*) + # Portland Group C++ compiler + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + ;; + cxx*) + # Compaq C++ + # Make sure the PIC flag is empty. It appears that all Alpha + # Linux and Compaq Tru64 Unix objects are PIC. + _LT_TAGVAR(lt_prog_compiler_pic, $1)= + _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' + ;; + xlc* | xlC*) + # IBM XL 8.0 on PPC + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink' + ;; + *) + case `$CC -V 2>&1 | sed 5q` in + *Sun\ C*) + # Sun C++ 5.9 + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' + ;; + esac + ;; + esac + ;; + lynxos*) + ;; + m88k*) + ;; + mvs*) + case $cc_basename in + cxx*) + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-W c,exportall' + ;; + *) + ;; + esac + ;; + netbsd* | netbsdelf*-gnu) + ;; + *qnx* | *nto*) + # QNX uses GNU C++, but need to define -shared option too, otherwise + # it will coredump. + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' + ;; + osf3* | osf4* | osf5*) + case $cc_basename in + KCC*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' + ;; + RCC*) + # Rational C++ 2.4.1 + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' + ;; + cxx*) + # Digital/Compaq C++ + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + # Make sure the PIC flag is empty. It appears that all Alpha + # Linux and Compaq Tru64 Unix objects are PIC. + _LT_TAGVAR(lt_prog_compiler_pic, $1)= + _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' + ;; + *) + ;; + esac + ;; + psos*) + ;; + solaris*) + case $cc_basename in + CC*) + # Sun C++ 4.2, 5.x and Centerline C++ + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' + ;; + gcx*) + # Green Hills C++ Compiler + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC' + ;; + *) + ;; + esac + ;; + sunos4*) + case $cc_basename in + CC*) + # Sun C++ 4.x + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + ;; + lcc*) + # Lucid + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' + ;; + *) + ;; + esac + ;; + sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*) + case $cc_basename in + CC*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + ;; + esac + ;; + tandem*) + case $cc_basename in + NCC*) + # NonStop-UX NCC 3.20 + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' + ;; + *) + ;; + esac + ;; + vxworks*) + ;; + *) + _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no + ;; + esac + fi +], +[ + if test "$GCC" = yes; then + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' + + case $host_os in + aix*) + # All AIX code is PIC. + if test "$host_cpu" = ia64; then + # AIX 5 now supports IA64 processor + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + fi + ;; + + amigaos*) + case $host_cpu in + powerpc) + # see comment about AmigaOS4 .so support + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' + ;; + m68k) + # FIXME: we need at least 68020 code to build shared libraries, but + # adding the `-m68020' flag to GCC prevents building anything better, + # like `-m68040'. + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' + ;; + esac + ;; + + beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) + # PIC is the default for these OSes. + ;; + + mingw* | cygwin* | pw32* | os2* | cegcc*) + # This hack is so that the source file can tell whether it is being + # built for inclusion in a dll (and should export symbols for example). + # Although the cygwin gcc ignores -fPIC, still need this for old-style + # (--disable-auto-import) libraries + m4_if([$1], [GCJ], [], + [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) + ;; + + darwin* | rhapsody*) + # PIC is the default on this platform + # Common symbols not allowed in MH_DYLIB files + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' + ;; + + hpux*) + # PIC is the default for 64-bit PA HP-UX, but not for 32-bit + # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag + # sets the default TLS model and affects inlining. + case $host_cpu in + hppa*64*) + # +Z the default + ;; + *) + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' + ;; + esac + ;; + + interix[[3-9]]*) + # Interix 3.x gcc -fpic/-fPIC options generate broken code. + # Instead, we relocate shared libraries at runtime. + ;; + + msdosdjgpp*) + # Just because we use GCC doesn't mean we suddenly get shared libraries + # on systems that don't support them. + _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no + enable_shared=no + ;; + + *nto* | *qnx*) + # QNX uses GNU C++, but need to define -shared option too, otherwise + # it will coredump. + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' + ;; + + sysv4*MP*) + if test -d /usr/nec; then + _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic + fi + ;; + + *) + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' + ;; + esac + else + # PORTME Check for flag to pass linker flags through the system compiler. + case $host_os in + aix*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + if test "$host_cpu" = ia64; then + # AIX 5 now supports IA64 processor + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + else + _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' + fi + ;; + + mingw* | cygwin* | pw32* | os2* | cegcc*) + # This hack is so that the source file can tell whether it is being + # built for inclusion in a dll (and should export symbols for example). + m4_if([$1], [GCJ], [], + [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) + ;; + + hpux9* | hpux10* | hpux11*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but + # not for PA HP-UX. + case $host_cpu in + hppa*64*|ia64*) + # +Z the default + ;; + *) + _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' + ;; + esac + # Is there a better lt_prog_compiler_static that works with the bundled CC? + _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' + ;; + + irix5* | irix6* | nonstopux*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + # PIC (with -KPIC) is the default. + _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' + ;; + + linux* | k*bsd*-gnu) + case $cc_basename in + # old Intel for x86_64 which still supported -KPIC. + ecc*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. + icc* | ifort*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' + ;; + # Lahey Fortran 8.1. + lf95*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='--shared' + _LT_TAGVAR(lt_prog_compiler_static, $1)='--static' + ;; + pgcc* | pgf77* | pgf90* | pgf95*) + # Portland Group compilers (*not* the Pentium gcc compiler, + # which looks to be a dead project) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + ;; + ccc*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + # All Alpha code is PIC. + _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' + ;; + xl*) + # IBM XL C 8.0/Fortran 10.1 on PPC + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink' + ;; + *) + case `$CC -V 2>&1 | sed 5q` in + *Sun\ C*) + # Sun C 5.9 + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + ;; + *Sun\ F*) + # Sun Fortran 8.3 passes all unrecognized flags to the linker + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + _LT_TAGVAR(lt_prog_compiler_wl, $1)='' + ;; + esac + ;; + esac + ;; + + newsos6) + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + ;; + + *nto* | *qnx*) + # QNX uses GNU C++, but need to define -shared option too, otherwise + # it will coredump. + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' + ;; + + osf3* | osf4* | osf5*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + # All OSF/1 code is PIC. + _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' + ;; + + rdos*) + _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' + ;; + + solaris*) + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + case $cc_basename in + f77* | f90* | f95*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ';; + *) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,';; + esac + ;; + + sunos4*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + ;; + + sysv4 | sysv4.2uw2* | sysv4.3*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + ;; + + sysv4*MP*) + if test -d /usr/nec ;then + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-Kconform_pic' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + fi + ;; + + sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + ;; + + unicos*) + _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' + _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no + ;; + + uts4*) + _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' + _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' + ;; + + *) + _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no + ;; + esac + fi +]) +case $host_os in + # For platforms which do not support PIC, -DPIC is meaningless: + *djgpp*) + _LT_TAGVAR(lt_prog_compiler_pic, $1)= + ;; + *) + _LT_TAGVAR(lt_prog_compiler_pic, $1)="$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t@m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])" + ;; +esac +AC_MSG_RESULT([$_LT_TAGVAR(lt_prog_compiler_pic, $1)]) +_LT_TAGDECL([wl], [lt_prog_compiler_wl], [1], + [How to pass a linker flag through the compiler]) + +# +# Check to make sure the PIC flag actually works. +# +if test -n "$_LT_TAGVAR(lt_prog_compiler_pic, $1)"; then + _LT_COMPILER_OPTION([if $compiler PIC flag $_LT_TAGVAR(lt_prog_compiler_pic, $1) works], + [_LT_TAGVAR(lt_cv_prog_compiler_pic_works, $1)], + [$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t@m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])], [], + [case $_LT_TAGVAR(lt_prog_compiler_pic, $1) in + "" | " "*) ;; + *) _LT_TAGVAR(lt_prog_compiler_pic, $1)=" $_LT_TAGVAR(lt_prog_compiler_pic, $1)" ;; + esac], + [_LT_TAGVAR(lt_prog_compiler_pic, $1)= + _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no]) +fi +_LT_TAGDECL([pic_flag], [lt_prog_compiler_pic], [1], + [Additional compiler flags for building library objects]) + +# +# Check to make sure the static flag actually works. +# +wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1) eval lt_tmp_static_flag=\"$_LT_TAGVAR(lt_prog_compiler_static, $1)\" +_LT_LINKER_OPTION([if $compiler static flag $lt_tmp_static_flag works], + _LT_TAGVAR(lt_cv_prog_compiler_static_works, $1), + $lt_tmp_static_flag, + [], + [_LT_TAGVAR(lt_prog_compiler_static, $1)=]) +_LT_TAGDECL([link_static_flag], [lt_prog_compiler_static], [1], + [Compiler flag to prevent dynamic linking]) +])# _LT_COMPILER_PIC + + +# _LT_LINKER_SHLIBS([TAGNAME]) +# ---------------------------- +# See if the linker supports building shared libraries. +m4_defun([_LT_LINKER_SHLIBS], +[AC_REQUIRE([LT_PATH_LD])dnl +AC_REQUIRE([LT_PATH_NM])dnl +m4_require([_LT_FILEUTILS_DEFAULTS])dnl +m4_require([_LT_DECL_EGREP])dnl +m4_require([_LT_DECL_SED])dnl +m4_require([_LT_CMD_GLOBAL_SYMBOLS])dnl +m4_require([_LT_TAG_COMPILER])dnl +AC_MSG_CHECKING([whether the $compiler linker ($LD) supports shared libraries]) +m4_if([$1], [CXX], [ + _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols' + case $host_os in + aix[[4-9]]*) + # If we're using GNU nm, then we don't want the "-C" option. + # -C means demangle to AIX nm, but means don't demangle with GNU nm + if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then + _LT_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols' + else + _LT_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols' + fi + ;; + pw32*) + _LT_TAGVAR(export_symbols_cmds, $1)="$ltdll_cmds" + ;; + cygwin* | mingw* | cegcc*) + _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1 DATA/;/^.*[[ ]]__nm__/s/^.*[[ ]]__nm__\([[^ ]]*\)[[ ]][[^ ]]*/\1 DATA/;/^I[[ ]]/d;/^[[AITW]][[ ]]/s/.* //'\'' | sort | uniq > $export_symbols' + ;; + linux* | k*bsd*-gnu) + _LT_TAGVAR(link_all_deplibs, $1)=no + ;; + *) + _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols' + ;; + esac + _LT_TAGVAR(exclude_expsyms, $1)=['_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'] +], [ + runpath_var= + _LT_TAGVAR(allow_undefined_flag, $1)= + _LT_TAGVAR(always_export_symbols, $1)=no + _LT_TAGVAR(archive_cmds, $1)= + _LT_TAGVAR(archive_expsym_cmds, $1)= + _LT_TAGVAR(compiler_needs_object, $1)=no + _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no + _LT_TAGVAR(export_dynamic_flag_spec, $1)= + _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols' + _LT_TAGVAR(hardcode_automatic, $1)=no + _LT_TAGVAR(hardcode_direct, $1)=no + _LT_TAGVAR(hardcode_direct_absolute, $1)=no + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)= + _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)= + _LT_TAGVAR(hardcode_libdir_separator, $1)= + _LT_TAGVAR(hardcode_minus_L, $1)=no + _LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported + _LT_TAGVAR(inherit_rpath, $1)=no + _LT_TAGVAR(link_all_deplibs, $1)=unknown + _LT_TAGVAR(module_cmds, $1)= + _LT_TAGVAR(module_expsym_cmds, $1)= + _LT_TAGVAR(old_archive_from_new_cmds, $1)= + _LT_TAGVAR(old_archive_from_expsyms_cmds, $1)= + _LT_TAGVAR(thread_safe_flag_spec, $1)= + _LT_TAGVAR(whole_archive_flag_spec, $1)= + # include_expsyms should be a list of space-separated symbols to be *always* + # included in the symbol list + _LT_TAGVAR(include_expsyms, $1)= + # exclude_expsyms can be an extended regexp of symbols to exclude + # it will be wrapped by ` (' and `)$', so one must not match beginning or + # end of line. Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc', + # as well as any symbol that contains `d'. + _LT_TAGVAR(exclude_expsyms, $1)=['_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'] + # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out + # platforms (ab)use it in PIC code, but their linkers get confused if + # the symbol is explicitly referenced. Since portable code cannot + # rely on this symbol name, it's probably fine to never include it in + # preloaded symbol tables. + # Exclude shared library initialization/finalization symbols. +dnl Note also adjust exclude_expsyms for C++ above. + extract_expsyms_cmds= + + case $host_os in + cygwin* | mingw* | pw32* | cegcc*) + # FIXME: the MSVC++ port hasn't been tested in a loooong time + # When not using gcc, we currently assume that we are using + # Microsoft Visual C++. + if test "$GCC" != yes; then + with_gnu_ld=no + fi + ;; + interix*) + # we just hope/assume this is gcc and not c89 (= MSVC++) + with_gnu_ld=yes + ;; + openbsd*) + with_gnu_ld=no + ;; + esac + + _LT_TAGVAR(ld_shlibs, $1)=yes + if test "$with_gnu_ld" = yes; then + # If archive_cmds runs LD, not CC, wlarc should be empty + wlarc='${wl}' + + # Set some defaults for GNU ld with shared library support. These + # are reset later if shared libraries are not supported. Putting them + # here allows them to be overridden if necessary. + runpath_var=LD_RUN_PATH + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic' + # ancient GNU ld didn't support --whole-archive et. al. + if $LD --help 2>&1 | $GREP 'no-whole-archive' > /dev/null; then + _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive' + else + _LT_TAGVAR(whole_archive_flag_spec, $1)= + fi + supports_anon_versioning=no + case `$LD -v 2>&1` in + *\ [[01]].* | *\ 2.[[0-9]].* | *\ 2.10.*) ;; # catch versions < 2.11 + *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ... + *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ... + *\ 2.11.*) ;; # other 2.11 versions + *) supports_anon_versioning=yes ;; + esac + + # See if GNU ld supports shared libraries. + case $host_os in + aix[[3-9]]*) + # On AIX/PPC, the GNU linker is very broken + if test "$host_cpu" != ia64; then + _LT_TAGVAR(ld_shlibs, $1)=no + cat <<_LT_EOF 1>&2 + +*** Warning: the GNU linker, at least up to release 2.9.1, is reported +*** to be unable to reliably create shared libraries on AIX. +*** Therefore, libtool is disabling shared libraries support. If you +*** really care for shared libraries, you may want to modify your PATH +*** so that a non-GNU linker is found, and then restart. + +_LT_EOF + fi + ;; + + amigaos*) + case $host_cpu in + powerpc) + # see comment about AmigaOS4 .so support + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='' + ;; + m68k) + _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' + _LT_TAGVAR(hardcode_minus_L, $1)=yes + ;; + esac + ;; + + beos*) + if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then + _LT_TAGVAR(allow_undefined_flag, $1)=unsupported + # Joseph Beckenbach says some releases of gcc + # support --undefined. This deserves some investigation. FIXME + _LT_TAGVAR(archive_cmds, $1)='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi + ;; + + cygwin* | mingw* | pw32* | cegcc*) + # _LT_TAGVAR(hardcode_libdir_flag_spec, $1) is actually meaningless, + # as there is no search path for DLLs. + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' + _LT_TAGVAR(allow_undefined_flag, $1)=unsupported + _LT_TAGVAR(always_export_symbols, $1)=no + _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes + _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1 DATA/'\'' | $SED -e '\''/^[[AITW]][[ ]]/s/.*[[ ]]//'\'' | sort | uniq > $export_symbols' + + if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' + # If the export-symbols file already is a .def file (1st line + # is EXPORTS), use it as is; otherwise, prepend... + _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then + cp $export_symbols $output_objdir/$soname.def; + else + echo EXPORTS > $output_objdir/$soname.def; + cat $export_symbols >> $output_objdir/$soname.def; + fi~ + $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi + ;; + + interix[[3-9]]*) + _LT_TAGVAR(hardcode_direct, $1)=no + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' + # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc. + # Instead, shared libraries are loaded at an image base (0x10000000 by + # default) and relocated if they conflict, which is a slow very memory + # consuming and fragmenting process. To avoid this, we pick a random, + # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link + # time. Moving up from 0x10000000 also allows more sbrk(2) space. + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib' + ;; + + gnu* | linux* | tpf* | k*bsd*-gnu) + tmp_diet=no + if test "$host_os" = linux-dietlibc; then + case $cc_basename in + diet\ *) tmp_diet=yes;; # linux-dietlibc with static linking (!diet-dyn) + esac + fi + if $LD --help 2>&1 | $EGREP ': supported targets:.* elf' > /dev/null \ + && test "$tmp_diet" = no + then + tmp_addflag= + tmp_sharedflag='-shared' + case $cc_basename,$host_cpu in + pgcc*) # Portland Group C compiler + _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag' + ;; + pgf77* | pgf90* | pgf95*) # Portland Group f77 and f90 compilers + _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag -Mnomain' ;; + ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; + efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; + ifc* | ifort*) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + _LT_TAGVAR(whole_archive_flag_spec, $1)= + tmp_sharedflag='--shared' ;; + xl[[cC]]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' + tmp_addflag= ;; + esac + case `$CC -V 2>&1 | sed 5q` in + *Sun\ C*) # Sun C 5.9 + _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' + _LT_TAGVAR(compiler_needs_object, $1)=yes + tmp_sharedflag='-G' ;; + *Sun\ F*) # Sun Fortran 8.3 + tmp_sharedflag='-G' ;; + esac + _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + + if test "x$supports_anon_versioning" = xyes; then + _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~ + cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ + echo "local: *; };" >> $output_objdir/$libname.ver~ + $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib' + fi + + case $cc_basename in + xlf*) + # IBM XL Fortran 10.1 on PPC cannot create shared libs itself + _LT_TAGVAR(whole_archive_flag_spec, $1)='--whole-archive$convenience --no-whole-archive' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)= + _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='-rpath $libdir' + _LT_TAGVAR(archive_cmds, $1)='$LD -shared $libobjs $deplibs $compiler_flags -soname $soname -o $lib' + if test "x$supports_anon_versioning" = xyes; then + _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~ + cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ + echo "local: *; };" >> $output_objdir/$libname.ver~ + $LD -shared $libobjs $deplibs $compiler_flags -soname $soname -version-script $output_objdir/$libname.ver -o $lib' + fi + ;; + esac + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi + ;; + + netbsd* | netbsdelf*-gnu) + if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then + _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib' + wlarc= + else + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' + fi + ;; + + solaris*) + if $LD -v 2>&1 | $GREP 'BFD 2\.8' > /dev/null; then + _LT_TAGVAR(ld_shlibs, $1)=no + cat <<_LT_EOF 1>&2 + +*** Warning: The releases 2.8.* of the GNU linker cannot reliably +*** create shared libraries on Solaris systems. Therefore, libtool +*** is disabling shared libraries support. We urge you to upgrade GNU +*** binutils to release 2.9.1 or newer. Another option is to modify +*** your PATH or compiler configuration so that the native linker is +*** used, and then restart. + +_LT_EOF + elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi + ;; + + sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*) + case `$LD -v 2>&1` in + *\ [[01]].* | *\ 2.[[0-9]].* | *\ 2.1[[0-5]].*) + _LT_TAGVAR(ld_shlibs, $1)=no + cat <<_LT_EOF 1>&2 + +*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not +*** reliably create shared libraries on SCO systems. Therefore, libtool +*** is disabling shared libraries support. We urge you to upgrade GNU +*** binutils to release 2.16.91.0.3 or newer. Another option is to modify +*** your PATH or compiler configuration so that the native linker is +*** used, and then restart. + +_LT_EOF + ;; + *) + # For security reasons, it is highly recommended that you always + # use absolute paths for naming shared libraries, and exclude the + # DT_RUNPATH tag from executables and libraries. But doing so + # requires that you compile everything twice, which is a pain. + if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi + ;; + esac + ;; + + sunos4*) + _LT_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags' + wlarc= + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + ;; + + *) + if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi + ;; + esac + + if test "$_LT_TAGVAR(ld_shlibs, $1)" = no; then + runpath_var= + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)= + _LT_TAGVAR(export_dynamic_flag_spec, $1)= + _LT_TAGVAR(whole_archive_flag_spec, $1)= + fi + else + # PORTME fill in a description of your system's linker (not GNU ld) + case $host_os in + aix3*) + _LT_TAGVAR(allow_undefined_flag, $1)=unsupported + _LT_TAGVAR(always_export_symbols, $1)=yes + _LT_TAGVAR(archive_expsym_cmds, $1)='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname' + # Note: this linker hardcodes the directories in LIBPATH if there + # are no directories specified by -L. + _LT_TAGVAR(hardcode_minus_L, $1)=yes + if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then + # Neither direct hardcoding nor static linking is supported with a + # broken collect2. + _LT_TAGVAR(hardcode_direct, $1)=unsupported + fi + ;; + + aix[[4-9]]*) + if test "$host_cpu" = ia64; then + # On IA64, the linker does run time linking by default, so we don't + # have to do anything special. + aix_use_runtimelinking=no + exp_sym_flag='-Bexport' + no_entry_flag="" + else + # If we're using GNU nm, then we don't want the "-C" option. + # -C means demangle to AIX nm, but means don't demangle with GNU nm + if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then + _LT_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols' + else + _LT_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols' + fi + aix_use_runtimelinking=no + + # Test if we are trying to use run time linking or normal + # AIX style linking. If -brtl is somewhere in LDFLAGS, we + # need to do runtime linking. + case $host_os in aix4.[[23]]|aix4.[[23]].*|aix[[5-9]]*) + for ld_flag in $LDFLAGS; do + if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then + aix_use_runtimelinking=yes + break + fi + done + ;; + esac + + exp_sym_flag='-bexport' + no_entry_flag='-bnoentry' + fi + + # When large executables or shared objects are built, AIX ld can + # have problems creating the table of contents. If linking a library + # or program results in "error TOC overflow" add -mminimal-toc to + # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not + # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS. + + _LT_TAGVAR(archive_cmds, $1)='' + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_direct_absolute, $1)=yes + _LT_TAGVAR(hardcode_libdir_separator, $1)=':' + _LT_TAGVAR(link_all_deplibs, $1)=yes + _LT_TAGVAR(file_list_spec, $1)='${wl}-f,' + + if test "$GCC" = yes; then + case $host_os in aix4.[[012]]|aix4.[[012]].*) + # We only want to do this on AIX 4.2 and lower, the check + # below for broken collect2 doesn't work under 4.3+ + collect2name=`${CC} -print-prog-name=collect2` + if test -f "$collect2name" && + strings "$collect2name" | $GREP resolve_lib_name >/dev/null + then + # We have reworked collect2 + : + else + # We have old collect2 + _LT_TAGVAR(hardcode_direct, $1)=unsupported + # It fails to find uninstalled libraries when the uninstalled + # path is not listed in the libpath. Setting hardcode_minus_L + # to unsupported forces relinking + _LT_TAGVAR(hardcode_minus_L, $1)=yes + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)= + fi + ;; + esac + shared_flag='-shared' + if test "$aix_use_runtimelinking" = yes; then + shared_flag="$shared_flag "'${wl}-G' + fi + _LT_TAGVAR(link_all_deplibs, $1)=no + else + # not using gcc + if test "$host_cpu" = ia64; then + # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release + # chokes on -Wl,-G. The following line is correct: + shared_flag='-G' + else + if test "$aix_use_runtimelinking" = yes; then + shared_flag='${wl}-G' + else + shared_flag='${wl}-bM:SRE' + fi + fi + fi + + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-bexpall' + # It seems that -bexpall does not export symbols beginning with + # underscore (_), so it is better to generate a list of symbols to export. + _LT_TAGVAR(always_export_symbols, $1)=yes + if test "$aix_use_runtimelinking" = yes; then + # Warning - without using the other runtime loading flags (-brtl), + # -berok will link without error, but may produce a broken library. + _LT_TAGVAR(allow_undefined_flag, $1)='-berok' + # Determine the default libpath from the value encoded in an + # empty executable. + _LT_SYS_MODULE_PATH_AIX + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath" + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" + else + if test "$host_cpu" = ia64; then + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib' + _LT_TAGVAR(allow_undefined_flag, $1)="-z nodefs" + _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" + else + # Determine the default libpath from the value encoded in an + # empty executable. + _LT_SYS_MODULE_PATH_AIX + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath" + # Warning - without using the other run time loading flags, + # -berok will link without error, but may produce a broken library. + _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok' + _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok' + # Exported symbols can be pulled into shared objects from archives + _LT_TAGVAR(whole_archive_flag_spec, $1)='$convenience' + _LT_TAGVAR(archive_cmds_need_lc, $1)=yes + # This is similar to how AIX traditionally builds its shared libraries. + _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' + fi + fi + ;; + + amigaos*) + case $host_cpu in + powerpc) + # see comment about AmigaOS4 .so support + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='' + ;; + m68k) + _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' + _LT_TAGVAR(hardcode_minus_L, $1)=yes + ;; + esac + ;; + + bsdi[[45]]*) + _LT_TAGVAR(export_dynamic_flag_spec, $1)=-rdynamic + ;; + + cygwin* | mingw* | pw32* | cegcc*) + # When not using gcc, we currently assume that we are using + # Microsoft Visual C++. + # hardcode_libdir_flag_spec is actually meaningless, as there is + # no search path for DLLs. + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=' ' + _LT_TAGVAR(allow_undefined_flag, $1)=unsupported + # Tell ltmain to make .lib files, not .a files. + libext=lib + # Tell ltmain to make .dll files, not .so files. + shrext_cmds=".dll" + # FIXME: Setting linknames here is a bad hack. + _LT_TAGVAR(archive_cmds, $1)='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames=' + # The linker will automatically build a .lib file if we build a DLL. + _LT_TAGVAR(old_archive_from_new_cmds, $1)='true' + # FIXME: Should let the user specify the lib program. + _LT_TAGVAR(old_archive_cmds, $1)='lib -OUT:$oldlib$oldobjs$old_deplibs' + _LT_TAGVAR(fix_srcfile_path, $1)='`cygpath -w "$srcfile"`' + _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes + ;; + + darwin* | rhapsody*) + _LT_DARWIN_LINKER_FEATURES($1) + ;; + + dgux*) + _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + ;; + + freebsd1*) + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + + # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor + # support. Future versions do this automatically, but an explicit c++rt0.o + # does not break anything, and helps significantly (at the cost of a little + # extra space). + freebsd2.2*) + _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + ;; + + # Unfortunately, older versions of FreeBSD 2 do not have this feature. + freebsd2*) + _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_minus_L, $1)=yes + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + ;; + + # FreeBSD 3 and greater uses gcc -shared to do shared libraries. + freebsd* | dragonfly*) + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + ;; + + hpux9*) + if test "$GCC" = yes; then + _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' + else + _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' + fi + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + _LT_TAGVAR(hardcode_direct, $1)=yes + + # hardcode_minus_L: Not really in the search PATH, + # but as the default location of the library. + _LT_TAGVAR(hardcode_minus_L, $1)=yes + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' + ;; + + hpux10*) + if test "$GCC" = yes -a "$with_gnu_ld" = no; then + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' + else + _LT_TAGVAR(archive_cmds, $1)='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' + fi + if test "$with_gnu_ld" = no; then + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir' + _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='+b $libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_direct_absolute, $1)=yes + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' + # hardcode_minus_L: Not really in the search PATH, + # but as the default location of the library. + _LT_TAGVAR(hardcode_minus_L, $1)=yes + fi + ;; + + hpux11*) + if test "$GCC" = yes -a "$with_gnu_ld" = no; then + case $host_cpu in + hppa*64*) + _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' + ;; + ia64*) + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' + ;; + *) + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' + ;; + esac + else + case $host_cpu in + hppa*64*) + _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' + ;; + ia64*) + _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' + ;; + *) + _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' + ;; + esac + fi + if test "$with_gnu_ld" = no; then + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + + case $host_cpu in + hppa*64*|ia64*) + _LT_TAGVAR(hardcode_direct, $1)=no + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + ;; + *) + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_direct_absolute, $1)=yes + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' + + # hardcode_minus_L: Not really in the search PATH, + # but as the default location of the library. + _LT_TAGVAR(hardcode_minus_L, $1)=yes + ;; + esac + fi + ;; + + irix5* | irix6* | nonstopux*) + if test "$GCC" = yes; then + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' + # Try to use the -exported_symbol ld option, if it does not + # work, assume that -exports_file does not work either and + # implicitly export all symbols. + save_LDFLAGS="$LDFLAGS" + LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null" + AC_LINK_IFELSE(int foo(void) {}, + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib' + ) + LDFLAGS="$save_LDFLAGS" + else + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib' + fi + _LT_TAGVAR(archive_cmds_need_lc, $1)='no' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + _LT_TAGVAR(inherit_rpath, $1)=yes + _LT_TAGVAR(link_all_deplibs, $1)=yes + ;; + + netbsd* | netbsdelf*-gnu) + if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then + _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out + else + _LT_TAGVAR(archive_cmds, $1)='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF + fi + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + ;; + + newsos6) + _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + ;; + + *nto* | *qnx*) + ;; + + openbsd*) + if test -f /usr/libexec/ld.so; then + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + _LT_TAGVAR(hardcode_direct_absolute, $1)=yes + if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' + else + case $host_os in + openbsd[[01]].* | openbsd2.[[0-7]] | openbsd2.[[0-7]].*) + _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' + ;; + *) + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' + ;; + esac + fi + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi + ;; + + os2*) + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' + _LT_TAGVAR(hardcode_minus_L, $1)=yes + _LT_TAGVAR(allow_undefined_flag, $1)=unsupported + _LT_TAGVAR(archive_cmds, $1)='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' + _LT_TAGVAR(old_archive_from_new_cmds, $1)='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' + ;; + + osf3*) + if test "$GCC" = yes; then + _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*' + _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' + else + _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*' + _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' + fi + _LT_TAGVAR(archive_cmds_need_lc, $1)='no' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + ;; + + osf4* | osf5*) # as osf3* with the addition of -msym flag + if test "$GCC" = yes; then + _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*' + _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' + else + _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*' + _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~ + $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp' + + # Both c and cxx compiler support -rpath directly + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir' + fi + _LT_TAGVAR(archive_cmds_need_lc, $1)='no' + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + ;; + + solaris*) + _LT_TAGVAR(no_undefined_flag, $1)=' -z defs' + if test "$GCC" = yes; then + wlarc='${wl}' + _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ + $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' + else + case `$CC -V 2>&1` in + *"Compilers 5.0"*) + wlarc='' + _LT_TAGVAR(archive_cmds, $1)='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ + $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp' + ;; + *) + wlarc='${wl}' + _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ + $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' + ;; + esac + fi + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + case $host_os in + solaris2.[[0-5]] | solaris2.[[0-5]].*) ;; + *) + # The compiler driver will combine and reorder linker options, + # but understands `-z linker_flag'. GCC discards it without `$wl', + # but is careful enough not to reorder. + # Supported since Solaris 2.6 (maybe 2.5.1?) + if test "$GCC" = yes; then + _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract' + else + _LT_TAGVAR(whole_archive_flag_spec, $1)='-z allextract$convenience -z defaultextract' + fi + ;; + esac + _LT_TAGVAR(link_all_deplibs, $1)=yes + ;; + + sunos4*) + if test "x$host_vendor" = xsequent; then + # Use $CC to link under sequent, because it throws in some extra .o + # files that make .init and .fini sections work. + _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags' + else + _LT_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags' + fi + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_minus_L, $1)=yes + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + ;; + + sysv4) + case $host_vendor in + sni) + _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + _LT_TAGVAR(hardcode_direct, $1)=yes # is this really true??? + ;; + siemens) + ## LD is ld it makes a PLAMLIB + ## CC just makes a GrossModule. + _LT_TAGVAR(archive_cmds, $1)='$LD -G -o $lib $libobjs $deplibs $linker_flags' + _LT_TAGVAR(reload_cmds, $1)='$CC -r -o $output$reload_objs' + _LT_TAGVAR(hardcode_direct, $1)=no + ;; + motorola) + _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + _LT_TAGVAR(hardcode_direct, $1)=no #Motorola manual says yes, but my tests say they lie + ;; + esac + runpath_var='LD_RUN_PATH' + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + ;; + + sysv4.3*) + _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + _LT_TAGVAR(export_dynamic_flag_spec, $1)='-Bexport' + ;; + + sysv4*MP*) + if test -d /usr/nec; then + _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + runpath_var=LD_RUN_PATH + hardcode_runpath_var=yes + _LT_TAGVAR(ld_shlibs, $1)=yes + fi + ;; + + sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[[01]].[[10]]* | unixware7* | sco3.2v5.0.[[024]]*) + _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text' + _LT_TAGVAR(archive_cmds_need_lc, $1)=no + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + runpath_var='LD_RUN_PATH' + + if test "$GCC" = yes; then + _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + else + _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + fi + ;; + + sysv5* | sco3.2v5* | sco5v6*) + # Note: We can NOT use -z defs as we might desire, because we do not + # link with -lc, and that would cause any symbols used from libc to + # always be unresolved, which means just about no library would + # ever link correctly. If we're not using GNU ld we use -z text + # though, which does catch some bad symbols but isn't as heavy-handed + # as -z defs. + _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text' + _LT_TAGVAR(allow_undefined_flag, $1)='${wl}-z,nodefs' + _LT_TAGVAR(archive_cmds_need_lc, $1)=no + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R,$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=':' + _LT_TAGVAR(link_all_deplibs, $1)=yes + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Bexport' + runpath_var='LD_RUN_PATH' + + if test "$GCC" = yes; then + _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + else + _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + fi + ;; + + uts4*) + _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + ;; + + *) + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + esac + + if test x$host_vendor = xsni; then + case $host in + sysv4 | sysv4.2uw2* | sysv4.3* | sysv5*) + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Blargedynsym' + ;; + esac + fi + fi +]) +AC_MSG_RESULT([$_LT_TAGVAR(ld_shlibs, $1)]) +test "$_LT_TAGVAR(ld_shlibs, $1)" = no && can_build_shared=no + +_LT_TAGVAR(with_gnu_ld, $1)=$with_gnu_ld + +_LT_DECL([], [libext], [0], [Old archive suffix (normally "a")])dnl +_LT_DECL([], [shrext_cmds], [1], [Shared library suffix (normally ".so")])dnl +_LT_DECL([], [extract_expsyms_cmds], [2], + [The commands to extract the exported symbol list from a shared archive]) + +# +# Do we need to explicitly link libc? +# +case "x$_LT_TAGVAR(archive_cmds_need_lc, $1)" in +x|xyes) + # Assume -lc should be added + _LT_TAGVAR(archive_cmds_need_lc, $1)=yes + + if test "$enable_shared" = yes && test "$GCC" = yes; then + case $_LT_TAGVAR(archive_cmds, $1) in + *'~'*) + # FIXME: we may have to deal with multi-command sequences. + ;; + '$CC '*) + # Test whether the compiler implicitly links with -lc since on some + # systems, -lgcc has to come before -lc. If gcc already passes -lc + # to ld, don't add -lc before -lgcc. + AC_MSG_CHECKING([whether -lc should be explicitly linked in]) + $RM conftest* + echo "$lt_simple_compile_test_code" > conftest.$ac_ext + + if AC_TRY_EVAL(ac_compile) 2>conftest.err; then + soname=conftest + lib=conftest + libobjs=conftest.$ac_objext + deplibs= + wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1) + pic_flag=$_LT_TAGVAR(lt_prog_compiler_pic, $1) + compiler_flags=-v + linker_flags=-v + verstring= + output_objdir=. + libname=conftest + lt_save_allow_undefined_flag=$_LT_TAGVAR(allow_undefined_flag, $1) + _LT_TAGVAR(allow_undefined_flag, $1)= + if AC_TRY_EVAL(_LT_TAGVAR(archive_cmds, $1) 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) + then + _LT_TAGVAR(archive_cmds_need_lc, $1)=no + else + _LT_TAGVAR(archive_cmds_need_lc, $1)=yes + fi + _LT_TAGVAR(allow_undefined_flag, $1)=$lt_save_allow_undefined_flag + else + cat conftest.err 1>&5 + fi + $RM conftest* + AC_MSG_RESULT([$_LT_TAGVAR(archive_cmds_need_lc, $1)]) + ;; + esac + fi + ;; +esac + +_LT_TAGDECL([build_libtool_need_lc], [archive_cmds_need_lc], [0], + [Whether or not to add -lc for building shared libraries]) +_LT_TAGDECL([allow_libtool_libs_with_static_runtimes], + [enable_shared_with_static_runtimes], [0], + [Whether or not to disallow shared libs when runtime libs are static]) +_LT_TAGDECL([], [export_dynamic_flag_spec], [1], + [Compiler flag to allow reflexive dlopens]) +_LT_TAGDECL([], [whole_archive_flag_spec], [1], + [Compiler flag to generate shared objects directly from archives]) +_LT_TAGDECL([], [compiler_needs_object], [1], + [Whether the compiler copes with passing no objects directly]) +_LT_TAGDECL([], [old_archive_from_new_cmds], [2], + [Create an old-style archive from a shared archive]) +_LT_TAGDECL([], [old_archive_from_expsyms_cmds], [2], + [Create a temporary old-style archive to link instead of a shared archive]) +_LT_TAGDECL([], [archive_cmds], [2], [Commands used to build a shared archive]) +_LT_TAGDECL([], [archive_expsym_cmds], [2]) +_LT_TAGDECL([], [module_cmds], [2], + [Commands used to build a loadable module if different from building + a shared archive.]) +_LT_TAGDECL([], [module_expsym_cmds], [2]) +_LT_TAGDECL([], [with_gnu_ld], [1], + [Whether we are building with GNU ld or not]) +_LT_TAGDECL([], [allow_undefined_flag], [1], + [Flag that allows shared libraries with undefined symbols to be built]) +_LT_TAGDECL([], [no_undefined_flag], [1], + [Flag that enforces no undefined symbols]) +_LT_TAGDECL([], [hardcode_libdir_flag_spec], [1], + [Flag to hardcode $libdir into a binary during linking. + This must work even if $libdir does not exist]) +_LT_TAGDECL([], [hardcode_libdir_flag_spec_ld], [1], + [[If ld is used when linking, flag to hardcode $libdir into a binary + during linking. This must work even if $libdir does not exist]]) +_LT_TAGDECL([], [hardcode_libdir_separator], [1], + [Whether we need a single "-rpath" flag with a separated argument]) +_LT_TAGDECL([], [hardcode_direct], [0], + [Set to "yes" if using DIR/libNAME${shared_ext} during linking hardcodes + DIR into the resulting binary]) +_LT_TAGDECL([], [hardcode_direct_absolute], [0], + [Set to "yes" if using DIR/libNAME${shared_ext} during linking hardcodes + DIR into the resulting binary and the resulting library dependency is + "absolute", i.e impossible to change by setting ${shlibpath_var} if the + library is relocated]) +_LT_TAGDECL([], [hardcode_minus_L], [0], + [Set to "yes" if using the -LDIR flag during linking hardcodes DIR + into the resulting binary]) +_LT_TAGDECL([], [hardcode_shlibpath_var], [0], + [Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR + into the resulting binary]) +_LT_TAGDECL([], [hardcode_automatic], [0], + [Set to "yes" if building a shared library automatically hardcodes DIR + into the library and all subsequent libraries and executables linked + against it]) +_LT_TAGDECL([], [inherit_rpath], [0], + [Set to yes if linker adds runtime paths of dependent libraries + to runtime path list]) +_LT_TAGDECL([], [link_all_deplibs], [0], + [Whether libtool must link a program against all its dependency libraries]) +_LT_TAGDECL([], [fix_srcfile_path], [1], + [Fix the shell variable $srcfile for the compiler]) +_LT_TAGDECL([], [always_export_symbols], [0], + [Set to "yes" if exported symbols are required]) +_LT_TAGDECL([], [export_symbols_cmds], [2], + [The commands to list exported symbols]) +_LT_TAGDECL([], [exclude_expsyms], [1], + [Symbols that should not be listed in the preloaded symbols]) +_LT_TAGDECL([], [include_expsyms], [1], + [Symbols that must always be exported]) +_LT_TAGDECL([], [prelink_cmds], [2], + [Commands necessary for linking programs (against libraries) with templates]) +_LT_TAGDECL([], [file_list_spec], [1], + [Specify filename containing input files]) +dnl FIXME: Not yet implemented +dnl _LT_TAGDECL([], [thread_safe_flag_spec], [1], +dnl [Compiler flag to generate thread safe objects]) +])# _LT_LINKER_SHLIBS + + +# _LT_LANG_C_CONFIG([TAG]) +# ------------------------ +# Ensure that the configuration variables for a C compiler are suitably +# defined. These variables are subsequently used by _LT_CONFIG to write +# the compiler configuration to `libtool'. +m4_defun([_LT_LANG_C_CONFIG], +[m4_require([_LT_DECL_EGREP])dnl +lt_save_CC="$CC" +AC_LANG_PUSH(C) + +# Source file extension for C test sources. +ac_ext=c + +# Object file extension for compiled C test sources. +objext=o +_LT_TAGVAR(objext, $1)=$objext + +# Code to be used in simple compile tests +lt_simple_compile_test_code="int some_variable = 0;" + +# Code to be used in simple link tests +lt_simple_link_test_code='int main(){return(0);}' + +_LT_TAG_COMPILER +# Save the default compiler, since it gets overwritten when the other +# tags are being tested, and _LT_TAGVAR(compiler, []) is a NOP. +compiler_DEFAULT=$CC + +# save warnings/boilerplate of simple test code +_LT_COMPILER_BOILERPLATE +_LT_LINKER_BOILERPLATE + +## CAVEAT EMPTOR: +## There is no encapsulation within the following macros, do not change +## the running order or otherwise move them around unless you know exactly +## what you are doing... +if test -n "$compiler"; then + _LT_COMPILER_NO_RTTI($1) + _LT_COMPILER_PIC($1) + _LT_COMPILER_C_O($1) + _LT_COMPILER_FILE_LOCKS($1) + _LT_LINKER_SHLIBS($1) + _LT_SYS_DYNAMIC_LINKER($1) + _LT_LINKER_HARDCODE_LIBPATH($1) + LT_SYS_DLOPEN_SELF + _LT_CMD_STRIPLIB + + # Report which library types will actually be built + AC_MSG_CHECKING([if libtool supports shared libraries]) + AC_MSG_RESULT([$can_build_shared]) + + AC_MSG_CHECKING([whether to build shared libraries]) + test "$can_build_shared" = "no" && enable_shared=no + + # On AIX, shared libraries and static libraries use the same namespace, and + # are all built from PIC. + case $host_os in + aix3*) + test "$enable_shared" = yes && enable_static=no + if test -n "$RANLIB"; then + archive_cmds="$archive_cmds~\$RANLIB \$lib" + postinstall_cmds='$RANLIB $lib' + fi + ;; + + aix[[4-9]]*) + if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then + test "$enable_shared" = yes && enable_static=no + fi + ;; + esac + AC_MSG_RESULT([$enable_shared]) + + AC_MSG_CHECKING([whether to build static libraries]) + # Make sure either enable_shared or enable_static is yes. + test "$enable_shared" = yes || enable_static=yes + AC_MSG_RESULT([$enable_static]) + + _LT_CONFIG($1) +fi +AC_LANG_POP +CC="$lt_save_CC" +])# _LT_LANG_C_CONFIG + + +# _LT_PROG_CXX +# ------------ +# Since AC_PROG_CXX is broken, in that it returns g++ if there is no c++ +# compiler, we have our own version here. +m4_defun([_LT_PROG_CXX], +[ +pushdef([AC_MSG_ERROR], [_lt_caught_CXX_error=yes]) +AC_PROG_CXX +if test -n "$CXX" && ( test "X$CXX" != "Xno" && + ( (test "X$CXX" = "Xg++" && `g++ -v >/dev/null 2>&1` ) || + (test "X$CXX" != "Xg++"))) ; then + AC_PROG_CXXCPP +else + _lt_caught_CXX_error=yes +fi +popdef([AC_MSG_ERROR]) +])# _LT_PROG_CXX + +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([_LT_PROG_CXX], []) + + +# _LT_LANG_CXX_CONFIG([TAG]) +# -------------------------- +# Ensure that the configuration variables for a C++ compiler are suitably +# defined. These variables are subsequently used by _LT_CONFIG to write +# the compiler configuration to `libtool'. +m4_defun([_LT_LANG_CXX_CONFIG], +[AC_REQUIRE([_LT_PROG_CXX])dnl +m4_require([_LT_FILEUTILS_DEFAULTS])dnl +m4_require([_LT_DECL_EGREP])dnl + +AC_LANG_PUSH(C++) +_LT_TAGVAR(archive_cmds_need_lc, $1)=no +_LT_TAGVAR(allow_undefined_flag, $1)= +_LT_TAGVAR(always_export_symbols, $1)=no +_LT_TAGVAR(archive_expsym_cmds, $1)= +_LT_TAGVAR(compiler_needs_object, $1)=no +_LT_TAGVAR(export_dynamic_flag_spec, $1)= +_LT_TAGVAR(hardcode_direct, $1)=no +_LT_TAGVAR(hardcode_direct_absolute, $1)=no +_LT_TAGVAR(hardcode_libdir_flag_spec, $1)= +_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)= +_LT_TAGVAR(hardcode_libdir_separator, $1)= +_LT_TAGVAR(hardcode_minus_L, $1)=no +_LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported +_LT_TAGVAR(hardcode_automatic, $1)=no +_LT_TAGVAR(inherit_rpath, $1)=no +_LT_TAGVAR(module_cmds, $1)= +_LT_TAGVAR(module_expsym_cmds, $1)= +_LT_TAGVAR(link_all_deplibs, $1)=unknown +_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds +_LT_TAGVAR(no_undefined_flag, $1)= +_LT_TAGVAR(whole_archive_flag_spec, $1)= +_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no + +# Source file extension for C++ test sources. +ac_ext=cpp + +# Object file extension for compiled C++ test sources. +objext=o +_LT_TAGVAR(objext, $1)=$objext + +# No sense in running all these tests if we already determined that +# the CXX compiler isn't working. Some variables (like enable_shared) +# are currently assumed to apply to all compilers on this platform, +# and will be corrupted by setting them based on a non-working compiler. +if test "$_lt_caught_CXX_error" != yes; then + # Code to be used in simple compile tests + lt_simple_compile_test_code="int some_variable = 0;" + + # Code to be used in simple link tests + lt_simple_link_test_code='int main(int, char *[[]]) { return(0); }' + + # ltmain only uses $CC for tagged configurations so make sure $CC is set. + _LT_TAG_COMPILER + + # save warnings/boilerplate of simple test code + _LT_COMPILER_BOILERPLATE + _LT_LINKER_BOILERPLATE + + # Allow CC to be a program name with arguments. + lt_save_CC=$CC + lt_save_LD=$LD + lt_save_GCC=$GCC + GCC=$GXX + lt_save_with_gnu_ld=$with_gnu_ld + lt_save_path_LD=$lt_cv_path_LD + if test -n "${lt_cv_prog_gnu_ldcxx+set}"; then + lt_cv_prog_gnu_ld=$lt_cv_prog_gnu_ldcxx + else + $as_unset lt_cv_prog_gnu_ld + fi + if test -n "${lt_cv_path_LDCXX+set}"; then + lt_cv_path_LD=$lt_cv_path_LDCXX + else + $as_unset lt_cv_path_LD + fi + test -z "${LDCXX+set}" || LD=$LDCXX + CC=${CXX-"c++"} + compiler=$CC + _LT_TAGVAR(compiler, $1)=$CC + _LT_CC_BASENAME([$compiler]) + + if test -n "$compiler"; then + # We don't want -fno-exception when compiling C++ code, so set the + # no_builtin_flag separately + if test "$GXX" = yes; then + _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin' + else + _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)= + fi + + if test "$GXX" = yes; then + # Set up default GNU C++ configuration + + LT_PATH_LD + + # Check if GNU C++ uses GNU ld as the underlying linker, since the + # archiving commands below assume that GNU ld is being used. + if test "$with_gnu_ld" = yes; then + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' + + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic' + + # If archive_cmds runs LD, not CC, wlarc should be empty + # XXX I think wlarc can be eliminated in ltcf-cxx, but I need to + # investigate it a little bit more. (MM) + wlarc='${wl}' + + # ancient GNU ld didn't support --whole-archive et. al. + if eval "`$CC -print-prog-name=ld` --help 2>&1" | + $GREP 'no-whole-archive' > /dev/null; then + _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive' + else + _LT_TAGVAR(whole_archive_flag_spec, $1)= + fi + else + with_gnu_ld=no + wlarc= + + # A generic and very simple default shared library creation + # command for GNU C++ for the case where it uses the native + # linker, instead of GNU ld. If possible, this setting should + # overridden to take advantage of the native linker features on + # the platform it is being used on. + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib' + fi + + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"' + + else + GXX=no + with_gnu_ld=no + wlarc= + fi + + # PORTME: fill in a description of your system's C++ link characteristics + AC_MSG_CHECKING([whether the $compiler linker ($LD) supports shared libraries]) + _LT_TAGVAR(ld_shlibs, $1)=yes + case $host_os in + aix3*) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + aix[[4-9]]*) + if test "$host_cpu" = ia64; then + # On IA64, the linker does run time linking by default, so we don't + # have to do anything special. + aix_use_runtimelinking=no + exp_sym_flag='-Bexport' + no_entry_flag="" + else + aix_use_runtimelinking=no + + # Test if we are trying to use run time linking or normal + # AIX style linking. If -brtl is somewhere in LDFLAGS, we + # need to do runtime linking. + case $host_os in aix4.[[23]]|aix4.[[23]].*|aix[[5-9]]*) + for ld_flag in $LDFLAGS; do + case $ld_flag in + *-brtl*) + aix_use_runtimelinking=yes + break + ;; + esac + done + ;; + esac + + exp_sym_flag='-bexport' + no_entry_flag='-bnoentry' + fi + + # When large executables or shared objects are built, AIX ld can + # have problems creating the table of contents. If linking a library + # or program results in "error TOC overflow" add -mminimal-toc to + # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not + # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS. + + _LT_TAGVAR(archive_cmds, $1)='' + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_direct_absolute, $1)=yes + _LT_TAGVAR(hardcode_libdir_separator, $1)=':' + _LT_TAGVAR(link_all_deplibs, $1)=yes + _LT_TAGVAR(file_list_spec, $1)='${wl}-f,' + + if test "$GXX" = yes; then + case $host_os in aix4.[[012]]|aix4.[[012]].*) + # We only want to do this on AIX 4.2 and lower, the check + # below for broken collect2 doesn't work under 4.3+ + collect2name=`${CC} -print-prog-name=collect2` + if test -f "$collect2name" && + strings "$collect2name" | $GREP resolve_lib_name >/dev/null + then + # We have reworked collect2 + : + else + # We have old collect2 + _LT_TAGVAR(hardcode_direct, $1)=unsupported + # It fails to find uninstalled libraries when the uninstalled + # path is not listed in the libpath. Setting hardcode_minus_L + # to unsupported forces relinking + _LT_TAGVAR(hardcode_minus_L, $1)=yes + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)= + fi + esac + shared_flag='-shared' + if test "$aix_use_runtimelinking" = yes; then + shared_flag="$shared_flag "'${wl}-G' + fi + else + # not using gcc + if test "$host_cpu" = ia64; then + # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release + # chokes on -Wl,-G. The following line is correct: + shared_flag='-G' + else + if test "$aix_use_runtimelinking" = yes; then + shared_flag='${wl}-G' + else + shared_flag='${wl}-bM:SRE' + fi + fi + fi + + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-bexpall' + # It seems that -bexpall does not export symbols beginning with + # underscore (_), so it is better to generate a list of symbols to + # export. + _LT_TAGVAR(always_export_symbols, $1)=yes + if test "$aix_use_runtimelinking" = yes; then + # Warning - without using the other runtime loading flags (-brtl), + # -berok will link without error, but may produce a broken library. + _LT_TAGVAR(allow_undefined_flag, $1)='-berok' + # Determine the default libpath from the value encoded in an empty + # executable. + _LT_SYS_MODULE_PATH_AIX + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath" + + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" + else + if test "$host_cpu" = ia64; then + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib' + _LT_TAGVAR(allow_undefined_flag, $1)="-z nodefs" + _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" + else + # Determine the default libpath from the value encoded in an + # empty executable. + _LT_SYS_MODULE_PATH_AIX + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath" + # Warning - without using the other run time loading flags, + # -berok will link without error, but may produce a broken library. + _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok' + _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok' + # Exported symbols can be pulled into shared objects from archives + _LT_TAGVAR(whole_archive_flag_spec, $1)='$convenience' + _LT_TAGVAR(archive_cmds_need_lc, $1)=yes + # This is similar to how AIX traditionally builds its shared + # libraries. + _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' + fi + fi + ;; + + beos*) + if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then + _LT_TAGVAR(allow_undefined_flag, $1)=unsupported + # Joseph Beckenbach says some releases of gcc + # support --undefined. This deserves some investigation. FIXME + _LT_TAGVAR(archive_cmds, $1)='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi + ;; + + chorus*) + case $cc_basename in + *) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + esac + ;; + + cygwin* | mingw* | pw32* | cegcc*) + # _LT_TAGVAR(hardcode_libdir_flag_spec, $1) is actually meaningless, + # as there is no search path for DLLs. + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' + _LT_TAGVAR(allow_undefined_flag, $1)=unsupported + _LT_TAGVAR(always_export_symbols, $1)=no + _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes + + if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' + # If the export-symbols file already is a .def file (1st line + # is EXPORTS), use it as is; otherwise, prepend... + _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then + cp $export_symbols $output_objdir/$soname.def; + else + echo EXPORTS > $output_objdir/$soname.def; + cat $export_symbols >> $output_objdir/$soname.def; + fi~ + $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi + ;; + darwin* | rhapsody*) + _LT_DARWIN_LINKER_FEATURES($1) + ;; + + dgux*) + case $cc_basename in + ec++*) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + ghcx*) + # Green Hills C++ Compiler + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + *) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + esac + ;; + + freebsd[[12]]*) + # C++ shared libraries reported to be fairly broken before + # switch to ELF + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + + freebsd-elf*) + _LT_TAGVAR(archive_cmds_need_lc, $1)=no + ;; + + freebsd* | dragonfly*) + # FreeBSD 3 and later use GNU C++ and GNU ld with standard ELF + # conventions + _LT_TAGVAR(ld_shlibs, $1)=yes + ;; + + gnu*) + ;; + + hpux9*) + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_minus_L, $1)=yes # Not in the search PATH, + # but as the default + # location of the library. + + case $cc_basename in + CC*) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + aCC*) + _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -b ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + # + # There doesn't appear to be a way to prevent this compiler from + # explicitly linking system object files so we need to strip them + # from the output so that they don't get included in the library + # dependencies. + output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $EGREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed' + ;; + *) + if test "$GXX" = yes; then + _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -shared -nostdlib -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' + else + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + fi + ;; + esac + ;; + + hpux10*|hpux11*) + if test $with_gnu_ld = no; then + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + + case $host_cpu in + hppa*64*|ia64*) + ;; + *) + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' + ;; + esac + fi + case $host_cpu in + hppa*64*|ia64*) + _LT_TAGVAR(hardcode_direct, $1)=no + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + ;; + *) + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_direct_absolute, $1)=yes + _LT_TAGVAR(hardcode_minus_L, $1)=yes # Not in the search PATH, + # but as the default + # location of the library. + ;; + esac + + case $cc_basename in + CC*) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + aCC*) + case $host_cpu in + hppa*64*) + _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' + ;; + ia64*) + _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' + ;; + *) + _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' + ;; + esac + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + # + # There doesn't appear to be a way to prevent this compiler from + # explicitly linking system object files so we need to strip them + # from the output so that they don't get included in the library + # dependencies. + output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $GREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed' + ;; + *) + if test "$GXX" = yes; then + if test $with_gnu_ld = no; then + case $host_cpu in + hppa*64*) + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' + ;; + ia64*) + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' + ;; + *) + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' + ;; + esac + fi + else + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + fi + ;; + esac + ;; + + interix[[3-9]]*) + _LT_TAGVAR(hardcode_direct, $1)=no + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' + # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc. + # Instead, shared libraries are loaded at an image base (0x10000000 by + # default) and relocated if they conflict, which is a slow very memory + # consuming and fragmenting process. To avoid this, we pick a random, + # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link + # time. Moving up from 0x10000000 also allows more sbrk(2) space. + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib' + ;; + irix5* | irix6*) + case $cc_basename in + CC*) + # SGI C++ + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -all -multigot $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' + + # Archives containing C++ object files must be created using + # "CC -ar", where "CC" is the IRIX C++ compiler. This is + # necessary to make sure instantiated templates are included + # in the archive. + _LT_TAGVAR(old_archive_cmds, $1)='$CC -ar -WR,-u -o $oldlib $oldobjs' + ;; + *) + if test "$GXX" = yes; then + if test "$with_gnu_ld" = no; then + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' + else + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` -o $lib' + fi + fi + _LT_TAGVAR(link_all_deplibs, $1)=yes + ;; + esac + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + _LT_TAGVAR(inherit_rpath, $1)=yes + ;; + + linux* | k*bsd*-gnu) + case $cc_basename in + KCC*) + # Kuck and Associates, Inc. (KAI) C++ Compiler + + # KCC will only create a shared library if the output file + # ends with ".so" (or ".sl" for HP-UX), so rename the library + # to its proper name (with version) after linking. + _LT_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib' + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + # + # There doesn't appear to be a way to prevent this compiler from + # explicitly linking system object files so we need to strip them + # from the output so that they don't get included in the library + # dependencies. + output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | $GREP "ld"`; rm -f libconftest$shared_ext; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed' + + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic' + + # Archives containing C++ object files must be created using + # "CC -Bstatic", where "CC" is the KAI C++ compiler. + _LT_TAGVAR(old_archive_cmds, $1)='$CC -Bstatic -o $oldlib $oldobjs' + ;; + icpc* | ecpc* ) + # Intel C++ + with_gnu_ld=yes + # version 8.0 and above of icpc choke on multiply defined symbols + # if we add $predep_objects and $postdep_objects, however 7.1 and + # earlier do not add the objects themselves. + case `$CC -V 2>&1` in + *"Version 7."*) + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' + ;; + *) # Version 8.0 or newer + tmp_idyn= + case $host_cpu in + ia64*) tmp_idyn=' -i_dynamic';; + esac + _LT_TAGVAR(archive_cmds, $1)='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' + ;; + esac + _LT_TAGVAR(archive_cmds_need_lc, $1)=no + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic' + _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive$convenience ${wl}--no-whole-archive' + ;; + pgCC* | pgcpp*) + # Portland Group C++ compiler + case `$CC -V` in + *pgCC\ [[1-5]]* | *pgcpp\ [[1-5]]*) + _LT_TAGVAR(prelink_cmds, $1)='tpldir=Template.dir~ + rm -rf $tpldir~ + $CC --prelink_objects --instantiation_dir $tpldir $objs $libobjs $compile_deplibs~ + compile_command="$compile_command `find $tpldir -name \*.o | $NL2SP`"' + _LT_TAGVAR(old_archive_cmds, $1)='tpldir=Template.dir~ + rm -rf $tpldir~ + $CC --prelink_objects --instantiation_dir $tpldir $oldobjs$old_deplibs~ + $AR $AR_FLAGS $oldlib$oldobjs$old_deplibs `find $tpldir -name \*.o | $NL2SP`~ + $RANLIB $oldlib' + _LT_TAGVAR(archive_cmds, $1)='tpldir=Template.dir~ + rm -rf $tpldir~ + $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~ + $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='tpldir=Template.dir~ + rm -rf $tpldir~ + $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~ + $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib' + ;; + *) # Version 6 will use weak symbols + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib' + ;; + esac + + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}--rpath ${wl}$libdir' + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic' + _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' + ;; + cxx*) + # Compaq C++ + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib ${wl}-retain-symbols-file $wl$export_symbols' + + runpath_var=LD_RUN_PATH + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + # + # There doesn't appear to be a way to prevent this compiler from + # explicitly linking system object files so we need to strip them + # from the output so that they don't get included in the library + # dependencies. + output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld .*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed' + ;; + xl*) + # IBM XL 8.0 on PPC, with GNU ld + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic' + _LT_TAGVAR(archive_cmds, $1)='$CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' + if test "x$supports_anon_versioning" = xyes; then + _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~ + cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ + echo "local: *; };" >> $output_objdir/$libname.ver~ + $CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib' + fi + ;; + *) + case `$CC -V 2>&1 | sed 5q` in + *Sun\ C*) + # Sun C++ 5.9 + _LT_TAGVAR(no_undefined_flag, $1)=' -zdefs' + _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file ${wl}$export_symbols' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' + _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' + _LT_TAGVAR(compiler_needs_object, $1)=yes + + # Not sure whether something based on + # $CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 + # would be better. + output_verbose_link_cmd='echo' + + # Archives containing C++ object files must be created using + # "CC -xar", where "CC" is the Sun C++ compiler. This is + # necessary to make sure instantiated templates are included + # in the archive. + _LT_TAGVAR(old_archive_cmds, $1)='$CC -xar -o $oldlib $oldobjs' + ;; + esac + ;; + esac + ;; + + lynxos*) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + + m88k*) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + + mvs*) + case $cc_basename in + cxx*) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + *) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + esac + ;; + + netbsd*) + if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then + _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $predep_objects $libobjs $deplibs $postdep_objects $linker_flags' + wlarc= + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + fi + # Workaround some broken pre-1.5 toolchains + output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP conftest.$objext | $SED -e "s:-lgcc -lc -lgcc::"' + ;; + + *nto* | *qnx*) + _LT_TAGVAR(ld_shlibs, $1)=yes + ;; + + openbsd2*) + # C++ shared libraries are fairly broken + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + + openbsd*) + if test -f /usr/libexec/ld.so; then + _LT_TAGVAR(hardcode_direct, $1)=yes + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + _LT_TAGVAR(hardcode_direct_absolute, $1)=yes + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' + if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file,$export_symbols -o $lib' + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' + _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive' + fi + output_verbose_link_cmd=echo + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi + ;; + + osf3* | osf4* | osf5*) + case $cc_basename in + KCC*) + # Kuck and Associates, Inc. (KAI) C++ Compiler + + # KCC will only create a shared library if the output file + # ends with ".so" (or ".sl" for HP-UX), so rename the library + # to its proper name (with version) after linking. + _LT_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo "$lib" | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib' + + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + + # Archives containing C++ object files must be created using + # the KAI C++ compiler. + case $host in + osf3*) _LT_TAGVAR(old_archive_cmds, $1)='$CC -Bstatic -o $oldlib $oldobjs' ;; + *) _LT_TAGVAR(old_archive_cmds, $1)='$CC -o $oldlib $oldobjs' ;; + esac + ;; + RCC*) + # Rational C++ 2.4.1 + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + cxx*) + case $host in + osf3*) + _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*' + _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $soname `test -n "$verstring" && $ECHO "X${wl}-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' + ;; + *) + _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*' + _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done~ + echo "-hidden">> $lib.exp~ + $CC -shared$allow_undefined_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname ${wl}-input ${wl}$lib.exp `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~ + $RM $lib.exp' + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir' + ;; + esac + + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + # + # There doesn't appear to be a way to prevent this compiler from + # explicitly linking system object files so we need to strip them + # from the output so that they don't get included in the library + # dependencies. + output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld" | $GREP -v "ld:"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed' + ;; + *) + if test "$GXX" = yes && test "$with_gnu_ld" = no; then + _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*' + case $host in + osf3*) + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' + ;; + *) + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' + ;; + esac + + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=: + + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"' + + else + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + fi + ;; + esac + ;; + + psos*) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + + sunos4*) + case $cc_basename in + CC*) + # Sun C++ 4.x + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + lcc*) + # Lucid + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + *) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + esac + ;; + + solaris*) + case $cc_basename in + CC*) + # Sun C++ 4.2, 5.x and Centerline C++ + _LT_TAGVAR(archive_cmds_need_lc,$1)=yes + _LT_TAGVAR(no_undefined_flag, $1)=' -zdefs' + _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ + $CC -G${allow_undefined_flag} ${wl}-M ${wl}$lib.exp -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp' + + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + case $host_os in + solaris2.[[0-5]] | solaris2.[[0-5]].*) ;; + *) + # The compiler driver will combine and reorder linker options, + # but understands `-z linker_flag'. + # Supported since Solaris 2.6 (maybe 2.5.1?) + _LT_TAGVAR(whole_archive_flag_spec, $1)='-z allextract$convenience -z defaultextract' + ;; + esac + _LT_TAGVAR(link_all_deplibs, $1)=yes + + output_verbose_link_cmd='echo' + + # Archives containing C++ object files must be created using + # "CC -xar", where "CC" is the Sun C++ compiler. This is + # necessary to make sure instantiated templates are included + # in the archive. + _LT_TAGVAR(old_archive_cmds, $1)='$CC -xar -o $oldlib $oldobjs' + ;; + gcx*) + # Green Hills C++ Compiler + _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib' + + # The C++ compiler must be used to create the archive. + _LT_TAGVAR(old_archive_cmds, $1)='$CC $LDFLAGS -archive -o $oldlib $oldobjs' + ;; + *) + # GNU C++ compiler with Solaris linker + if test "$GXX" = yes && test "$with_gnu_ld" = no; then + _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-z ${wl}defs' + if $CC --version | $GREP -v '^2\.7' > /dev/null; then + _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ + $CC -shared -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp' + + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"' + else + # g++ 2.7 appears to require `-G' NOT `-shared' on this + # platform. + _LT_TAGVAR(archive_cmds, $1)='$CC -G -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib' + _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ + $CC -G -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp' + + # Commands to make compiler produce verbose output that lists + # what "hidden" libraries, object files and flags are used when + # linking a shared library. + output_verbose_link_cmd='$CC -G $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"' + fi + + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $wl$libdir' + case $host_os in + solaris2.[[0-5]] | solaris2.[[0-5]].*) ;; + *) + _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract' + ;; + esac + fi + ;; + esac + ;; + + sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[[01]].[[10]]* | unixware7* | sco3.2v5.0.[[024]]*) + _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text' + _LT_TAGVAR(archive_cmds_need_lc, $1)=no + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + runpath_var='LD_RUN_PATH' + + case $cc_basename in + CC*) + _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + ;; + *) + _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + ;; + esac + ;; + + sysv5* | sco3.2v5* | sco5v6*) + # Note: We can NOT use -z defs as we might desire, because we do not + # link with -lc, and that would cause any symbols used from libc to + # always be unresolved, which means just about no library would + # ever link correctly. If we're not using GNU ld we use -z text + # though, which does catch some bad symbols but isn't as heavy-handed + # as -z defs. + _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text' + _LT_TAGVAR(allow_undefined_flag, $1)='${wl}-z,nodefs' + _LT_TAGVAR(archive_cmds_need_lc, $1)=no + _LT_TAGVAR(hardcode_shlibpath_var, $1)=no + _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R,$libdir' + _LT_TAGVAR(hardcode_libdir_separator, $1)=':' + _LT_TAGVAR(link_all_deplibs, $1)=yes + _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Bexport' + runpath_var='LD_RUN_PATH' + + case $cc_basename in + CC*) + _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + ;; + *) + _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' + ;; + esac + ;; + + tandem*) + case $cc_basename in + NCC*) + # NonStop-UX NCC 3.20 + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + *) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + esac + ;; + + vxworks*) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + + *) + # FIXME: insert proper C++ library support + _LT_TAGVAR(ld_shlibs, $1)=no + ;; + esac + + AC_MSG_RESULT([$_LT_TAGVAR(ld_shlibs, $1)]) + test "$_LT_TAGVAR(ld_shlibs, $1)" = no && can_build_shared=no + + _LT_TAGVAR(GCC, $1)="$GXX" + _LT_TAGVAR(LD, $1)="$LD" + + ## CAVEAT EMPTOR: + ## There is no encapsulation within the following macros, do not change + ## the running order or otherwise move them around unless you know exactly + ## what you are doing... + _LT_SYS_HIDDEN_LIBDEPS($1) + _LT_COMPILER_PIC($1) + _LT_COMPILER_C_O($1) + _LT_COMPILER_FILE_LOCKS($1) + _LT_LINKER_SHLIBS($1) + _LT_SYS_DYNAMIC_LINKER($1) + _LT_LINKER_HARDCODE_LIBPATH($1) + + _LT_CONFIG($1) + fi # test -n "$compiler" + + CC=$lt_save_CC + LDCXX=$LD + LD=$lt_save_LD + GCC=$lt_save_GCC + with_gnu_ld=$lt_save_with_gnu_ld + lt_cv_path_LDCXX=$lt_cv_path_LD + lt_cv_path_LD=$lt_save_path_LD + lt_cv_prog_gnu_ldcxx=$lt_cv_prog_gnu_ld + lt_cv_prog_gnu_ld=$lt_save_with_gnu_ld +fi # test "$_lt_caught_CXX_error" != yes + +AC_LANG_POP +])# _LT_LANG_CXX_CONFIG + + +# _LT_SYS_HIDDEN_LIBDEPS([TAGNAME]) +# --------------------------------- +# Figure out "hidden" library dependencies from verbose +# compiler output when linking a shared library. +# Parse the compiler output and extract the necessary +# objects, libraries and library flags. +m4_defun([_LT_SYS_HIDDEN_LIBDEPS], +[m4_require([_LT_FILEUTILS_DEFAULTS])dnl +# Dependencies to place before and after the object being linked: +_LT_TAGVAR(predep_objects, $1)= +_LT_TAGVAR(postdep_objects, $1)= +_LT_TAGVAR(predeps, $1)= +_LT_TAGVAR(postdeps, $1)= +_LT_TAGVAR(compiler_lib_search_path, $1)= + +dnl we can't use the lt_simple_compile_test_code here, +dnl because it contains code intended for an executable, +dnl not a library. It's possible we should let each +dnl tag define a new lt_????_link_test_code variable, +dnl but it's only used here... +m4_if([$1], [], [cat > conftest.$ac_ext <<_LT_EOF +int a; +void foo (void) { a = 0; } +_LT_EOF +], [$1], [CXX], [cat > conftest.$ac_ext <<_LT_EOF +class Foo +{ +public: + Foo (void) { a = 0; } +private: + int a; +}; +_LT_EOF +], [$1], [F77], [cat > conftest.$ac_ext <<_LT_EOF + subroutine foo + implicit none + integer*4 a + a=0 + return + end +_LT_EOF +], [$1], [FC], [cat > conftest.$ac_ext <<_LT_EOF + subroutine foo + implicit none + integer a + a=0 + return + end +_LT_EOF +], [$1], [GCJ], [cat > conftest.$ac_ext <<_LT_EOF +public class foo { + private int a; + public void bar (void) { + a = 0; + } +}; +_LT_EOF +]) +dnl Parse the compiler output and extract the necessary +dnl objects, libraries and library flags. +if AC_TRY_EVAL(ac_compile); then + # Parse the compiler output and extract the necessary + # objects, libraries and library flags. + + # Sentinel used to keep track of whether or not we are before + # the conftest object file. + pre_test_object_deps_done=no + + for p in `eval "$output_verbose_link_cmd"`; do + case $p in + + -L* | -R* | -l*) + # Some compilers place space between "-{L,R}" and the path. + # Remove the space. + if test $p = "-L" || + test $p = "-R"; then + prev=$p + continue + else + prev= + fi + + if test "$pre_test_object_deps_done" = no; then + case $p in + -L* | -R*) + # Internal compiler library paths should come after those + # provided the user. The postdeps already come after the + # user supplied libs so there is no need to process them. + if test -z "$_LT_TAGVAR(compiler_lib_search_path, $1)"; then + _LT_TAGVAR(compiler_lib_search_path, $1)="${prev}${p}" + else + _LT_TAGVAR(compiler_lib_search_path, $1)="${_LT_TAGVAR(compiler_lib_search_path, $1)} ${prev}${p}" + fi + ;; + # The "-l" case would never come before the object being + # linked, so don't bother handling this case. + esac + else + if test -z "$_LT_TAGVAR(postdeps, $1)"; then + _LT_TAGVAR(postdeps, $1)="${prev}${p}" + else + _LT_TAGVAR(postdeps, $1)="${_LT_TAGVAR(postdeps, $1)} ${prev}${p}" + fi + fi + ;; + + *.$objext) + # This assumes that the test object file only shows up + # once in the compiler output. + if test "$p" = "conftest.$objext"; then + pre_test_object_deps_done=yes + continue + fi + + if test "$pre_test_object_deps_done" = no; then + if test -z "$_LT_TAGVAR(predep_objects, $1)"; then + _LT_TAGVAR(predep_objects, $1)="$p" + else + _LT_TAGVAR(predep_objects, $1)="$_LT_TAGVAR(predep_objects, $1) $p" + fi + else + if test -z "$_LT_TAGVAR(postdep_objects, $1)"; then + _LT_TAGVAR(postdep_objects, $1)="$p" + else + _LT_TAGVAR(postdep_objects, $1)="$_LT_TAGVAR(postdep_objects, $1) $p" + fi + fi + ;; + + *) ;; # Ignore the rest. + + esac + done + + # Clean up. + rm -f a.out a.exe +else + echo "libtool.m4: error: problem compiling $1 test program" +fi + +$RM -f confest.$objext + +# PORTME: override above test on systems where it is broken +m4_if([$1], [CXX], +[case $host_os in +interix[[3-9]]*) + # Interix 3.5 installs completely hosed .la files for C++, so rather than + # hack all around it, let's just trust "g++" to DTRT. + _LT_TAGVAR(predep_objects,$1)= + _LT_TAGVAR(postdep_objects,$1)= + _LT_TAGVAR(postdeps,$1)= + ;; + +linux*) + case `$CC -V 2>&1 | sed 5q` in + *Sun\ C*) + # Sun C++ 5.9 + + # The more standards-conforming stlport4 library is + # incompatible with the Cstd library. Avoid specifying + # it if it's in CXXFLAGS. Ignore libCrun as + # -library=stlport4 depends on it. + case " $CXX $CXXFLAGS " in + *" -library=stlport4 "*) + solaris_use_stlport4=yes + ;; + esac + + if test "$solaris_use_stlport4" != yes; then + _LT_TAGVAR(postdeps,$1)='-library=Cstd -library=Crun' + fi + ;; + esac + ;; + +solaris*) + case $cc_basename in + CC*) + # The more standards-conforming stlport4 library is + # incompatible with the Cstd library. Avoid specifying + # it if it's in CXXFLAGS. Ignore libCrun as + # -library=stlport4 depends on it. + case " $CXX $CXXFLAGS " in + *" -library=stlport4 "*) + solaris_use_stlport4=yes + ;; + esac + + # Adding this requires a known-good setup of shared libraries for + # Sun compiler versions before 5.6, else PIC objects from an old + # archive will be linked into the output, leading to subtle bugs. + if test "$solaris_use_stlport4" != yes; then + _LT_TAGVAR(postdeps,$1)='-library=Cstd -library=Crun' + fi + ;; + esac + ;; +esac +]) + +case " $_LT_TAGVAR(postdeps, $1) " in +*" -lc "*) _LT_TAGVAR(archive_cmds_need_lc, $1)=no ;; +esac + _LT_TAGVAR(compiler_lib_search_dirs, $1)= +if test -n "${_LT_TAGVAR(compiler_lib_search_path, $1)}"; then + _LT_TAGVAR(compiler_lib_search_dirs, $1)=`echo " ${_LT_TAGVAR(compiler_lib_search_path, $1)}" | ${SED} -e 's! -L! !g' -e 's!^ !!'` +fi +_LT_TAGDECL([], [compiler_lib_search_dirs], [1], + [The directories searched by this compiler when creating a shared library]) +_LT_TAGDECL([], [predep_objects], [1], + [Dependencies to place before and after the objects being linked to + create a shared library]) +_LT_TAGDECL([], [postdep_objects], [1]) +_LT_TAGDECL([], [predeps], [1]) +_LT_TAGDECL([], [postdeps], [1]) +_LT_TAGDECL([], [compiler_lib_search_path], [1], + [The library search path used internally by the compiler when linking + a shared library]) +])# _LT_SYS_HIDDEN_LIBDEPS + + +# _LT_PROG_F77 +# ------------ +# Since AC_PROG_F77 is broken, in that it returns the empty string +# if there is no fortran compiler, we have our own version here. +m4_defun([_LT_PROG_F77], +[ +pushdef([AC_MSG_ERROR], [_lt_disable_F77=yes]) +AC_PROG_F77 +if test -z "$F77" || test "X$F77" = "Xno"; then + _lt_disable_F77=yes +fi +popdef([AC_MSG_ERROR]) +])# _LT_PROG_F77 + +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([_LT_PROG_F77], []) + + +# _LT_LANG_F77_CONFIG([TAG]) +# -------------------------- +# Ensure that the configuration variables for a Fortran 77 compiler are +# suitably defined. These variables are subsequently used by _LT_CONFIG +# to write the compiler configuration to `libtool'. +m4_defun([_LT_LANG_F77_CONFIG], +[AC_REQUIRE([_LT_PROG_F77])dnl +AC_LANG_PUSH(Fortran 77) + +_LT_TAGVAR(archive_cmds_need_lc, $1)=no +_LT_TAGVAR(allow_undefined_flag, $1)= +_LT_TAGVAR(always_export_symbols, $1)=no +_LT_TAGVAR(archive_expsym_cmds, $1)= +_LT_TAGVAR(export_dynamic_flag_spec, $1)= +_LT_TAGVAR(hardcode_direct, $1)=no +_LT_TAGVAR(hardcode_direct_absolute, $1)=no +_LT_TAGVAR(hardcode_libdir_flag_spec, $1)= +_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)= +_LT_TAGVAR(hardcode_libdir_separator, $1)= +_LT_TAGVAR(hardcode_minus_L, $1)=no +_LT_TAGVAR(hardcode_automatic, $1)=no +_LT_TAGVAR(inherit_rpath, $1)=no +_LT_TAGVAR(module_cmds, $1)= +_LT_TAGVAR(module_expsym_cmds, $1)= +_LT_TAGVAR(link_all_deplibs, $1)=unknown +_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds +_LT_TAGVAR(no_undefined_flag, $1)= +_LT_TAGVAR(whole_archive_flag_spec, $1)= +_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no + +# Source file extension for f77 test sources. +ac_ext=f + +# Object file extension for compiled f77 test sources. +objext=o +_LT_TAGVAR(objext, $1)=$objext + +# No sense in running all these tests if we already determined that +# the F77 compiler isn't working. Some variables (like enable_shared) +# are currently assumed to apply to all compilers on this platform, +# and will be corrupted by setting them based on a non-working compiler. +if test "$_lt_disable_F77" != yes; then + # Code to be used in simple compile tests + lt_simple_compile_test_code="\ + subroutine t + return + end +" + + # Code to be used in simple link tests + lt_simple_link_test_code="\ + program t + end +" + + # ltmain only uses $CC for tagged configurations so make sure $CC is set. + _LT_TAG_COMPILER + + # save warnings/boilerplate of simple test code + _LT_COMPILER_BOILERPLATE + _LT_LINKER_BOILERPLATE + + # Allow CC to be a program name with arguments. + lt_save_CC="$CC" + lt_save_GCC=$GCC + CC=${F77-"f77"} + compiler=$CC + _LT_TAGVAR(compiler, $1)=$CC + _LT_CC_BASENAME([$compiler]) + GCC=$G77 + if test -n "$compiler"; then + AC_MSG_CHECKING([if libtool supports shared libraries]) + AC_MSG_RESULT([$can_build_shared]) + + AC_MSG_CHECKING([whether to build shared libraries]) + test "$can_build_shared" = "no" && enable_shared=no + + # On AIX, shared libraries and static libraries use the same namespace, and + # are all built from PIC. + case $host_os in + aix3*) + test "$enable_shared" = yes && enable_static=no + if test -n "$RANLIB"; then + archive_cmds="$archive_cmds~\$RANLIB \$lib" + postinstall_cmds='$RANLIB $lib' + fi + ;; + aix[[4-9]]*) + if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then + test "$enable_shared" = yes && enable_static=no + fi + ;; + esac + AC_MSG_RESULT([$enable_shared]) + + AC_MSG_CHECKING([whether to build static libraries]) + # Make sure either enable_shared or enable_static is yes. + test "$enable_shared" = yes || enable_static=yes + AC_MSG_RESULT([$enable_static]) + + _LT_TAGVAR(GCC, $1)="$G77" + _LT_TAGVAR(LD, $1)="$LD" + + ## CAVEAT EMPTOR: + ## There is no encapsulation within the following macros, do not change + ## the running order or otherwise move them around unless you know exactly + ## what you are doing... + _LT_COMPILER_PIC($1) + _LT_COMPILER_C_O($1) + _LT_COMPILER_FILE_LOCKS($1) + _LT_LINKER_SHLIBS($1) + _LT_SYS_DYNAMIC_LINKER($1) + _LT_LINKER_HARDCODE_LIBPATH($1) + + _LT_CONFIG($1) + fi # test -n "$compiler" + + GCC=$lt_save_GCC + CC="$lt_save_CC" +fi # test "$_lt_disable_F77" != yes + +AC_LANG_POP +])# _LT_LANG_F77_CONFIG + + +# _LT_PROG_FC +# ----------- +# Since AC_PROG_FC is broken, in that it returns the empty string +# if there is no fortran compiler, we have our own version here. +m4_defun([_LT_PROG_FC], +[ +pushdef([AC_MSG_ERROR], [_lt_disable_FC=yes]) +AC_PROG_FC +if test -z "$FC" || test "X$FC" = "Xno"; then + _lt_disable_FC=yes +fi +popdef([AC_MSG_ERROR]) +])# _LT_PROG_FC + +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([_LT_PROG_FC], []) + + +# _LT_LANG_FC_CONFIG([TAG]) +# ------------------------- +# Ensure that the configuration variables for a Fortran compiler are +# suitably defined. These variables are subsequently used by _LT_CONFIG +# to write the compiler configuration to `libtool'. +m4_defun([_LT_LANG_FC_CONFIG], +[AC_REQUIRE([_LT_PROG_FC])dnl +AC_LANG_PUSH(Fortran) + +_LT_TAGVAR(archive_cmds_need_lc, $1)=no +_LT_TAGVAR(allow_undefined_flag, $1)= +_LT_TAGVAR(always_export_symbols, $1)=no +_LT_TAGVAR(archive_expsym_cmds, $1)= +_LT_TAGVAR(export_dynamic_flag_spec, $1)= +_LT_TAGVAR(hardcode_direct, $1)=no +_LT_TAGVAR(hardcode_direct_absolute, $1)=no +_LT_TAGVAR(hardcode_libdir_flag_spec, $1)= +_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)= +_LT_TAGVAR(hardcode_libdir_separator, $1)= +_LT_TAGVAR(hardcode_minus_L, $1)=no +_LT_TAGVAR(hardcode_automatic, $1)=no +_LT_TAGVAR(inherit_rpath, $1)=no +_LT_TAGVAR(module_cmds, $1)= +_LT_TAGVAR(module_expsym_cmds, $1)= +_LT_TAGVAR(link_all_deplibs, $1)=unknown +_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds +_LT_TAGVAR(no_undefined_flag, $1)= +_LT_TAGVAR(whole_archive_flag_spec, $1)= +_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no + +# Source file extension for fc test sources. +ac_ext=${ac_fc_srcext-f} + +# Object file extension for compiled fc test sources. +objext=o +_LT_TAGVAR(objext, $1)=$objext + +# No sense in running all these tests if we already determined that +# the FC compiler isn't working. Some variables (like enable_shared) +# are currently assumed to apply to all compilers on this platform, +# and will be corrupted by setting them based on a non-working compiler. +if test "$_lt_disable_FC" != yes; then + # Code to be used in simple compile tests + lt_simple_compile_test_code="\ + subroutine t + return + end +" + + # Code to be used in simple link tests + lt_simple_link_test_code="\ + program t + end +" + + # ltmain only uses $CC for tagged configurations so make sure $CC is set. + _LT_TAG_COMPILER + + # save warnings/boilerplate of simple test code + _LT_COMPILER_BOILERPLATE + _LT_LINKER_BOILERPLATE + + # Allow CC to be a program name with arguments. + lt_save_CC="$CC" + lt_save_GCC=$GCC + CC=${FC-"f95"} + compiler=$CC + GCC=$ac_cv_fc_compiler_gnu + + _LT_TAGVAR(compiler, $1)=$CC + _LT_CC_BASENAME([$compiler]) + + if test -n "$compiler"; then + AC_MSG_CHECKING([if libtool supports shared libraries]) + AC_MSG_RESULT([$can_build_shared]) + + AC_MSG_CHECKING([whether to build shared libraries]) + test "$can_build_shared" = "no" && enable_shared=no + + # On AIX, shared libraries and static libraries use the same namespace, and + # are all built from PIC. + case $host_os in + aix3*) + test "$enable_shared" = yes && enable_static=no + if test -n "$RANLIB"; then + archive_cmds="$archive_cmds~\$RANLIB \$lib" + postinstall_cmds='$RANLIB $lib' + fi + ;; + aix[[4-9]]*) + if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then + test "$enable_shared" = yes && enable_static=no + fi + ;; + esac + AC_MSG_RESULT([$enable_shared]) + + AC_MSG_CHECKING([whether to build static libraries]) + # Make sure either enable_shared or enable_static is yes. + test "$enable_shared" = yes || enable_static=yes + AC_MSG_RESULT([$enable_static]) + + _LT_TAGVAR(GCC, $1)="$ac_cv_fc_compiler_gnu" + _LT_TAGVAR(LD, $1)="$LD" + + ## CAVEAT EMPTOR: + ## There is no encapsulation within the following macros, do not change + ## the running order or otherwise move them around unless you know exactly + ## what you are doing... + _LT_SYS_HIDDEN_LIBDEPS($1) + _LT_COMPILER_PIC($1) + _LT_COMPILER_C_O($1) + _LT_COMPILER_FILE_LOCKS($1) + _LT_LINKER_SHLIBS($1) + _LT_SYS_DYNAMIC_LINKER($1) + _LT_LINKER_HARDCODE_LIBPATH($1) + + _LT_CONFIG($1) + fi # test -n "$compiler" + + GCC=$lt_save_GCC + CC="$lt_save_CC" +fi # test "$_lt_disable_FC" != yes + +AC_LANG_POP +])# _LT_LANG_FC_CONFIG + + +# _LT_LANG_GCJ_CONFIG([TAG]) +# -------------------------- +# Ensure that the configuration variables for the GNU Java Compiler compiler +# are suitably defined. These variables are subsequently used by _LT_CONFIG +# to write the compiler configuration to `libtool'. +m4_defun([_LT_LANG_GCJ_CONFIG], +[AC_REQUIRE([LT_PROG_GCJ])dnl +AC_LANG_SAVE + +# Source file extension for Java test sources. +ac_ext=java + +# Object file extension for compiled Java test sources. +objext=o +_LT_TAGVAR(objext, $1)=$objext + +# Code to be used in simple compile tests +lt_simple_compile_test_code="class foo {}" + +# Code to be used in simple link tests +lt_simple_link_test_code='public class conftest { public static void main(String[[]] argv) {}; }' + +# ltmain only uses $CC for tagged configurations so make sure $CC is set. +_LT_TAG_COMPILER + +# save warnings/boilerplate of simple test code +_LT_COMPILER_BOILERPLATE +_LT_LINKER_BOILERPLATE + +# Allow CC to be a program name with arguments. +lt_save_CC="$CC" +lt_save_GCC=$GCC +GCC=yes +CC=${GCJ-"gcj"} +compiler=$CC +_LT_TAGVAR(compiler, $1)=$CC +_LT_TAGVAR(LD, $1)="$LD" +_LT_CC_BASENAME([$compiler]) + +# GCJ did not exist at the time GCC didn't implicitly link libc in. +_LT_TAGVAR(archive_cmds_need_lc, $1)=no + +_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds + +## CAVEAT EMPTOR: +## There is no encapsulation within the following macros, do not change +## the running order or otherwise move them around unless you know exactly +## what you are doing... +if test -n "$compiler"; then + _LT_COMPILER_NO_RTTI($1) + _LT_COMPILER_PIC($1) + _LT_COMPILER_C_O($1) + _LT_COMPILER_FILE_LOCKS($1) + _LT_LINKER_SHLIBS($1) + _LT_LINKER_HARDCODE_LIBPATH($1) + + _LT_CONFIG($1) +fi + +AC_LANG_RESTORE + +GCC=$lt_save_GCC +CC="$lt_save_CC" +])# _LT_LANG_GCJ_CONFIG + + +# _LT_LANG_RC_CONFIG([TAG]) +# ------------------------- +# Ensure that the configuration variables for the Windows resource compiler +# are suitably defined. These variables are subsequently used by _LT_CONFIG +# to write the compiler configuration to `libtool'. +m4_defun([_LT_LANG_RC_CONFIG], +[AC_REQUIRE([LT_PROG_RC])dnl +AC_LANG_SAVE + +# Source file extension for RC test sources. +ac_ext=rc + +# Object file extension for compiled RC test sources. +objext=o +_LT_TAGVAR(objext, $1)=$objext + +# Code to be used in simple compile tests +lt_simple_compile_test_code='sample MENU { MENUITEM "&Soup", 100, CHECKED }' + +# Code to be used in simple link tests +lt_simple_link_test_code="$lt_simple_compile_test_code" + +# ltmain only uses $CC for tagged configurations so make sure $CC is set. +_LT_TAG_COMPILER + +# save warnings/boilerplate of simple test code +_LT_COMPILER_BOILERPLATE +_LT_LINKER_BOILERPLATE + +# Allow CC to be a program name with arguments. +lt_save_CC="$CC" +lt_save_GCC=$GCC +GCC= +CC=${RC-"windres"} +compiler=$CC +_LT_TAGVAR(compiler, $1)=$CC +_LT_CC_BASENAME([$compiler]) +_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=yes + +if test -n "$compiler"; then + : + _LT_CONFIG($1) +fi + +GCC=$lt_save_GCC +AC_LANG_RESTORE +CC="$lt_save_CC" +])# _LT_LANG_RC_CONFIG + + +# LT_PROG_GCJ +# ----------- +AC_DEFUN([LT_PROG_GCJ], +[m4_ifdef([AC_PROG_GCJ], [AC_PROG_GCJ], + [m4_ifdef([A][M_PROG_GCJ], [A][M_PROG_GCJ], + [AC_CHECK_TOOL(GCJ, gcj,) + test "x${GCJFLAGS+set}" = xset || GCJFLAGS="-g -O2" + AC_SUBST(GCJFLAGS)])])[]dnl +]) + +# Old name: +AU_ALIAS([LT_AC_PROG_GCJ], [LT_PROG_GCJ]) +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([LT_AC_PROG_GCJ], []) + + +# LT_PROG_RC +# ---------- +AC_DEFUN([LT_PROG_RC], +[AC_CHECK_TOOL(RC, windres,) +]) + +# Old name: +AU_ALIAS([LT_AC_PROG_RC], [LT_PROG_RC]) +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([LT_AC_PROG_RC], []) + + +# _LT_DECL_EGREP +# -------------- +# If we don't have a new enough Autoconf to choose the best grep +# available, choose the one first in the user's PATH. +m4_defun([_LT_DECL_EGREP], +[AC_REQUIRE([AC_PROG_EGREP])dnl +AC_REQUIRE([AC_PROG_FGREP])dnl +test -z "$GREP" && GREP=grep +_LT_DECL([], [GREP], [1], [A grep program that handles long lines]) +_LT_DECL([], [EGREP], [1], [An ERE matcher]) +_LT_DECL([], [FGREP], [1], [A literal string matcher]) +dnl Non-bleeding-edge autoconf doesn't subst GREP, so do it here too +AC_SUBST([GREP]) +]) + + +# _LT_DECL_OBJDUMP +# -------------- +# If we don't have a new enough Autoconf to choose the best objdump +# available, choose the one first in the user's PATH. +m4_defun([_LT_DECL_OBJDUMP], +[AC_CHECK_TOOL(OBJDUMP, objdump, false) +test -z "$OBJDUMP" && OBJDUMP=objdump +_LT_DECL([], [OBJDUMP], [1], [An object symbol dumper]) +AC_SUBST([OBJDUMP]) +]) + + +# _LT_DECL_SED +# ------------ +# Check for a fully-functional sed program, that truncates +# as few characters as possible. Prefer GNU sed if found. +m4_defun([_LT_DECL_SED], +[AC_PROG_SED +test -z "$SED" && SED=sed +Xsed="$SED -e 1s/^X//" +_LT_DECL([], [SED], [1], [A sed program that does not truncate output]) +_LT_DECL([], [Xsed], ["\$SED -e 1s/^X//"], + [Sed that helps us avoid accidentally triggering echo(1) options like -n]) +])# _LT_DECL_SED + +m4_ifndef([AC_PROG_SED], [ +############################################################ +# NOTE: This macro has been submitted for inclusion into # +# GNU Autoconf as AC_PROG_SED. When it is available in # +# a released version of Autoconf we should remove this # +# macro and use it instead. # +############################################################ + +m4_defun([AC_PROG_SED], +[AC_MSG_CHECKING([for a sed that does not truncate output]) +AC_CACHE_VAL(lt_cv_path_SED, +[# Loop through the user's path and test for sed and gsed. +# Then use that list of sed's as ones to test for truncation. +as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + for lt_ac_prog in sed gsed; do + for ac_exec_ext in '' $ac_executable_extensions; do + if $as_executable_p "$as_dir/$lt_ac_prog$ac_exec_ext"; then + lt_ac_sed_list="$lt_ac_sed_list $as_dir/$lt_ac_prog$ac_exec_ext" + fi + done + done +done +IFS=$as_save_IFS +lt_ac_max=0 +lt_ac_count=0 +# Add /usr/xpg4/bin/sed as it is typically found on Solaris +# along with /bin/sed that truncates output. +for lt_ac_sed in $lt_ac_sed_list /usr/xpg4/bin/sed; do + test ! -f $lt_ac_sed && continue + cat /dev/null > conftest.in + lt_ac_count=0 + echo $ECHO_N "0123456789$ECHO_C" >conftest.in + # Check for GNU sed and select it if it is found. + if "$lt_ac_sed" --version 2>&1 < /dev/null | grep 'GNU' > /dev/null; then + lt_cv_path_SED=$lt_ac_sed + break + fi + while true; do + cat conftest.in conftest.in >conftest.tmp + mv conftest.tmp conftest.in + cp conftest.in conftest.nl + echo >>conftest.nl + $lt_ac_sed -e 's/a$//' < conftest.nl >conftest.out || break + cmp -s conftest.out conftest.nl || break + # 10000 chars as input seems more than enough + test $lt_ac_count -gt 10 && break + lt_ac_count=`expr $lt_ac_count + 1` + if test $lt_ac_count -gt $lt_ac_max; then + lt_ac_max=$lt_ac_count + lt_cv_path_SED=$lt_ac_sed + fi + done +done +]) +SED=$lt_cv_path_SED +AC_SUBST([SED]) +AC_MSG_RESULT([$SED]) +])#AC_PROG_SED +])#m4_ifndef + +# Old name: +AU_ALIAS([LT_AC_PROG_SED], [AC_PROG_SED]) +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([LT_AC_PROG_SED], []) + + +# _LT_CHECK_SHELL_FEATURES +# ------------------------ +# Find out whether the shell is Bourne or XSI compatible, +# or has some other useful features. +m4_defun([_LT_CHECK_SHELL_FEATURES], +[AC_MSG_CHECKING([whether the shell understands some XSI constructs]) +# Try some XSI features +xsi_shell=no +( _lt_dummy="a/b/c" + test "${_lt_dummy##*/},${_lt_dummy%/*},"${_lt_dummy%"$_lt_dummy"}, \ + = c,a/b,, \ + && eval 'test $(( 1 + 1 )) -eq 2 \ + && test "${#_lt_dummy}" -eq 5' ) >/dev/null 2>&1 \ + && xsi_shell=yes +AC_MSG_RESULT([$xsi_shell]) +_LT_CONFIG_LIBTOOL_INIT([xsi_shell='$xsi_shell']) + +AC_MSG_CHECKING([whether the shell understands "+="]) +lt_shell_append=no +( foo=bar; set foo baz; eval "$[1]+=\$[2]" && test "$foo" = barbaz ) \ + >/dev/null 2>&1 \ + && lt_shell_append=yes +AC_MSG_RESULT([$lt_shell_append]) +_LT_CONFIG_LIBTOOL_INIT([lt_shell_append='$lt_shell_append']) + +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + lt_unset=unset +else + lt_unset=false +fi +_LT_DECL([], [lt_unset], [0], [whether the shell understands "unset"])dnl + +# test EBCDIC or ASCII +case `echo X|tr X '\101'` in + A) # ASCII based system + # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr + lt_SP2NL='tr \040 \012' + lt_NL2SP='tr \015\012 \040\040' + ;; + *) # EBCDIC based system + lt_SP2NL='tr \100 \n' + lt_NL2SP='tr \r\n \100\100' + ;; +esac +_LT_DECL([SP2NL], [lt_SP2NL], [1], [turn spaces into newlines])dnl +_LT_DECL([NL2SP], [lt_NL2SP], [1], [turn newlines into spaces])dnl +])# _LT_CHECK_SHELL_FEATURES + + +# _LT_PROG_XSI_SHELLFNS +# --------------------- +# Bourne and XSI compatible variants of some useful shell functions. +m4_defun([_LT_PROG_XSI_SHELLFNS], +[case $xsi_shell in + yes) + cat << \_LT_EOF >> "$cfgfile" + +# func_dirname file append nondir_replacement +# Compute the dirname of FILE. If nonempty, add APPEND to the result, +# otherwise set result to NONDIR_REPLACEMENT. +func_dirname () +{ + case ${1} in + */*) func_dirname_result="${1%/*}${2}" ;; + * ) func_dirname_result="${3}" ;; + esac +} + +# func_basename file +func_basename () +{ + func_basename_result="${1##*/}" +} + +# func_dirname_and_basename file append nondir_replacement +# perform func_basename and func_dirname in a single function +# call: +# dirname: Compute the dirname of FILE. If nonempty, +# add APPEND to the result, otherwise set result +# to NONDIR_REPLACEMENT. +# value returned in "$func_dirname_result" +# basename: Compute filename of FILE. +# value retuned in "$func_basename_result" +# Implementation must be kept synchronized with func_dirname +# and func_basename. For efficiency, we do not delegate to +# those functions but instead duplicate the functionality here. +func_dirname_and_basename () +{ + case ${1} in + */*) func_dirname_result="${1%/*}${2}" ;; + * ) func_dirname_result="${3}" ;; + esac + func_basename_result="${1##*/}" +} + +# func_stripname prefix suffix name +# strip PREFIX and SUFFIX off of NAME. +# PREFIX and SUFFIX must not contain globbing or regex special +# characters, hashes, percent signs, but SUFFIX may contain a leading +# dot (in which case that matches only a dot). +func_stripname () +{ + # pdksh 5.2.14 does not do ${X%$Y} correctly if both X and Y are + # positional parameters, so assign one to ordinary parameter first. + func_stripname_result=${3} + func_stripname_result=${func_stripname_result#"${1}"} + func_stripname_result=${func_stripname_result%"${2}"} +} + +# func_opt_split +func_opt_split () +{ + func_opt_split_opt=${1%%=*} + func_opt_split_arg=${1#*=} +} + +# func_lo2o object +func_lo2o () +{ + case ${1} in + *.lo) func_lo2o_result=${1%.lo}.${objext} ;; + *) func_lo2o_result=${1} ;; + esac +} + +# func_xform libobj-or-source +func_xform () +{ + func_xform_result=${1%.*}.lo +} + +# func_arith arithmetic-term... +func_arith () +{ + func_arith_result=$(( $[*] )) +} + +# func_len string +# STRING may not start with a hyphen. +func_len () +{ + func_len_result=${#1} +} + +_LT_EOF + ;; + *) # Bourne compatible functions. + cat << \_LT_EOF >> "$cfgfile" + +# func_dirname file append nondir_replacement +# Compute the dirname of FILE. If nonempty, add APPEND to the result, +# otherwise set result to NONDIR_REPLACEMENT. +func_dirname () +{ + # Extract subdirectory from the argument. + func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"` + if test "X$func_dirname_result" = "X${1}"; then + func_dirname_result="${3}" + else + func_dirname_result="$func_dirname_result${2}" + fi +} + +# func_basename file +func_basename () +{ + func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"` +} + +dnl func_dirname_and_basename +dnl A portable version of this function is already defined in general.m4sh +dnl so there is no need for it here. + +# func_stripname prefix suffix name +# strip PREFIX and SUFFIX off of NAME. +# PREFIX and SUFFIX must not contain globbing or regex special +# characters, hashes, percent signs, but SUFFIX may contain a leading +# dot (in which case that matches only a dot). +# func_strip_suffix prefix name +func_stripname () +{ + case ${2} in + .*) func_stripname_result=`$ECHO "X${3}" \ + | $Xsed -e "s%^${1}%%" -e "s%\\\\${2}\$%%"`;; + *) func_stripname_result=`$ECHO "X${3}" \ + | $Xsed -e "s%^${1}%%" -e "s%${2}\$%%"`;; + esac +} + +# sed scripts: +my_sed_long_opt='1s/^\(-[[^=]]*\)=.*/\1/;q' +my_sed_long_arg='1s/^-[[^=]]*=//' + +# func_opt_split +func_opt_split () +{ + func_opt_split_opt=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_opt"` + func_opt_split_arg=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_arg"` +} + +# func_lo2o object +func_lo2o () +{ + func_lo2o_result=`$ECHO "X${1}" | $Xsed -e "$lo2o"` +} + +# func_xform libobj-or-source +func_xform () +{ + func_xform_result=`$ECHO "X${1}" | $Xsed -e 's/\.[[^.]]*$/.lo/'` +} + +# func_arith arithmetic-term... +func_arith () +{ + func_arith_result=`expr "$[@]"` +} + +# func_len string +# STRING may not start with a hyphen. +func_len () +{ + func_len_result=`expr "$[1]" : ".*" 2>/dev/null || echo $max_cmd_len` +} + +_LT_EOF +esac + +case $lt_shell_append in + yes) + cat << \_LT_EOF >> "$cfgfile" + +# func_append var value +# Append VALUE to the end of shell variable VAR. +func_append () +{ + eval "$[1]+=\$[2]" +} +_LT_EOF + ;; + *) + cat << \_LT_EOF >> "$cfgfile" + +# func_append var value +# Append VALUE to the end of shell variable VAR. +func_append () +{ + eval "$[1]=\$$[1]\$[2]" +} + +_LT_EOF + ;; + esac +]) diff --git a/binaries/src/clustalo/m4/ltoptions.m4 b/binaries/src/clustalo/m4/ltoptions.m4 new file mode 100644 index 0000000..34151a3 --- /dev/null +++ b/binaries/src/clustalo/m4/ltoptions.m4 @@ -0,0 +1,368 @@ +# Helper functions for option handling. -*- Autoconf -*- +# +# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc. +# Written by Gary V. Vaughan, 2004 +# +# This file is free software; the Free Software Foundation gives +# unlimited permission to copy and/or distribute it, with or without +# modifications, as long as this notice is preserved. + +# serial 6 ltoptions.m4 + +# This is to help aclocal find these macros, as it can't see m4_define. +AC_DEFUN([LTOPTIONS_VERSION], [m4_if([1])]) + + +# _LT_MANGLE_OPTION(MACRO-NAME, OPTION-NAME) +# ------------------------------------------ +m4_define([_LT_MANGLE_OPTION], +[[_LT_OPTION_]m4_bpatsubst($1__$2, [[^a-zA-Z0-9_]], [_])]) + + +# _LT_SET_OPTION(MACRO-NAME, OPTION-NAME) +# --------------------------------------- +# Set option OPTION-NAME for macro MACRO-NAME, and if there is a +# matching handler defined, dispatch to it. Other OPTION-NAMEs are +# saved as a flag. +m4_define([_LT_SET_OPTION], +[m4_define(_LT_MANGLE_OPTION([$1], [$2]))dnl +m4_ifdef(_LT_MANGLE_DEFUN([$1], [$2]), + _LT_MANGLE_DEFUN([$1], [$2]), + [m4_warning([Unknown $1 option `$2'])])[]dnl +]) + + +# _LT_IF_OPTION(MACRO-NAME, OPTION-NAME, IF-SET, [IF-NOT-SET]) +# ------------------------------------------------------------ +# Execute IF-SET if OPTION is set, IF-NOT-SET otherwise. +m4_define([_LT_IF_OPTION], +[m4_ifdef(_LT_MANGLE_OPTION([$1], [$2]), [$3], [$4])]) + + +# _LT_UNLESS_OPTIONS(MACRO-NAME, OPTION-LIST, IF-NOT-SET) +# ------------------------------------------------------- +# Execute IF-NOT-SET unless all options in OPTION-LIST for MACRO-NAME +# are set. +m4_define([_LT_UNLESS_OPTIONS], +[m4_foreach([_LT_Option], m4_split(m4_normalize([$2])), + [m4_ifdef(_LT_MANGLE_OPTION([$1], _LT_Option), + [m4_define([$0_found])])])[]dnl +m4_ifdef([$0_found], [m4_undefine([$0_found])], [$3 +])[]dnl +]) + + +# _LT_SET_OPTIONS(MACRO-NAME, OPTION-LIST) +# ---------------------------------------- +# OPTION-LIST is a space-separated list of Libtool options associated +# with MACRO-NAME. If any OPTION has a matching handler declared with +# LT_OPTION_DEFINE, dispatch to that macro; otherwise complain about +# the unknown option and exit. +m4_defun([_LT_SET_OPTIONS], +[# Set options +m4_foreach([_LT_Option], m4_split(m4_normalize([$2])), + [_LT_SET_OPTION([$1], _LT_Option)]) + +m4_if([$1],[LT_INIT],[ + dnl + dnl Simply set some default values (i.e off) if boolean options were not + dnl specified: + _LT_UNLESS_OPTIONS([LT_INIT], [dlopen], [enable_dlopen=no + ]) + _LT_UNLESS_OPTIONS([LT_INIT], [win32-dll], [enable_win32_dll=no + ]) + dnl + dnl If no reference was made to various pairs of opposing options, then + dnl we run the default mode handler for the pair. For example, if neither + dnl `shared' nor `disable-shared' was passed, we enable building of shared + dnl archives by default: + _LT_UNLESS_OPTIONS([LT_INIT], [shared disable-shared], [_LT_ENABLE_SHARED]) + _LT_UNLESS_OPTIONS([LT_INIT], [static disable-static], [_LT_ENABLE_STATIC]) + _LT_UNLESS_OPTIONS([LT_INIT], [pic-only no-pic], [_LT_WITH_PIC]) + _LT_UNLESS_OPTIONS([LT_INIT], [fast-install disable-fast-install], + [_LT_ENABLE_FAST_INSTALL]) + ]) +])# _LT_SET_OPTIONS + + +## --------------------------------- ## +## Macros to handle LT_INIT options. ## +## --------------------------------- ## + +# _LT_MANGLE_DEFUN(MACRO-NAME, OPTION-NAME) +# ----------------------------------------- +m4_define([_LT_MANGLE_DEFUN], +[[_LT_OPTION_DEFUN_]m4_bpatsubst(m4_toupper([$1__$2]), [[^A-Z0-9_]], [_])]) + + +# LT_OPTION_DEFINE(MACRO-NAME, OPTION-NAME, CODE) +# ----------------------------------------------- +m4_define([LT_OPTION_DEFINE], +[m4_define(_LT_MANGLE_DEFUN([$1], [$2]), [$3])[]dnl +])# LT_OPTION_DEFINE + + +# dlopen +# ------ +LT_OPTION_DEFINE([LT_INIT], [dlopen], [enable_dlopen=yes +]) + +AU_DEFUN([AC_LIBTOOL_DLOPEN], +[_LT_SET_OPTION([LT_INIT], [dlopen]) +AC_DIAGNOSE([obsolete], +[$0: Remove this warning and the call to _LT_SET_OPTION when you +put the `dlopen' option into LT_INIT's first parameter.]) +]) + +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AC_LIBTOOL_DLOPEN], []) + + +# win32-dll +# --------- +# Declare package support for building win32 dll's. +LT_OPTION_DEFINE([LT_INIT], [win32-dll], +[enable_win32_dll=yes + +case $host in +*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-cegcc*) + AC_CHECK_TOOL(AS, as, false) + AC_CHECK_TOOL(DLLTOOL, dlltool, false) + AC_CHECK_TOOL(OBJDUMP, objdump, false) + ;; +esac + +test -z "$AS" && AS=as +_LT_DECL([], [AS], [0], [Assembler program])dnl + +test -z "$DLLTOOL" && DLLTOOL=dlltool +_LT_DECL([], [DLLTOOL], [0], [DLL creation program])dnl + +test -z "$OBJDUMP" && OBJDUMP=objdump +_LT_DECL([], [OBJDUMP], [0], [Object dumper program])dnl +])# win32-dll + +AU_DEFUN([AC_LIBTOOL_WIN32_DLL], +[AC_REQUIRE([AC_CANONICAL_HOST])dnl +_LT_SET_OPTION([LT_INIT], [win32-dll]) +AC_DIAGNOSE([obsolete], +[$0: Remove this warning and the call to _LT_SET_OPTION when you +put the `win32-dll' option into LT_INIT's first parameter.]) +]) + +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AC_LIBTOOL_WIN32_DLL], []) + + +# _LT_ENABLE_SHARED([DEFAULT]) +# ---------------------------- +# implement the --enable-shared flag, and supports the `shared' and +# `disable-shared' LT_INIT options. +# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'. +m4_define([_LT_ENABLE_SHARED], +[m4_define([_LT_ENABLE_SHARED_DEFAULT], [m4_if($1, no, no, yes)])dnl +AC_ARG_ENABLE([shared], + [AS_HELP_STRING([--enable-shared@<:@=PKGS@:>@], + [build shared libraries @<:@default=]_LT_ENABLE_SHARED_DEFAULT[@:>@])], + [p=${PACKAGE-default} + case $enableval in + yes) enable_shared=yes ;; + no) enable_shared=no ;; + *) + enable_shared=no + # Look at the argument we got. We use all the common list separators. + lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," + for pkg in $enableval; do + IFS="$lt_save_ifs" + if test "X$pkg" = "X$p"; then + enable_shared=yes + fi + done + IFS="$lt_save_ifs" + ;; + esac], + [enable_shared=]_LT_ENABLE_SHARED_DEFAULT) + + _LT_DECL([build_libtool_libs], [enable_shared], [0], + [Whether or not to build shared libraries]) +])# _LT_ENABLE_SHARED + +LT_OPTION_DEFINE([LT_INIT], [shared], [_LT_ENABLE_SHARED([yes])]) +LT_OPTION_DEFINE([LT_INIT], [disable-shared], [_LT_ENABLE_SHARED([no])]) + +# Old names: +AC_DEFUN([AC_ENABLE_SHARED], +[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[shared]) +]) + +AC_DEFUN([AC_DISABLE_SHARED], +[_LT_SET_OPTION([LT_INIT], [disable-shared]) +]) + +AU_DEFUN([AM_ENABLE_SHARED], [AC_ENABLE_SHARED($@)]) +AU_DEFUN([AM_DISABLE_SHARED], [AC_DISABLE_SHARED($@)]) + +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AM_ENABLE_SHARED], []) +dnl AC_DEFUN([AM_DISABLE_SHARED], []) + + + +# _LT_ENABLE_STATIC([DEFAULT]) +# ---------------------------- +# implement the --enable-static flag, and support the `static' and +# `disable-static' LT_INIT options. +# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'. +m4_define([_LT_ENABLE_STATIC], +[m4_define([_LT_ENABLE_STATIC_DEFAULT], [m4_if($1, no, no, yes)])dnl +AC_ARG_ENABLE([static], + [AS_HELP_STRING([--enable-static@<:@=PKGS@:>@], + [build static libraries @<:@default=]_LT_ENABLE_STATIC_DEFAULT[@:>@])], + [p=${PACKAGE-default} + case $enableval in + yes) enable_static=yes ;; + no) enable_static=no ;; + *) + enable_static=no + # Look at the argument we got. We use all the common list separators. + lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," + for pkg in $enableval; do + IFS="$lt_save_ifs" + if test "X$pkg" = "X$p"; then + enable_static=yes + fi + done + IFS="$lt_save_ifs" + ;; + esac], + [enable_static=]_LT_ENABLE_STATIC_DEFAULT) + + _LT_DECL([build_old_libs], [enable_static], [0], + [Whether or not to build static libraries]) +])# _LT_ENABLE_STATIC + +LT_OPTION_DEFINE([LT_INIT], [static], [_LT_ENABLE_STATIC([yes])]) +LT_OPTION_DEFINE([LT_INIT], [disable-static], [_LT_ENABLE_STATIC([no])]) + +# Old names: +AC_DEFUN([AC_ENABLE_STATIC], +[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[static]) +]) + +AC_DEFUN([AC_DISABLE_STATIC], +[_LT_SET_OPTION([LT_INIT], [disable-static]) +]) + +AU_DEFUN([AM_ENABLE_STATIC], [AC_ENABLE_STATIC($@)]) +AU_DEFUN([AM_DISABLE_STATIC], [AC_DISABLE_STATIC($@)]) + +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AM_ENABLE_STATIC], []) +dnl AC_DEFUN([AM_DISABLE_STATIC], []) + + + +# _LT_ENABLE_FAST_INSTALL([DEFAULT]) +# ---------------------------------- +# implement the --enable-fast-install flag, and support the `fast-install' +# and `disable-fast-install' LT_INIT options. +# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'. +m4_define([_LT_ENABLE_FAST_INSTALL], +[m4_define([_LT_ENABLE_FAST_INSTALL_DEFAULT], [m4_if($1, no, no, yes)])dnl +AC_ARG_ENABLE([fast-install], + [AS_HELP_STRING([--enable-fast-install@<:@=PKGS@:>@], + [optimize for fast installation @<:@default=]_LT_ENABLE_FAST_INSTALL_DEFAULT[@:>@])], + [p=${PACKAGE-default} + case $enableval in + yes) enable_fast_install=yes ;; + no) enable_fast_install=no ;; + *) + enable_fast_install=no + # Look at the argument we got. We use all the common list separators. + lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," + for pkg in $enableval; do + IFS="$lt_save_ifs" + if test "X$pkg" = "X$p"; then + enable_fast_install=yes + fi + done + IFS="$lt_save_ifs" + ;; + esac], + [enable_fast_install=]_LT_ENABLE_FAST_INSTALL_DEFAULT) + +_LT_DECL([fast_install], [enable_fast_install], [0], + [Whether or not to optimize for fast installation])dnl +])# _LT_ENABLE_FAST_INSTALL + +LT_OPTION_DEFINE([LT_INIT], [fast-install], [_LT_ENABLE_FAST_INSTALL([yes])]) +LT_OPTION_DEFINE([LT_INIT], [disable-fast-install], [_LT_ENABLE_FAST_INSTALL([no])]) + +# Old names: +AU_DEFUN([AC_ENABLE_FAST_INSTALL], +[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[fast-install]) +AC_DIAGNOSE([obsolete], +[$0: Remove this warning and the call to _LT_SET_OPTION when you put +the `fast-install' option into LT_INIT's first parameter.]) +]) + +AU_DEFUN([AC_DISABLE_FAST_INSTALL], +[_LT_SET_OPTION([LT_INIT], [disable-fast-install]) +AC_DIAGNOSE([obsolete], +[$0: Remove this warning and the call to _LT_SET_OPTION when you put +the `disable-fast-install' option into LT_INIT's first parameter.]) +]) + +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AC_ENABLE_FAST_INSTALL], []) +dnl AC_DEFUN([AM_DISABLE_FAST_INSTALL], []) + + +# _LT_WITH_PIC([MODE]) +# -------------------- +# implement the --with-pic flag, and support the `pic-only' and `no-pic' +# LT_INIT options. +# MODE is either `yes' or `no'. If omitted, it defaults to `both'. +m4_define([_LT_WITH_PIC], +[AC_ARG_WITH([pic], + [AS_HELP_STRING([--with-pic], + [try to use only PIC/non-PIC objects @<:@default=use both@:>@])], + [pic_mode="$withval"], + [pic_mode=default]) + +test -z "$pic_mode" && pic_mode=m4_default([$1], [default]) + +_LT_DECL([], [pic_mode], [0], [What type of objects to build])dnl +])# _LT_WITH_PIC + +LT_OPTION_DEFINE([LT_INIT], [pic-only], [_LT_WITH_PIC([yes])]) +LT_OPTION_DEFINE([LT_INIT], [no-pic], [_LT_WITH_PIC([no])]) + +# Old name: +AU_DEFUN([AC_LIBTOOL_PICMODE], +[_LT_SET_OPTION([LT_INIT], [pic-only]) +AC_DIAGNOSE([obsolete], +[$0: Remove this warning and the call to _LT_SET_OPTION when you +put the `pic-only' option into LT_INIT's first parameter.]) +]) + +dnl aclocal-1.4 backwards compatibility: +dnl AC_DEFUN([AC_LIBTOOL_PICMODE], []) + +## ----------------- ## +## LTDL_INIT Options ## +## ----------------- ## + +m4_define([_LTDL_MODE], []) +LT_OPTION_DEFINE([LTDL_INIT], [nonrecursive], + [m4_define([_LTDL_MODE], [nonrecursive])]) +LT_OPTION_DEFINE([LTDL_INIT], [recursive], + [m4_define([_LTDL_MODE], [recursive])]) +LT_OPTION_DEFINE([LTDL_INIT], [subproject], + [m4_define([_LTDL_MODE], [subproject])]) + +m4_define([_LTDL_TYPE], []) +LT_OPTION_DEFINE([LTDL_INIT], [installable], + [m4_define([_LTDL_TYPE], [installable])]) +LT_OPTION_DEFINE([LTDL_INIT], [convenience], + [m4_define([_LTDL_TYPE], [convenience])]) diff --git a/binaries/src/clustalo/m4/ltsugar.m4 b/binaries/src/clustalo/m4/ltsugar.m4 new file mode 100644 index 0000000..9000a05 --- /dev/null +++ b/binaries/src/clustalo/m4/ltsugar.m4 @@ -0,0 +1,123 @@ +# ltsugar.m4 -- libtool m4 base layer. -*-Autoconf-*- +# +# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc. +# Written by Gary V. Vaughan, 2004 +# +# This file is free software; the Free Software Foundation gives +# unlimited permission to copy and/or distribute it, with or without +# modifications, as long as this notice is preserved. + +# serial 6 ltsugar.m4 + +# This is to help aclocal find these macros, as it can't see m4_define. +AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])]) + + +# lt_join(SEP, ARG1, [ARG2...]) +# ----------------------------- +# Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their +# associated separator. +# Needed until we can rely on m4_join from Autoconf 2.62, since all earlier +# versions in m4sugar had bugs. +m4_define([lt_join], +[m4_if([$#], [1], [], + [$#], [2], [[$2]], + [m4_if([$2], [], [], [[$2]_])$0([$1], m4_shift(m4_shift($@)))])]) +m4_define([_lt_join], +[m4_if([$#$2], [2], [], + [m4_if([$2], [], [], [[$1$2]])$0([$1], m4_shift(m4_shift($@)))])]) + + +# lt_car(LIST) +# lt_cdr(LIST) +# ------------ +# Manipulate m4 lists. +# These macros are necessary as long as will still need to support +# Autoconf-2.59 which quotes differently. +m4_define([lt_car], [[$1]]) +m4_define([lt_cdr], +[m4_if([$#], 0, [m4_fatal([$0: cannot be called without arguments])], + [$#], 1, [], + [m4_dquote(m4_shift($@))])]) +m4_define([lt_unquote], $1) + + +# lt_append(MACRO-NAME, STRING, [SEPARATOR]) +# ------------------------------------------ +# Redefine MACRO-NAME to hold its former content plus `SEPARATOR'`STRING'. +# Note that neither SEPARATOR nor STRING are expanded; they are appended +# to MACRO-NAME as is (leaving the expansion for when MACRO-NAME is invoked). +# No SEPARATOR is output if MACRO-NAME was previously undefined (different +# than defined and empty). +# +# This macro is needed until we can rely on Autoconf 2.62, since earlier +# versions of m4sugar mistakenly expanded SEPARATOR but not STRING. +m4_define([lt_append], +[m4_define([$1], + m4_ifdef([$1], [m4_defn([$1])[$3]])[$2])]) + + + +# lt_combine(SEP, PREFIX-LIST, INFIX, SUFFIX1, [SUFFIX2...]) +# ---------------------------------------------------------- +# Produce a SEP delimited list of all paired combinations of elements of +# PREFIX-LIST with SUFFIX1 through SUFFIXn. Each element of the list +# has the form PREFIXmINFIXSUFFIXn. +# Needed until we can rely on m4_combine added in Autoconf 2.62. +m4_define([lt_combine], +[m4_if(m4_eval([$# > 3]), [1], + [m4_pushdef([_Lt_sep], [m4_define([_Lt_sep], m4_defn([lt_car]))])]]dnl +[[m4_foreach([_Lt_prefix], [$2], + [m4_foreach([_Lt_suffix], + ]m4_dquote(m4_dquote(m4_shift(m4_shift(m4_shift($@)))))[, + [_Lt_sep([$1])[]m4_defn([_Lt_prefix])[$3]m4_defn([_Lt_suffix])])])])]) + + +# lt_if_append_uniq(MACRO-NAME, VARNAME, [SEPARATOR], [UNIQ], [NOT-UNIQ]) +# ----------------------------------------------------------------------- +# Iff MACRO-NAME does not yet contain VARNAME, then append it (delimited +# by SEPARATOR if supplied) and expand UNIQ, else NOT-UNIQ. +m4_define([lt_if_append_uniq], +[m4_ifdef([$1], + [m4_if(m4_index([$3]m4_defn([$1])[$3], [$3$2$3]), [-1], + [lt_append([$1], [$2], [$3])$4], + [$5])], + [lt_append([$1], [$2], [$3])$4])]) + + +# lt_dict_add(DICT, KEY, VALUE) +# ----------------------------- +m4_define([lt_dict_add], +[m4_define([$1($2)], [$3])]) + + +# lt_dict_add_subkey(DICT, KEY, SUBKEY, VALUE) +# -------------------------------------------- +m4_define([lt_dict_add_subkey], +[m4_define([$1($2:$3)], [$4])]) + + +# lt_dict_fetch(DICT, KEY, [SUBKEY]) +# ---------------------------------- +m4_define([lt_dict_fetch], +[m4_ifval([$3], + m4_ifdef([$1($2:$3)], [m4_defn([$1($2:$3)])]), + m4_ifdef([$1($2)], [m4_defn([$1($2)])]))]) + + +# lt_if_dict_fetch(DICT, KEY, [SUBKEY], VALUE, IF-TRUE, [IF-FALSE]) +# ----------------------------------------------------------------- +m4_define([lt_if_dict_fetch], +[m4_if(lt_dict_fetch([$1], [$2], [$3]), [$4], + [$5], + [$6])]) + + +# lt_dict_filter(DICT, [SUBKEY], VALUE, [SEPARATOR], KEY, [...]) +# -------------------------------------------------------------- +m4_define([lt_dict_filter], +[m4_if([$5], [], [], + [lt_join(m4_quote(m4_default([$4], [[, ]])), + lt_unquote(m4_split(m4_normalize(m4_foreach(_Lt_key, lt_car([m4_shiftn(4, $@)]), + [lt_if_dict_fetch([$1], _Lt_key, [$2], [$3], [_Lt_key ])])))))])[]dnl +]) diff --git a/binaries/src/clustalo/m4/ltversion.m4 b/binaries/src/clustalo/m4/ltversion.m4 new file mode 100644 index 0000000..b8e154f --- /dev/null +++ b/binaries/src/clustalo/m4/ltversion.m4 @@ -0,0 +1,23 @@ +# ltversion.m4 -- version numbers -*- Autoconf -*- +# +# Copyright (C) 2004 Free Software Foundation, Inc. +# Written by Scott James Remnant, 2004 +# +# This file is free software; the Free Software Foundation gives +# unlimited permission to copy and/or distribute it, with or without +# modifications, as long as this notice is preserved. + +# Generated from ltversion.in. + +# serial 3012 ltversion.m4 +# This file is part of GNU Libtool + +m4_define([LT_PACKAGE_VERSION], [2.2.6]) +m4_define([LT_PACKAGE_REVISION], [1.3012]) + +AC_DEFUN([LTVERSION_VERSION], +[macro_version='2.2.6' +macro_revision='1.3012' +_LT_DECL(, macro_version, 0, [Which release of libtool.m4 was used?]) +_LT_DECL(, macro_revision, 0) +]) diff --git a/binaries/src/clustalo/m4/lt~obsolete.m4 b/binaries/src/clustalo/m4/lt~obsolete.m4 new file mode 100644 index 0000000..637bb20 --- /dev/null +++ b/binaries/src/clustalo/m4/lt~obsolete.m4 @@ -0,0 +1,92 @@ +# lt~obsolete.m4 -- aclocal satisfying obsolete definitions. -*-Autoconf-*- +# +# Copyright (C) 2004, 2005, 2007 Free Software Foundation, Inc. +# Written by Scott James Remnant, 2004. +# +# This file is free software; the Free Software Foundation gives +# unlimited permission to copy and/or distribute it, with or without +# modifications, as long as this notice is preserved. + +# serial 4 lt~obsolete.m4 + +# These exist entirely to fool aclocal when bootstrapping libtool. +# +# In the past libtool.m4 has provided macros via AC_DEFUN (or AU_DEFUN) +# which have later been changed to m4_define as they aren't part of the +# exported API, or moved to Autoconf or Automake where they belong. +# +# The trouble is, aclocal is a bit thick. It'll see the old AC_DEFUN +# in /usr/share/aclocal/libtool.m4 and remember it, then when it sees us +# using a macro with the same name in our local m4/libtool.m4 it'll +# pull the old libtool.m4 in (it doesn't see our shiny new m4_define +# and doesn't know about Autoconf macros at all.) +# +# So we provide this file, which has a silly filename so it's always +# included after everything else. This provides aclocal with the +# AC_DEFUNs it wants, but when m4 processes it, it doesn't do anything +# because those macros already exist, or will be overwritten later. +# We use AC_DEFUN over AU_DEFUN for compatibility with aclocal-1.6. +# +# Anytime we withdraw an AC_DEFUN or AU_DEFUN, remember to add it here. +# Yes, that means every name once taken will need to remain here until +# we give up compatibility with versions before 1.7, at which point +# we need to keep only those names which we still refer to. + +# This is to help aclocal find these macros, as it can't see m4_define. +AC_DEFUN([LTOBSOLETE_VERSION], [m4_if([1])]) + +m4_ifndef([AC_LIBTOOL_LINKER_OPTION], [AC_DEFUN([AC_LIBTOOL_LINKER_OPTION])]) +m4_ifndef([AC_PROG_EGREP], [AC_DEFUN([AC_PROG_EGREP])]) +m4_ifndef([_LT_AC_PROG_ECHO_BACKSLASH], [AC_DEFUN([_LT_AC_PROG_ECHO_BACKSLASH])]) +m4_ifndef([_LT_AC_SHELL_INIT], [AC_DEFUN([_LT_AC_SHELL_INIT])]) +m4_ifndef([_LT_AC_SYS_LIBPATH_AIX], [AC_DEFUN([_LT_AC_SYS_LIBPATH_AIX])]) +m4_ifndef([_LT_PROG_LTMAIN], [AC_DEFUN([_LT_PROG_LTMAIN])]) +m4_ifndef([_LT_AC_TAGVAR], [AC_DEFUN([_LT_AC_TAGVAR])]) +m4_ifndef([AC_LTDL_ENABLE_INSTALL], [AC_DEFUN([AC_LTDL_ENABLE_INSTALL])]) +m4_ifndef([AC_LTDL_PREOPEN], [AC_DEFUN([AC_LTDL_PREOPEN])]) +m4_ifndef([_LT_AC_SYS_COMPILER], [AC_DEFUN([_LT_AC_SYS_COMPILER])]) +m4_ifndef([_LT_AC_LOCK], [AC_DEFUN([_LT_AC_LOCK])]) +m4_ifndef([AC_LIBTOOL_SYS_OLD_ARCHIVE], [AC_DEFUN([AC_LIBTOOL_SYS_OLD_ARCHIVE])]) +m4_ifndef([_LT_AC_TRY_DLOPEN_SELF], [AC_DEFUN([_LT_AC_TRY_DLOPEN_SELF])]) +m4_ifndef([AC_LIBTOOL_PROG_CC_C_O], [AC_DEFUN([AC_LIBTOOL_PROG_CC_C_O])]) +m4_ifndef([AC_LIBTOOL_SYS_HARD_LINK_LOCKS], [AC_DEFUN([AC_LIBTOOL_SYS_HARD_LINK_LOCKS])]) +m4_ifndef([AC_LIBTOOL_OBJDIR], [AC_DEFUN([AC_LIBTOOL_OBJDIR])]) +m4_ifndef([AC_LTDL_OBJDIR], [AC_DEFUN([AC_LTDL_OBJDIR])]) +m4_ifndef([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH], [AC_DEFUN([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH])]) +m4_ifndef([AC_LIBTOOL_SYS_LIB_STRIP], [AC_DEFUN([AC_LIBTOOL_SYS_LIB_STRIP])]) +m4_ifndef([AC_PATH_MAGIC], [AC_DEFUN([AC_PATH_MAGIC])]) +m4_ifndef([AC_PROG_LD_GNU], [AC_DEFUN([AC_PROG_LD_GNU])]) +m4_ifndef([AC_PROG_LD_RELOAD_FLAG], [AC_DEFUN([AC_PROG_LD_RELOAD_FLAG])]) +m4_ifndef([AC_DEPLIBS_CHECK_METHOD], [AC_DEFUN([AC_DEPLIBS_CHECK_METHOD])]) +m4_ifndef([AC_LIBTOOL_PROG_COMPILER_NO_RTTI], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_NO_RTTI])]) +m4_ifndef([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE], [AC_DEFUN([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE])]) +m4_ifndef([AC_LIBTOOL_PROG_COMPILER_PIC], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_PIC])]) +m4_ifndef([AC_LIBTOOL_PROG_LD_SHLIBS], [AC_DEFUN([AC_LIBTOOL_PROG_LD_SHLIBS])]) +m4_ifndef([AC_LIBTOOL_POSTDEP_PREDEP], [AC_DEFUN([AC_LIBTOOL_POSTDEP_PREDEP])]) +m4_ifndef([LT_AC_PROG_EGREP], [AC_DEFUN([LT_AC_PROG_EGREP])]) +m4_ifndef([LT_AC_PROG_SED], [AC_DEFUN([LT_AC_PROG_SED])]) +m4_ifndef([_LT_CC_BASENAME], [AC_DEFUN([_LT_CC_BASENAME])]) +m4_ifndef([_LT_COMPILER_BOILERPLATE], [AC_DEFUN([_LT_COMPILER_BOILERPLATE])]) +m4_ifndef([_LT_LINKER_BOILERPLATE], [AC_DEFUN([_LT_LINKER_BOILERPLATE])]) +m4_ifndef([_AC_PROG_LIBTOOL], [AC_DEFUN([_AC_PROG_LIBTOOL])]) +m4_ifndef([AC_LIBTOOL_SETUP], [AC_DEFUN([AC_LIBTOOL_SETUP])]) +m4_ifndef([_LT_AC_CHECK_DLFCN], [AC_DEFUN([_LT_AC_CHECK_DLFCN])]) +m4_ifndef([AC_LIBTOOL_SYS_DYNAMIC_LINKER], [AC_DEFUN([AC_LIBTOOL_SYS_DYNAMIC_LINKER])]) +m4_ifndef([_LT_AC_TAGCONFIG], [AC_DEFUN([_LT_AC_TAGCONFIG])]) +m4_ifndef([AC_DISABLE_FAST_INSTALL], [AC_DEFUN([AC_DISABLE_FAST_INSTALL])]) +m4_ifndef([_LT_AC_LANG_CXX], [AC_DEFUN([_LT_AC_LANG_CXX])]) +m4_ifndef([_LT_AC_LANG_F77], [AC_DEFUN([_LT_AC_LANG_F77])]) +m4_ifndef([_LT_AC_LANG_GCJ], [AC_DEFUN([_LT_AC_LANG_GCJ])]) +m4_ifndef([AC_LIBTOOL_RC], [AC_DEFUN([AC_LIBTOOL_RC])]) +m4_ifndef([AC_LIBTOOL_LANG_C_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_C_CONFIG])]) +m4_ifndef([_LT_AC_LANG_C_CONFIG], [AC_DEFUN([_LT_AC_LANG_C_CONFIG])]) +m4_ifndef([AC_LIBTOOL_LANG_CXX_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_CXX_CONFIG])]) +m4_ifndef([_LT_AC_LANG_CXX_CONFIG], [AC_DEFUN([_LT_AC_LANG_CXX_CONFIG])]) +m4_ifndef([AC_LIBTOOL_LANG_F77_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_F77_CONFIG])]) +m4_ifndef([_LT_AC_LANG_F77_CONFIG], [AC_DEFUN([_LT_AC_LANG_F77_CONFIG])]) +m4_ifndef([AC_LIBTOOL_LANG_GCJ_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_GCJ_CONFIG])]) +m4_ifndef([_LT_AC_LANG_GCJ_CONFIG], [AC_DEFUN([_LT_AC_LANG_GCJ_CONFIG])]) +m4_ifndef([AC_LIBTOOL_LANG_RC_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_RC_CONFIG])]) +m4_ifndef([_LT_AC_LANG_RC_CONFIG], [AC_DEFUN([_LT_AC_LANG_RC_CONFIG])]) +m4_ifndef([AC_LIBTOOL_CONFIG], [AC_DEFUN([AC_LIBTOOL_CONFIG])]) +m4_ifndef([_LT_AC_FILE_LTDLL_C], [AC_DEFUN([_LT_AC_FILE_LTDLL_C])]) diff --git a/binaries/src/clustalo/missing b/binaries/src/clustalo/missing new file mode 100644 index 0000000..28055d2 --- /dev/null +++ b/binaries/src/clustalo/missing @@ -0,0 +1,376 @@ +#! /bin/sh +# Common stub for a few missing GNU programs while installing. + +scriptversion=2009-04-28.21; # UTC + +# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006, +# 2008, 2009 Free Software Foundation, Inc. +# Originally by Fran,cois Pinard , 1996. + +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2, or (at your option) +# any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that program. + +if test $# -eq 0; then + echo 1>&2 "Try \`$0 --help' for more information" + exit 1 +fi + +run=: +sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p' +sed_minuso='s/.* -o \([^ ]*\).*/\1/p' + +# In the cases where this matters, `missing' is being run in the +# srcdir already. +if test -f configure.ac; then + configure_ac=configure.ac +else + configure_ac=configure.in +fi + +msg="missing on your system" + +case $1 in +--run) + # Try to run requested program, and just exit if it succeeds. + run= + shift + "$@" && exit 0 + # Exit code 63 means version mismatch. This often happens + # when the user try to use an ancient version of a tool on + # a file that requires a minimum version. In this case we + # we should proceed has if the program had been absent, or + # if --run hadn't been passed. + if test $? = 63; then + run=: + msg="probably too old" + fi + ;; + + -h|--h|--he|--hel|--help) + echo "\ +$0 [OPTION]... PROGRAM [ARGUMENT]... + +Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an +error status if there is no known handling for PROGRAM. + +Options: + -h, --help display this help and exit + -v, --version output version information and exit + --run try to run the given command, and emulate it if it fails + +Supported PROGRAM values: + aclocal touch file \`aclocal.m4' + autoconf touch file \`configure' + autoheader touch file \`config.h.in' + autom4te touch the output file, or create a stub one + automake touch all \`Makefile.in' files + bison create \`y.tab.[ch]', if possible, from existing .[ch] + flex create \`lex.yy.c', if possible, from existing .c + help2man touch the output file + lex create \`lex.yy.c', if possible, from existing .c + makeinfo touch the output file + tar try tar, gnutar, gtar, then tar without non-portable flags + yacc create \`y.tab.[ch]', if possible, from existing .[ch] + +Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and +\`g' are ignored when checking the name. + +Send bug reports to ." + exit $? + ;; + + -v|--v|--ve|--ver|--vers|--versi|--versio|--version) + echo "missing $scriptversion (GNU Automake)" + exit $? + ;; + + -*) + echo 1>&2 "$0: Unknown \`$1' option" + echo 1>&2 "Try \`$0 --help' for more information" + exit 1 + ;; + +esac + +# normalize program name to check for. +program=`echo "$1" | sed ' + s/^gnu-//; t + s/^gnu//; t + s/^g//; t'` + +# Now exit if we have it, but it failed. Also exit now if we +# don't have it and --version was passed (most likely to detect +# the program). This is about non-GNU programs, so use $1 not +# $program. +case $1 in + lex*|yacc*) + # Not GNU programs, they don't have --version. + ;; + + tar*) + if test -n "$run"; then + echo 1>&2 "ERROR: \`tar' requires --run" + exit 1 + elif test "x$2" = "x--version" || test "x$2" = "x--help"; then + exit 1 + fi + ;; + + *) + if test -z "$run" && ($1 --version) > /dev/null 2>&1; then + # We have it, but it failed. + exit 1 + elif test "x$2" = "x--version" || test "x$2" = "x--help"; then + # Could not run --version or --help. This is probably someone + # running `$TOOL --version' or `$TOOL --help' to check whether + # $TOOL exists and not knowing $TOOL uses missing. + exit 1 + fi + ;; +esac + +# If it does not exist, or fails to run (possibly an outdated version), +# try to emulate it. +case $program in + aclocal*) + echo 1>&2 "\ +WARNING: \`$1' is $msg. You should only need it if + you modified \`acinclude.m4' or \`${configure_ac}'. You might want + to install the \`Automake' and \`Perl' packages. Grab them from + any GNU archive site." + touch aclocal.m4 + ;; + + autoconf*) + echo 1>&2 "\ +WARNING: \`$1' is $msg. You should only need it if + you modified \`${configure_ac}'. You might want to install the + \`Autoconf' and \`GNU m4' packages. Grab them from any GNU + archive site." + touch configure + ;; + + autoheader*) + echo 1>&2 "\ +WARNING: \`$1' is $msg. You should only need it if + you modified \`acconfig.h' or \`${configure_ac}'. You might want + to install the \`Autoconf' and \`GNU m4' packages. Grab them + from any GNU archive site." + files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}` + test -z "$files" && files="config.h" + touch_files= + for f in $files; do + case $f in + *:*) touch_files="$touch_files "`echo "$f" | + sed -e 's/^[^:]*://' -e 's/:.*//'`;; + *) touch_files="$touch_files $f.in";; + esac + done + touch $touch_files + ;; + + automake*) + echo 1>&2 "\ +WARNING: \`$1' is $msg. You should only need it if + you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'. + You might want to install the \`Automake' and \`Perl' packages. + Grab them from any GNU archive site." + find . -type f -name Makefile.am -print | + sed 's/\.am$/.in/' | + while read f; do touch "$f"; done + ;; + + autom4te*) + echo 1>&2 "\ +WARNING: \`$1' is needed, but is $msg. + You might have modified some files without having the + proper tools for further handling them. + You can get \`$1' as part of \`Autoconf' from any GNU + archive site." + + file=`echo "$*" | sed -n "$sed_output"` + test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"` + if test -f "$file"; then + touch $file + else + test -z "$file" || exec >$file + echo "#! /bin/sh" + echo "# Created by GNU Automake missing as a replacement of" + echo "# $ $@" + echo "exit 0" + chmod +x $file + exit 1 + fi + ;; + + bison*|yacc*) + echo 1>&2 "\ +WARNING: \`$1' $msg. You should only need it if + you modified a \`.y' file. You may need the \`Bison' package + in order for those modifications to take effect. You can get + \`Bison' from any GNU archive site." + rm -f y.tab.c y.tab.h + if test $# -ne 1; then + eval LASTARG="\${$#}" + case $LASTARG in + *.y) + SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'` + if test -f "$SRCFILE"; then + cp "$SRCFILE" y.tab.c + fi + SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'` + if test -f "$SRCFILE"; then + cp "$SRCFILE" y.tab.h + fi + ;; + esac + fi + if test ! -f y.tab.h; then + echo >y.tab.h + fi + if test ! -f y.tab.c; then + echo 'main() { return 0; }' >y.tab.c + fi + ;; + + lex*|flex*) + echo 1>&2 "\ +WARNING: \`$1' is $msg. You should only need it if + you modified a \`.l' file. You may need the \`Flex' package + in order for those modifications to take effect. You can get + \`Flex' from any GNU archive site." + rm -f lex.yy.c + if test $# -ne 1; then + eval LASTARG="\${$#}" + case $LASTARG in + *.l) + SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'` + if test -f "$SRCFILE"; then + cp "$SRCFILE" lex.yy.c + fi + ;; + esac + fi + if test ! -f lex.yy.c; then + echo 'main() { return 0; }' >lex.yy.c + fi + ;; + + help2man*) + echo 1>&2 "\ +WARNING: \`$1' is $msg. You should only need it if + you modified a dependency of a manual page. You may need the + \`Help2man' package in order for those modifications to take + effect. You can get \`Help2man' from any GNU archive site." + + file=`echo "$*" | sed -n "$sed_output"` + test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"` + if test -f "$file"; then + touch $file + else + test -z "$file" || exec >$file + echo ".ab help2man is required to generate this page" + exit $? + fi + ;; + + makeinfo*) + echo 1>&2 "\ +WARNING: \`$1' is $msg. You should only need it if + you modified a \`.texi' or \`.texinfo' file, or any other file + indirectly affecting the aspect of the manual. The spurious + call might also be the consequence of using a buggy \`make' (AIX, + DU, IRIX). You might want to install the \`Texinfo' package or + the \`GNU make' package. Grab either from any GNU archive site." + # The file to touch is that specified with -o ... + file=`echo "$*" | sed -n "$sed_output"` + test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"` + if test -z "$file"; then + # ... or it is the one specified with @setfilename ... + infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'` + file=`sed -n ' + /^@setfilename/{ + s/.* \([^ ]*\) *$/\1/ + p + q + }' $infile` + # ... or it is derived from the source name (dir/f.texi becomes f.info) + test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info + fi + # If the file does not exist, the user really needs makeinfo; + # let's fail without touching anything. + test -f $file || exit 1 + touch $file + ;; + + tar*) + shift + + # We have already tried tar in the generic part. + # Look for gnutar/gtar before invocation to avoid ugly error + # messages. + if (gnutar --version > /dev/null 2>&1); then + gnutar "$@" && exit 0 + fi + if (gtar --version > /dev/null 2>&1); then + gtar "$@" && exit 0 + fi + firstarg="$1" + if shift; then + case $firstarg in + *o*) + firstarg=`echo "$firstarg" | sed s/o//` + tar "$firstarg" "$@" && exit 0 + ;; + esac + case $firstarg in + *h*) + firstarg=`echo "$firstarg" | sed s/h//` + tar "$firstarg" "$@" && exit 0 + ;; + esac + fi + + echo 1>&2 "\ +WARNING: I can't seem to be able to run \`tar' with the given arguments. + You may want to install GNU tar or Free paxutils, or check the + command line arguments." + exit 1 + ;; + + *) + echo 1>&2 "\ +WARNING: \`$1' is needed, and is $msg. + You might have modified some files without having the + proper tools for further handling them. Check the \`README' file, + it often tells you about the needed prerequisites for installing + this package. You may also peek at any GNU archive site, in case + some other package would contain this missing \`$1' program." + exit 1 + ;; +esac + +exit 0 + +# Local variables: +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "scriptversion=" +# time-stamp-format: "%:y-%02m-%02d.%02H" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" +# End: diff --git a/binaries/src/clustalo/src/Makefile.am b/binaries/src/clustalo/src/Makefile.am new file mode 100644 index 0000000..9eb57b9 --- /dev/null +++ b/binaries/src/clustalo/src/Makefile.am @@ -0,0 +1,31 @@ +EXTRA_DIST = clustalo-api-test.c + +SUBDIRS = hhalign squid kmpp clustal + +AM_LDFLAGS = @AM_LDFLAGS@ +AM_CXXFLAGS = @AM_CXXFLAGS@ @OPENMP_CXXFLAGS@ +AM_CFLAGS = @AM_CFLAGS@ @OPENMP_CFLAGS@ + + +# the following is the clustalo convenience library which wraps all +# the other noinst libraries + +lib_LTLIBRARIES = libclustalo.la + +libclustalo_la_SOURCES = clustal-omega.c +libclustalo_la_LIBADD = clustal/libclustal.la \ + 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a/binaries/src/clustalo/src/clustal-omega-config.h b/binaries/src/clustalo/src/clustal-omega-config.h new file mode 100644 index 0000000..765f97f --- /dev/null +++ b/binaries/src/clustalo/src/clustal-omega-config.h @@ -0,0 +1,348 @@ +#ifndef _SRC_CLUSTAL_OMEGA_CONFIG_H +#define _SRC_CLUSTAL_OMEGA_CONFIG_H 1 + +/* src/clustal-omega-config.h. Generated automatically at end of configure. */ +/* src/config.h. Generated from config.h.in by configure. */ +/* src/config.h.in. Generated from configure.ac by autoheader. */ + +/* Define if building universal (internal helper macro) */ +/* #undef AC_APPLE_UNIVERSAL_BUILD */ + +/* Let all files know they are being used inside Clustal Omega */ +#ifndef CLUSTAL_OMEGA_CLUSTALO +#define CLUSTAL_OMEGA_CLUSTALO 1 +#endif + +/* This is a CYGWIN system */ +/* #undef CYGWIN */ + +/* This is a Darwin system */ +/* #undef DARWIN */ + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_ARGTABLE2_H +#define CLUSTAL_OMEGA_HAVE_ARGTABLE2_H 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_ASSERT_H +#define CLUSTAL_OMEGA_HAVE_ASSERT_H 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_CTYPE_H +#define CLUSTAL_OMEGA_HAVE_CTYPE_H 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_DLFCN_H +#define CLUSTAL_OMEGA_HAVE_DLFCN_H 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_FLOAT_H +#define CLUSTAL_OMEGA_HAVE_FLOAT_H 1 +#endif + +/* Define to 1 if you have the `fseek64' function. */ +/* #undef HAVE_FSEEK64 */ + +/* Define to 1 if you have the `fseeko' function. */ +#ifndef CLUSTAL_OMEGA_HAVE_FSEEKO +#define CLUSTAL_OMEGA_HAVE_FSEEKO 1 +#endif + +/* Define to 1 if you have the `fseeko64' function. */ +#ifndef CLUSTAL_OMEGA_HAVE_FSEEKO64 +#define CLUSTAL_OMEGA_HAVE_FSEEKO64 1 +#endif + +/* Define to 1 if you have the `ftell64' function. */ +/* #undef HAVE_FTELL64 */ + +/* Define to 1 if you have the `ftello' function. */ +#ifndef CLUSTAL_OMEGA_HAVE_FTELLO +#define CLUSTAL_OMEGA_HAVE_FTELLO 1 +#endif + +/* Define to 1 if you have the `ftello64' function. */ +#ifndef CLUSTAL_OMEGA_HAVE_FTELLO64 +#define CLUSTAL_OMEGA_HAVE_FTELLO64 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_INTTYPES_H +#define CLUSTAL_OMEGA_HAVE_INTTYPES_H 1 +#endif + +/* Define to 1 if you have the `argtable2' library (-largtable2). */ +#ifndef CLUSTAL_OMEGA_HAVE_LIBARGTABLE2 +#define CLUSTAL_OMEGA_HAVE_LIBARGTABLE2 1 +#endif + +/* Define to 1 if you have the `m' library (-lm). */ +#ifndef CLUSTAL_OMEGA_HAVE_LIBM +#define CLUSTAL_OMEGA_HAVE_LIBM 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_LIMITS_H +#define CLUSTAL_OMEGA_HAVE_LIMITS_H 1 +#endif + +/* Has log2() */ +#ifndef CLUSTAL_OMEGA_HAVE_LOG2 +#define CLUSTAL_OMEGA_HAVE_LOG2 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_MATH_H +#define CLUSTAL_OMEGA_HAVE_MATH_H 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_MEMORY_H +#define CLUSTAL_OMEGA_HAVE_MEMORY_H 1 +#endif + +/* Define to 1 if you have the `ntohl' function. */ +#ifndef CLUSTAL_OMEGA_HAVE_NTOHL +#define CLUSTAL_OMEGA_HAVE_NTOHL 1 +#endif + +/* Define to 1 if you have the `ntohs' function. */ +#ifndef CLUSTAL_OMEGA_HAVE_NTOHS +#define CLUSTAL_OMEGA_HAVE_NTOHS 1 +#endif + +/* Define to 1 if you have the `ntonl' function. */ +/* #undef HAVE_NTONL */ + +/* Define to 1 if you have the `ntons' function. */ +/* #undef HAVE_NTONS */ + +/* Defined if OpenMP should and can be used */ +#ifndef CLUSTAL_OMEGA_HAVE_OPENMP +#define CLUSTAL_OMEGA_HAVE_OPENMP 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_STDARG_H +#define CLUSTAL_OMEGA_HAVE_STDARG_H 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_STDINT_H +#define CLUSTAL_OMEGA_HAVE_STDINT_H 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_STDIO_H +#define CLUSTAL_OMEGA_HAVE_STDIO_H 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_STDLIB_H +#define CLUSTAL_OMEGA_HAVE_STDLIB_H 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_STRINGS_H +#define CLUSTAL_OMEGA_HAVE_STRINGS_H 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_STRING_H +#define CLUSTAL_OMEGA_HAVE_STRING_H 1 +#endif + +/* Define to 1 if you have the `stroul' function. */ +/* #undef HAVE_STROUL */ + +/* Define to 1 if you have the `strtoull' function. */ +#ifndef CLUSTAL_OMEGA_HAVE_STRTOULL +#define CLUSTAL_OMEGA_HAVE_STRTOULL 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_SYS_STAT_H +#define CLUSTAL_OMEGA_HAVE_SYS_STAT_H 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_SYS_TYPES_H +#define CLUSTAL_OMEGA_HAVE_SYS_TYPES_H 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_TIME_H +#define CLUSTAL_OMEGA_HAVE_TIME_H 1 +#endif + +/* Define to 1 if you have the header file. */ +#ifndef CLUSTAL_OMEGA_HAVE_UNISTD_H +#define CLUSTAL_OMEGA_HAVE_UNISTD_H 1 +#endif + +/* This is a LINUX system */ +#ifndef CLUSTAL_OMEGA_LINUX +#define CLUSTAL_OMEGA_LINUX 1 +#endif + +/* Define to the sub-directory in which libtool stores uninstalled libraries. + */ +#ifndef CLUSTAL_OMEGA_LT_OBJDIR +#define CLUSTAL_OMEGA_LT_OBJDIR ".libs/" +#endif + +/* This is a MinGW system */ +/* #undef MINGW */ + +/* No-debug Mode */ +#ifndef CLUSTAL_OMEGA_NDEBUG +#define CLUSTAL_OMEGA_NDEBUG /**/ +#endif + +/* Some strange OS */ +/* #undef OTHEROS */ + +/* Name of package */ +#ifndef CLUSTAL_OMEGA_PACKAGE +#define CLUSTAL_OMEGA_PACKAGE "clustal-omega" +#endif + +/* Define to the address where bug reports for this package should be sent. */ +#ifndef CLUSTAL_OMEGA_PACKAGE_BUGREPORT +#define CLUSTAL_OMEGA_PACKAGE_BUGREPORT "clustalw@ucd.ie" +#endif + +/* The package code name */ +#ifndef CLUSTAL_OMEGA_PACKAGE_CODENAME +#define CLUSTAL_OMEGA_PACKAGE_CODENAME "DeshilHollesEamus" +#endif + +/* Define to the full name of this package. */ +#ifndef CLUSTAL_OMEGA_PACKAGE_NAME +#define CLUSTAL_OMEGA_PACKAGE_NAME "Clustal Omega" +#endif + +/* Define to the full name and version of this package. */ +#ifndef CLUSTAL_OMEGA_PACKAGE_STRING +#define CLUSTAL_OMEGA_PACKAGE_STRING "Clustal Omega 1.0.2" +#endif + +/* Define to the one symbol short name of this package. */ +#ifndef CLUSTAL_OMEGA_PACKAGE_TARNAME +#define CLUSTAL_OMEGA_PACKAGE_TARNAME "clustal-omega" +#endif + +/* Define to the version of this package. */ +#ifndef CLUSTAL_OMEGA_PACKAGE_VERSION +#define CLUSTAL_OMEGA_PACKAGE_VERSION "1.0.2" +#endif + +/* The size of `fpos_t', as computed by sizeof. */ +#ifndef CLUSTAL_OMEGA_SIZEOF_FPOS_T +#define CLUSTAL_OMEGA_SIZEOF_FPOS_T 16 +#endif + +/* The size of `unsigned int', as computed by sizeof. */ +#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_INT +#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_INT 4 +#endif + +/* The size of `unsigned long', as computed by sizeof. */ +#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG +#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG 8 +#endif + +/* The size of `unsigned long long', as computed by sizeof. */ +#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG_LONG +#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG_LONG 8 +#endif + +/* The size of `unsigned short', as computed by sizeof. */ +#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_SHORT +#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_SHORT 2 +#endif + +/* This is a Solaris system */ +/* #undef SOLARIS */ + +/* This is a BSD system */ +/* #undef SOMEBSD */ + +/* Define to 1 if you have the ANSI C header files. */ +#ifndef CLUSTAL_OMEGA_STDC_HEADERS +#define CLUSTAL_OMEGA_STDC_HEADERS 1 +#endif + +/* Enable extensions on AIX 3, Interix. */ +#ifndef _ALL_SOURCE +# define _ALL_SOURCE 1 +#endif +/* Enable GNU extensions on systems that have them. */ +#ifndef _GNU_SOURCE +# define _GNU_SOURCE 1 +#endif +/* Enable threading extensions on Solaris. */ +#ifndef _POSIX_PTHREAD_SEMANTICS +# define _POSIX_PTHREAD_SEMANTICS 1 +#endif +/* Enable extensions on HP NonStop. */ +#ifndef _TANDEM_SOURCE +# define _TANDEM_SOURCE 1 +#endif +/* Enable general extensions on Solaris. */ +#ifndef __EXTENSIONS__ +# define __EXTENSIONS__ 1 +#endif + + +/* Version number of package */ +#ifndef CLUSTAL_OMEGA_VERSION +#define CLUSTAL_OMEGA_VERSION "1.0.2" +#endif + +/* Define if using the dmalloc debugging malloc package */ +/* #undef WITH_DMALLOC */ + +/* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most + significant byte first (like Motorola and SPARC, unlike Intel). */ +#if defined AC_APPLE_UNIVERSAL_BUILD +# if defined __BIG_ENDIAN__ +# define WORDS_BIGENDIAN 1 +# endif +#else +# ifndef WORDS_BIGENDIAN +/* # undef WORDS_BIGENDIAN */ +# endif +#endif + +/* Define to 1 if on MINIX. */ +/* #undef _MINIX */ + +/* Define to 2 if the system does not provide POSIX.1 features except with + this defined. */ +/* #undef _POSIX_1_SOURCE */ + +/* Define to 1 if you need to in order for `stat' and other things to work. */ +/* #undef _POSIX_SOURCE */ + +/* Define to empty if `const' does not conform to ANSI C. */ +/* #undef const */ + +/* Define to `__inline__' or `__inline' if that's what the C compiler + calls it, or to nothing if 'inline' is not supported under any name. */ +#ifndef __cplusplus +/* #undef inline */ +#endif + +/* Define to `long int' if does not define. */ +/* #undef off_t */ + +/* Define to `unsigned int' if does not define. */ +/* #undef size_t */ + +/* once: _SRC_CLUSTAL_OMEGA_CONFIG_H */ +#endif diff --git a/binaries/src/clustalo/src/clustal-omega.c b/binaries/src/clustalo/src/clustal-omega.c new file mode 100644 index 0000000..376e078 --- /dev/null +++ b/binaries/src/clustalo/src/clustal-omega.c @@ -0,0 +1,1385 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: clustal-omega.c 254 2011-06-21 13:07:50Z andreas $ + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include + +#include "clustal-omega.h" +#include "hhalign/general.h" + +/* The following comment block contains the frontpage/mainpage of the doxygen + * documentation. Please add some more info. FIXME add more + */ + +/** + * + * @mainpage Clustal-Omega Documentation + * + * @section intro_sec Introduction + * + * For more information see http://www.clustal.org/ + * + * @section api_section API + * + * @subsection example_prog_subsection An Example Program + * + * To use libclustalo you will have to include the clustal-omega.h header and + * link against libclustalo. For linking against libclustalo you will have to + * use a C++ compiler, no matter if your program was written in C or C++. + * + * First compile (no linking) your source (for an example see section "\ref + * example_src_subsubsec"): + * + * @code + * $ gcc -c -ansi -Wall clustalo-api-test.c + * @endcode + * + * Then link against libclustalo (we recommend the use of pkg-config as + * explained in \ref pkgconfig_subsubsec). Assuming Clustal Omega was installed + * in system-wide default directory (e.g. /usr) just type: + * + * @code + * $ g++ -ansi -Wall -o clustalo-api-test clustalo-api-test.o -lclustalo + * @endcode + * + * Voila! Now you have your own alignment program which can be run with + * + * @code + * $ ./clustalo-api-test + * @endcode + * + * It's best to use the same compiler that you used for compiling libclustal. + * If libclustal was compiled with OpenMP support, you will have to use OpenMP + * flags for you program as well. + * + * + * @subsubsection pkgconfig_subsubsec Using pkg-config / Figuring out compiler flags + * + * Clustal Omega comes with support for pkg-config, which means you + * can run + * + * @code + * $ pkg-config --cflags --libs clustalo + * @endcode + * + * to figure out cflags and library flags needed to compile and link against + * libclustalo. This is especially handy if Clustal Omega was installed to a + * non-standard directory. + * + * You might have to change PKG_CONFIG_PATH. For example, if you used the prefix $HOME/local/ for + * installation then you will first need to set PKG_CONFIG_PATH: + * + * @code + * $ export PKG_CONFIG_PATH=$HOME/local/lib/pkgconfig + * $ pkg-config --cflags --libs clustalo + * @endcode + * + * + * To compile your source use: + * + * @code + * $ export PKG_CONFIG_PATH=$HOME/local/lib/pkgconfig + * $ gcc -c -ansi -Wall clustalo-api-test.c $(pkg-config --cflags clustalo) + * $ g++ -ansi -Wall -o clustalo-api-test clustalo-api-test.o $(pkg-config --libs clustalo) + * @endcode + * + * + * @subsubsection example_src_subsubsec Example Source Code + * + * @include "clustalo-api-test.c" + * + * + */ + + + + +/* FIXME: doc */ +/* the following are temporary flags while the code is still under construction; + had problems internalising hhmake, so as temporary crutch + write alignment to file and get external hmmer/hhmake via system call + to read alignment and convert into HMM + All this will go, once hhmake is properly internalised */ +#define INDIRECT_HMM 0 /* temp flag: (1) write aln to file, use system(hmmer/hhmake), (0) internal hhmake */ +#define USEHMMER 1 /* temp flag: use system(hmmer) to build HMM */ +#define USEHHMAKE (!USEHMMER) /* temp flag: use system(hhmake) to build HMM */ + + +/* shuffle order of input sequences */ +#define SHUFFLE_INPUT_SEQ_ORDER 0 + +/* sort input sequences by length */ +#define SORT_INPUT_SEQS 0 + + +int iNumberOfThreads; + +/* broken, unused and lonely */ +static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01; + + +/** + * @brief Print Long version information to pre-allocated char. + * + * @note short version + * information is equivalent to PACKAGE_VERSION + * + * @param[out] pcStr + * char pointer to write to preallocated to hold iSize chars. + * @param[in] iSize + * size of pcStr + */ +void +PrintLongVersion(char *pcStr, int iSize) +{ + snprintf(pcStr, iSize, "version %s; code-name '%s'; build date %s", + PACKAGE_VERSION, PACKAGE_CODENAME, __DATE__); +} +/* end of PrintLongVersion() */ + + + +/** + * @brief free aln opts members + * + */ +void +FreeAlnOpts(opts_t *prAlnOpts) { + if (NULL != prAlnOpts->pcGuidetreeInfile) { + CKFREE(prAlnOpts->pcGuidetreeInfile); + } + if (NULL != prAlnOpts->pcGuidetreeOutfile) { + CKFREE(prAlnOpts->pcGuidetreeOutfile); + } + if (NULL != prAlnOpts->pcDistmatOutfile) { + CKFREE(prAlnOpts->pcDistmatOutfile); + } + if (NULL != prAlnOpts->pcDistmatInfile) { + CKFREE(prAlnOpts->pcDistmatInfile); + } +} +/* end of FreeAlnOpts() */ + + + +/** + * @brief Sets members of given user opts struct to default values + * + * @param[out] prOpts + * User opt struct to initialise + * + */ +void +SetDefaultAlnOpts(opts_t *prOpts) { + prOpts->bAutoOptions = FALSE; + + prOpts->pcDistmatInfile = NULL; + prOpts->pcDistmatOutfile = NULL; + + prOpts->iClusteringType = CLUSTERING_UPGMA; + prOpts->iPairDistType = PAIRDIST_KTUPLE; + prOpts->bUseMbed = TRUE; /* FS, r250 -> */ + prOpts->bUseMbedForIteration = TRUE; /* FS, r250 -> */ + prOpts->pcGuidetreeOutfile = NULL; + prOpts->pcGuidetreeInfile = NULL; + + prOpts->ppcHMMInput = NULL; + prOpts->iHMMInputFiles = 0; + + prOpts->iNumIterations = 0; + prOpts->bIterationsAuto = FALSE; + prOpts->iMaxGuidetreeIterations = INT_MAX; + prOpts->iMaxHMMIterations = INT_MAX; + prOpts->iMacRam = 2048; /* give 2GB to MAC algorithm. FS, r240 -> r241 */ + } +/* end of SetDefaultAlnOpts() */ + + + +/** + * @brief Check logic of parsed user options. Will exit (call Log(&rLog, LOG_FATAL, )) + * on Fatal logic error + * + * @param[in] prOpts + * Already parsed user options + * + */ +void +AlnOptsLogicCheck(opts_t *prOpts) +{ + /* guide-tree & distmat + * + */ + if (prOpts->pcDistmatInfile && prOpts->pcGuidetreeInfile) { + Log(&rLog, LOG_FATAL, "Read distances *and* guide-tree from file doesn't make sense."); + } + + if (prOpts->pcDistmatOutfile && prOpts->pcGuidetreeInfile) { + Log(&rLog, LOG_FATAL, "Won't be able to save distances to file, because I got a guide-tree as input."); + } + + /* combination of options that don't make sense when not iterating + */ + if (prOpts->iNumIterations==0 && prOpts->bIterationsAuto != TRUE) { + + if (prOpts->pcGuidetreeInfile && prOpts->pcGuidetreeOutfile) { + Log(&rLog, LOG_FATAL, "Got a guide-tree as input and output which doesn't make sense when not iterating."); + } + /* + if (prOpts->pcGuidetreeInfile && prOpts->bUseMbed > 0) { + Log(&rLog, LOG_FATAL, "Got a guide-tree as input and was requested to cluster with mBed, which doesn't make sense when not iterating."); + } + */ + /* + AW: bUseMbedForIteration default since at least R252 + if (prOpts->bUseMbedForIteration > 0) { + Log(&rLog, LOG_FATAL, "No iteration requested, but mbed for iteration was set. Paranoia exit."); + } + */ + } + + if (prOpts->iMacRam < 512) { + + Log(&rLog, LOG_INFO, "Memory for MAC Algorithm quite low, Viterbi Algorithm may be triggered."); + + if (prOpts->iMacRam < 1) { + + Log(&rLog, LOG_WARN, "Viterbi Algorithm always turned on, increase MAC-RAM to turn on MAC."); + } + } + + return; +} +/* end of AlnOptsLogicCheck() */ + + +/** + * @brief FIXME doc + */ +void +PrintAlnOpts(FILE *prFile, opts_t *prOpts) +{ + int iAux; + + + /* keep in same order as struct */ + fprintf(prFile, "option: auto-options = %d\n", prOpts->bAutoOptions); + fprintf(prFile, "option: distmat-infile = %s\n", + NULL != prOpts->pcDistmatInfile? prOpts->pcDistmatInfile: "(null)"); + fprintf(prFile, "option: distmat-outfile = %s\n", + NULL != prOpts->pcDistmatOutfile? prOpts->pcDistmatOutfile: "(null)"); + fprintf(prFile, "option: clustering-type = %d\n", prOpts->iClusteringType); + fprintf(prFile, "option: pair-dist-type = %d\n", prOpts->iPairDistType); + fprintf(prFile, "option: use-mbed = %d\n", prOpts->bUseMbed); + fprintf(prFile, "option: use-mbed-for-iteration = %d\n", prOpts->bUseMbedForIteration); + fprintf(prFile, "option: guidetree-outfile = %s\n", + NULL != prOpts->pcGuidetreeOutfile? prOpts->pcGuidetreeOutfile: "(null)"); + fprintf(prFile, "option: guidetree-infile = %s\n", + NULL != prOpts->pcGuidetreeInfile? prOpts->pcGuidetreeInfile: "(null)"); + for (iAux=0; iAuxiHMMInputFiles; iAux++) { + fprintf(prFile, "option: hmm-input no %d = %s\n", iAux, prOpts->ppcHMMInput[iAux]); + } + fprintf(prFile, "option: hmm-input-files = %d\n", prOpts->iHMMInputFiles); + fprintf(prFile, "option: num-iterations = %d\n", prOpts->iNumIterations); + fprintf(prFile, "option: iterations-auto = %d\n", prOpts->bIterationsAuto); + fprintf(prFile, "option: max-hmm-iterations = %d\n", prOpts->iMaxHMMIterations); + fprintf(prFile, "option: max-guidetree-iterations = %d\n", prOpts->iMaxGuidetreeIterations); +} +/* end of PrintAlnOpts() */ + + + +/** + * @brief Returns major version of HMMER. Whichever hmmbuild version + * is found first in your PATH will be used + * + * @return -1 on error, major hmmer version otherwise + * + */ +int +HmmerVersion() +{ + char zcHmmerTestCall[] = "hmmbuild -h"; + FILE *fp = NULL; + int iMajorVersion = 0; + char zcLine[16384]; + + if (NULL == (fp = popen(zcHmmerTestCall, "r"))) { + Log(&rLog, LOG_ERROR, "Couldn't exec %s", zcHmmerTestCall); + return -1; + } + while (fgets(zcLine, sizeof(zcLine), fp)) { + char *pcLocate; + if ((pcLocate = strstr(zcLine, "HMMER "))) { + iMajorVersion = atoi(&pcLocate[6]); + break; + } + } + pclose(fp); + + return iMajorVersion; +} +/* end of HmmerVersion() */ + + + +/** + * @brief Create a HHM file from aligned sequences + * + * @warning Should be eliminated in the future + * as building routine should not create intermediate files + * + * @param[in] prMSeq + * Aligned mseq_t + * @param[in] pcHMMOut + * HMM output file name + * + * @return Non-zero on error + * + */ +int +AlnToHHMFile(mseq_t *prMSeq, char *pcHMMOut) +{ + char *tmp_aln = NULL; + int retcode = OK; + + assert(NULL!=prMSeq); + assert(NULL!=pcHMMOut); + + if (FALSE == prMSeq->aligned) { + Log(&rLog, LOG_ERROR, "Sequences need to be aligned to create an HMM"); + return FAILURE; + } + + /* Convert alignment to a2m, and call hhmake + * + * can't be static templates, or mktemp fails (at least on os x + * (with a bus error)) + * + * gcc says we should use mkstemp to avoid race conditions, + * but that returns a file descriptor, which is of no use to + * us + */ + /* NOTE: the following won't work on windows: missing /tmp/ */ + tmp_aln = CkStrdup("/tmp/clustalo_tmpaln_XXXXXX"); + if (NULL == mktemp(tmp_aln)) { + Log(&rLog, LOG_ERROR, "Could not create temporary alignment filename"); + retcode = FAILURE; + goto cleanup_and_return; + } + if (WriteAlignment(prMSeq, tmp_aln, MSAFILE_A2M)) { + Log(&rLog, LOG_ERROR, "Could not save alignment to %s", tmp_aln); + retcode = FAILURE; + goto cleanup_and_return; + } + + if (HHMake_Wrapper(tmp_aln, pcHMMOut)){ + Log(&rLog, LOG_ERROR, "Could not convert alignment %s into HHM", tmp_aln); + retcode = FAILURE; + goto cleanup_and_return; + } + + + cleanup_and_return: + + if (NULL != tmp_aln) { + if (FileExists(tmp_aln)) { + if (remove(tmp_aln)) { + Log(&rLog, LOG_WARN, "Removing %s failed. Continuing anyway", tmp_aln); + } + } + CKFREE(tmp_aln); + } + + return retcode; + +} /* end of AlnToHHMFile() */ + + + +/** + * @brief Create a HMM file from aligned sequences + * + * @warning Should be replaced in the future by some internal HMM + * building routine that does not call external programs + * + * @param[in] prMSeq + * Aligned mseq_t + * @param[in] pcHMMOut + * HMM output file name + * + * @return Non-zero on error + * + + */ +int +AlnToHMMFile(mseq_t *prMSeq, const char *pcHMMOut) +{ + char *tmp_aln = NULL; + char *tmp_hmm = NULL; /* only needed for hmmer3 to hmmer2 conversion */ + char cmdbuf[16384]; + int iHmmerVersion = 0; + int retcode = OK; + + assert(NULL!=prMSeq); + assert(NULL!=pcHMMOut); + + if (FALSE == prMSeq->aligned) { + Log(&rLog, LOG_ERROR, "Sequences need to be aligned to create an HMM"); + return FAILURE; + } + + iHmmerVersion = HmmerVersion(); + if (2 != iHmmerVersion && 3 != iHmmerVersion) { + Log(&rLog, LOG_ERROR, "Could not find suitable HMMER binaries"); + return FAILURE; + } + + /* Convert alignment to stockholm, call hmmbuild and then + * either hmmconvert (hmmer3) or hmmcalibrate (hmmer2) + * + * can't be static templates, or mktemp fails (at least on os x + * (with a bus error)) + * + * gcc says we should use mkstemp to avoid race conditions, + * but that returns a file descriptor, which is of no use to + * us + */ + /* NOTE: the following won't work on windows: missing /tmp/ */ + tmp_aln = CkStrdup("/tmp/clustalo_tmpaln_XXXXXX"); + if (NULL == mktemp(tmp_aln)) { + Log(&rLog, LOG_ERROR, "Could not create temporary alignment filename"); + retcode = FAILURE; + goto cleanup_and_return; + } + if (WriteAlignment(prMSeq, tmp_aln, MSAFILE_STOCKHOLM)) { + Log(&rLog, LOG_ERROR, "Could not save alignment to %s", tmp_aln); + retcode = FAILURE; + goto cleanup_and_return; + } + + if (2 == iHmmerVersion) { + sprintf(cmdbuf, "hmmbuild %s %s >/dev/null && hmmcalibrate %s >/dev/null", + pcHMMOut, tmp_aln, pcHMMOut); + if (system(cmdbuf)) { + Log(&rLog, LOG_ERROR, "Command '%s' failed", cmdbuf); + retcode = FAILURE; + goto cleanup_and_return; + } + } else if (3 == iHmmerVersion) { + /* NOTE: the following won't work on windows: missing /tmp/ */ + tmp_hmm = CkStrdup("/tmp/clustalo_tmphmm2_XXXXXX"); + if (NULL == mktemp(tmp_hmm)) { + Log(&rLog, LOG_ERROR, "Could not create temporary hmm filename"); + retcode = FAILURE; + goto cleanup_and_return; + } + sprintf(cmdbuf, "hmmbuild %s %s >/dev/null && hmmconvert -2 %s > %s", + tmp_hmm, tmp_aln, tmp_hmm, pcHMMOut); + if (system(cmdbuf)) { + Log(&rLog, LOG_ERROR, "Command '%s' failed", cmdbuf); + retcode = FAILURE; + goto cleanup_and_return; + } + } else { + CKFREE(tmp_aln); + Log(&rLog, LOG_FATAL, "Internal error: Unknown Hmmer version %d", iHmmerVersion); + } + + + cleanup_and_return: + + if (NULL != tmp_aln) { + if (FileExists(tmp_aln)) { + if (remove(tmp_aln)) { + Log(&rLog, LOG_WARN, "Removing %s failed. Continuing anyway", tmp_aln); + } + } + CKFREE(tmp_aln); + } + if (NULL != tmp_hmm) { + if (FileExists(tmp_hmm)) { + if (remove(tmp_hmm)) { + Log(&rLog, LOG_WARN, "Removing %s failed. Continuing anyway", tmp_hmm); + } + } + CKFREE(tmp_hmm); + } + + return retcode; +} +/* end of AlnToHMMFile() */ + + + +/** + * @brief Convert a multiple sequence structure into a HMM + * + * @param[out] prHMM + * Pointer to preallocted HMM which will be set here + * @param[in] prMSeq + * Pointer to an alignment + * + * @return 0 on error, non-0 otherwise + * + * @see AlnToHMMFile() + * + */ +int +AlnToHMM(hmm_light *prHMM, mseq_t *prMSeq) +{ + char *pcHMM; /* temp hmm file */ + + Log(&rLog, LOG_INFO, + "Using HMMER version %d to calculate a new HMM.", + HmmerVersion()); + /* FIXME replace all this with internal HMM computation (HHmake) */ + + /** + * @warning the following probably won't work on windows: missing + * /tmp/. Should be ok on Cygwin though + */ + pcHMM = CkStrdup("/tmp/clustalo-hmm-iter_XXXXXX"); + if (NULL == mktemp(pcHMM)) { + Log(&rLog, LOG_ERROR, "Could not create temporary hmm filename"); + CKFREE(pcHMM); + return FAILURE; + } + + /* Create a HMM representing the current alignment + */ +#if USEHMMER + if (AlnToHMMFile(prMSeq, pcHMM)) { + Log(&rLog, LOG_ERROR, "AlnToHMMFile() on %s failed.", pcHMM); + CKFREE(pcHMM); + return FAILURE; + } +#elif USEHHMAKE + if (AlnToHHMFile(prMSeq, pcHMM)) { + Log(&rLog, LOG_ERROR, "AlnToHHMFile() on %s failed.", pcHMM); + CKFREE(pcHMM); + return FAILURE; + } + /* Log(&rLog, LOG_FATAL, "Method to create HHM (HMM using hhmake) not installed yet"); */ +#else + Log(&rLog, LOG_FATAL, "Unknown method to create temporary HMM"); +#endif + + /* Read HMM information + */ + if (OK != readHMMWrapper(prHMM, pcHMM)){ + Log(&rLog, LOG_ERROR, "Processing of HMM file %s failed", pcHMM); + CKFREE(pcHMM); + return FAILURE; + } + + if (remove(pcHMM)) { + Log(&rLog, LOG_WARN, "Removing %s failed. Continuing anyway", pcHMM); + } + CKFREE(pcHMM); + + return OK; +} +/* end of AlnToHMM() */ + + + +/** + * @brief FIXME + * + */ +void +InitClustalOmega(int iNumThreadsRequested) +{ + +#ifdef HAVE_OPENMP + iNumberOfThreads = iNumThreadsRequested; + omp_set_num_threads(iNumberOfThreads); +#else + if (iNumThreadsRequested>1) { + Log(&rLog, LOG_FATAL, "Cannot change number of threads to %d. %s was build without OpenMP support.", + iNumThreadsRequested, PACKAGE_NAME); + } + iNumberOfThreads = 1; /* need to set this, even if build without support */ +#endif + + Log(&rLog, LOG_INFO, "Using %d threads", + iNumberOfThreads); + +} +/* end of InitClustalOmega() */ + + + +/** + * @brief Defines an alignment order, which adds sequences + * sequentially, i.e. one at a time starting with seq 1 & 2 + * + * @param[out] piOrderLR_p + * order in which nodes/profiles are to be merged/aligned + * @param[in] iNumSeq + * Number of sequences + * + * @see TraverseTree() + * + */ +void +SequentialAlignmentOrder(int **piOrderLR_p, int iNumSeq) +{ + unsigned int uNodes = iNumSeq*2-1; + unsigned int uNodeCounter = 0; + unsigned int uSeqCounter = 0; + + Log(&rLog, LOG_FATAL, "FIXME: Untested..."); + + (*piOrderLR_p) = (int *)CKCALLOC(DIFF_NODE * uNodes, sizeof(int)); + /* loop over merge nodes, which have per definition even indices + * and set up children which have odd indices + */ + uSeqCounter = 0; + for (uNodeCounter=iNumSeq; uNodeCounternseqs) { + Log(&rLog, LOG_VERBOSE, + "Have only two sequences: No need to compute pairwise score and compute a tree."); + + (*piOrderLR_p) = (int*) CKMALLOC(DIFF_NODE * 3 * sizeof(int)); + (*piOrderLR_p)[DIFF_NODE*0+LEFT_NODE] = 0; + (*piOrderLR_p)[DIFF_NODE*0+RGHT_NODE] = 0; + (*piOrderLR_p)[DIFF_NODE*0+PRNT_NODE] = 0; + + (*piOrderLR_p)[DIFF_NODE*1+LEFT_NODE] = 1; + (*piOrderLR_p)[DIFF_NODE*1+RGHT_NODE] = 1; + (*piOrderLR_p)[DIFF_NODE*1+PRNT_NODE] = 1; + + /* root */ + (*piOrderLR_p)[DIFF_NODE*2+LEFT_NODE] = 0; + (*piOrderLR_p)[DIFF_NODE*2+RGHT_NODE] = 1; + (*piOrderLR_p)[DIFF_NODE*2+PRNT_NODE] = 2; + + /* Same logic as CalcClustalWeights(). Changes there will + have to be reflected here as well. */ +#if USE_WEIGHTS + (*pdWeights_p) = (double *) CKMALLOC(uNodeCount * sizeof(double)); + (*pdWeights_p)[0] = 0.5; + (*pdWeights_p)[1] = 0.5; +#endif + + return OK; + } + + + /* compute distance & guide tree, alternatively read distances or + * guide tree from file + * + */ + if (NULL != pcGuidetreeInfile) { + Log(&rLog, LOG_INFO, "Reading guide-tree from %s", pcGuidetreeInfile); + if (GuideTreeFromFile(&prTree, prMSeq, pcGuidetreeInfile)) { + Log(&rLog, LOG_ERROR, "Reading of guide tree %s failed.", pcGuidetreeInfile); + return FAILURE; + } + + } else { + + if (bUseMbed) { + if (Mbed(&prTree, prMSeq, iPairDistType, pcGuidetreeOutfile)) { + Log(&rLog, LOG_ERROR, "mbed execution failed."); + return FAILURE; + } + Log(&rLog, LOG_INFO, "Guide-tree computation (mBed) done."); + if (NULL != pcDistmatOutfile) { + Log(&rLog, LOG_INFO, + "Ignoring request to write distance matrix (am in mBed mode)"); + } + } else { + + if (PairDistances(&distmat, prMSeq, iPairDistType, + 0, prMSeq->nseqs, 0, prMSeq->nseqs, + pcDistmatInfile, pcDistmatOutfile)) { + Log(&rLog, LOG_ERROR, "Couldn't compute pair distances"); + return FAILURE; + } + + /* clustering of distances to get guide tree + */ + if (CLUSTERING_UPGMA == iClusteringType) { + char **labels; + labels = (char**) CKMALLOC(prMSeq->nseqs * sizeof(char*)); + for (i=0; inseqs; i++) { + labels[i] = prMSeq->sqinfo[i].name; + } + + GuideTreeUpgma(&prTree, labels, distmat, pcGuidetreeOutfile); + Log(&rLog, LOG_INFO, "Guide-tree computation done."); + + CKFREE(labels); + } else { + Log(&rLog, LOG_FATAL, "INTERNAL ERROR %s", + "clustering method should have been checked before"); + } + } + } + +#if USE_WEIGHTS + /* derive sequence weights from tree + * + */ + Log(&rLog, LOG_INFO, "Calculating sequence weights"); + CalcClustalWeights(pdSeqWeights_p, prTree); + for (i = 0; i < GetLeafCount(prTree); i++) { + Log(&rLog, LOG_VERBOSE, + "Weight for seq no %d: %s = %f", + i, prMSeq->sqinfo[i].name, (*pdSeqWeights_p)[i]); + } +#else + Log(&rLog, LOG_DEBUG, "Not using weights"); +#endif + + + /* define traversing order of tree + * + */ + TraverseTree(piOrderLR_p, prTree, prMSeq); + if (rLog.iLogLevelEnabled <= LOG_DEBUG) { + /* FIXME: debug only, FS */ + uint uNodeIndex; + FILE *fp = LogGetFP(&rLog, LOG_INFO); + Log(&rLog, LOG_DEBUG, "left/right order after tree traversal"); + for (uNodeIndex = 0; uNodeIndex < GetNodeCount(prTree); uNodeIndex++) { + fprintf(fp, "%3d:\t%2d/%2d -> %d\n", i, + (*piOrderLR_p)[DIFF_NODE*uNodeIndex+LEFT_NODE], + (*piOrderLR_p)[DIFF_NODE*uNodeIndex+RGHT_NODE], + (*piOrderLR_p)[DIFF_NODE*uNodeIndex+PRNT_NODE]); + } + } + + FreeMuscleTree(prTree); + FreeSymMatrix(&distmat); + +#if 0 + Log(&rLog, LOG_FATAL, "DEBUG EXIT before leaving %s", __FUNCTION__); +#endif + return OK; +} +/* end of AlignmentOrder() */ + + + +/** + * @brief Set some options automatically based on number of sequences. Might + * overwrite some user-set options. + * + * @param[out] prOpts + * Pointer to alignment options structure + * @param[in] iNumSeq + * Number of sequences to align + */ +void +SetAutoOptions(opts_t *prOpts, int iNumSeq) { + + Log(&rLog, LOG_INFO, + "Setting options automatically based on input sequence characteristics (might overwrite some of your options)."); + + /* AW: new version of mbed is always good (uses subclusters) */ + if (FALSE == prOpts->bUseMbed) { + Log(&rLog, LOG_INFO, "Auto settings: Enabling mBed."); + prOpts->bUseMbed = TRUE; + } + + if (iNumSeq >= 1000) { + if (0 != prOpts->iNumIterations) { + Log(&rLog, LOG_INFO, "Auto settings: Disabling iterations."); + prOpts->iNumIterations = 0; + } + + } else if (iNumSeq < 1000) { + if (1 != prOpts->iNumIterations) { + Log(&rLog, LOG_INFO, "Auto settings: Setting iteration to 1."); + prOpts->iNumIterations = 1; + } + } +} +/* end of */ + + + +/** + * @brief The main alignment function which wraps everything else. + * + * @param[out] prMSeq + * *the* multiple sequences structure + * @param[in] prMSeqProfile + * optional profile to align against + * @param[in] prOpts + * alignmemnt options to use + * + * @return 0 on success, -1 on failure + * + */ +int +Align(mseq_t *prMSeq, + mseq_t *prMSeqProfile, + opts_t *prOpts, + hhalign_para rHhalignPara) { + + /* HMM + */ + /* structs with pseudocounts etc; one for each HMM infile, i.e. + * index range: 0..iHMMInputFiles */ + hmm_light *prHMMs = NULL; + + /* MSA order in which nodes/profiles are to be merged/aligned + (order of nodes in guide tree (left/right)*/ + int *piOrderLR = NULL; + + /* weights per sequence */ + double *pdSeqWeights = NULL; + + /* Iteration + */ + int iIterationCounter = 0; + double dAlnScore; + /* last dAlnScore for iteration */ + double dLastAlnScore = -666.666; + + int i, j; /* aux */ + + assert(NULL != prMSeq); + if (NULL != prMSeqProfile) { + assert(TRUE == prMSeqProfile->aligned); + } + + + /* automatic setting of options + * + */ + if (prOpts->bAutoOptions) { + SetAutoOptions(prOpts, prMSeq->nseqs); + } + + +#if SHUFFLE_INPUT_SEQ_ORDER + /* + * shuffle input: only useful for testing/debugging + */ + Log(&rLog, LOG_WARN, "Shuffling input sequences! (Will also change output order)"); + ShuffleMSeq(prMSeq); +#endif + + +#if SORT_INPUT_SEQS + /* + * sort input: + * + * would ensure we *always* (unless we get into the mbed k-means stage) + * get the same answer. usually you don't, because most pairwise alignment + * scores are in theory not symmetric, therefore sequence ordering might + * have an effect on the guide-tree. Sorting by length should get rid of + * this (and takes no time even for 100k seqs). Benchmark results on + * Balibase show almost no difference after sorting. + */ + Log(&rLog, LOG_WARN, "Sorting input seq by length! This will also change the output order"); + SortMSeqByLength(prMSeq, 'd'); + +#endif + + + /* Read backgrounds HMMs and store in prHMMs + * + */ + if (0 < prOpts->iHMMInputFiles) { + int iHMMInfileIndex; + + /** + * @warning old structure used to be initialised like this: + * hmm_light rHMM = {0}; + */ + prHMMs = (hmm_light *) CKMALLOC(prOpts->iHMMInputFiles * sizeof(hmm_light)); + + for (iHMMInfileIndex=0; iHMMInfileIndexiHMMInputFiles; iHMMInfileIndex++) { + char *pcHMMInput = prOpts->ppcHMMInput[iHMMInfileIndex]; + if (OK != readHMMWrapper(&prHMMs[iHMMInfileIndex], pcHMMInput)){ + Log(&rLog, LOG_ERROR, "Processing of HMM file %s failed", pcHMMInput); + return -1; + } + +#if 0 + Log(&rLog, LOG_FORCED_DEBUG, "HMM length is %d", prHMMs[iHMMInfileIndex].L); + Log(&rLog, LOG_FORCED_DEBUG, "n-display is %d", prHMMs[iHMMInfileIndex].n_display); + for (i = 0; NULL != prHMMs[prOpts->iHMMInputFiles].seq[i]; i++){ + printf("seq[%d]: %s\n", i, prHMMs[iHMMInfileIndex].seq[i]); + } + Log(&rLog, LOG_FORCED_DEBUG, "Neff_HMM is %f", prHMMs[iHMMInfileIndex].Neff_HMM); +#endif + if (rLog.iLogLevelEnabled <= LOG_DEBUG){ + Log(&rLog, LOG_DEBUG, "print frequencies"); + for (i = 0; i < prHMMs[iHMMInfileIndex].L; i++){ +#define PRINT_TAIL 5 + if ( (PRINT_TAIL+1 == i) && (prHMMs[iHMMInfileIndex].L-PRINT_TAIL != i) ){ + printf("....\n"); + } + if ( (i > PRINT_TAIL) && (i < prHMMs[iHMMInfileIndex].L-PRINT_TAIL) ){ + continue; + } + printf("%3d:", i); + for (j = 0; j < 20; j++){ + printf("\t%1.3f", prHMMs[iHMMInfileIndex].f[i][j]); + } + printf("\n"); + } + } /* debug print block */ + + CKFREE(prOpts->ppcHMMInput[iHMMInfileIndex]); + } /* for each background HMM file */ + CKFREE(prOpts->ppcHMMInput); + } /* there were background HMM files */ + + + + /* If the input ("non-profile") sequences are aligned, then turn + * the alignment into a HMM and add to the list of background HMMs + * + */ + if (TRUE == prMSeq->aligned) { + /* FIXME: gcc warns about missing initialiser here (-Wall -Wextra -pedantic) */ + hmm_light rHMMLocal = {0}; + + Log(&rLog, LOG_INFO, + "Input sequences are aligned. Will turn alignment into HMM and add it to the user provided background HMMs."); + if (OK != +#if INDIRECT_HMM + AlnToHMM(&rHMMLocal, prMSeq) +#else + AlnToHMM2(&rHMMLocal, prMSeq->seq, prMSeq->nseqs) +#endif + ) { + Log(&rLog, LOG_ERROR, "Couldn't convert aligned input sequences to HMM. Will try to continue"); + } else { + prHMMs = (hmm_light *) CKREALLOC(prHMMs, ((prOpts->iHMMInputFiles+1) * sizeof(hmm_light))); + memcpy(&(prHMMs[prOpts->iHMMInputFiles]), &rHMMLocal, sizeof(hmm_light)); + prOpts->iHMMInputFiles++; + } + } + + + /* If we have a profile turn it into a HMM and add to + * the list of background HMMs. + * + */ + if (NULL != prMSeqProfile) { + /* FIXME: gcc warns about missing initialiser here (-Wall -Wextra -pedantic) */ + hmm_light rHMMLocal = {0}; + Log(&rLog, LOG_INFO, + "Turning profile1 into HMM and will use it during progressive alignment."); + if (OK != +#if INDIRECT_HMM + AlnToHMM(&rHMMLocal, prMSeqProfile) +#else + AlnToHMM2(&rHMMLocal, prMSeqProfile->seq, prMSeqProfile->nseqs) +#endif + ) { + Log(&rLog, LOG_ERROR, "Couldn't convert profile1 to HMM. Will try to continue"); + } else { + prHMMs = (hmm_light *) CKREALLOC(prHMMs, ((prOpts->iHMMInputFiles+1) * sizeof(hmm_light))); + memcpy(&(prHMMs[prOpts->iHMMInputFiles]), &rHMMLocal, sizeof(hmm_light)); + prOpts->iHMMInputFiles++; + } + } + + + /* Now do a first alignment of the input sequences (prMSeq) adding + * all collected background HMMs + * + */ + /* Determine progressive alignment order + */ + if (TRUE == prMSeq->aligned) { + Log(&rLog, LOG_INFO, "%s %s", + "Input sequences are aligned.", + "Will use Kimura distances of aligned sequences."); + prOpts->iPairDistType = PAIRDIST_SQUIDID_KIMURA; + } + +#if 0 + Log(&rLog, LOG_WARN, "Using a sequential alignment order."); + SequentialAlignmentOrder(&piOrderLR, prMSeq->nseqs); +#else + if (OK != AlignmentOrder(&piOrderLR, &pdSeqWeights, prMSeq, + prOpts->iPairDistType, + prOpts->pcDistmatInfile, prOpts->pcDistmatOutfile, + prOpts->iClusteringType, + prOpts->pcGuidetreeInfile, prOpts->pcGuidetreeOutfile, + prOpts->bUseMbed)) { + Log(&rLog, LOG_ERROR, "AlignmentOrder() failed. Cannot continue"); + return -1; + } +#endif + + /* Progressive alignment of input sequences. Order defined by + * branching of guide tree (piOrderLR). Use optional + * background HMM information (prHMMs[0..prOpts->iHMMInputFiles-1]) + * + */ + dAlnScore = HHalignWrapper(prMSeq, piOrderLR, pdSeqWeights, + 2*prMSeq->nseqs -1/* nodes */, + prHMMs, prOpts->iHMMInputFiles, -1, rHhalignPara); + dLastAlnScore = dAlnScore; + Log(&rLog, LOG_VERBOSE, + "Alignment score for first alignment = %f", dAlnScore); + + + + + /* ------------------------------------------------------------ + * + * prMSeq is aligned now. Now start iterations if requested and save the + * alignment at the very end. + * + * @note We discard the background HMM information at this point, + * because it was already used. Could consider to make this choice + * optional. FIXME + * + * ------------------------------------------------------------ */ + + + /* iteration after first alignment was computed (if not profile-profile + * alignment) + * + */ + for (iIterationCounter=0; + (iIterationCounter < prOpts->iNumIterations || prOpts->bIterationsAuto); + iIterationCounter++) { + + hmm_light rHMMLocal = {0}; + /* FIXME Keep copy of old alignment in case new one sucks? */ + + + if (iIterationCounter >= prOpts->iMaxHMMIterations + && + iIterationCounter >= prOpts->iMaxGuidetreeIterations) { + Log(&rLog, LOG_VERBOSE, "Reached maximum number of HMM and guide-tree iterations"); + break; + } + + if (! prOpts->bIterationsAuto) { + Log(&rLog, LOG_INFO, "Iteration step %d out of %d", + iIterationCounter+1, prOpts->iNumIterations); + } else { + Log(&rLog, LOG_INFO, "Iteration step %d out of ", + iIterationCounter+1); + } +#if 0 + if (rLog.iLogLevelEnabled <= LOG_VERBOSE) { + char zcIntermediate[1000] = {0}; + char *pcFormat = "fasta"; + sprintf(zcIntermediate, "clustalo-aln-iter~%d~", iIterationCounter); + if (WriteAlignment(prMSeq, zcIntermediate, MSAFILE_A2M)) { + Log(&rLog, LOG_ERROR, "Could not save alignment to %s", zcIntermediate); + return -1; + } + } +#endif + + + /* new guide-tree + * + */ + if (iIterationCounter < prOpts->iMaxGuidetreeIterations) { + /* determine progressive alignment order + * + * few things are different now when calling AlignmentOrder: + * - we have to ignore prOpts->pcDistmatInfile and pcGuidetreeInfile + * as they were used before + * - the corresponding outfiles are still valid though + */ + /* Free stuff that has already been allocated by or further + * downstream of AlignmentOrder() + */ + if (NULL != piOrderLR) + CKFREE(piOrderLR); + if (NULL != pdSeqWeights) + CKFREE(pdSeqWeights); + if (AlignmentOrder(&piOrderLR, &pdSeqWeights, prMSeq, + PAIRDIST_SQUIDID_KIMURA /* override */, NULL, prOpts->pcDistmatOutfile, + prOpts->iClusteringType, NULL, prOpts->pcGuidetreeOutfile, + prOpts->bUseMbedForIteration)) { + Log(&rLog, LOG_ERROR, "AlignmentOrder() failed. Cannot continue"); + return -1; + } + } else { + Log(&rLog, LOG_INFO, "Skipping guide-tree iteration at iteration step %d (reached maximum)", + iIterationCounter); + } + + + /* new local hmm iteration + * + */ + if (iIterationCounter < prOpts->iMaxHMMIterations) { + if (OK != +#if INDIRECT_HMM + AlnToHMM(&rHMMLocal, prMSeq) +#else + AlnToHMM2(&rHMMLocal, prMSeq->seq, prMSeq->nseqs) +#endif + ) { + Log(&rLog, LOG_ERROR, "Couldn't convert alignment to HMM. Will stop iterating now..."); + break; + } + } else { + Log(&rLog, LOG_INFO, "Skipping HMM iteration at iteration step %d (reached maximum)", + iIterationCounter); + } + + + /* align the sequences (again) + */ + dAlnScore = HHalignWrapper(prMSeq, piOrderLR, pdSeqWeights, + 2*prMSeq->nseqs -1/* nodes */, &rHMMLocal, 1, -1, rHhalignPara); + Log(&rLog, LOG_VERBOSE, + "Alignment score for alignmnent in hmm-iteration no %d = %f (last score = %f)", + iIterationCounter+1, dAlnScore, dLastAlnScore); + + + FreeHMMstruct(&rHMMLocal); + +#if 0 + /* FIXME: need a better score for automatic iteration */ + if (prOpts->bIterationsAuto) { + /* automatic iteration: break if score improvement was not + * big enough + */ + double dScoreImprovement = (dAlnScore-dLastAlnScore)/dLastAlnScore; + if (dScoreImprovement < ITERATION_SCORE_IMPROVEMENT_THRESHOLD) { + Log(&rLog, LOG_INFO, + "Stopping after %d guide-tree iterations. No further alignment score improvement achieved.", + iIterationCounter+1); + /* use previous alignment */ + FreeMSeq(&prMSeq); + Log(&rLog, LOG_FORCED_DEBUG, "FIXME: %s", "CopyMSeq breaks things in this context"); + CopyMSeq(&prMSeq, prMSeqCopy); + /* FIXME: prOpts->pcDistmatOutfile and pcGuidetreeOutfile + * might have been updated, but then discarded here? + */ + break; + } else { + Log(&rLog, LOG_INFO, + "Got a %d%% better score in iteration step %d", + (int)dScoreImprovement*100, iIterationCounter+1); + FreeMSeq(&prMSeqCopy); + } + } + dLastAlnScore = dAlnScore; +#endif + + } + /* end of iterations */ + + + + /* Last step: if a profile was also provided then align now-aligned mseq + * with this profile + * + * Don't use the backgrounds HMMs anymore and don't iterate. + * (which was done before). + * + */ + if (NULL != prMSeqProfile) { + if (AlignProfiles(prMSeq, prMSeqProfile, rHhalignPara)) { + Log(&rLog, LOG_ERROR, "An error occured during the profile/profile alignment"); + return -1; + } + } + + + if (NULL != piOrderLR) { + CKFREE(piOrderLR); + } + if (NULL != pdSeqWeights) { + CKFREE(pdSeqWeights); + } + if (0 < prOpts->iHMMInputFiles) { + for (i=0; iiHMMInputFiles; i++) { + FreeHMMstruct(&prHMMs[i]); + } + CKFREE(prHMMs); + } + + return 0; +} +/* end of Align() */ + + + + +/** + * @brief Align two profiles, ie two sets of prealigned sequences. Already + * aligned columns won't be changed. + * + * @param[out] prMSeqProfile1 + * First profile/aligned set of sequences. Merged alignment will be found in + * here. + * @param[in] prMSeqProfile2 + * First profile/aligned set of sequences + * + * @return 0 on success, -1 on failure + * + */ +int +AlignProfiles(mseq_t *prMSeqProfile1, + mseq_t *prMSeqProfile2, hhalign_para rHhalignPara) { + + double dAlnScore; + + /* number of seqs in first half of joined profile */ + int iProfProfSeparator = prMSeqProfile1->nseqs; + + assert(TRUE == prMSeqProfile1->aligned); + assert(TRUE == prMSeqProfile2->aligned); + + Log(&rLog, LOG_INFO, "Performing profile/profile alignment"); + + /* Combine the available mseqs into prMSeq + * which will be aligned afterwards. + */ + JoinMSeqs(&prMSeqProfile1, prMSeqProfile2); + + + /* set alignment flag explicitly to FALSE */ + prMSeqProfile1->aligned = FALSE; + + dAlnScore = HHalignWrapper(prMSeqProfile1, + NULL, /* no order */ + NULL, /* no weights */ + 3, /* nodes: root+2profiles */ + NULL, 0 /* no bg-hmms */, + iProfProfSeparator, rHhalignPara); + + Log(&rLog, LOG_VERBOSE, "Alignment score is = %f", dAlnScore); + + return 0; +} +/* end of AlignProfiles() */ + + diff --git a/binaries/src/clustalo/src/clustal-omega.h b/binaries/src/clustalo/src/clustal-omega.h new file mode 100644 index 0000000..4f38e6f --- /dev/null +++ b/binaries/src/clustalo/src/clustal-omega.h @@ -0,0 +1,167 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: clustal-omega.h 212 2011-03-10 15:09:46Z andreas $ + */ + +#ifndef CLUSTALO_H +#define CLUSTALO_H + + + +#ifdef HAVE_OPENMP +#include +#endif + +#include "clustal-omega-config.h" + +/* the following needs to be kept in sync with library_include_HEADERS of all + * subdir Makefile.am's + */ + +/* hhalign */ +#include "hhalign/general.h" +#include "hhalign/hhfunc.h" + + +/* clustal */ +#include "clustal/log.h" +#include "clustal/util.h" +#include "clustal/symmatrix.h" +#include "clustal/tree.h" +#include "clustal/seq.h" +#include "clustal/mbed.h" +#include "clustal/weights.h" +#include "clustal/pair_dist.h" +#include "clustal/hhalign_wrapper.h" + + + +#define CLUSTERING_UNKNOWN 0 +#define CLUSTERING_UPGMA 1 + +/* weights will be computed if 1. but are not really used for now and they + * might slow things down. also, mbed's screws up branch lengths which will + * have a negative effect on weights +*/ +#define USE_WEIGHTS 0 + +extern int iNumberOfThreads; + + +/** user/commandline options + * + * changes here will have to be reflected in ParseCommandLine() + * and during setup of the default opts + * + */ +typedef struct { + /* auto: Clustal (know what) is good for you + */ + bool bAutoOptions; + + /* Distance matrix + */ + /** distance matrix input file */ + char *pcDistmatInfile; + /** distance matrix output file */ + char *pcDistmatOutfile; + + /* Clustering / guide-tree + */ + /** clustering type (from cmdline arg) */ + int iClusteringType; + /** pairwise distance method */ + int iPairDistType; + /** use mbed-like clustering */ + bool bUseMbed; + /** use mbed-like clustering also during iteration */ + bool bUseMbedForIteration; + /** guidetree output file */ + char *pcGuidetreeOutfile; + /** guidetree input file */ + char *pcGuidetreeInfile; + + /* HMMs + */ + /** HMM input files. index range: 0..iHMMInputFiles */ + char **ppcHMMInput; + /** number of provided HMM input files. not really a user + option but need for ppcHMMInput */ + int iHMMInputFiles; + + /* Iteration + */ + /** number of iterations */ + int iNumIterations; + /** determine number of iterations automatically */ + bool bIterationsAuto; + /** maximum number of hmm iterations */ + int iMaxHMMIterations; + /** max number of guidetree iterations */ + int iMaxGuidetreeIterations; + + /** max MAC RAM (maximum amount of RAM set aside for MAC algorithm) */ + int iMacRam; /* FS, r240 -> */ + + /* changes here will have to be reflected in FreeAlnOpts(), + * SetDefaultAlnOpts(), AlnOptsLogicCheck() etc + */ +} opts_t; + + + + + +extern void +PrintLongVersion(char *pcStr, int iSize); + +extern void +SetDefaultAlnOpts(opts_t *opts); + +extern void +FreeAlnOpts(opts_t *aln_opts); + +extern void +AlnOptsLogicCheck(opts_t *opts); + +extern void +PrintAlnOpts(FILE *prFile, opts_t *opts); + +extern void +InitClustalOmega(int iNumThreadsToUse); + +extern void +SequentialAlignmentOrder(int **piOrderLR_p, int iNumSeq); + +extern int +AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, + int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, + int iClusteringType, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, + bool bUseMBed); + +extern int +Align(mseq_t *prMSeq, + mseq_t *prMSeqProfile, + opts_t *prOpts, + hhalign_para rHhalignPara); + +extern int +AlignProfiles(mseq_t *prMSeqProfile1, + mseq_t *prMSeqProfile2, hhalign_para rHhalignPara); + +#endif diff --git a/binaries/src/clustalo/src/clustal/Makefile.am b/binaries/src/clustalo/src/clustal/Makefile.am new file mode 100644 index 0000000..b348384 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/Makefile.am @@ -0,0 +1,38 @@ +AM_CFLAGS = @OPENMP_CFLAGS@ @AM_CFLAGS@ +AM_LDFLAGS = @AM_LDFLAGS@ + +noinst_LTLIBRARIES = libclustal.la + +libclustal_la_SOURCES = \ + hhalign_wrapper.c hhalign_wrapper.h \ + ktuple_pair.c ktuple_pair.h \ + list.c list.h \ + log.c log.h \ + muscle_upgma.c muscle_upgma.h \ + muscle_tree.c muscle_tree.h \ + mbed.c mbed.h \ + pair_dist.h pair_dist.c \ + progress.c progress.h \ + queue.h \ + seq.c seq.h \ + symmatrix.c symmatrix.h \ + tree.c tree.h \ + util.c util.h \ + weights.c weights.h + +library_includedir=$(includedir)/clustalo/clustal + +library_include_HEADERS = \ + hhalign_wrapper.h \ + ktuple_pair.h \ + log.h \ + mbed.h \ + muscle_tree.h \ + pair_dist.h \ + progress.h \ + seq.h \ + symmatrix.h \ + tree.h \ + util.h \ + weights.h + diff --git a/binaries/src/clustalo/src/clustal/Makefile.in b/binaries/src/clustalo/src/clustal/Makefile.in new file mode 100644 index 0000000..5077ca7 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/Makefile.in @@ -0,0 +1,527 @@ +# Makefile.in generated by automake 1.10.2 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, +# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +# This Makefile.in is free software; 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tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: hhalign_wrapper.c 256 2011-06-23 13:57:28Z fabian $ + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include + +#include "seq.h" +#include "tree.h" +#include "progress.h" +#include "hhalign/general.h" +#include "hhalign/hhfunc.h" +#include "hhalign/hhalign.h" + +/* up to this level (from leaf) will background HMM info be applied */ +#define APPLY_BG_HMM_UP_TO_TREE_DEPTH 10 + +#define TIMING 0 + +#define TRACE 0 + +/** + * @brief get rid of unknown residues + * + * @note HHalignWrapper can be entered in 2 different ways: (i) all + * sequences are un-aligned (ii) there are 2 (aligned) profiles. in + * the un-aligned case (i) the sequences come straight from Squid, + * that is, they have been sanitised, all non-alphabetic residues + * have been rendered as X's. In profile mode (ii) one profile may + * have been produced internally. In that case residues may have + * been translated back into their 'native' form, that is, they may + * contain un-sanitised residues. These will cause trouble during + * alignment + * FS, r213->214 + */ +void +SanitiseUnknown(mseq_t *mseq) +{ + + int iS; /* iterator for sequence */ + int iR; /* iterator for residue */ + int iLen; /* length of sequence */ + char *pcRes = NULL; + + + for (iS = 0; iS < mseq->nseqs; iS++){ + + for (pcRes = mseq->seq[iS]; '\0' != *pcRes; pcRes++){ + + if (isgap(*pcRes)){ + continue; + } + + if (mseq->seqtype==SEQTYPE_PROTEIN) { + if (NULL == strchr(AMINO_ALPHABET, toupper(*pcRes))) { + *pcRes = AMINOACID_ANY; + } + } else if (mseq->seqtype==SEQTYPE_DNA) { + if (NULL == strchr(DNA_ALPHABET, toupper(*pcRes))) { + *pcRes = NUCLEOTIDE_ANY; + } + } else if (mseq->seqtype==SEQTYPE_RNA) { + if (NULL == strchr(RNA_ALPHABET, toupper(*pcRes))) { + *pcRes = NUCLEOTIDE_ANY; + } + } + + } /* !EO String */ + + } /* 0 <= iS < mseq->nseqs */ + + return; + +} /*** end: SanitiseUnknown() ***/ + +/** + * @brief translate unknown residues back to ambiguity codes; + * hhalign translates ambiguity codes (B,Z) into unknown residue (X). + * we still have the original (un-aligned) residue information, + * by iterating along the original and aligned sequences we can + * reconstruct where codes have been changed and restore them + * to their original value + * + * @param[in,out] mseq + * sequence/profile data, mseq->seq [in,out] is changed to conform + * with mseq->orig_seq [in] + * + */ +void +TranslateUnknown2Ambiguity(mseq_t *mseq) +{ + + int iS; /* iterator for sequence */ + int iR, iRo; /* iterator for residue (original) */ + int iChange, iCase, iAmbi; /* counts how many replacements */ + static int siOffset = 'a' - 'A'; + + for (iS = 0; iS < mseq->nseqs; iS++){ + + iR = iRo = 0; + iChange = iCase = iAmbi = 0; + + while(('\0' != mseq->seq[iS][iR]) && + ('\0' != mseq->orig_seq[iS][iRo])) { + + /* skip gaps in aligned sequences */ + while(isgap(mseq->seq[iS][iR])) { + iR++; + } /* was gap in unaligned seq + * this should probably not happen */ + while(isgap(mseq->orig_seq[iS][iRo])) { + iRo++; + } /* was gap in aligned seq */ + + /* check if we reached the end of the sequence after + * skipping the gaps */ + if ( ('\0' == mseq->seq[iS][iR]) || + ('\0' == mseq->orig_seq[iS][iRo]) ){ + break; + } + + + if (mseq->seq[iS][iR] != mseq->orig_seq[iS][iRo]){ + /* FIXME: count replacements, discard case changes */ + iChange++; + if ( (mseq->seq[iS][iR] == mseq->orig_seq[iS][iRo]+siOffset) || + (mseq->seq[iS][iR] == mseq->orig_seq[iS][iRo]-siOffset) ){ + iCase++; + } + else { + iAmbi++; + } +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "seq=%d, pos=(%d:%d), (%c:%c)", + iS, iR, iRo, + mseq->seq[iS][iR], mseq->orig_seq[iS][iRo]); +#endif + mseq->seq[iS][iR] = mseq->orig_seq[iS][iRo]; + } + + iR++; + iRo++; + + } /* !EO seq */ + + Log(&rLog, LOG_DEBUG, + "in seq %d re-translated %d residue codes (%d true, %d case)", + iS, iChange, iAmbi, iCase); + + /* assert that both sequences (un/aligned) have terminated */ + /* skip gaps in aligned sequences */ + while(isgap(mseq->seq[iS][iR])) { + iR++; + } /* was gap in unaligned seq + * this should probably not happen */ + while(isgap(mseq->orig_seq[iS][iRo])) { + iRo++; + } /* was gap in aligned seq */ + + + if ( ('\0' != mseq->seq[iS][iR]) || + ('\0' != mseq->orig_seq[iS][iRo]) ){ + + Log(&rLog, LOG_FATAL, "inconsistency in un/aligned sequence %d\n>%s\n>%s\n", + iS, mseq->seq[iS], mseq->orig_seq[iS]); + } + + } /* 0 <= iS < mseq->nseqs */ + +} /*** end: TranslateUnknown2Ambiguity() ***/ + + +/** + * @brief re-attach leading and trailing gaps to alignment + * + * @param[in,out] prMSeq, + * alignment structure (at this stage there should be no un-aligned sequences) + * @param[in] iProfProfSeparator + * gives sizes of input profiles, -1 if no input-profiles but un-aligned sequences + * + * @note leading and tailing profile columns + * that only contain gaps have no effect on the alignment + * and are removed during the alignment. if they are + * encountered a warning message is printed to screen. + * some users like to preserve these gap columns + * FS, r213->214 + */ +void +ReAttachLeadingGaps(mseq_t *prMSeq, int iProfProfSeparator) +{ + + int i, j; + int iSize1 = 0; /* #seqs in 1st profile */ + int iSize2 = 0; /* #seqs in 2nd profile */ + int iPPS = iProfProfSeparator; + int iLeadO1 = 0; /* leading gaps in 1st seq of 1st profile */ + int iLeadO2 = 0; /* leading gaps in 1st seq of 2nd profile */ + int iLeadA1 = 0; /* leading gaps in 1st seq of final alignment */ + int iLeadA2 = 0; /* leading gaps in PPS seq of final alignment */ + int iTrailO1 = 0; /* trailing gaps in 1st seq of 1st profile */ + int iTrailO2 = 0; /* trailing gaps in 1st seq of 2nd profile */ + int iTrailA1 = 0; /* trailing gaps in 1st seq of final alignment */ + int iTrailA2 = 0; /* trailing gaps in PPS seq of final alignment */ + int iLen = 0; /* length of final alignment */ + int iLen1 = 0; /* length of 1st profile */ + int iLen2 = 0; /* length of 2nd profile */ + int iCutHead = 0; /* make up truncation at head */ + int iCutTail = 0; /* make up truncation at tail */ + char *pcIter = NULL; + + if (-1 == iProfProfSeparator){ + return; + } + else { + assert(prMSeq->aligned); + assert(prMSeq->nseqs > iProfProfSeparator); + } + iSize1 = iProfProfSeparator; + iSize2 = prMSeq->nseqs - iProfProfSeparator; + iLen = strlen(prMSeq->seq[0]); + iLen1 = strlen(prMSeq->orig_seq[0]); + iLen2 = strlen(prMSeq->orig_seq[iPPS]); + + /* count leading/trailing gaps in 1st sequence of 1st/2nd profile and final alignmant */ + for (iLeadO1 = 0, pcIter = prMSeq->orig_seq[0]; isgap(*pcIter); pcIter++, iLeadO1++); + for (iLeadO2 = 0, pcIter = prMSeq->orig_seq[iPPS]; isgap(*pcIter); pcIter++, iLeadO2++); + for (iLeadA1 = 0, pcIter = prMSeq->seq[0]; isgap(*pcIter); pcIter++, iLeadA1++); + for (iLeadA2 = 0, pcIter = prMSeq->seq[iPPS]; isgap(*pcIter); pcIter++, iLeadA2++); + for (iTrailO1 = 0, pcIter = &prMSeq->orig_seq[0][iLen1-1]; isgap(*pcIter); pcIter--, iTrailO1++); + for (iTrailO2 = 0, pcIter = &prMSeq->orig_seq[iPPS][iLen2-1]; isgap(*pcIter); pcIter--, iTrailO2++); + for (iTrailA1 = 0, pcIter = &prMSeq->seq[0][iLen-1]; isgap(*pcIter); pcIter--, iTrailA1++); + for (iTrailA2 = 0, pcIter = &prMSeq->seq[iPPS][iLen-1]; isgap(*pcIter); pcIter--, iTrailA2++); + + + /* turn leading/trailing gaps into truncation */ + iLeadO1 = iLeadO1 > iLeadA1 ? iLeadO1-iLeadA1 : 0; + iLeadO2 = iLeadO2 > iLeadA2 ? iLeadO2-iLeadA2 : 0; + iTrailO1 = iTrailO1 > iTrailA1 ? iTrailO1-iTrailA1 : 0; + iTrailO2 = iTrailO2 > iTrailA2 ? iTrailO2-iTrailA2 : 0; + iCutHead = iLeadO1 > iLeadO2 ? iLeadO1 : iLeadO2; + iCutTail = iTrailO1 > iTrailO2 ? iTrailO1 : iTrailO2; + + /* re-allocate and shift memory */ + if ( (iCutHead > 0) || (iCutTail > 0) ){ /* skip if no re-attachment, FS, r244 -> r245 */ + for (i = 0; i < prMSeq->nseqs; i++){ + + CKREALLOC(prMSeq->seq[i], iLen+iCutHead+iCutTail+2); + if (iCutHead > 0){ /* skip if no re-attachment, FS, r244 -> r245 */ + memmove(prMSeq->seq[i]+iCutHead, prMSeq->seq[i], iLen); + } + for (j = 0; j < iCutHead; j++){ + prMSeq->seq[i][j] = '-'; + } + for (j = iLen+iCutHead; j < iLen+iCutHead+iCutTail; j++){ + prMSeq->seq[i][j] = '-'; + } + prMSeq->seq[i][j] = '\0'; + } + } /* (iCutHead > 0) || (iCutTail > 0) */ + +} /*** end: ReAttachLeadingGaps() ***/ + +/** + * @brief reallocate enough memory for alignment and + * attach sequence pointers to profiles + * + * @param[in,out] mseq + * sequence/profile data, increase memory for sequences in profiles + * @param[out] ppcProfile1 + * pointers to sequencese in 1st profile + * @param[out] ppcProfile2 + * pointers to sequencese in 2nd profile + * @param[out] pdWeightsL + * weights (normalised to 1.0) for sequences in left profile + * @param[out] pdWeightsR + * weights (normalised to 1.0) for sequences in right profile + * @param[in] pdSeqWeights + * weights for _all_ sequences in alignment + * @param[in] iLeafCountL + * number of sequences in 1st profile + * @param[in] piLeafListL + * array of integer IDs of sequences in 1st profile + * @param[in] iLeafCountR + * number of sequences in 2nd profile + * @param[in] piLeafListR + * array of integer IDs of sequences in 2nd profile + * + */ +void +PrepareAlignment(mseq_t *mseq, char **ppcProfile1, char **ppcProfile2, + double *pdWeightsL, double *pdWeightsR, double *pdSeqWeights, + int iLeafCountL, int *piLeafListL, + int iLeafCountR, int *piLeafListR) +{ + + int iLenL = 0; /* length of 1st profile */ + int iLenR = 0; /* length of 2nd profile */ + int iMaxLen = 0; /* maximum possible length of alignment */ + int i; /* aux */ + double dWeight = 0.00; + double dWeightInv = 0.00; + + assert(NULL!=mseq); + assert(NULL!=ppcProfile1); + assert(NULL!=ppcProfile2); + assert(NULL!=piLeafListL); + assert(NULL!=piLeafListR); + + /* get length of profiles, + * in a profile all sequences should have same length so only look at 1st + */ + iLenL = strlen(mseq->seq[piLeafListL[0]]); + iLenR = strlen(mseq->seq[piLeafListR[0]]); + iMaxLen = iLenL + iLenR + 1; + + /* reallocate enough memory for sequences in alignment (for adding + * gaps) + */ + for (i = 0; i < iLeafCountL; i++){ + mseq->seq[piLeafListL[i]] = + CKREALLOC(mseq->seq[piLeafListL[i]], iMaxLen); + } + for (i = 0; i < iLeafCountR; i++){ + mseq->seq[piLeafListR[i]] = + CKREALLOC(mseq->seq[piLeafListR[i]], iMaxLen); + } + + /* attach sequences to profiles + */ + for (i = 0; i < iLeafCountL; i++){ + ppcProfile1[i] = mseq->seq[piLeafListL[i]]; + } + ppcProfile1[i] = NULL; + + for (i = 0; i < iLeafCountR; i++){ + ppcProfile2[i] = mseq->seq[piLeafListR[i]]; + } + ppcProfile2[i] = NULL; + + + /* remove terminal 'X' for single sequences: + * it is a quirk of hhalign() to delete 2 individual sequences + * if 2 terminal X's meet during alignment, + * just replace (one of) them. + * this can be undone at the end. + * profiles -consisting of more than 1 sequence- + * appear to be all-right. + * there seems to be no problem with B's and Z's + */ + if ( (1 == iLeafCountL) && (1 == iLeafCountR) ){ + + if ( ('X' == ppcProfile1[0][0]) && ('X' == ppcProfile2[0][0]) ){ +#define NOTX 'N' + ppcProfile1[0][0] = NOTX; /* FIXME: arbitrary assignment */ + ppcProfile2[0][0] = NOTX; /* FIXME: arbitrary assignment */ + } + if ( ('X' == ppcProfile1[0][iLenL-1]) && ('X' == ppcProfile2[0][iLenR-1]) ){ + ppcProfile1[0][iLenL-1] = NOTX; /* FIXME: arbitrary assignment */ + ppcProfile2[0][iLenR-1] = NOTX; /* FIXME: arbitrary assignment */ + } + } + + /* obtain sequence weights + */ + if (NULL != pdSeqWeights){ + + dWeight = 0.00; + for (i = 0; i < iLeafCountL; i++){ + register double dAux = pdSeqWeights[piLeafListL[i]]; +#ifndef NDEBUG + if (dAux <= 0.00){ + Log(&rLog, LOG_DEBUG, "seq-weight %d = %f", piLeafListL[i], dAux); + } +#endif + pdWeightsL[i] = dAux; + dWeight += dAux; + } /* 0 <= i < iLeafCountL */ + dWeightInv = 1.00 / dWeight; + for (i = 0; i < iLeafCountL; i++){ + pdWeightsL[i] *= dWeightInv; + } + + dWeight = 0.00; + for (i = 0; i < iLeafCountR; i++){ + register double dAux = pdSeqWeights[piLeafListR[i]]; +#ifndef NDEBUG + if (dAux <= 0.00){ + Log(&rLog, LOG_DEBUG, "seq-weight %d = %f", piLeafListR[i], dAux); + } +#endif + pdWeightsR[i] = dAux; + dWeight += dAux; + } /* 0 <= i < iLeafCountL */ + dWeightInv = 1.00 / dWeight; + for (i = 0; i < iLeafCountR; i++){ + pdWeightsR[i] *= dWeightInv; + } + } /* (NULL != pdSeqWeights) */ + else { + pdWeightsL[0] = pdWeightsR[0] = -1.00; + } + +#if TRACE + for (i = 0; i < iLeafCountL; i++){ + Log(&rLog, LOG_FORCED_DEBUG, "ppcProfile1[%d/%d] pointing to mseq %d = %s", + i, iLeafCountR, piLeafListL[i], ppcProfile1[i]); + } + for (i = 0; i < iLeafCountR; i++){ + Log(&rLog, LOG_FORCED_DEBUG, "ppcProfile2[%d/%d] pointing to mseq %d = %s", + i, iLeafCountR, piLeafListR[i], ppcProfile2[i]); + } +#endif + + return; + +} /*** end: PrepareAlignment() ***/ + + +/** + * @brief wrapper for hhalign. This is a frontend function to + * the ported hhalign code. + * + * @param[in,out] prMSeq + * holds the unaligned sequences [in] and the final alignment [out] + * @param[in] piOrderLR + * holds order in which sequences/profiles are to be aligned, + * even elements specify left nodes, odd elements right nodes, + * if even and odd are same then it is a leaf + * @param[in] pdSeqWeights + * Weight per sequence. No weights used if NULL + * @param[in] iNodeCount + * number of nodes in tree, piOrderLR has 2*iNodeCount elements + * @param[in] prHMMList + * List of background HMMs (transition/emission probabilities) + * @param[in] iHMMCount + * Number of input background HMMs + * @param[in] iProfProfSeparator + * Gives the number of sequences in the first profile, if in + * profile/profile alignment mode (iNodeCount==3). That assumes mseqs + * holds the sequences of profile 1 and profile 2. + * @param[in] rHhalignPara + * various parameters read from commandline + * + * @return score of the alignment FIXME what is this? + * + * @note complex function. could use some simplification, more and + * documentation and a struct'uring of piOrderLR + * + * @note HHalignWrapper can be entered in 2 different ways: + * (i) all sequences are un-aligned (ii) there are 2 (aligned) profiles. + * in the un-aligned case (i) the sequences come straight from Squid, + * that is, they have been sanitised, all non-alphabetic residues + * have been rendered as X's. In profile mode (ii) one profile may + * have been produced internally. In that case residues may have + * been translated back into their 'native' form, that is, they + * may contain un-sanitised residues. These will cause trouble + * during alignment + * + * @note: introduced argument hhalign_para rHhalignPara; FS, r240 -> r241 + * @note: if hhalign() fails then try with Viterbi by setting MAC-RAM=0; FS, r241 -> r243 + */ + +double +HHalignWrapper(mseq_t *prMSeq, int *piOrderLR, + double *pdSeqWeights, int iNodeCount, + hmm_light *prHMMList, int iHMMCount, + int iProfProfSeparator, hhalign_para rHhalignPara) +{ + int iN; /* node iterator */ + int *piLeafCount = NULL; /* number of leaves beneath a certain node */ + int **ppiLeafList = NULL; /* list of leaves beneath a certain node */ + char **ppcProfile1 = NULL; /* pointer to sequences in profile */ + char **ppcProfile2 = NULL; /* pointer to sequences in profile */ + char *pcReprsnt1 = NULL; /* representative of HMM aligned to left */ + char *pcReprsnt2 = NULL; /* representative of HMM aligned to right */ + char **ppcReprsnt1 = &pcReprsnt1; /* representative of HMM aligned to L */ + char **ppcReprsnt2 = &pcReprsnt2; /* representative of HMM aligned to R */ + char *pcConsens1 = NULL; /* copy of left sequence */ + char *pcConsens2 = NULL; /* copy of right sequence */ + char **ppcCopy1 = /*&pcCopy1*/NULL; /* copy of left sequences */ + char **ppcCopy2 = /*&pcCopy2*/NULL; /* copy of right sequences */ + double *pdScores = NULL; /* alignment scores (seq/HMM) */ + double dScore = 0.0; /* alignment score (seq/HMM) */ + int iAux_FS = 0; + char zcAux[10000] = {0}; + char zcError[10000] = {0}; + int i; /* aux */ + progress_t *prProgress; + int iAlnLen; /* alignment length */ + double *pdWeightsL = NULL; /* sequence weights of left profile */ + double *pdWeightsR = NULL; /* sequence weights of right profile */ + int iMergeNodeCounter = 0; + hmm_light *prHMM = NULL; + bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE; +#if TIMING + char zcStopwatchMsg[1024]; + Stopwatch_t *stopwatch = StopwatchCreate(); + StopwatchZero(stopwatch); + StopwatchStart(stopwatch); +#endif + + + if (NULL != prHMMList) { + if (iHMMCount>1) { + Log(&rLog, LOG_WARN, "FIXME: Using only first of %u HMMs (needs implementation)", iHMMCount); + } + prHMM = &(prHMMList[0]); + } else { + /* FIXME: prHMM not allowed to be NULL and therefore pseudo allocated here */ + prHMM = (hmm_light *) CKCALLOC(1, sizeof(hmm_light)); + } + + assert(NULL!=prMSeq); + + if (NULL==piOrderLR) { + assert(3==iNodeCount); + } + SanitiseUnknown(prMSeq); + + /* hhalign was not made for DNA/RNA. So warn if sequences are not + * protein + */ + if (SEQTYPE_PROTEIN != prMSeq->seqtype) { + Log(&rLog, LOG_WARN, "Sequence type is %s. HHalign has only been tested on protein.", + SeqTypeToStr(prMSeq->seqtype)); + } + + /* hhalign produces funny results if sequences contain gaps, so + * dealign. Only way to use alignment info is to use it as a + * background HMM + */ + if (TRUE == prMSeq->aligned) { + Log(&rLog, LOG_DEBUG, "Dealigning aligned sequences (inside %s)", __FUNCTION__); + DealignMSeq(prMSeq); + } + +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "iNodeCount = %d", iNodeCount); +#endif + + + /* allocate top-level memory for leaf tracking arrays and profiles, + * and sequence weights*/ + piLeafCount = CKCALLOC(iNodeCount, sizeof(int)); + ppiLeafList = CKCALLOC(iNodeCount, sizeof(int *)); + ppcProfile1 = CKCALLOC(prMSeq->nseqs*2-1, sizeof(char *)); + ppcProfile2 = CKCALLOC(prMSeq->nseqs*2-1, sizeof(char *)); + pdScores = CKCALLOC(iNodeCount, sizeof(double)); + pdWeightsL = CKCALLOC(iNodeCount, sizeof(double)); + pdWeightsR = CKCALLOC(iNodeCount, sizeof(double)); + + NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO), + "Progressive alignment progress", bPrintCR); + + + /* Profile-profile alignment? Then setup piLeafCount and + * piLeafList here. FIXME this is just an awful haaaack + */ + if (iNodeCount==3 && NULL==piOrderLR) { + int iSizeProf1 = iProfProfSeparator; + int iSizeProf2 = prMSeq->nseqs - iProfProfSeparator; + + piLeafCount[0] = iSizeProf1; + ppiLeafList[0] = (int *)CKMALLOC(iSizeProf1 * sizeof(int)); + for (i=0;isqinfo[riLeaf].name); + } else { + Log(&rLog, LOG_FORCED_DEBUG, "node %d is a leaf with entry %d (seq %s) and weight %f", + iN, riLeaf, prMSeq->sqinfo[riLeaf].name, pdSeqWeights[riLeaf]); + } +#endif + /* left/right entry same, this is a leaf */ + piLeafCount[piOrderLR[riAux+PRNT_NODE]] = 1; /* number of leaves is '1' */ + ppiLeafList[piOrderLR[riAux+PRNT_NODE]] = (int *)CKMALLOC(1 * sizeof(int)); + ppiLeafList[piOrderLR[riAux+PRNT_NODE]][0] = riLeaf; + + } /* was a leaf */ + else { + int iL, iR, iP; /* ID of left/right nodes, parent */ + int i, j; /* aux */ + + Log(&rLog, LOG_DEBUG, + "merge profiles at node %d", iN, piOrderLR[riAux]); + + /* iNodeCount - prMSeq->nseqs = total # of merge-nodes + * unless in profile/profile alignment mode + */ + if (1 == iNodeCount) { + ProgressLog(prProgress, ++iMergeNodeCounter, + 1, FALSE); + } else { + ProgressLog(prProgress, ++iMergeNodeCounter, + iNodeCount - prMSeq->nseqs, FALSE); + } + + /* left/right entry are not same, this is a merge node */ + iL = piOrderLR[riAux+LEFT_NODE]; + iR = piOrderLR[riAux+RGHT_NODE]; + iP = piOrderLR[riAux+PRNT_NODE]; + piLeafCount[iP] = piLeafCount[iL] + piLeafCount[iR]; + ppiLeafList[iP] = (int *)CKMALLOC(piLeafCount[iP] * sizeof(int)); + + for (i = j = 0; i < piLeafCount[iL]; i++, j++){ + ppiLeafList[iP][j] = ppiLeafList[iL][i]; + } + for (i = 0; i < piLeafCount[iR]; i++, j++){ + ppiLeafList[iP][j] = ppiLeafList[iR][i]; + } + + /* prepare simulation arena: + * - make sure enough memory in sequences + * - attach sequence pointers to profiles + */ + /* idea: switch template and query according to nseq? */ + + PrepareAlignment(prMSeq, ppcProfile1, ppcProfile2, + pdWeightsL, pdWeightsR, pdSeqWeights, + piLeafCount[iL], ppiLeafList[iL], + piLeafCount[iR], ppiLeafList[iR]); + if (rLog.iLogLevelEnabled <= LOG_DEBUG){ + int i; + FILE *fp = LogGetFP(&rLog, LOG_DEBUG); + Log(&rLog, LOG_DEBUG, "merging profiles %d & %d", iL, iR); + for (i = 0; i < piLeafCount[iL]; i++){ + fprintf(fp, "L/#=%3d (ID=%3d, w=%f): %s\n", + i, ppiLeafList[iL][i], pdWeightsL[i], ppcProfile1[i]); + } + for (i = 0; i < piLeafCount[iR]; i++){ + fprintf(fp, "R/#=%3d (ID=%3d, w=%f): %s\n", + i, ppiLeafList[iR][i], pdWeightsR[i], ppcProfile2[i]); + } + } + + + + /* align individual sequences to HMM; + * - use representative sequence to get gapping + * - create copies of both, individual/representative sequences + * as we don't want to introduce gaps into original + * + * FIXME: representative sequence is crutch, should use + * full HMM but that does not seem to work at all + * -- try harder! Fail better! + */ + if ( (piLeafCount[iL] <= APPLY_BG_HMM_UP_TO_TREE_DEPTH) && (0 != prHMM->L) ){ + int i, j; + pcReprsnt1 = CKCALLOC(prHMM->L+strlen(ppcProfile1[0])+1, sizeof(char)); + for (i = 0; i < prHMM->L; i++){ + pcReprsnt1[i] = prHMM->seq[prHMM->ncons][i+1]; + } + ppcCopy1 = CKCALLOC(piLeafCount[iL], sizeof(char *)); + for (j = 0; j < piLeafCount[iL]; j++){ + ppcCopy1[j] = CKCALLOC(prHMM->L+strlen(ppcProfile1[0])+1, sizeof(char)); + for (i = 0; i < (int) strlen(ppcProfile1[0]); i++){ + ppcCopy1[j][i] = ppcProfile1[j][i]; + } + } + + { + /* the size of the elements in the forward/backward matrices + depends very much on the lengths of the profiles _and_ + in which position (1st/2nd) the longer/shorter profile/HMM is. + the matrix elements can easily exceed the size of a (long?) double + if the longer profile/HMM is associated with the query (q) and the + shorter with the target (t). + FIXME: however, pseudo-count adding may also depend on position, + this is only really tested for the HMM being in the 1st position (q) + MUST TEST THIS MORE THOROUGHLY + + this switch appears to be most easily (although unelegantly) + effected here. Don't want to do it (upstairs) in PrepareAlignment() + because it might jumble up the nodes. Don't want to do it in hhalign() + either because ppcProfile1/2 and q/t may be used independently. + FS, r236 -> r237 + */ + int iLenA = strlen(ppcCopy1[0]); + int iLenH = prHMM->L; + int iHHret = 0; + + if (iLenH < iLenA){ + iHHret = hhalign(ppcReprsnt1, 0/* only one representative seq*/, NULL, + ppcCopy1, piLeafCount[iL], pdWeightsL, + &dScore, prHMM, + NULL, NULL, NULL, NULL, + rHhalignPara, + iAux_FS++, /* DEBUG ARGUMENT */ + zcAux, zcError); + } + else { + iHHret = hhalign(ppcCopy1, piLeafCount[iL], pdWeightsL, + ppcReprsnt1, 0/* only one representative seq*/, NULL, + &dScore, prHMM, + NULL, NULL, NULL, NULL, + rHhalignPara, + iAux_FS++, /* DEBUG ARGUMENT */ + zcAux, zcError); + } + if (0 != iHHret){ /* FS, r255 -> */ + fprintf(stderr, "%s:%s:%d: (not essential) HMM pre-alignment failed, error %d, \n" + "\t#=%d (len=%d), lead-seq=%s, len(HMM)=%d\tCARRY ON REGARDLESS\n", + __FUNCTION__, __FILE__, __LINE__, iHHret, + piLeafCount[iL], (int)strlen(ppcCopy1[0]), prMSeq->sqinfo[ppiLeafList[iL][0]].name, (int)strlen(ppcReprsnt1[0])); + } + } + pdScores[ppiLeafList[iL][0]] = dScore; +#if 0 + printf("score: %f\nL: %s\nH: %s\n", + dScore, ppcCopy1[0], ppcReprsnt1[0]); +#endif + /* assemble 'consensus'; + * this is not a real consensus, it is more a gap indicator, + * for each position it consists of residues/gaps in the 1st sequences, + * or a residue (if any) of the other sequences. + * it only contains a gap if all sequences of the profile + * have a gap at this position + */ + pcConsens1 = CKCALLOC(prHMM->L+strlen(ppcProfile1[0])+1, sizeof(char)); + for (i = 0; i < prHMM->L; i++){ + for (j = 0, pcConsens1[i] = '-'; (j < piLeafCount[iL]) && ('-' == pcConsens1[i]); j++){ + pcConsens1[i] = ppcCopy1[j][i]; + } + } +#if 0 + for (j = 0; (j < piLeafCount[iL]); j++){ + printf("L%d:%s\n", j, ppcCopy1[j]); + } + printf("LC:%s\n", pcConsens1); +#endif + } /* ( (1 == piLeafCount[iL]) && (0 != prHMM->L) ) */ + + if ( (piLeafCount[iR] <= APPLY_BG_HMM_UP_TO_TREE_DEPTH) && (0 != prHMM->L) ){ + int i, j; + + pcReprsnt2 = CKCALLOC(prHMM->L+strlen(ppcProfile2[0])+1, sizeof(char)); + for (i = 0; i < prHMM->L; i++){ + pcReprsnt2[i] = prHMM->seq[prHMM->ncons][i+1]; + } + ppcCopy2 = CKCALLOC(piLeafCount[iR], sizeof(char *)); + for (j = 0; j < piLeafCount[iR]; j++){ + ppcCopy2[j] = CKCALLOC(prHMM->L+strlen(ppcProfile2[0])+1, sizeof(char)); + for (i = 0; i < (int) strlen(ppcProfile2[0]); i++){ + ppcCopy2[j][i] = ppcProfile2[j][i]; + } + } + + { + /* the size of the elements in the forward/backward matrices + depends very much on the lengths of the profiles _and_ + in which position (1st/2nd) the longer/shorter profile/HMM is. + the matrix elements can easily exceed the size of a (long?) double + if the longer profile/HMM is associated with the query (q) and the + shorter with the target (t). + FIXME: however, pseudo-count adding may also depend on position, + this is only really tested for the HMM being in the 1st position (q) + MUST TEST THIS MORE THOROUGHLY + + this switch appears to be most easily (although unelegantly) + effected here. Don't want to do it (upstairs) in PrepareAlignment() + because it might jumble up the nodes. Don't want to do it in hhalign() + either because ppcProfile1/2 and q/t may be used independently. + FS, r236 -> r237 + */ + int iLenA = strlen(ppcCopy2[0]); + int iLenH = prHMM->L; + int iHHret = 0; + + if (iLenH < iLenA){ + iHHret = hhalign(ppcReprsnt2, 0/* only one representative seq */, NULL, + ppcCopy2, piLeafCount[iR], pdWeightsR, + &dScore, prHMM, + NULL, NULL, NULL, NULL, + rHhalignPara, + iAux_FS++, /* DEBUG ARGUMENT */ + zcAux, zcError); + } + else { + iHHret = hhalign(ppcCopy2, piLeafCount[iR], pdWeightsR, + ppcReprsnt2, 0/* only one representative seq */, NULL, + &dScore, prHMM, + NULL, NULL, NULL, NULL, + rHhalignPara, + iAux_FS++, /* DEBUG ARGUMENT */ + zcAux, zcError); + } + if (0 != iHHret){ /* FS, r255 -> */ + fprintf(stderr, "%s:%s:%d: (not essential) HMM pre-alignment failed, error %d, \n" + "\t#=%d (len=%d), lead-seq=%s, len(HMM)=%d\tCARRY ON REGARDLESS\n", + __FUNCTION__, __FILE__, __LINE__, iHHret, + piLeafCount[iR], (int)strlen(ppcCopy2[0]), prMSeq->sqinfo[ppiLeafList[iR][0]].name, (int)strlen(ppcReprsnt2[0])); + } + } + pdScores[ppiLeafList[iR][0]] = dScore; +#if 0 + printf("H: %s\nR: %s\nscore: %f\n", + ppcReprsnt2[0], ppcCopy2[0], dScore); +#endif + /* assemble 'consensus'; + * this is not a real consensus, it is more a gap indicator, + * for each position it consists of residues/gaps in the 1st sequences, + * or a residue (if any) of the other sequences. + * it only contains a gap if all sequences of the profile + * have a gap at this position + */ + pcConsens2 = CKCALLOC(prHMM->L+strlen(ppcProfile2[0])+1, sizeof(char)); + for (i = 0; i < prHMM->L; i++){ + for (j = 0, pcConsens2[i] = '-'; (j < piLeafCount[iR]) && ('-' == pcConsens2[i]); j++){ + pcConsens2[i] = ppcCopy2[j][i]; + } + } +#if 0 + for (j = 0; (j < piLeafCount[iR]); j++){ + printf("R%d:%s\n", j, ppcCopy2[j]); + } + printf("RC:%s\n", pcConsens2); +#endif + } /* ( (1 == piLeafCount[iR]) && (0 != prHMM->L) ) */ + + + + /* do alignment here (before free) + */ + { + /* the size of the elements in the forward/backward matrices + depends very much on the lengths of the profiles _and_ + in which position (1st/2nd) the longer/shorter profile is. + the matrix elements can easily exceed the size of a (long?) double + if the longer profile is associated with the query (q) and the + shorter with the target (t). + this switch appears to be most easily (although unelegantly) + effected here. Don't want to do it (upstairs) in PrepareAlignment() + because it might jumble up the nodes. Don't want to do it in hhalign() + either because ppcProfile1/2 and q/t may be used independently. + FS, r228 -> 229 + */ + int iLen1 = strlen(ppcProfile1[0]); + int iLen2 = strlen(ppcProfile2[0]); + /* potential problem with empty profiles, FS, r249 -> r250 */ + if ( (0 == iLen1) || (0 == iLen2) ){ + Log(&rLog, LOG_FATAL, "strlen(prof1)=%d, strlen(prof2)=%d -- nothing to align\n", + iLen1, iLen2); + } + + + if (iLen1 < iLen2){ + int iHHret = 0; + int iOldMacRam = rHhalignPara.iMacRamMB; + iHHret = hhalign(ppcProfile1, piLeafCount[iL], pdWeightsL, + ppcProfile2, piLeafCount[iR], pdWeightsR, + &dScore, prHMM, + pcConsens1, pcReprsnt1, + pcConsens2, pcReprsnt2, + rHhalignPara, + iAux_FS++, /* DEBUG ARGUMENT */ + zcAux, zcError); + + if (RETURN_OK != iHHret){ /* FS, r241 -> */ + fprintf(stderr, + "%s:%s:%d: problem in alignment (profile sizes: %d + %d) (%s + %s), forcing Viterbi\n" + "\thh-error-code=%d (mac-ram=%d)\n", + __FUNCTION__, __FILE__, __LINE__, piLeafCount[iL], piLeafCount[iR], + prMSeq->sqinfo[ppiLeafList[iL][0]].name, prMSeq->sqinfo[ppiLeafList[iR][0]].name, + iHHret, rHhalignPara.iMacRamMB); + /* at this stage hhalign() has failed, + the only thing we can do (easily) is to re-run it in Viterbi mode, + for this set MAC-RAM=0, set it back to its original value after 2nd try. + FS, r241 -> r243 */ + if (RETURN_FROM_MAC == iHHret){ + /* Note: the default way to run hhalign() is to initially select MAC + by giving it all the memory it needs. MAC may fail due to overflow (repeats?). + alternatively, the problem may be (genuinely) too big for MAC. + in thses cases it is legitimate to switch to Viterbi. + However, selecting Viterbi from the outset is an abuse (abomination!), + should this 1st invocation of Viterbi fail, then we (FS) will overrule + the user and hammer the system with a massive memory request. + (Jos 2:19) If anyone goes outside your house into the street, + his blood will be on his own head; we will not be responsible. FS, r246 -> r247 */ + rHhalignPara.iMacRamMB = 0; + } + else { + rHhalignPara.iMacRamMB = REALLY_BIG_MEMORY_MB; + } + + iHHret = hhalign(ppcProfile1, piLeafCount[iL], pdWeightsL, + ppcProfile2, piLeafCount[iR], pdWeightsR, + &dScore, prHMM, + pcConsens1, pcReprsnt1, + pcConsens2, pcReprsnt2, + rHhalignPara, + iAux_FS++, /* DEBUG ARGUMENT */ + zcAux, zcError); + if (RETURN_OK != iHHret){ /* at this stage hhalign() has failed twice, + 1st time MAC, 2nd time Viterbi, don't know what to do else. FS, r241 -> r243 */ + fprintf(stderr, "%s:%s:%d: problem in alignment, even Viterbi did not work\n" + "\thh-error-code=%d (mac-ram=%d)\n", + __FUNCTION__, __FILE__, __LINE__, iHHret, rHhalignPara.iMacRamMB); + Log(&rLog, LOG_FATAL, "could not perform alignment -- bailing out\n"); + } + else { + fprintf(stderr, "%s:%s:%d: 2nd attempt worked", __FUNCTION__, __FILE__, __LINE__); + } + rHhalignPara.iMacRamMB = iOldMacRam; + } /* 1st invocation failed */ + + } /* 1st profile was shorter than 2nd */ + else { + int iHHret = 0; + int iOldMacRam = rHhalignPara.iMacRamMB; + iHHret = hhalign(ppcProfile2, piLeafCount[iR], pdWeightsR, + ppcProfile1, piLeafCount[iL], pdWeightsL, + &dScore, prHMM, + pcConsens2, pcReprsnt2, + pcConsens1, pcReprsnt1, + rHhalignPara, + iAux_FS++, /* DEBUG ARGUMENT */ + zcAux, zcError); + + if (RETURN_OK != iHHret){ /* FS, r241 -> r243 */ + fprintf(stderr, + "%s:%s:%d: problem in alignment (profile sizes: %d + %d) (%s + %s), forcing Viterbi\n" + "\thh-error-code=%d (mac-ram=%d)\n", + __FUNCTION__, __FILE__, __LINE__, piLeafCount[iL], piLeafCount[iR], + prMSeq->sqinfo[ppiLeafList[iL][0]].name, prMSeq->sqinfo[ppiLeafList[iR][0]].name, + iHHret, rHhalignPara.iMacRamMB); + /* at this stage hhalign() has failed, + the only thing we can do (easily) is to re-run it in Viterbi mode, + for this set MAC-RAM=0, set it back to its original value after 2nd try. + FS, r241 -> r243 */ + if (RETURN_FROM_MAC == iHHret){ + /* see above */ + rHhalignPara.iMacRamMB = 0; + } + else { + rHhalignPara.iMacRamMB = REALLY_BIG_MEMORY_MB; + } + + iHHret = hhalign(ppcProfile2, piLeafCount[iR], pdWeightsR, + ppcProfile1, piLeafCount[iL], pdWeightsL, + &dScore, prHMM, + pcConsens2, pcReprsnt2, + pcConsens1, pcReprsnt1, + rHhalignPara, + iAux_FS++, /* DEBUG ARGUMENT */ + zcAux, zcError); + if (RETURN_OK != iHHret){ /* at this stage hhalign() has failed twice, + 1st time MAC, 2nd time Viterbi, don't know what to do else. FS, r241 -> r243 */ + fprintf(stderr, "%s:%s:%d: problem in alignment, even Viterbi did not work\n" + "\thh-error-code=%d (mac-ram=%d)\n", + __FUNCTION__, __FILE__, __LINE__, iHHret, rHhalignPara.iMacRamMB); + Log(&rLog, LOG_FATAL, "could not perform alignment -- bailing out\n"); + } + else { + fprintf(stderr, "%s:%s:%d: 2nd attempt worked", __FUNCTION__, __FILE__, __LINE__); + } + rHhalignPara.iMacRamMB = iOldMacRam; + } /* 1st invocation failed */ + + } /* 2nd profile was shorter than 1st */ + + } + /* free left/right node lists, + * after alignment left/right profiles no longer needed + */ + if (NULL != ppcCopy1){ + int i; + for (i = 0; i < piLeafCount[iL]; i++){ + CKFREE(ppcCopy1[i]); + } + CKFREE(ppcCopy1); + CKFREE(pcReprsnt1); + CKFREE(pcConsens1); + } + if (NULL != ppcCopy2){ + int i; + for (i = 0; i < piLeafCount[iR]; i++){ + CKFREE(ppcCopy2[i]); + } + CKFREE(ppcCopy2); + CKFREE(pcReprsnt2); + CKFREE(pcConsens2); + } + ppiLeafList[iL] = CKFREE(ppiLeafList[iL]); + ppiLeafList[iR] = CKFREE(ppiLeafList[iR]); + piLeafCount[iL] = piLeafCount[iR] = 0; + + } /* was a merge node */ + + if (rLog.iLogLevelEnabled <= LOG_DEBUG){ + int i, j; + FILE *fp = LogGetFP(&rLog, LOG_DEBUG); + for (i = 0; i < iNodeCount; i++){ + if (0 == piLeafCount[i]){ + continue; + } + fprintf(fp, "node %3d, #leaves=%d:\t", i, piLeafCount[i]); + for (j = 0; ppiLeafList && (j < piLeafCount[i]); j++){ + fprintf(fp, "%d,", ppiLeafList[i][j]); + } + fprintf(fp, "\n"); + } + } + + + } /* 0 <= iN < iNodeCount */ + ProgressDone(prProgress); + + + /* check length and set length info + */ + iAlnLen = strlen(prMSeq->seq[0]); + for (i=0; inseqs; i++) { +#if 0 + Log(&rLog, LOG_FORCED_DEBUG, "seq no %d: name %s; len %d; %s", + i, prMSeq->sqinfo[i].name, strlen(prMSeq->seq[i]), prMSeq->seq[i]); +#endif + +#ifndef NDEBUG + assert(iAlnLen == strlen(prMSeq->seq[i])); +#endif + prMSeq->sqinfo[i].len = iAlnLen; + } + prMSeq->aligned = TRUE; + + + if (rLog.iLogLevelEnabled <= LOG_DEBUG){ + if (0 != prHMM->L){ + int i; + Log(&rLog, LOG_DEBUG, "Alignment scores with HMM:"); + for (i = 0; /*pdScores[i] > 0.0*/i < prMSeq->nseqs; i++){ + Log(&rLog, LOG_DEBUG, "%2d:\t%f\n", i, pdScores[i]); + } + } + } + + + /** translate back ambiguity residues + * hhalign translates ambiguity codes (B,Z) into unknown residues (X). + * as we still have the original input we can substitute them back + */ + TranslateUnknown2Ambiguity(prMSeq); + ReAttachLeadingGaps(prMSeq, iProfProfSeparator); + + if (NULL == prHMMList){ + CKFREE(prHMM); + } + CKFREE(ppcProfile2); + CKFREE(ppcProfile1); + CKFREE(ppiLeafList[piOrderLR[DIFF_NODE*(iNodeCount-1)+PRNT_NODE]]); + CKFREE(ppiLeafList); + CKFREE(piLeafCount); + CKFREE(pdScores); + FreeProgress(&prProgress); + CKFREE(pdWeightsL); + CKFREE(pdWeightsR); + +#if TIMING + StopwatchStop(stopwatch); + StopwatchDisplay(stdout, "Total time for HHalignWrapper():" , stopwatch); + StopwatchFree(stopwatch); +#endif + + return dScore; /* FIXME alternative: return averaged pdScores */ + +} +/*** end: HHalignWrapper() ***/ diff --git a/binaries/src/clustalo/src/clustal/hhalign_wrapper.h b/binaries/src/clustalo/src/clustal/hhalign_wrapper.h new file mode 100644 index 0000000..385a7ec --- /dev/null +++ b/binaries/src/clustalo/src/clustal/hhalign_wrapper.h @@ -0,0 +1,24 @@ +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: hhalign_wrapper.h 241 2011-05-04 14:37:17Z fabian $ + */ + + +extern double +HHalignWrapper(mseq_t *mseq, int *piOrderLR, + double *pdSeqWeights, int iNodeCount, + hmm_light *prHMMList, int iHMMCount, + int iProfProfSeparator, hhalign_para rHhalignPara); diff --git a/binaries/src/clustalo/src/clustal/ktuple_pair.c b/binaries/src/clustalo/src/clustal/ktuple_pair.c new file mode 100644 index 0000000..3ea9ca9 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/ktuple_pair.c @@ -0,0 +1,842 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: ktuple_pair.c 230 2011-04-09 15:37:50Z andreas $ + * + * + * K-Tuple code for pairwise alignment (Wilbur and Lipman, 1983; PMID + * 6572363). Most code taken from showpair.c (Clustal 1.83) + * DD: some functions now have lots of parameters as static variables + * were removed to make code OpenMP-friendly + * + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + + +#include +#include +#include +#include +#include +#include + +#ifdef HAVE_OPENMP +#include +#endif + +#include "squid/squid.h" +#include "util.h" +#include "symmatrix.h" +#include "ktuple_pair.h" +#include "log.h" +#include "progress.h" + +#define END_MARK -3 /* see interface.c in 1.83 */ +#define NUMRES 32 /* max size of comparison matrix */ + +/* see notes below */ +#undef SORT_LAST_ELEMENT_AS_WELL + +/* gap_pos1 = NUMRES-2; /@ code for gaps inserted by clustalw @/ */ +static const int GAP_POS2 = NUMRES-1; /* code for gaps already in alignment */ +static bool DNAFLAG = FALSE; + +static const char *AMINO_ACID_CODES = "ABCDEFGHIKLMNPQRSTUVWXYZ-"; +static const char *NUCLEIC_ACID_CODES = "ACGTUN-"; +/* As far as I understand the gap symbol should not be necessary here, + * because we use isgap for testing later anyway. But changing this, + * will affect max_res_code and max_nuc as well. So I leave it for now + * as it is. AW + */ + +static bool percent = TRUE; + +static void make_ptrs(int *tptr, int *pl, const int naseq, const int l, const int ktup, const int max_res_code, char **seq_array); +static void put_frag(const int fs, const int v1, const int v2, const int flen, const int curr_frag, int *next, int *maxsf, int **accum); +static bool frag_rel_pos(int a1, int b1, int a2, int b2, int ktup); +static void des_quick_sort(int *array1, int *array2, const int array_size); +static void pair_align(int seq_no, int l1, int l2, int max_res_code, ktuple_param_t *aln_param, + char **seq_array, int *maxsf, int **accum, int max_aln_length, + int *zza, int *zzb, int *zzc, int *zzd); +static void encode(char *seq, char *naseq, int l, const char *res_codes); +static int res_index(const char *lookup, char c); + + +typedef struct { + int i1; + int i2; +} two_ints_t; + + + +/* default ktuple pairwise alignment parameters + * + */ +/* protein + */ +/* designated initializer */ +const ktuple_param_t default_protein_param = { + .ktup = 1, + .wind_gap = 3, + .signif = 5, + .window = 5, +}; +/* dna + */ +/* designated initializer */ +const ktuple_param_t default_dna_param = { + .ktup = 2, + .wind_gap = 5, + .signif = 4, + .window = 4, +}; + + +/** + * note: naseq should be unit-offset + */ +static void +encode(char *seq, char *naseq, int l, const char *res_codes) +{ + /* code seq as ints .. use GAP_POS2 for gap */ + register int i; + bool seq_contains_unknown_char = FALSE; + /*LOG_DEBUG("seq=%s naseq=%p l=%d", &(seq[1]), naseq, l); */ + + + for (i=1; i<=l; i++) { + char res = toupper(seq[i]); + if (isgap(res)) { + naseq[i] = GAP_POS2; /* gap in input */ + } else { + naseq[i] = res_index(res_codes, res); + } + + /*LOG_DEBUG("Character '%c' at pos %d", res, i);*/ + if (-1 == naseq[i]) { + seq_contains_unknown_char = TRUE; + /*LOG_DEBUG("Unknown character '%c' at pos %d", res, i);*/ + } + /*LOG_DEBUG("na_seq[%d]=%d", i, naseq[i]);*/ + } + + if (TRUE == seq_contains_unknown_char) + Log(&rLog, LOG_WARN, "Unknown character in seq '%s'", &(seq[1])); + + naseq[i] = END_MARK; + + return; +} +/* end of encode */ + + +/** + * + */ +static int +res_index(const char *t, char c) +{ + register int i; + for (i=0; t[i] && t[i] != c; i++) + ; + if (t[i]) { + return (i); + } else { + return -1; + } +} +/* end of res_index */ + + +/** + * + */ +static void +make_ptrs(int *tptr, int *pl, const int naseq, const int l, const int ktup, const int max_res_code, char **seq_array) +{ + /* FIXME make 10 a constant and give it a nice name */ + static int a[10]; + int i, j, code, flag; + char residue; + const int limit = (int) pow((double)(max_res_code+1),(double)ktup); + + for (i=1;i<=ktup;i++) + a[i] = (int) pow((double)(max_res_code+1),(double)(i-1)); + + for (i=1; i<=limit; ++i) + pl[i]=0; + for (i=1; i<=l; ++i) + tptr[i]=0; + + for (i=1; i<=(l-ktup+1); ++i) { + code=0; + flag=FALSE; + for (j=1; j<=ktup; ++j) { + /* Log(&rLog, LOG_FORCED_DEBUG, "naseq=%d i=%d j=%d seq_array[naseq]=%p", + * naseq, i, j, seq_array[naseq]); + */ + residue = seq_array[naseq][i+j-1]; + /* Log(&rLog, LOG_FORCED_DEBUG, "residue = %d", residue); */ + if ((residue<0) || (residue > max_res_code)){ + flag=TRUE; + break; + } + code += ((residue) * a[j]); + } + if (flag) + continue; + ++code; + if (0 != pl[code]) + tptr[i] =pl[code]; + pl[code] = i; + } + + return; +} +/* end of make_ptrs */ + + +/** + * + * FIXME Why hardcoding of 5? + */ +static void +put_frag(const int fs, const int v1, const int v2, const int flen, const int curr_frag, int *next, int *maxsf, int **accum) +{ + int end; + accum[0][curr_frag]=fs; + accum[1][curr_frag]=v1; + accum[2][curr_frag]=v2; + accum[3][curr_frag]=flen; + + if (!*maxsf) { + *maxsf=1; + accum[4][curr_frag]=0; + return; + } + + if (fs >= accum[0][*maxsf]) { + accum[4][curr_frag]=*maxsf; + *maxsf=curr_frag; + return; + } else { + *next=*maxsf; + while (TRUE) { + end=*next; + *next=accum[4][*next]; + if (fs>=accum[0][*next]) + break; + } + accum[4][curr_frag]=*next; + accum[4][end]=curr_frag; + } + + return; +} +/* end of put_frag */ + + +/** + * + */ +static bool +frag_rel_pos(int a1, int b1, int a2, int b2, int ktup) +{ + if (a1-b1 == a2-b2) { + if (a2 0) { + if (lst[p] >= ust[p]) { + p--; + } else { + i = lst[p] - 1; + j = ust[p]; + pivlin = array1[j]; + while (i < j) { + for (i=i+1; array1[i] < pivlin; i++) + ; + for (j=j-1; j > i; j--) + if (array1[j] <= pivlin) break; + if (i < j) { + temp1 = array1[i]; + array1[i] = array1[j]; + array1[j] = temp1; + + temp2 = array2[i]; + array2[i] = array2[j]; + array2[j] = temp2; + } + } + + j = ust[p]; + + temp1 = array1[i]; + array1[i] = array1[j]; + array1[j] = temp1; + + temp2 = array2[i]; + array2[i] = array2[j]; + array2[j] = temp2; + + if (i-lst[p] < ust[p] - i) { + lst[p+1] = lst[p]; + ust[p+1] = i - 1; + lst[p] = i + 1; + + } else { + lst[p+1] = i + 1; + ust[p+1] = ust[p]; + ust[p] = i - 1; + } + p = p + 1; + } + } + +#if 0 + for (i=1; i<=array_size; i++) { + Log(&rLog, LOG_FORCED_DEBUG, "after sort array1[%d]=%d array2[%d]=%d", i, array1[i], i, array2[i]); + } +#endif + + return; +} +/* end of des_quick_sort */ + + + +/** + * + * FIXME together with des_quick_sort most time consuming routine + * according to gprof on r110 + * + */ +static void +pair_align(int seq_no, int l1, int l2, int max_res_code, ktuple_param_t *aln_param, + char **seq_array, int *maxsf, int **accum, int max_aln_length, + int *zza, int *zzb, int *zzc, int *zzd) +{ + int next; /* forrmerly static */ + int pot[8],i, j, l, m, flag, limit, pos, vn1, vn2, flen, osptr, fs; + int tv1, tv2, encrypt, subt1, subt2, rmndr; + char residue; + int *diag_index; + int *displ; + char *slopes; + int curr_frag; + const int tl1 = (l1+l2)-1; + + assert(NULL!=aln_param); + + /* + Log(&rLog, LOG_FORCED_DEBUG, "DNAFLAG=%d seq_no=%d l1=%d l2=%d window=%d ktup=%d signif=%d wind_gap=%d", + DNAFLAG, seq_no, l1, l2, window, ktup, signif, + wind_gap); + */ + + slopes = (char *) CKCALLOC(tl1+1, sizeof(char)); + displ = (int *) CKCALLOC(tl1+1, sizeof(int)); + diag_index = (int *) CKMALLOC((tl1+1) * sizeof(int)); + + for (i=1; i<=tl1; ++i) { + /* unnecessary, because we calloced: slopes[i] = displ[i] = 0; */ + diag_index[i] = i; + } + + for (i=1;i<=aln_param->ktup;i++) + pot[i] = (int) pow((double)(max_res_code+1),(double)(i-1)); + limit = (int) pow((double)(max_res_code+1),(double)aln_param->ktup); + + + + /* increment diagonal score for each k_tuple match */ + + for (i=1; i<=limit; ++i) { + vn1=zzc[i]; + while (TRUE) { + if (!vn1) break; + vn2 = zzd[i]; + while (0 != vn2) { + osptr = vn1-vn2+l2; + ++displ[osptr]; + vn2 = zzb[vn2]; + } + vn1=zza[vn1]; + } + } + + + /* choose the top SIGNIF diagonals + */ + +#ifdef QSORT_REPLACEMENT + /* This was an attempt to replace des_quick_sort with qsort(), + * which turns out to be much slower, so don't use this + */ + + /* FIXME: if we use this branch, we don't need to init diag_index + * before, because that is done in QSortAndTrackIndex() + * automatically. + */ +#if 0 + for (i=1; i<=tl1; i++) { + Log(&rLog, LOG_FORCED_DEBUG, "b4 sort disp[%d]=%d diag_index[%d]=%d", i, diag_index[i], i, displ[i]); + } +#endif + + QSortAndTrackIndex(&(diag_index[1]), &(displ[1]), tl1, 'a', TRUE); + +#if 0 + for (i=1; i<=tl1; i++) { + Log(&rLog, LOG_FORCED_DEBUG, "after sort disp[%d]=%d diag_index[%d]=%d", i, diag_index[i], i, displ[i]); + } +#endif + +#else + + des_quick_sort(displ, diag_index, tl1); + +#endif + + j = tl1 - aln_param->signif + 1; + + if (j < 1) { + j = 1; + } + + /* flag all diagonals within WINDOW of a top diagonal */ + + for (i=tl1; i>=j; i--) { + if (displ[i] > 0) { + pos = diag_index[i]; + l = (1 > pos - aln_param->window) ? + 1 : pos - aln_param->window; + m = (tl1 < pos + aln_param->window) ? + tl1 : pos + aln_param->window; + for (; l <= m; l++) + slopes[l] = 1; + } + } + + for (i=1; i<=tl1; i++) { + displ[i] = 0; + } + + curr_frag=*maxsf=0; + + for (i=1; i<=(l1-aln_param->ktup+1); ++i) { + encrypt=flag=0; + for (j=1; j<=aln_param->ktup; ++j) { + residue = seq_array[seq_no][i+j-1]; + if ((residue<0) || (residue>max_res_code)) { + flag=TRUE; + break; + } + encrypt += ((residue)*pot[j]); + } + if (flag) { + continue; + } + ++encrypt; + + vn2=zzd[encrypt]; + + flag=FALSE; + while (TRUE) { + if (!vn2) { + flag=TRUE; + break; + } + osptr=i-vn2+l2; + if (1 != slopes[osptr]) { + vn2=zzb[vn2]; + continue; + } + flen=0; + fs=aln_param->ktup; + next=*maxsf; + + /* + * A-loop + */ + + while (TRUE) { + if (!next) { + ++curr_frag; + if (curr_frag >= 2*max_aln_length) { + Log(&rLog, LOG_VERBOSE, "(Partial alignment)"); + goto free_and_exit; /* Yesss! Always wanted to + * use a goto (AW) */ + } + displ[osptr]=curr_frag; + put_frag(fs, i, vn2, flen, curr_frag, &next, maxsf, accum); + + } else { + tv1=accum[1][next]; + tv2=accum[2][next]; + + if (frag_rel_pos(i, vn2, tv1, tv2, aln_param->ktup)) { + if (i-vn2 == accum[1][next]-accum[2][next]) { + if (i > accum[1][next]+(aln_param->ktup-1)) { + fs = accum[0][next]+aln_param->ktup; + } else { + rmndr = i-accum[1][next]; + fs = accum[0][next]+rmndr; + } + flen=next; + next=0; + continue; + + } else { + if (0 == displ[osptr]) { + subt1=aln_param->ktup; + } else { + if (i > accum[1][displ[osptr]]+(aln_param->ktup-1)) { + subt1=accum[0][displ[osptr]]+aln_param->ktup; + } else { + rmndr=i-accum[1][displ[osptr]]; + subt1=accum[0][displ[osptr]]+rmndr; + } + } + subt2=accum[0][next] - aln_param->wind_gap + aln_param->ktup; + if (subt2>subt1) { + flen=next; + fs=subt2; + } else { + flen=displ[osptr]; + fs=subt1; + } + next=0; + continue; + } + } else { + next=accum[4][next]; + continue; + } + } + break; + } + /* + * End of Aloop + */ + + vn2=zzb[vn2]; + } + } + +free_and_exit: + CKFREE(displ); + CKFREE(slopes); + CKFREE(diag_index); + + return; +} +/* end of pair_align */ + + + +/** + * + * Will compute ktuple scores and store in tmat + * Following values will be set: tmat[i][j], where + * istart <= i nseqs+1) * sizeof(int)); + for (i=0; inseqs; i++) { + seqlen_array[i+1] = mseq->sqinfo[i].len; + } + + /* setup alignment parameters + */ + if (SEQTYPE_PROTEIN == mseq->seqtype) { + DNAFLAG = FALSE; + max_res_code = strlen(AMINO_ACID_CODES)-2; + aln_param = default_protein_param; + + } else if (SEQTYPE_RNA == mseq->seqtype || SEQTYPE_DNA == mseq->seqtype) { + DNAFLAG = TRUE; + max_res_code = strlen(NUCLEIC_ACID_CODES)-2; + aln_param = default_dna_param; + + } else { + Log(&rLog, LOG_FATAL, "Internal error in %s: Unknown sequence type.", __FUNCTION__); + } + + if (NULL!=param_override) { + aln_param.ktup = param_override->ktup; + aln_param.wind_gap = param_override->wind_gap; + aln_param.signif = param_override->signif; + aln_param.window = param_override->window; + } + + /*LOG_DEBUG("DNAFLAG = %d max_res_code = %d", DNAFLAG, max_res_code);*/ + + /* convert mseq to clustal's old-style int encoded sequences (unit-offset) + */ + max_aln_length = 0; + max_seq_len = 0; + seq_array = (char **) CKMALLOC((mseq->nseqs+1) * sizeof(char *)); + seq_array[0] = NULL; + /* FIXME check that non of the seqs is smaller than ktup (?). + * Otherwise segfault occurs + */ + for (i=0; inseqs; i++) { + seq_array[i+1] = (char *) CKMALLOC((seqlen_array[i+1]+2) * sizeof (char));; + } + for (i=0; inseqs; i++) { + /*LOG_DEBUG("calling encode with seq_array[%d+1] len=%d and seq=%s", + i, seqlen_array[i+1], mseq->seq[i]);*/ + if (TRUE == DNAFLAG) { + encode(&(mseq->seq[i][-1]), seq_array[i+1], + seqlen_array[i+1], NUCLEIC_ACID_CODES); + } else { + encode(&(mseq->seq[i][-1]), seq_array[i+1], + seqlen_array[i+1], AMINO_ACID_CODES); + } + + if (seqlen_array[i+1]>max_seq_len) { + max_seq_len = seqlen_array[i+1]; + } + } + max_aln_length = max_seq_len * 2; + /* see sequence.c in old source */ + + /* FIXME: short sequences can cause seg-fault + * because max_aln_length can get shorter + * than (max_res_code+1)^k + * FS, r222->r223 */ + max_aln_length = max_aln_length > pow((max_res_code+1), aln_param.ktup)+1 ? + max_aln_length : pow((max_res_code+1), aln_param.ktup)+1; + + /* + * + * conversion to old style clustal done (in no time) */ + + + accum = (int **) CKCALLOC(5, sizeof (int *)); + for (i=0;i<5;i++) { + accum[i] = (int *) CKCALLOC((2*max_aln_length+1), sizeof(int)); + } + zza = (int *) CKCALLOC( (max_aln_length+1), sizeof(int)); + zzb = (int *) CKCALLOC( (max_aln_length+1), sizeof(int)); + zzc = (int *) CKCALLOC( (max_aln_length+1), sizeof(int)); + zzd = (int *) CKCALLOC( (max_aln_length+1), sizeof(int)); + + /* estimation of total number of steps (if istart and jstart are + * both 0) (now handled in the calling routine) + */ + /* uTotalStepNo = iend*jend - iend*iend/2 + iend/2; + uStepNo = 0; */ + /*LOG_DEBUG("istart=%d iend=%d jstart=%d jend=%d", istart, iend, jstart, jend);*/ + + for (i=istart+1; i<=iend; ++i) { + /* by definition a sequence compared to itself should give + a score of 0. AW */ + SymMatrixSetValue(tmat, i-1, i-1, 0.0); + make_ptrs(zza, zzc, i, seqlen_array[i], aln_param.ktup, max_res_code, seq_array); + +#ifdef HAVE_OPENMP + #pragma omp critical(ktuple) +#endif + { + ProgressLog(prProgress, *ulStepNo, ulTotalStepNo, FALSE); + } + + for (j=MAX(i+1, jstart+1); j<=jend; ++j) { + (*ulStepNo)++; + private_step_no++; + /*LOG_DEBUG("comparing pair %d:%d", i, j);*/ + + make_ptrs(zzb, zzd, j, seqlen_array[j], aln_param.ktup, max_res_code, seq_array); + pair_align(i, seqlen_array[i], seqlen_array[j], max_res_code, &aln_param, + seq_array, &maxsf, accum, max_aln_length, zza, zzb, zzc, zzd); + + if (!maxsf) { + calc_score=0.0; + } else { + calc_score=(double)accum[0][maxsf]; + if (percent) { + dsr=(seqlen_array[i]nseqs; i++) { + CKFREE(seq_array[i]); + } + CKFREE(seq_array); +} +/* end of KTuplePairDist */ diff --git a/binaries/src/clustalo/src/clustal/ktuple_pair.h b/binaries/src/clustalo/src/clustal/ktuple_pair.h new file mode 100644 index 0000000..013248f --- /dev/null +++ b/binaries/src/clustalo/src/clustal/ktuple_pair.h @@ -0,0 +1,47 @@ +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: ktuple_pair.h 193 2011-02-07 15:45:21Z andreas $ + */ + +/* K-Tuple code for pairwise alignment (Wilbur and Lipman (1983) + * Most code taken from showpair (Clustal 1.83) + */ + + +#ifndef CLUSTALO_KTUPLE_PAIR_H +#define CLUSTALO_KTUPLE_PAIR_H + +#include "seq.h" +#include "symmatrix.h" +#include "progress.h" + +typedef struct { + int ktup; + int window; + int wind_gap; + int signif; +} ktuple_param_t; + + +extern void +KTuplePairDist(symmatrix_t *tmat, mseq_t *mseq, + int istart, int iend, + int jstart, int jend, + ktuple_param_t *aln_param, + progress_t *prProgress, + unsigned long int *ulStepNo, unsigned long int ulTotalStepNo); + +#endif diff --git a/binaries/src/clustalo/src/clustal/list.c b/binaries/src/clustalo/src/clustal/list.c new file mode 100644 index 0000000..29c6a35 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/list.c @@ -0,0 +1,389 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: list.c 156 2010-11-18 10:52:40Z andreas $ + * + * Single linked list and FIFO/Queue + * + * Based on Kyle Loudon's Mastering Algorithms with C + * http://oreilly.com/catalog/9781565924536 + * + * Allows generic data types by using void* pointers, which works fine + * as long as your data is just pointers. + * + */ + + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include /* for memset */ + +#include "list.h" + +#ifdef LIST_TEST +#include +#include "queue.h" +#include "time.h" +#endif + +/** + * @brief Initialise data members of a list + * + * @param[in] prList + * List to initialise + * @param[in] destroy + * A function to be called with pointer to data when destroying the + * list. NULL if in doubt, free in most other cases. + * Note: doxygen will always fail to parse this... + */ +void +ListInit(list_t *prList, void (*destroy)(void *data)) { + prList->size = 0; + prList->destroy = destroy; + prList->head = NULL; + prList->tail = NULL; + + return; +} +/* end of ListInit() */ + + + +/** + * @brief Calls user defined function to free data in list and resets + * the list to NULL. Call even if your destroy function is NULL. + * + * @param[in] prList + * The list to destroy + * + */ +void +ListDestroy(list_t *prList) { + void *pvData; + + while (LIST_SIZE(prList) > 0) { + if (0 == ListRemoveNext(prList, NULL, (void **)&pvData) + && + NULL != prList->destroy) { + prList->destroy(pvData); + } + } + /* precaution */ + memset(prList, 0, sizeof(list_t)); + + return; +} +/* end of ListDestroy() */ + + + +/** + * + * @brief Insert data next to given element + * + * @param[in] prList + * List into which to insert + * @param[in] prElement + * Current position/element. Element after which to insert. If NULL + * head is used. + * @param[in] pvData + * Pointer to data to store + * + * @return Non-zero on failure + */ +int +ListInsertNext(list_t *prList, list_elem_t *prElement, const void *pvData) +{ + list_elem_t *prNewElement; + + if (NULL == (prNewElement = (list_elem_t *) malloc(sizeof(list_elem_t)))) + return -1; + + prNewElement->data = (void *)pvData; + + if (NULL == prElement) { + /* insertion at head */ + if (LIST_SIZE(prList) == 0) + prList->tail = prNewElement; + prNewElement->next = prList->head; + prList->head = prNewElement; + + } else { + /* insert somewhere other than at head */ + if (NULL == prElement->next) + prList->tail = prNewElement; + prNewElement->next = prElement->next; + prElement->next = prNewElement; + } + + prList->size++; + + return 0; +} +/* end of ListInsertNext() */ + + + +/** + * @brief Remove next element from current element/position. + * + * @param[in] prList + * List from which an element is to be removed. + * @param[in] prElement + * Current element/position. Next item will be removed. If NULL head + * is used. + * @param[out] pvData_p + * Will be pointed to removed elements data. + * + * @return Non-zero on failure + */ +int +ListRemoveNext(list_t *prList, list_elem_t *prElement, void **pvData_p) +{ + list_elem_t *prOldElement; + + if (0 == LIST_SIZE(prList)) + return -1; + + if (NULL == prElement) { + /* handle removal from the head of the list */ + *pvData_p = prList->head->data; + prOldElement = prList->head; + prList->head = prList->head->next; + if (1 == LIST_SIZE(prList)) + prList->tail = NULL; + + } else { + /* handle removal from somewhere other than the head */ + if (NULL == prElement->next) + return -1; + + *pvData_p = prElement->next->data; + prOldElement = prElement->next; + prElement->next = prElement->next->next; + + if (NULL == prElement->next) + prList->tail = prElement; + } + + free(prOldElement); + + prList->size--; + + return 0; +} +/* end of ListRemoveNext() */ + + + +/** + * @brief Insert int next to given element + * + * @param[in] prList + * List into which to insert + * @param[in] prElement + * Current position/element. Element after which to insert. If NULL + * head is used. + * @param[in] data + * int to store + * + * @return Non-zero on failure + * + */ +int +IntListInsertNext(list_t *prList, list_elem_t *prElement, const int data) +{ + int *piInt; + + if (NULL == (piInt = malloc(sizeof(int)))) { + return -1; + } + *piInt = data; + + return ListInsertNext(prList, prElement, piInt); + } +/* end if IntListInsertNext() */ + + +/** + * @brief Remove next element from current element/position. + * + * @param[in] prList + * List from which an element is to be removed. + * @param[in] prElement + * Current element/position. Next item will be removed. If NULL head + * is used. + * @param[out] iData_p + * Will be pointed to removed elements data. + * + * @return Non-zero on failure + * + */ +int +IntListRemoveNext(list_t *prList, list_elem_t *prElement, int *iData_p) +{ + int *piData; + int res; + res = ListRemoveNext(prList, prElement, (void **)&piData); + *iData_p = *piData; + prList->destroy(piData); + return res; +} +/* end of IntListRemoveNext */ + + + + +#ifdef LIST_TEST +/* gcc list.c -o list_test -ansi -Wall -DLIST_TEST */ + +int main(int argc, char **argv) +{ + + int i; + list_t *mylist; + int_list_t *myintlist; + queue_t *myqueue; + int_queue_t *myintqueue; + int res; + + int iSeed = (int)time(NULL); + srand((unsigned int)iSeed); + + printf("%s", "list test! also delete #include!\n"); + + + mylist = malloc(sizeof(list_t)); + ListInit(mylist, NULL); + + printf("LIST test\n"); + + for (i=0; i + +typedef struct list_elem_s { + void *data; + struct list_elem_s *next; +} list_elem_t; + +typedef struct { + /* size of list */ + int size; + /* user defined function for freeing data */ + void (*destroy)(void *data); + list_elem_t *head; + list_elem_t *tail; +} list_t; + +void ListInit(list_t *prList, void (*destroy)(void *data)); + +void ListDestroy(list_t *prList); + +int ListInsertNext(list_t *prList, list_elem_t *prElement, const void *data); + +#define LIST_APPEND(prList, data) ListInsertNext((prList), LIST_TAIL(prList), (data)) + +#define LIST_PREPEND(prList, data) ListInsertNext((prList), CLUSTALO_LIST_HEAD(prList), (data)) + +int ListRemoveNext(list_t *prList, list_elem_t *prElement, void **data); + +#define LIST_SIZE(prList) ((prList)->size) + +#define CLUSTALO_LIST_HEAD(prList) ((prList)->head) + +#define LIST_TAIL(prList) ((prList)->tail) + +#define LIST_IS_HEAD(prList, prElement) ((prElement) == (prList)->head ? 1 : 0) + +#define LIST_IS_TAIL(prElement) ((prElement)->next == NULL ? 1 : 0) + +#define LIST_DATA(prElement) ((prElement)->data) + +#define LIST_NEXT(prElement) ((prElement)->next) + + + + + +/* special int list: stores ints by copying them (instead of storing + * pointers as generic list) + * + */ + +typedef list_t int_list_t; + +#define INT_LIST_INIT(prList) ListInit((prList), free) + +#define INT_LIST_DESTROY(prList) ListDestroy((prList)); + +int IntListInsertNext(list_t *prList, list_elem_t *prElement, const int data); + +#define INT_LIST_APPEND(prList, data) IntListInsertNext((prList), LIST_TAIL(prList), (data)) + +#define INT_LIST_PREPEND(prList, data) IntListInsertNext((prList), CLUSTALO_LIST_HEAD(prList), (data)) + +int IntListRemoveNext(list_t *prList, list_elem_t *prElement, int *data); + +#define INT_LIST_SIZE(prList) LIST_SIZE(prList) + +#define INT_CLUSTALO_LIST_HEAD(prList) CLUSTALO_LIST_HEAD_INT((prList)) + +#define INT_LIST_TAIL(prList) LIST_TAIL_INT((prList) ) + +#define INT_LIST_IS_HEAD(prList, prElement) LIST_IS_HEAD(prList, prElement) + +#define INT_LIST_IS_TAIL(prElement) LIST_IS_TAIL((prElement)) + +#define INT_LIST_DATA(prElement) LIST_DATA((prElement)) + +#define INT_LIST_NEXT(prElement) LIST_NEXT((prElement)) + + +#endif diff --git a/binaries/src/clustalo/src/clustal/log.c b/binaries/src/clustalo/src/clustal/log.c new file mode 100644 index 0000000..e503303 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/log.c @@ -0,0 +1,379 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id$ + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + + +#include +#include +#include +#include + +#include "log.h" + +/* a default standard logger */ +log_t rLog; + + + +void +LogVfprintf(FILE *prFP, char *pcFmt, va_list rVArgList); +void +LogWarn(FILE *prFP, char *pcFmt, va_list rVArgList); +void +LogError(FILE *prFP, char *pcFmt, va_list rVArgList); +void +LogCritical(FILE *prFP, char *pcFmt, va_list rVArgList); +void +LogFatal(FILE *prFP, char *pcFmt, va_list rVArgList); +void +LogForcedDebug(FILE *prFP, char *pcFmt, va_list rVArgList); + + + + +/** + * @brief Plain, default print function + * + * Newline character is automatically appended to message. + * + */ +void +LogVfprintf(FILE *prFP, char *pcFmt, va_list rVArgList) +{ + /* print prefix */ + vfprintf(prFP, pcFmt, rVArgList); + fprintf(prFP,"\n"); + +#ifndef NDEBUG + fflush(prFP); +#endif +} +/* end of LogVfprintf() */ + + + +/** + * @brief + * + */ +void +LogWarn(FILE *prFP, char *pcFmt, va_list rVArgList) +{ + fprintf(prFP, "WARNING: "); + LogVfprintf(prFP, pcFmt, rVArgList); +} +/* end of LogWarn() */ + + + +/** + * @brief + * + */ +void +LogError(FILE *prFP, char *pcFmt, va_list rVArgList) +{ + fprintf(prFP, "ERROR: "); + LogVfprintf(prFP, pcFmt, rVArgList); +} +/* end of LogError() */ + + + +/** + * @brief + * + */ +void +LogCritical(FILE *prFP, char *pcFmt, va_list rVArgList) +{ + fprintf(prFP, "CRITICAL ERROR: "); + LogVfprintf(prFP, pcFmt, rVArgList); +} +/* end of LogCritical() */ + + + +/** + * @brief Will also exit! + */ +void +LogFatal(FILE *prFP, char *pcFmt, va_list rVArgList) +{ + fprintf(prFP, "FATAL: "); + LogVfprintf(prFP, pcFmt, rVArgList); + + exit(EXIT_FAILURE); +} +/* end of LogFatal() */ + + + +/** + * @brief + * + */ +void +LogForcedDebug(FILE *prFP, char *pcFmt, va_list rVArgList) +{ + fprintf(prFP, "FORCED DEBUG: "); + LogVfprintf(prFP, pcFmt, rVArgList); +} +/* end of LogForcedDebug() */ + + + +/** + * + * @brief Sets up default function pointers + * + */ +void +LogDefaultSetup(log_t *log) +{ + log->iLogLevelEnabled = LOG_WARN; + + log->prFP[LOG_DEBUG] = stdout; + log->prFP[LOG_INFO] = stdout; + log->prFP[LOG_WARN] = stderr; + log->prFP[LOG_ERROR] = stderr; + log->prFP[LOG_CRITICAL] = stderr; + log->prFP[LOG_FATAL] = stderr; + log->prFP[LOG_FORCED_DEBUG] = stderr; + + log->prFunc[LOG_DEBUG] = &LogVfprintf; + log->prFunc[LOG_INFO] = &LogVfprintf; + log->prFunc[LOG_WARN] = &LogWarn; + log->prFunc[LOG_ERROR] = &LogError; + log->prFunc[LOG_CRITICAL] = &LogCritical; + log->prFunc[LOG_FATAL] = &LogFatal; + log->prFunc[LOG_FORCED_DEBUG] = &LogForcedDebug; +} +/* end of LogDefaultSetup() */ + + + +/** + * @brief Log to certain level + * + * See also comp.lang.c FAQ list · Question 15.12 + * http://c-faq.com/varargs/handoff.html How can I write a function which + * takes a variable number of arguments and passes them to some other function + * (which takes a variable number of arguments)? + * + */ +void +Log(log_t *prLog, int iLevel, char *pcFmt, ...) +{ + va_list rVArgList; + void (*prFunc) (FILE *prFP, char *pcFormat, va_list rVArgList); + FILE *prFP; + + assert(iLevel>=0 && iLevel<=LOG_NUM_LEVELS); + + /* fprintf(stderr, "DEBUG: iLevel=%d and iLogLevelEnabled=%d\n", iLevel, prLog->iLogLevelEnabled); */ + + /* return if below current loglevel */ + if (iLevel < prLog->iLogLevelEnabled) { + return; + } + + prFunc = prLog->prFunc[iLevel]; + prFP = prLog->prFP[iLevel]; + + /* return if muted */ + if (NULL == prFunc) { + return; + } + + va_start(rVArgList, pcFmt); + prFunc(prFP, pcFmt, rVArgList); + va_end(rVArgList); +} +/* end of Log() */ + + + +/** + * + * @brief Change file pointer for certain level + * + */ +void +LogSetFP(log_t *prLog, int iLevel, FILE *prFP) +{ + assert(iLevel>=0 && iLevel<=LOG_NUM_LEVELS); + + prLog->prFP[iLevel] = prFP; +} +/* end of LogSetFP() */ + + + +/** + * + * @brief Return file pointer for certain level + * + */ +FILE * +LogGetFP(log_t *prLog, int iLevel) +{ + assert(iLevel>=0 && iLevel<=LOG_NUM_LEVELS); + + return prLog->prFP[iLevel]; +} +/* end of LogGetFP() */ + + + + + +/** + * + * @brief Change file pointer for all levels + * + */ +void +LogSetFPForAll(log_t *prLog, FILE *prFP) +{ + int iAux; + + for (iAux=0; iAuxprFP[iAux] = prFP; + } +} +/* end of LogSetFP() */ + + + +/** + * + * @brief Mute certain level (i.e set the corresponding function to NULL) + * + */ +void +LogMute(log_t *prLog, int iLevel) +{ + assert(iLevel>=0 && iLevel<=LOG_NUM_LEVELS); + + prLog->prFunc[iLevel] = NULL; +} +/* end of LogMute() */ + + +/** + * + * @brief Mute all channels + * + */ +void +LogMuteAll(log_t *prLog) +{ + int iAux; + + for (iAux=0; iAux=0 && iLevel<=LOG_NUM_LEVELS); + + prLog->prFunc[iLevel] = Func; + +} +/* end of LogFuncOverwrite() */ + + + +#ifdef LOG_TEST + + +#define TEXT "Lorem ipsum dolor sit amet" + +void +PrintSomeTextToAll(log_t *prLog) { + int iAux; + for (iAux=0; iAux +#include + +#ifndef LOG_H +#define LOG_H + + +#define LOG_DEBUG 0 +#define LOG_VERBOSE 1 +#define LOG_INFO 2 +#define LOG_WARN 3 +#define LOG_FORCED_DEBUG 4 +#define LOG_ERROR 5 +#define LOG_CRITICAL 6 +#define LOG_FATAL 7 + +#define LOG_NUM_LEVELS 8 + + +typedef struct { + /* the higher the level, the more priority it has. numbers must be + * sequential + */ + + /* array of function pointers */ + void (*prFunc[LOG_NUM_LEVELS]) (FILE *prFP, char *pcFormat, va_list rVArgList); + FILE *prFP[LOG_NUM_LEVELS]; + char *prPrefix[LOG_NUM_LEVELS]; + + /* everything above this level will be printed */ + int iLogLevelEnabled; +} log_t; + + + +/* a standard logger */ +extern log_t rLog; + + + +void +LogDefaultSetup(log_t *log); +void +Log(log_t *prLog, int iLevel, char *pcFmt, ...); +void +LogSetFP(log_t *log, int level, FILE *fp); +void +LogSetFPForAll(log_t *log, FILE *fp); +FILE * +LogGetFP(log_t *prLog, int iLevel); +void +LogMute(log_t *log, int level); +void +LogMuteAll(log_t *log); +void +LogFuncOverwrite(log_t *prLog, int iLevel, + void (*Func) (FILE *prFP, char *pcFormat, va_list rVArgList)); + + +#endif diff --git a/binaries/src/clustalo/src/clustal/mbed.c b/binaries/src/clustalo/src/clustal/mbed.c new file mode 100644 index 0000000..f143fe0 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/mbed.c @@ -0,0 +1,1574 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: mbed.c 254 2011-06-21 13:07:50Z andreas $ + * + * + * Reimplementation from scratch of mBed: + * Blackshields et al. (2010); PMID 20470396 + * + * + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include + +#include "mbed.h" +#include "pair_dist.h" +#include "symmatrix.h" +#include "ktuple_pair.h" +#include "tree.h" +#include "util.h" +#include "progress.h" +#include "queue.h" + +#include "log.h" +#include "kmpp/KMeans.h" +#include "mbed.h" + +#define TIMING 0 +#if TIMING +#include "squid/stopwatch.h" +#endif + + +/* If FULL_WITHIN_CLUSTER_DISTANCES is not 0, distances within each + * bisecting kmeans subcluster are not estimated using the vectors, + * but calculated normally (using ktuple or kimura). Surprisingly this + * results in 3% loss on a Homfam p24-h2010-08-09 subset (100-5000 + * seqs in test, at least 5 ref seqs; MAX_SEQ 100 vs 10000; NUM_SEEDS + * log2 instead of log2^2). And of course it slows things down. + */ +#define FULL_WITHIN_CLUSTER_DISTANCES 1 + +#define COMPUTE_WITHIN_SUBCLUSTER_AVERAGE 0 + +/* Cluster size limits. Maximum is a soft limit, which might be + * exceeded if a K-Means split was unsuccesful, where unsuccesful + * might also mean that the minimum required number seqs. was not + * reached */ +#if FULL_WITHIN_CLUSTER_DISTANCES +static const int MAX_ALLOWED_SEQ_PER_PRECLUSTER = 100; +static const int MIN_REQUIRED_SEQ_PER_PRECLUSTER = 1; +#else +static const int MAX_ALLOWED_SEQ_PER_PRECLUSTER = 10000; +static const int MIN_REQUIRED_SEQ_PER_PRECLUSTER = 100; +#endif + +/* How many restarts per bisecting kmeans split. 10 give 0.5% increase + * in quality on original HOMFAM over just 1. It also increases kmeans + * time by a factor of ~3, but overall time is insignificant + * compared to pairdist/progressive alignment part. + */ +static const int RESTARTS_PER_SPLIT = 10; + + +/* Use standard kmeans (lloyds) or kmeans++. Both are almost + * indistinguishable here, although kmeans++ is slightly ahead the + * fewer seeds you pick (and it should be better in theory) + */ +#define USE_KMEANS_LLOYDS 0 + + +#ifndef HAVE_LOG2 +#define log2(x) (log(x) / 0.69314718055994530942) +#endif +#define NUMBER_OF_SEEDS(n) pow(log2(((double)n)), 2) + + +/* Seed selection method: SAMPLE_SEEDS_BY_LENGTH is the original mBed + * approach: Sample iSeeds sequence with constant stride from length-sorted X. + * It might be better to pick the seeds randomly, because length sorting might + * be more prone to including outliers (e.g. very long and very short seqs). + * However, we could never observer such a thing. So just stick to the + * original version as this also removes the random element. + */ +enum SEED_SELECTION_TYPE { + SELECT_SEEDS_RANDOMLY, + SELECT_SEEDS_BY_LENGTH +}; +#define SEED_SELECTION SELECT_SEEDS_BY_LENGTH + + +/* Tests on BAliBase (RV11,12,20,30,40,50; 10 runs each) show there is + * no difference between mbed-trees created from cosine or euclidean + * distances (simple version, just using disparities). + */ +#define USE_EUCLIDEAN_DISTANCE 1 + + +/* print some mbed pre-cluster usage to screen */ +#define PRINT_CLUSTER_DISTRIBUTION 0 + + +#define TRACE 0 + + +typedef struct { + /* Number of final clusters + */ + int iNClusters; + + /* Coordinates (columns) for each cluster (rows) + * valid indices: [0...iNClusters][0...dim-1] + */ + double **ppdClusterCenters; + + /* Dimensionality of input data and cluster center coordinates + */ + int iDim; + + /* Number of objects per cluster + */ + int *piNObjsPerCluster; + + /* Objects (indices) for each cluster. [i][j] will point to (index + * of) object j in cluster i + */ + int **ppiObjIndicesPerCluster; +} bisecting_kmeans_result_t; + + + +/** + * @brief Free KMeans result structure. + * + * @param[out] prResult_p + * K-Means result to free + * + * @see NewKMeansResult() + */ +void +FreeKMeansResult(bisecting_kmeans_result_t **prResult_p) +{ + int iAux; + CKFREE((*prResult_p)->piNObjsPerCluster); + for (iAux=0; iAux<(*prResult_p)->iNClusters; iAux++) { + CKFREE((*prResult_p)->ppiObjIndicesPerCluster[iAux]); + CKFREE((*prResult_p)->ppdClusterCenters[iAux]); + } + CKFREE((*prResult_p)->ppiObjIndicesPerCluster); + CKFREE((*prResult_p)->ppdClusterCenters); + (*prResult_p)->iNClusters = 0; + (*prResult_p)->iDim = 0; + CKFREE(*prResult_p); +} +/*** end: FreeKMeansResult() ***/ + + + +/** + * @brief Allocate new KMeans result + * + * @param[out] prKMeansResult_p + * K-Means result to free + * + * @see NewKMeansResult() + */ +void +NewKMeansResult(bisecting_kmeans_result_t **prKMeansResult_p) +{ + (*prKMeansResult_p) = (bisecting_kmeans_result_t *) + CKCALLOC(1, sizeof(bisecting_kmeans_result_t)); + (*prKMeansResult_p)->iNClusters = 0; + (*prKMeansResult_p)->iDim = 0; + (*prKMeansResult_p)->ppdClusterCenters = NULL; + (*prKMeansResult_p)->piNObjsPerCluster = NULL; + (*prKMeansResult_p)->ppiObjIndicesPerCluster = NULL; + +} +/*** end: NewKMeansResult() ***/ + + + +/** + * @brief Calculate the euclidean distance between two vectors + * + * @param[in] v1 + * First vector with dim dimensions + * @param[in] v2 + * Second vector with dim dimensions + * @param[in] dim + * Dimensionality of v1 and v2 + * + * @return euclidean distance as double + * + * @note Could probably be inlined. Also perfect for SSE + */ +double +EuclDist(const double *v1, const double *v2, const int dim) +{ + int i; /* aux */ + double dist; /* returned distance */ + + assert(v1!=NULL); + assert(v2!=NULL); + + dist = 0.0; + for (i=0; i0 && iNumSeeds<=prMSeq->nseqs); + + piSortedSeeds = CKMALLOC(iNumSeeds * sizeof(int)); + memcpy(piSortedSeeds, piSeeds, iNumSeeds*sizeof(int)); + + /* need them sorted, otherwise the swapping approach below might + * break + */ + qsort(piSortedSeeds, iNumSeeds, sizeof(int), IntCmp); + + + /* rearrange mseq order so that we can use ktuple_pairdist code as + * is. That is, swap seeds and non-seeds such that the seeds end + * up in front of mseq. This way we can use the KTuplePairDist() + * code, without making a copy of mseq. Also, keep an array of + * indices which serves to restore the original sequence order + * after putting the seeds in front + * + */ + restore = (int *) CKMALLOC(prMSeq->nseqs * sizeof(int)); + for (iSeqIndex=0; iSeqIndexnseqs; iSeqIndex++) { + restore[iSeqIndex] = iSeqIndex; + } + for (iSeedIndex=0; iSeedIndexnseqs; iSeqIndex++) { + Log(&rLog, LOG_FORCED_DEBUG, "swapped seq no %d now: seq = %s", + iSeqIndex, prMSeq->sqinfo[iSeqIndex].name); + } +#endif + + + /* convert sequences into vectors of distances by calling pairwise + * distance function for each seq/seed pair + * + */ + if (0 != PairDistances(&prDistmat, prMSeq, iPairDistType, + 0, iNumSeeds, 0, prMSeq->nseqs, + NULL, NULL)) { + Log(&rLog, LOG_ERROR, "Could not compute pairwise distances for mbed."); + FreeSymMatrix(&prDistmat); + CKFREE(piSortedSeeds); + CKFREE(restore); + return -1; + } +#if TRACE + { + char **labels; + labels = (char **) CKMALLOC(prMSeq->nseqs * sizeof(char *)); + for (iSeqIndex=0; iSeqIndexnseqs; iSeqIndex++) { + labels[iSeqIndex] = prMSeq->sqinfo[iSeqIndex].name; + } + SymMatrixPrint(prDistmat, labels, NULL); + CKFREE(labels); + } +#endif + + + /* update ppdSeqVec according to prDistmat. keep in mind that we + * changed mseq order + * + */ + for (iSeqIndex=0; iSeqIndexnseqs; iSeqIndex++) { + for (iSeedIndex=0; iSeedIndexnseqs; iSeqIndex++) { + Log(&rLog, LOG_FORCED_DEBUG, "restored seq no %d: seq = %s %s", + iSeqIndex, prMSeq->sqinfo[iSeqIndex].name, prMSeq->seq[iSeqIndex]); + } +#endif + +#if TRACE + for (iSeqIndex=0; iSeqIndexnseqs; iSeqIndex++) { + printf("DEBUG: seq %-4u as distance vector =", iSeqIndex); + for (iSeedIndex=0; iSeedIndexnseqs); + + PermutationArray(&piPermArray, iNumSeeds); + /* copy to piSeeds */ + for (iSeedIndex=0; iSeedIndexnseqs * sizeof(int)); + int *piOrder = CKMALLOC(prMSeq->nseqs * sizeof(int)); + + Log(&rLog, LOG_INFO, + "Using %d seeds (chosen with constant stride from length sorted seqs) for mBed (from a total of %d sequences)", + iNumSeeds, prMSeq->nseqs); + + iStep = prMSeq->nseqs / iNumSeeds; /* iStep will never get too big + * due to rounding */ + /* first get an array of seq indices order according to + corresponding sequence length: piOrder */ + for (iSeqIndex=0; iSeqIndexnseqs; iSeqIndex++) { + piSeqLen[iSeqIndex] = prMSeq->sqinfo[iSeqIndex].len; + } + QSortAndTrackIndex(piOrder, piSeqLen, prMSeq->nseqs, 'd', FALSE); +#if 0 + for (iSeqIndex=0; iSeqIndexnseqs; iSeqIndex++) { + Log(&rLog, LOG_FORCED_DEBUG, "Descending order (no %d): seq %d has len %d)", + iSeqIndex, piOrder[iSeqIndex], piSeqLen[piOrder[iSeqIndex]]); + } +#endif + CKFREE(piSeqLen); + iSeedIndex = 0; + for (iSeqIndex=0; iSeedIndexnseqs * sizeof(int)); + double *pdKMeansClusterCenters = CKCALLOC(iNumSeeds * iNumSeeds, sizeof(double)); + /* create a copy of ppdSeqVec suitable for KMeans */ + double *pdKMeansVectors = CKMALLOC(prMSeq->nseqs * iNumSeeds * sizeof(double)); + bool *pbClusterUsed = CKCALLOC(iNumSeeds, sizeof(bool)); + + Log(&rLog, LOG_FORCED_DEBUG, "%s", "FIXME Experimental feature: K-means on first round embedding to get better seeds"); + Log(&rLog, LOG_FORCED_DEBUG, "%s", "FIXME Reuse seeds from clusters"); + Log(&rLog, LOG_FORCED_DEBUG, "%s", "FIXME Could try log(n) instead of log(n)^2 in first round"); + Log(&rLog, LOG_FORCED_DEBUG, "%s", "FIXME hardcoded iPairDistType PAIRDIST_KTUPLE"); + Log(&rLog, LOG_FORCED_DEBUG, "%s", "FIXME Show that this is fast *and* good"); + + /* + Log(&rLog, LOG_FORCED_DEBUG, "%s", "Overriding iNumSeeds"); + iNumSeeds = (int) pow(log2((double)prMSeq->nseqs), 2); + */ + + ppdSeqVec = (double **) CKMALLOC(prMSeq->nseqs * sizeof(double *)); + for (iSeqIndex=0; iSeqIndexnseqs; iSeqIndex++) { + ppdSeqVec[iSeqIndex] = (double *) CKMALLOC(iNumSeeds * sizeof(double)); + } + if (0 != SeqToVec(ppdSeqVec, prMSeq, piSeeds, iNumSeeds, PAIRDIST_KTUPLE)) { + Log(&rLog, LOG_ERROR, "Could not convert sequences into vectors for mbed"); + return -1; + } + + for (iSeqIndex=0; iSeqIndexnseqs; iSeqIndex++) { + int iDim; + for (iDim=0; iDimnseqs, iNumSeeds, iNumSeeds, + pdKMeansVectors, + RESTARTS_PER_SPLIT, USE_KMEANS_LLOYDS, + pdKMeansClusterCenters, piKMeansClusterAssignments); + Log(&rLog, LOG_FORCED_DEBUG, "Best split cost = %f", dCost); + + Log(&rLog, LOG_FORCED_DEBUG, "%s", "FIXME Check for Nan in cluster centers"); + +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "%s", "K-Means output:"); + for (iSeqIndex=0; iSeqIndexnseqs; iSeqIndex++) { + Log(&rLog, LOG_FORCED_DEBUG, " Raw assignment: Seq %u (%s) to cluster %d", + iSeqIndex, prMSeq->sqinfo[iSeqIndex].name, + piKMeansClusterAssignments[iSeqIndex]); + } +#endif + + Log(&rLog, LOG_FORCED_DEBUG, "FIXME %s", "proof of concept implementation: Pick first sequences from each clusters instead of reusing seeds"); + iSeedIndex = 0; + for (iSeqIndex=0; iSeqIndexnseqs; iSeqIndex++) { + int iAssignedCluster = piKMeansClusterAssignments[iSeqIndex]; + if (pbClusterUsed[iAssignedCluster]) { + continue; + } else { + /*LOG_DEBUG("Picked seed %d from cluster %d", iSeqIndex,iAssignedCluster);*/ + piSeeds[iSeedIndex++] = iSeqIndex; + pbClusterUsed[iAssignedCluster] = TRUE; + } + } + CKFREE(pbClusterUsed); + + CKFREE(pdKMeansVectors); + CKFREE(pdKMeansClusterCenters); + CKFREE(piKMeansClusterAssignments); + + } + /* if (1) */ +#endif + + + if (LOG_DEBUG <= rLog.iLogLevelEnabled) { + for (iSeedIndex=0; iSeedIndexsqinfo[piSeeds[iSeedIndex]].name, iSeedIndex); + } + } + + return 0; +} +/* end of SeedSelection() */ + + + + +/** + * @brief Bisecting K-Means clustering. Repeatedly calls K-Means with + * a K of 2 until no cluster has more than iMaxAllowedObjsPerCluster. + * + * @param[out] prKMeansResult_p + * Result of Bisecting KMeans. Will be allocated here. + * Caller has to free. See @see FreeKMeansResult() + * @param[in] iNObjs + * Number of objects/sequences to cluster + * @param[in] iDim + * Dimensionality of input data + * @param[in] ppdVectors + * each row holds iDim points for this object's coordinates + * @param[in] iMinRequiredObjsPerCluster + * Minimum number of objects per Cluster (inclusive)/ + * @param[in] iMaxAllowedObjsPerCluster + * Maximum number of objects per Cluster (inclusive). Function returns once no + * cluster contains more then this number of objects. Soft limit! + * + * @note Convoluted code. Could use some restructuring. My apologies. + * AW + * + */ +void +BisectingKmeans(bisecting_kmeans_result_t **prKMeansResult_p, + const int iNObjs, const int iDim, double **ppdVectors, + const int iMinRequiredObjsPerCluster, + const int iMaxAllowedObjsPerCluster) +{ + int iN, iD; + /* cluster centers for each cluster created at each split */ + double *pdKClusterCenters; + /* keep track of updated object indices per newly created + * cluster */ + int *piCurObjToUpdate; + /* number of times we called 2-means */ + int iNRounds; + /* flag for unsuccessful cluster split */ + bool bNaNDetected = FALSE; + /* flag for detected small cluster after split */ + bool bSmallClusterDetected; + /* queue of clusters which are to be split */ + int_queue_t rClusterSplitQueue; + +#if TIMING + Stopwatch_t *stopwatch = StopwatchCreate(); +#endif + + + piCurObjToUpdate = (int *) CKMALLOC(2 * sizeof(int)); + + NewKMeansResult(prKMeansResult_p); + + /* new cluster centers created at each split/KMeans run + */ + pdKClusterCenters = (double *) CKCALLOC(2 * iDim, sizeof(double)); + + /* init results by setting a first cluster that contains all objects + */ + (*prKMeansResult_p)->iNClusters = 1; + (*prKMeansResult_p)->iDim = iDim; + /* fake center coordinates of first cluster */ + (*prKMeansResult_p)->ppdClusterCenters = + (double **) CKMALLOC(1 * sizeof(double *)); + (*prKMeansResult_p)->ppdClusterCenters[0] = + (double *) CKMALLOC(iDim * sizeof(double)); + /* objects per cluster */ + (*prKMeansResult_p)->piNObjsPerCluster = + (int *) CKMALLOC(1 * sizeof(int)); + (*prKMeansResult_p)->piNObjsPerCluster[0] = iNObjs; + /* object indices per cluster */ + (*prKMeansResult_p)->ppiObjIndicesPerCluster = + (int **) CKMALLOC(1 * sizeof(int *)); + (*prKMeansResult_p)->ppiObjIndicesPerCluster[0] = (int *) + CKMALLOC(iNObjs * sizeof(int)); + for (iN=0; iNppiObjIndicesPerCluster[0][iN] = iN; + } + + + + /* Starting with the first cluster that now contains all the + * sequences keep splitting until no cluster contains more than + * iMaxAllowedObjsPerCluster + * + * Keep a queue of clusters (rClusterSplitQueue) to split + * + * At each split values/memory of the just split cluster will be + * reused and exactly one new only allocated. + * + * Example: + * Given the following cluster assignments + * 0 0 0 0 1 1 2 2 2 3 3 3 3 3 3 3 4 4 + * and a K-Means split in cluster 3 at |: + * 0 0 0 0 1 1 2 2 2 3 3 3 | 3 3 3 3 4 4 + * The result should be this: + * 0 0 0 0 1 1 2 2 2 3 3 3 | 5 5 5 5 4 4 + * + * + */ + INT_QUEUE_INIT(&rClusterSplitQueue); + if (iNObjs>iMaxAllowedObjsPerCluster) { + /* pish fake first cluster index */ + INT_QUEUE_PUSH(&rClusterSplitQueue, 0); + } + iNRounds = 0; + while (! INT_QUEUE_EMPTY(&rClusterSplitQueue)) { + /* assignments for each seq to the K newly created clusters */ + int *piKClusterAssignments; + /* number of objects in cluster that is to be split */ + int iNObjsInClusterToSplit; + /* coordinates of points in cluster that is to be split + * array of size n*d where [d*i + j] gives coordinate j of point i + */ + double *pdVectorsInClusterToSplit; + /* copy of object indices in split cluster */ + int *piObjIndicesOfSplitCluster; + /* best cost of kmeans rounds */ + double dCost = -1.0; + + /* indices for the two created clusters + */ + /* index of cluster to split */ + int iClusterToSplot; + /* index of newly created cluster at each round. data for the + other created cluster goes to the one just split, + i.e. (*piClusterToSplot) */ + int iNewClusterIdx; + +#if TIMING + StopwatchZero(stopwatch); + StopwatchStart(stopwatch); +#endif + + INT_QUEUE_POP(&rClusterSplitQueue, &iClusterToSplot); + + iNObjsInClusterToSplit = (*prKMeansResult_p)->piNObjsPerCluster[iClusterToSplot]; + piKClusterAssignments = (int *) + CKMALLOC(iNObjsInClusterToSplit * sizeof(int)); + + pdVectorsInClusterToSplit = (double *) + CKMALLOC(iNObjsInClusterToSplit * iDim * sizeof(double)); + for (iN=0; iNppiObjIndicesPerCluster[iClusterToSplot][iN]; + pdVectorsInClusterToSplit[iDim*iN + iD] = ppdVectors[iThisObjIdx][iD]; + } + } + +#if TRACE + Log(&rLog, LOG_FOCRED_DEBUG, "Round %d: Will split cluster %d which has %d objects", + iNRounds, iClusterToSplot, iNObjsInClusterToSplit); + fprintf(stderr, "DEBUG(%s|%s():%d): Object indices in cluster to split are:", + __FILE__, __FUNCTION__, __LINE__); + for (iN=0; iNppiObjIndicesPerCluster[iClusterToSplot][iN]); + } + fprintf(stderr, "\n"); + (void) fflush(stderr); +#endif + +#if TRACE + for (iN=0; iNppiObjIndicesPerCluster[iClusterToSplot][iN]); + for (iD=0; iDiNClusters; + + + /* We don't want Clusters which are too small. Check here if a + * split created a small cluster and if yes, discard the + * solution. Because the cluster has already been removed from + * the queue, we can just continue. + */ + bSmallClusterDetected = FALSE; + if (iMinRequiredObjsPerCluster>1) { + int iNObjsCluster[2]; + iNObjsCluster[0] = 0; /* first cluster */ + iNObjsCluster[1] = 0; /* second cluster */ + for (iN=0; iNppdClusterCenters[iClusterToSplot][iN] = dCoord; + } + /* realloc and set new one + */ + (*prKMeansResult_p)->ppdClusterCenters = (double **) + CKREALLOC((*prKMeansResult_p)->ppdClusterCenters, + ((*prKMeansResult_p)->iNClusters+1) * sizeof(double *)); + (*prKMeansResult_p)->ppdClusterCenters[iNewClusterIdx] = (double *) + CKMALLOC(iDim * sizeof(double)); + for (iD=0; iDppdClusterCenters[iNewClusterIdx][iD] = dCoord; + } +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "%s", "* Update of cluster centers done. Cluster centers so far:"); + for (iN=0; iN<(*prKMeansResult_p)->iNClusters+1; iN++) { + fprintf(stderr, "DEBUG(%s|%s():%d): Center %u =", + __FILE__, __FUNCTION__, __LINE__, iN); + for (iD=0; iDppdClusterCenters[iN][iD]); + } + fprintf(stderr, "\n"); + (void) fflush(stderr); + } +#endif + + + /* update #seqs per cluster: piNObjsPerCluster + * + */ + (*prKMeansResult_p)->piNObjsPerCluster = (int *) + CKREALLOC((*prKMeansResult_p)->piNObjsPerCluster, + ((*prKMeansResult_p)->iNClusters+1) * sizeof(int)); + /* init new and old one to zero */ + (*prKMeansResult_p)->piNObjsPerCluster[iClusterToSplot] = 0; + (*prKMeansResult_p)->piNObjsPerCluster[iNewClusterIdx] = 0; + /* now update values */ + for (iN=0; iNpiNObjsPerCluster[iClusterToSplot] += 1; + } else if (1 == piKClusterAssignments[iN]) { + (*prKMeansResult_p)->piNObjsPerCluster[iNewClusterIdx] += 1; + } else { + /* there used to be code for iK>=2 in r101 */ + Log(&rLog, LOG_FATAL, "Internal error: split into more than two clusters (got assignment %d)", + piKClusterAssignments[iN]); + } + } +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "%s", "* Update of NObjs per cluster done:"); + for (iN=0; iN<(*prKMeansResult_p)->iNClusters+1; iN++) { + Log(&rLog, LOG_FORCED_DEBUG, "Cluster %d contains %d sequences", + iN, (*prKMeansResult_p)->piNObjsPerCluster[iN]); + } +#endif + /* queue clusters if still they are still too big + */ + if ((*prKMeansResult_p)->piNObjsPerCluster[iClusterToSplot] > iMaxAllowedObjsPerCluster) { + INT_QUEUE_PUSH(&rClusterSplitQueue, iClusterToSplot); + } + if ((*prKMeansResult_p)->piNObjsPerCluster[iNewClusterIdx] > iMaxAllowedObjsPerCluster) { + INT_QUEUE_PUSH(&rClusterSplitQueue, iNewClusterIdx); + } + + + + /* update which objects belong to which cluster: + * + * note: piNObjsPerCluster needs to be already updated + * + */ + /* create a copy of the object indices in the split cluster + * (original will be overwritten) + */ + piObjIndicesOfSplitCluster = (int *) CKMALLOC(iNObjsInClusterToSplit * sizeof(int)); + memcpy(piObjIndicesOfSplitCluster, + (*prKMeansResult_p)->ppiObjIndicesPerCluster[iClusterToSplot], + iNObjsInClusterToSplit * sizeof(int)); + + (*prKMeansResult_p)->ppiObjIndicesPerCluster = (int **) + CKREALLOC((*prKMeansResult_p)->ppiObjIndicesPerCluster, + ((*prKMeansResult_p)->iNClusters+1) * sizeof(int *)); + + + (*prKMeansResult_p)->ppiObjIndicesPerCluster[iClusterToSplot] = + (int *) CKREALLOC((*prKMeansResult_p)->ppiObjIndicesPerCluster[iClusterToSplot], + (*prKMeansResult_p)->piNObjsPerCluster[iClusterToSplot] * sizeof(int)); + + (*prKMeansResult_p)->ppiObjIndicesPerCluster[iNewClusterIdx] = + (int *) CKMALLOC((*prKMeansResult_p)->piNObjsPerCluster[iNewClusterIdx] * sizeof(int)); + + + /* now reassign the object indices to the assigned cluster + */ + piCurObjToUpdate[0] = 0; + piCurObjToUpdate[1] = 0; + for (iN=0; iN=2 in r101 */ + Log(&rLog, LOG_FATAL, "Internal error: split into more than two clusters (got assignment %d)", + piKClusterAssignments[iN]); + } +#if 0 + Log(&rLog, LOG_FORCED_DEBUG, "Setting (*prKMeansResult_p)->ppiObjIndicesPerCluster[%d][%d] = %d", + iThisClusterIndex, iThisOffset, iThisObjIdx); +#endif + (*prKMeansResult_p)->ppiObjIndicesPerCluster[iThisClusterIndex][iThisOffset] = iThisObjIdx; + piCurObjToUpdate[iThisClusterAssignment]+=1; + } + CKFREE(piObjIndicesOfSplitCluster); +#if TRACE + for (iN=0; iN<(*prKMeansResult_p)->iNClusters+1; iN++) { + int iObj; + fprintf(stderr, "DEBUG(%s|%s():%d): Objects in cluster %u: ", + __FILE__, __FUNCTION__, __LINE__, iN); + for (iObj=0; iObj<(*prKMeansResult_p)->piNObjsPerCluster[iN]; iObj++) { + fprintf(stderr, " %u", (*prKMeansResult_p)->ppiObjIndicesPerCluster[iN][iObj]); + } + fprintf(stderr, "\n"); + (void) fflush(stderr); + } +#endif + + +#if TIMING + StopwatchStop(stopwatch); + StopwatchDisplay(stdout, "Total time after next round in Bisecting-KMeans: ", stopwatch); +#endif + + + /* finally: increase number of clusters + */ + (*prKMeansResult_p)->iNClusters += 1; + iNRounds += 1; + CKFREE(piKClusterAssignments); + CKFREE(pdVectorsInClusterToSplit); + + } /* while */ + INT_QUEUE_DESTROY(&rClusterSplitQueue); + + + Log(&rLog, LOG_DEBUG, + "Bisecting K-means finished after %d rounds (no more clusters to split)", + iNRounds); + +#if TIMING + StopwatchFree(stopwatch); +#endif + + /* @note could use progress/timer */ + + CKFREE(pdKClusterCenters); + CKFREE(piCurObjToUpdate); + + return; +} +/*** end: BisectingKmeans() ***/ + + + +/** + * + * @brief From scratch reimplementation of mBed: Blackshields et al. + * (2010); PMID 20470396. + * + * Idea is a follows: + * - convert sequences into vectors of distances + * - cluster the vectors using k-means + * - cluster each of the k clusters using upgma (used cached distances + * from above?) + * - join the sub-clusters to create on tree (use UPGMA on k-means + * medoids) + * + * + * @param[out] prMbedTree_p + * Created upgma tree. will be allocated here. use FreeMuscleTree() + * to free + * @param[in] prMSeq + * Multiple sequences + * @param[in] iPairDistType + * Distance measure for pairwise alignments + * @param[in] pcGuidetreeOut + * Passed down to GuideTreeUpgma() + * + * @return Zero on success, non-zero on error + * + */ +int +Mbed(tree_t **prMbedTree_p, mseq_t *prMSeq, const int iPairDistType, + const char *pcGuidetreeOut) +{ + /* number of seeds */ + int iNumSeeds; + /* seed indices matching prMSeq */ + int *piSeeds; + /* seqs represented as distance vectors */ + double **ppdSeqVec; + /* kmeans result */ + bisecting_kmeans_result_t *prKMeansResult = NULL; + /* distance matrix of kmeans (pre-)cluster centers */ + symmatrix_t *prPreClusterDistmat = NULL; + /* auxiliary for symmetric matrix output; tree routines etc */ + char **ppcLabels; + int iNodeIndex; + /* mapping of cluster-center tree node indices to corresponding + cluster */ + int *piClusterToTreeNode; + int iClusterIndex; + int iI, iJ; + FILE *pfOut; + progress_t *prSubClusterDistanceProgress; + bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE; + +#if FULL_WITHIN_CLUSTER_DISTANCES + Log(&rLog, LOG_DEBUG, "Computing real distances within subclusters for mBed."); +#else + Log(&rLog, LOG_DEBUG, "Computing vector distances within subclusters for mBed."); +#endif + +#if MBED_TIMING + Stopwatch_t *stopwatch = StopwatchCreate(); +#endif + + assert(NULL != prMbedTree_p); + assert(NULL != prMSeq); + + + iNumSeeds = (int) NUMBER_OF_SEEDS(prMSeq->nseqs); + if (iNumSeeds >= prMSeq->nseqs) { + /* -1 is condition for RandomUniqueIntArray */ + iNumSeeds = prMSeq->nseqs-1; + Log(&rLog, LOG_DEBUG, + "Automatically determined number of seeds is bigger (or equal) the number of sequences. Will set it to %d", + iNumSeeds); + } + + + /* Turn sequences into vectors of distances to the seeds + * + */ + piSeeds = (int *) CKMALLOC(iNumSeeds * sizeof(int)); + if (0 != SeedSelection(piSeeds, iNumSeeds, SEED_SELECTION, prMSeq)) { + Log(&rLog, LOG_ERROR, "Something went wrong during seed selection for mbed"); + return -1; + } + ppdSeqVec = (double **) CKMALLOC(prMSeq->nseqs * sizeof(double *)); + for (iI=0; iInseqs; iI++) { + ppdSeqVec[iI] = (double *) CKMALLOC(iNumSeeds * sizeof(double)); + } + if (0 != SeqToVec(ppdSeqVec, prMSeq, piSeeds, iNumSeeds, iPairDistType)) { + Log(&rLog, LOG_ERROR, "Could not convert sequences into vectors for mbed"); + return -1; + } + CKFREE(piSeeds); + + + /* Calculate (pre-)clusters of sequence vectors by applying + * bisecting kmeans + * + */ +#if MBED_TIMING + /* start clock only here, to make sure we don't include pairwise + * distance computation */ + StopwatchZero(stopwatch); + StopwatchStart(stopwatch); +#endif + + BisectingKmeans(&prKMeansResult, prMSeq->nseqs, iNumSeeds, ppdSeqVec, + MIN_REQUIRED_SEQ_PER_PRECLUSTER, + MAX_ALLOWED_SEQ_PER_PRECLUSTER); + Log(&rLog, LOG_INFO, + "mBed created %u cluster/s (with a minimum of %d and a soft maximum of %d sequences each)", + prKMeansResult->iNClusters, + MIN_REQUIRED_SEQ_PER_PRECLUSTER, + MAX_ALLOWED_SEQ_PER_PRECLUSTER); + + +#if PRINT_CLUSTER_DISTRIBUTION + Log(&rLog, LOG_FORCED_DEBUG, "Bisecting Kmeans returned %d clusters", prKMeansResult->iNClusters); + for (iI=0; iIiNClusters; iI++) { +#if TRACE + int iD; + Log(&rLog, LOG_FORCED_DEBUG, "Diagnostic output for cluster %d follows:", iI); + fprintf(stderr, "DEBUG(%s|%s():%d): center coordinates =", + __FILE__, __FUNCTION__, __LINE__); + for (iD=0; iDppdClusterCenters[iI][iD]); + } + fprintf(stderr, "\n"); + fflush(stderr); +#endif + Log(&rLog, LOG_FORCED_DEBUG, "Cluster %d has %d objects assigned", + iI, prKMeansResult->piNObjsPerCluster[iI]); +#if TRACE + for (iJ=0; iJpiNObjsPerCluster[iI]; iJ++) { + int iRealIndex = prKMeansResult->ppiObjIndicesPerCluster[iI][iJ]; + + Log(&rLog, LOG_FORCED_DEBUG, "Cluster %u: object %u has index %u (= seq %s)", + iI, iJ, iRealIndex, prMSeq->sqinfo[iRealIndex].name); + } +#endif + } +#endif + + + /* Cluster pre-clusters produced by k-means. + * + * Do this by calculating the vector distances of the cluster + * centers and applying UPGMA. + * + * @note could try to force-balance the tree here + * + */ + if (0 != NewSymMatrix(&prPreClusterDistmat, + prKMeansResult->iNClusters, prKMeansResult->iNClusters)) { + Log(&rLog, LOG_FATAL, "%s", "Memory allocation for pre-cluster distance-matrix failed"); + } + for (iI=0; iIiNClusters; iI++) { + for (iJ=iI+1; iJiNClusters; iJ++) { + double dDist; + dDist = EuclDist(prKMeansResult->ppdClusterCenters[iI], + prKMeansResult->ppdClusterCenters[iJ], + iNumSeeds); + SymMatrixSetValue(prPreClusterDistmat, iI, iJ, dDist); + /* Log(&rLog, LOG_FORCED_DEBUG, "Euclidean distance between clusters %d and %d = %f", + iI, iJ, dDist); */ + } + } + + + /* labels needed for the guide tree building routine only */ + ppcLabels = (char **) CKMALLOC(prKMeansResult->iNClusters * sizeof(char*)); + for (iI=0; iIiNClusters; iI++) { + ppcLabels[iI] = (char *) CKMALLOC(32 * sizeof(char)); + (void) snprintf(ppcLabels[iI], 32, "Subcluster-%u", iI); + } +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "%s", "Distance matrix for pre-cluster centers:"); + SymMatrixPrint(prPreClusterDistmat, ppcLabels, NULL); +#endif + + GuideTreeUpgma(prMbedTree_p, + ppcLabels, prPreClusterDistmat, NULL); + + for (iI=0; iIiNClusters; iI++) { + CKFREE(ppcLabels[iI]); + } + CKFREE(ppcLabels); +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "%s", "Cluster-center guide-tree:"); + LogTree(*prMbedTree_p); +#endif + + + + /* Now replace each leaf in the pre-cluster-center tree + * appropriately, i.e. with the corresponding sub-cluster. + * + * For each leaf/sub-cluster, create a distance matrix for the + * corresponding sequences. Use distances between vectors as + * approximated distances between sequences. Then create a + * guide-tree by applying UPGMA. + * + */ + + /* Get a mapping of (pre)cluster number and leaf-node indices in + * the cluster-center tree. We can add trees to prMbedTree_p + * because AppendTrees() guarantees that no other than the node to + * append to changes. + */ + piClusterToTreeNode = (int*) + CKMALLOC(prKMeansResult->iNClusters * sizeof(int)); + iNodeIndex = FirstDepthFirstNode(*prMbedTree_p); + do { + if (IsLeaf(iNodeIndex, *prMbedTree_p)) { + int iLeafId = GetLeafId(iNodeIndex, *prMbedTree_p); + piClusterToTreeNode[iLeafId] = iNodeIndex; + } + iNodeIndex = NextDepthFirstNode(iNodeIndex, *prMbedTree_p); + } while (NULL_NEIGHBOR != iNodeIndex); + + + + + /* Now step through all the leafs and replace them with the + * corresponding sub-trees + */ + NewProgress(&prSubClusterDistanceProgress, LogGetFP(&rLog, LOG_INFO), + "Distance calculation within sub-clusters", bPrintCR); + /* for each cluster */ + for (iClusterIndex=0; + iClusterIndex < prKMeansResult->iNClusters; iClusterIndex++) { + /* distance matrix for the sub-cluster */ + symmatrix_t *prWithinClusterDistances = NULL; + int iNSeqInCluster; + tree_t *prSubClusterTree = NULL; + + ProgressLog(prSubClusterDistanceProgress, + iClusterIndex, prKMeansResult->iNClusters, FALSE); + +#if FULL_WITHIN_CLUSTER_DISTANCES + mseq_t *prSubClusterMSeq; + int iPairDistType; + int iSeqIndex; + int iOldLogLevel; + + Log(&rLog, LOG_DEBUG, + "%s\n", "Calling new Mbed use makes only sense if nseq>MAX_ALLOWED_SEQ_PER_PRECLUSTER"); + + if (TRUE == prMSeq->aligned) { + iPairDistType = PAIRDIST_SQUIDID_KIMURA; + } else { + iPairDistType = PAIRDIST_KTUPLE; + } +#endif + + iNSeqInCluster = prKMeansResult->piNObjsPerCluster[iClusterIndex]; +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "#seqs in subcluster no %d = %d", + iClusterIndex, iNSeqInCluster); +#endif + +#if FULL_WITHIN_CLUSTER_DISTANCES + /* create an mseq structure for sequences in this cluster + * don't need most of the members (e.g. orig_seq) but copy + * them anyway for the sake of completeness + */ + NewMSeq(&prSubClusterMSeq); + + prSubClusterMSeq->nseqs = iNSeqInCluster; + prSubClusterMSeq->seqtype = prMSeq->seqtype; + if (NULL!=prMSeq->filename) { + prSubClusterMSeq->filename = CkStrdup(prMSeq->filename); + } + prSubClusterMSeq->aligned = prMSeq->aligned; /* FS, r252 */ + prSubClusterMSeq->seq = (char **) + CKMALLOC(prSubClusterMSeq->nseqs * sizeof(char *)); + prSubClusterMSeq->orig_seq = (char **) + CKMALLOC(prSubClusterMSeq->nseqs * sizeof(char *)); + prSubClusterMSeq->sqinfo = (SQINFO *) + CKMALLOC(prSubClusterMSeq->nseqs * sizeof(SQINFO)); + + for (iSeqIndex=0; iSeqIndexppiObjIndicesPerCluster[iClusterIndex][iSeqIndex]; + prSubClusterMSeq->seq[iSeqIndex] = CkStrdup(prMSeq->seq[iRealSeqIndex]); + prSubClusterMSeq->orig_seq[iSeqIndex] = CkStrdup(prMSeq->orig_seq[iRealSeqIndex]); + SeqinfoCopy(&prSubClusterMSeq->sqinfo[iSeqIndex], &prMSeq->sqinfo[iRealSeqIndex]); +#if TRACE + Log(&rLog, LOG_DEBUG, "seq no %d in cluster %d is %s (real index = %d)", + iSeqIndex, iClusterIndex, prSubClusterMSeq->sqinfo[iSeqIndex].name, + iRealSeqIndex); +#endif + } +#endif + + + /* Create a distance matrix for this sub-cluster + * (prWithinClusterDistances) by using the vector distances or + * ktuple distances. + * + * Then apply UPGMA to get a subcluster tree + * (prSubClusterTree) and append created tree to the + * pre-cluster-tree (prMbedTree_p) + * + */ +#if FULL_WITHIN_CLUSTER_DISTANCES + + iOldLogLevel = rLog.iLogLevelEnabled; + rLog.iLogLevelEnabled = LOG_WARN; + /* compute distances, but be quiet */ + if (PairDistances(&prWithinClusterDistances, prSubClusterMSeq, iPairDistType, + 0, prSubClusterMSeq->nseqs, 0, prSubClusterMSeq->nseqs, + NULL, NULL)) { + Log(&rLog, LOG_ERROR, "Couldn't compute pair distances"); + return -1; + } + rLog.iLogLevelEnabled = iOldLogLevel; + +#if COMPUTE_WITHIN_SUBCLUSTER_AVERAGE + { + double dSum = 0.0; + for (iI=0; iInseqs; iI++) { + for (iJ=iI+1; iJnseqs; iJ++) { + dSum += SymMatrixGetValue(prWithinClusterDistances, iI, iJ); + } + } + Log(&rLog, LOG_FORCED_DEBUG, + "mean pair-wise distance within subcluster %d of %d = %f", + iClusterIndex, prKMeansResult->iNClusters, dSum/prSubClusterMSeq->nseqs); + } +#endif + +#else + if (NewSymMatrix(&prWithinClusterDistances, iNSeqInCluster, iNSeqInCluster)!=0) { + Log(&rLog, LOG_FATAL, "%s", "Memory allocation for disparity matrix failed"); + } + for (iI=0; iIppiObjIndicesPerCluster[iClusterIndex][iI]; + + for (iJ=iI+1; iJppiObjIndicesPerCluster[iClusterIndex][iJ]; + double dist; + + /* Log(&rLog, LOG_FORCED_DEBUG, "Cluster %d: compute distance between %d:%s and %d:%s", + iClusterIndex, i, prMSeq->sqinfo[iRealIndexI].name, + iJ, prMSeq->sqinfo[iRealIndexJ].name); */ + + if (1 == USE_EUCLIDEAN_DISTANCE) { + dist = EuclDist(ppdSeqVec[iRealIndexI], + ppdSeqVec[iRealIndexJ], iNumSeeds); + } else { + dist = CosDist(ppdSeqVec[iRealIndexI], + ppdSeqVec[iRealIndexJ], iNumSeeds); + } + SymMatrixSetValue(prWithinClusterDistances, iI, iJ, dist); + } + } +#endif + + /* labels needed for the guide tree building routine only */ + ppcLabels = (char**) CKMALLOC(iNSeqInCluster * sizeof(char*)); + for (iI=0; iIsqinfo[iI].name; +#else + int iRealIndex = prKMeansResult->ppiObjIndicesPerCluster[iClusterIndex][iI]; + ppcLabels[iI] = prMSeq->sqinfo[iRealIndex].name; +#endif + } +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "Distance matrix for seqs within sub cluster %d/%d", + iClusterIndex, prKMeansResult->iNClusters); + SymMatrixPrint(prWithinClusterDistances, ppcLabels, NULL); +#endif + + + GuideTreeUpgma(&prSubClusterTree, ppcLabels, + prWithinClusterDistances, NULL); + + CKFREE(ppcLabels); /* don't free members, they just point */ +#if 0 + Log(&rLog, LOG_FORCED_DEBUG, "Cluster %d guide-tree:", iClusterIndex); + LogTree(prSubClusterTree); +#endif + + + /* The guide tree id's (that point to the sequences) now start + * from 0, i.e. the association with the prMSeq numbering is + * broken and fixed in the following + */ + for (iNodeIndex = 0; iNodeIndex < (int)GetNodeCount(prSubClusterTree); iNodeIndex++) { + if (IsLeaf(iNodeIndex, prSubClusterTree)) { + int iLeafId = GetLeafId(iNodeIndex, prSubClusterTree); + int iRealId = prKMeansResult->ppiObjIndicesPerCluster[iClusterIndex][iLeafId]; +#if 0 + Log(&rLog, LOG_FORCED_DEBUG, "Correcting leaf node %d which has (wrong) id %d and name %s to id %d (prMSeq name %s)", + iNodeIndex, iLeafId, + GetLeafName(iNodeIndex, prSubClusterTree), + iRealId, prMSeq->sqinfo[iRealId].name); +#endif + SetLeafId(prSubClusterTree, iNodeIndex, iRealId); + } + } + + + /* Append the newly created tree (prSubClusterTree) to the + * corresponding node index of prMbedTree_p. + */ +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "Will join trees at leaf node %d = %s", + piClusterToTreeNode[iClusterIndex], + GetLeafName(piClusterToTreeNode[iClusterIndex], *prMbedTree_p)); +#endif + + AppendTree(*prMbedTree_p, + piClusterToTreeNode[iClusterIndex], + prSubClusterTree); + /* Note: piClusterToTreeNode is still valid, because + * AppendTrees() guarantees that no other than the node to + * append to changes. */ + +#if 0 + Log(&rLog, LOG_FORCED_DEBUG, "%s", "prMbedTree_p after cluster %d has appended:", iClusterIndex); + LogTree(*prMbedTree_p); + + if (0) { + char fname[] = "mbed-joined-tree.dnd"; + FILE *pfOut; + if (NULL == (pfOut = fopen(fname, "w"))) { + Log(&rLog, LOG_FATAL, "Couldn't open %s for writing", fname); + } + MuscleTreeToFile(pfOut, *prMbedTree_p); + Log(&rLog, LOG_FORCED_DEBUG, "Joined tree written to %s", fname); + fclose(pfOut); + Log(&rLog, LOG_FATAL, "DEBUG EXIT"); + } +#endif + + /* cleanup + */ + FreeMuscleTree(prSubClusterTree); + FreeSymMatrix(&prWithinClusterDistances); +#if FULL_WITHIN_CLUSTER_DISTANCES + FreeMSeq(&prSubClusterMSeq); +#endif + } /* end for each cluster */ + ProgressDone(prSubClusterDistanceProgress); + FreeProgress(&prSubClusterDistanceProgress); + + + if (NULL != pcGuidetreeOut) { + if (NULL == (pfOut = fopen(pcGuidetreeOut, "w"))) { + Log(&rLog, LOG_ERROR, "Couldn't open %s for writing", pcGuidetreeOut); + } else { + MuscleTreeToFile(pfOut, *prMbedTree_p); + Log(&rLog, LOG_INFO, "Guide tree written to %s", pcGuidetreeOut); + (void) fclose(pfOut); + } + } + + + /* cleanup + * + */ +#if MBED_TIMING + StopwatchStop(stopwatch); + StopwatchDisplay(stdout, "mBed time (without pairwise distance computation): ", stopwatch); + StopwatchFree(stopwatch); +#endif + + FreeKMeansResult(&prKMeansResult); + FreeSymMatrix(&prPreClusterDistmat); + for (iI=0; iInseqs; iI++) { + CKFREE(ppdSeqVec[iI]); + } + CKFREE(ppdSeqVec); + CKFREE(piClusterToTreeNode); + +#ifndef NDEBUG + TreeValidate(*prMbedTree_p); +#endif + + return 0; +} +/*** end: Mbed() ***/ diff --git a/binaries/src/clustalo/src/clustal/mbed.h b/binaries/src/clustalo/src/clustal/mbed.h new file mode 100644 index 0000000..84b7a3a --- /dev/null +++ b/binaries/src/clustalo/src/clustal/mbed.h @@ -0,0 +1,30 @@ +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: mbed.h 193 2011-02-07 15:45:21Z andreas $ + */ + +#ifndef CLUSTALO_MBED_H +#define CLUSTALO_MBED_H + +#include "muscle_tree.h" +#include "seq.h" + + +extern int +Mbed(tree_t **tree, mseq_t *prMSeq, + const int iPairDistType, const char *pcGuidetreeOutfile); + +#endif diff --git a/binaries/src/clustalo/src/clustal/muscle_tree.c b/binaries/src/clustalo/src/clustal/muscle_tree.c new file mode 100644 index 0000000..c4ba70d --- /dev/null +++ b/binaries/src/clustalo/src/clustal/muscle_tree.c @@ -0,0 +1,2017 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/* This a mix of tree functions and data-structures from + * Bob Edgar's Muscle (version 3.7) ported to pure C, topped up with + * some of our own stuff. + * + * Used files: phy.cpp, tree.h, phytofile.cpp and phyfromclust.cpp + * + * Muscle's code is public domain and so is this code here. + + * From http://www.drive5.com/muscle/license.htm: + * """ + * MUSCLE is public domain software + * + * The MUSCLE software, including object and source code and + * documentation, is hereby donated to the public domain. + * + * Disclaimer of warranty + * THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, + * EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * """ + * + */ + +/* + * RCS $Id: muscle_tree.c 230 2011-04-09 15:37:50Z andreas $ + */ + +#include +#include +#include +#include +#include +#include + +#include "util.h" +#include "log.h" +#include "muscle_tree.h" + + +static const double VERY_NEGATIVE_DOUBLE = -9e29; +/*const double dInsane = VERY_NEGATIVE_DOUBLE;*/ +static const double dInsane = -9e29; +static const unsigned uInsane = 8888888; + +typedef enum +{ + NTT_Unknown, + + /* Returned from Tree::GetToken: */ + NTT_Lparen, + NTT_Rparen, + NTT_Colon, + NTT_Comma, + NTT_Semicolon, + NTT_String, + + /* Following are never returned from Tree::GetToken: */ + NTT_SingleQuotedString, + NTT_DoubleQuotedString, + NTT_Comment +} NEWICK_TOKEN_TYPE; + + +static void +InitCache(uint uCacheCount, tree_t *tree); +static void +TreeZero(tree_t *tree); +static uint +GetNeighborCount(unsigned uNodeIndex, tree_t *tree); +static bool +IsEdge(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree); +static bool +HasEdgeLength(uint uNodeIndex1, uint uNodeIndex2, tree_t *tree); +static void +TreeToFileNodeRooted(tree_t *tree, uint m_uRootNodeIndex, FILE *fp); +static void +ValidateNode(uint uNodeIndex, tree_t *tree); +static void +AssertAreNeighbors(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree); +static void +ExpandCache(tree_t *tree); +static void +TreeCreateRooted(tree_t *tree); +static bool +GetGroupFromFile(FILE *fp, uint uNodeIndex, double *ptrdEdgeLength, tree_t *tree); +static NEWICK_TOKEN_TYPE +GetToken(FILE *fp, char szToken[], uint uBytes); +/* stuff from textfile.cpp */ +static void +FileSkipWhite(FILE *fp); +static bool +FileSkipWhiteX(FILE *fp); +static void +SetLeafName(uint uNodeIndex, const char *ptrName, tree_t *tree); +uint +AppendBranch(tree_t *tree, uint uExistingLeafIndex); +static void +SetEdgeLength(uint uNodeIndex1, uint uNodeIndex2, + double dLength, tree_t *tree); +static uint +UnrootFromFile(tree_t *tree); +uint +GetNeighbor(uint uNodeIndex, uint uNeighborSubscript, tree_t *tree); +static void +InitNode(tree_t *prTree, uint uNodeIndex); + + +/** + * @param[in] uNodeIndex + * node to examine + * @param[in] tree + * tree to examine + * @return id of left node + * @note called GetRight in Muscle3.7 + */ +uint +GetLeft(uint uNodeIndex, tree_t *tree) +{ + assert(NULL != tree); + assert(tree->m_bRooted && uNodeIndex < tree->m_uNodeCount); + return tree->m_uNeighbor2[uNodeIndex]; +} +/*** end: GetLeft ***/ + + + +/** + * @param[in] uNodeIndex + * node to examine + * @param[in] tree + * tree to examine + * @return id of right node + * @note called GetRight in Muscle3.7 + */ +uint +GetRight(uint uNodeIndex, tree_t *tree) +{ + assert(NULL != tree); + assert(tree->m_bRooted && uNodeIndex < tree->m_uNodeCount); + return tree->m_uNeighbor3[uNodeIndex]; +} +/*** end: GetRight ***/ + + + +/** + * @param[in] uNodeIndex + * node to examine + * @param[in] tree + * tree to examine + * @return leaf id of current node + */ +uint +GetLeafId(uint uNodeIndex, tree_t *tree) +{ + assert(NULL != tree); + assert(uNodeIndex < tree->m_uNodeCount); + assert(IsLeaf(uNodeIndex, tree)); + + return tree->m_Ids[uNodeIndex]; +} +/*** end: GetLeafId ***/ + + + +/** + * @note originally called GetLeafName + * + */ +char * +GetLeafName(unsigned uNodeIndex, tree_t *tree) +{ + assert(NULL != tree); + assert(uNodeIndex < tree->m_uNodeCount); + assert(IsLeaf(uNodeIndex, tree)); + return tree->m_ptrName[uNodeIndex]; +} +/*** end: GetLeafName ***/ + + + +/** + * @brief returns first leaf node for a depth-first traversal of tree + * + * @param[in] tree + * tree to traverse + * + * @return node index of first leaf node for depth-first traversal + * + * @note called FirstDepthFirstNode in Muscle3.7 + * + */ +uint +FirstDepthFirstNode(tree_t *tree) +{ + uint uNodeIndex; + + assert(NULL != tree); + assert(IsRooted(tree)); + + /* Descend via left branches until we hit a leaf */ + uNodeIndex = tree->m_uRootNodeIndex; + while (!IsLeaf(uNodeIndex, tree)) + uNodeIndex = GetLeft(uNodeIndex, tree); + return uNodeIndex; +} +/*** end: FirstDepthFirstNode ***/ + + +/** + * @brief returns next leaf node index for depth-first traversal of + * tree + * + * @param[in] tree + * tree to traverse + * @param[in] uNodeIndex + * Current node index + * + * @return node index of next leaf node during depth-first traversal + * + * @note called NextDepthFirstNode in Muscle3.7 + */ +uint +NextDepthFirstNode(uint uNodeIndex, tree_t *tree) +{ + uint uParent; + + assert(NULL != tree); + assert(IsRooted(tree)); + assert(uNodeIndex < tree->m_uNodeCount); + + if (IsRoot(uNodeIndex, tree)) + { + /* Node uNodeIndex is root, end of traversal */ + return NULL_NEIGHBOR; + } + + uParent = GetParent(uNodeIndex, tree); + if (GetRight(uParent, tree) == uNodeIndex) { + /* Is right branch, return parent=uParent */ + return uParent; + } + + uNodeIndex = GetRight(uParent, tree); + /* Descend left from right sibling uNodeIndex */ + while (!IsLeaf(uNodeIndex, tree)) { + uNodeIndex = GetLeft(uNodeIndex, tree); + } + + /* bottom out at leaf uNodeIndex */ + return uNodeIndex; +} +/*** end: NextDepthFirstNode ***/ + + + +/** + * @brief check if tree is a rooted tree + * @param[in] tree + * tree to check + * @return TRUE if given tree is rooted, FALSE otherwise + * + */ +bool +IsRooted(tree_t *tree) +{ + assert(NULL != tree); + return tree->m_bRooted; +} +/*** end: IsRooted ***/ + + +/** + * + */ +void +FreeMuscleTree(tree_t *tree) +{ + uint i; + + assert(tree!=NULL); + + + /* FIXME use GetLeafNodeIndex? or + for (unsigned uNodeIndex = 0; uNodeIndex < m_uNodeCount; ++uNodeIndex) + { + if (tree.IsLeaf(uNodeIndex)) + { + const char *ptrName = + tree.GetLeafName(uNodeIndex); + */ + /* IsLeaf needs m_uNodeCount and all m_uNeighbor's + * so free first + */ + for (i=0; im_uNodeCount; i++) { + /* IsLeaf needs neighbour count, so free those guys later */ + if (IsLeaf(i, tree)) { + CKFREE(tree->m_ptrName[i]); + } + } + CKFREE(tree->m_ptrName); + + CKFREE(tree->m_uNeighbor1); + CKFREE(tree->m_uNeighbor2); + CKFREE(tree->m_uNeighbor3); + + CKFREE(tree->m_Ids); + + CKFREE(tree->m_dEdgeLength1); + CKFREE(tree->m_dEdgeLength2); + CKFREE(tree->m_dEdgeLength3); +#if USE_HEIGHT + CKFREE(tree->m_dHeight); + CKFREE(tree->m_bHasHeight); +#endif + CKFREE(tree->m_bHasEdgeLength1); + CKFREE(tree->m_bHasEdgeLength2); + CKFREE(tree->m_bHasEdgeLength3); + + TreeZero(tree); + + free(tree); +} +/*** end: FreeMuscleTree ***/ + + + +/** + * @brief create a muscle tree + * + * @note Original comment in Muscle code: "Create rooted tree from a + * vector description. Node indexes are 0..N-1 for leaves, N..2N-2 for + * internal nodes. Vector subscripts are i-N and have values for + * internal nodes only, but those values are node indexes 0..2N-2. So + * e.g. if N=6 and Left[2]=1, this means that the third internal node + * (node index 8) has the second leaf (node index 1) as its left + * child. uRoot gives the vector subscript of the root, so add N to + * get the node index." + * + * @param[out] tree + * newly created tree + * @param[in] uLeafCount + * number of leaf nodes + * @param[in] uRoot + * Internal node index of root node + * @param[in] Left + * Node index of left sibling of an internal node. + * Index range: 0--uLeafCount-1 + * @param[in] Right + * Node index of right sibling of an internal node. + * Index range: 0--uLeafCount-1 + * @param[in] LeftLength + * Branch length of left branch of an internal node. + * Index range: 0--uLeafCount-1 + * @param[in] RightLength + * Branch length of right branch of an internal node. + * Index range: 0--uLeafCount-1 + * @param[in] LeafIds + * Leaf id. Index range: 0--uLeafCount + * @param[in] LeafNames + * Leaf label. Index range: 0--uLeafCount + * + */ +void +MuscleTreeCreate(tree_t *tree, + uint uLeafCount, uint uRoot, + const uint *Left, const uint *Right, + const float *LeftLength, const float* RightLength, + const uint *LeafIds, char **LeafNames) +{ + uint uNodeIndex; + + TreeZero(tree); + tree->m_uNodeCount = 2*uLeafCount - 1; + InitCache(tree->m_uNodeCount, tree); + + for (uNodeIndex = 0; uNodeIndex < uLeafCount; ++uNodeIndex) { + tree->m_Ids[uNodeIndex] = LeafIds[uNodeIndex]; + tree->m_ptrName[uNodeIndex] = CkStrdup(LeafNames[uNodeIndex]); + } + + for (uNodeIndex = uLeafCount; uNodeIndex < tree->m_uNodeCount; ++uNodeIndex) { + uint v = uNodeIndex - uLeafCount; + uint uLeft = Left[v]; + uint uRight = Right[v]; + float fLeft = LeftLength[v]; + float fRight = RightLength[v]; + + tree->m_uNeighbor2[uNodeIndex] = uLeft; + tree->m_uNeighbor3[uNodeIndex] = uRight; + + tree->m_bHasEdgeLength2[uNodeIndex] = TRUE; + tree->m_bHasEdgeLength3[uNodeIndex] = TRUE; + + tree->m_dEdgeLength2[uNodeIndex] = fLeft; + tree->m_dEdgeLength3[uNodeIndex] = fRight; + + tree->m_uNeighbor1[uLeft] = uNodeIndex; + tree->m_uNeighbor1[uRight] = uNodeIndex; + + tree->m_dEdgeLength1[uLeft] = fLeft; + tree->m_dEdgeLength1[uRight] = fRight; + + tree->m_bHasEdgeLength1[uLeft] = TRUE; + tree->m_bHasEdgeLength1[uRight] = TRUE; + } + + tree->m_bRooted = TRUE; + tree->m_uRootNodeIndex = uRoot + uLeafCount; +#ifndef NDEBUG + TreeValidate(tree); +#endif +} +/*** end: MuscleTreeCreate ***/ + + + +/** + * @param[in] tree + * tree to write + * @param[out] fp + * filepointer to write to2 + * + * @brief write a muscle tree to a file in newick format (distances + * and all names) + * + * + */ +void +MuscleTreeToFile(FILE *fp, tree_t *tree) +{ + assert(NULL != tree); + if (IsRooted(tree)) { + TreeToFileNodeRooted(tree, tree->m_uRootNodeIndex, fp); + fprintf(fp, ";\n"); + return; + } else { + Log(&rLog, LOG_FATAL, "FIXME: output of unrooted muscle trees not implemented"); + } +} +/*** end: MuscleTreeToFile ***/ + + + +/** + * @brief check if given node is a leaf node + * + * @param[in] uNodeIndex + * the node index + * @param tree + * the tree + * + * @return TRUE if given node is a leaf, FALSE otherwise + * + * @note called IsLeaf in Muscle3.7. See tree.h in original code + */ +bool +IsLeaf(uint uNodeIndex, tree_t *tree) +{ + assert(NULL != tree); + assert(uNodeIndex < tree->m_uNodeCount); + if (1 == tree->m_uNodeCount) + return TRUE; + return 1 == GetNeighborCount(uNodeIndex, tree); +} +/*** end: IsLeaf ***/ + + + +/** + */ +bool +IsRoot(uint uNodeIndex, tree_t *tree) +{ + assert(NULL != tree); + return IsRooted(tree) && tree->m_uRootNodeIndex == uNodeIndex; +} +/*** end: IsRoot ***/ + + + +/** + */ +uint +GetNeighborCount(uint uNodeIndex, tree_t *tree) +{ + uint n1, n2, n3; + assert(uNodeIndex < tree->m_uNodeCount); + assert(NULL != tree); + assert(NULL != tree->m_uNeighbor1); + assert(NULL != tree->m_uNeighbor2); + assert(NULL != tree->m_uNeighbor3); + n1 = tree->m_uNeighbor1[uNodeIndex]; + n2 = tree->m_uNeighbor2[uNodeIndex]; + n3 = tree->m_uNeighbor3[uNodeIndex]; + return (NULL_NEIGHBOR != n1) + (NULL_NEIGHBOR != n2) + (NULL_NEIGHBOR != n3); +} +/*** end: GetNeighborCount ***/ + + +/** + */ +uint +GetParent(unsigned uNodeIndex, tree_t *tree) +{ + assert(NULL != tree); + assert(tree->m_bRooted && uNodeIndex < tree->m_uNodeCount); + return tree->m_uNeighbor1[uNodeIndex]; +} +/*** end: GetParent ***/ + + + +/** + */ +bool +IsEdge(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree) +{ + assert(uNodeIndex1 < tree->m_uNodeCount && uNodeIndex2 < tree->m_uNodeCount); + assert(NULL != tree); + + return tree->m_uNeighbor1[uNodeIndex1] == uNodeIndex2 || + tree->m_uNeighbor2[uNodeIndex1] == uNodeIndex2 || + tree->m_uNeighbor3[uNodeIndex1] == uNodeIndex2; +} +/*** end: IsEdge ***/ + + + +/** + */ +bool +HasEdgeLength(uint uNodeIndex1, uint uNodeIndex2, tree_t *tree) +{ + assert(NULL != tree); + assert(uNodeIndex1 < tree->m_uNodeCount); + assert(uNodeIndex2 < tree->m_uNodeCount); + assert(IsEdge(uNodeIndex1, uNodeIndex2, tree)); + + if (tree->m_uNeighbor1[uNodeIndex1] == uNodeIndex2) + return tree->m_bHasEdgeLength1[uNodeIndex1]; + else if (tree->m_uNeighbor2[uNodeIndex1] == uNodeIndex2) + return tree->m_bHasEdgeLength2[uNodeIndex1]; + assert(tree->m_uNeighbor3[uNodeIndex1] == uNodeIndex2); + return tree->m_bHasEdgeLength3[uNodeIndex1]; +} +/*** end: ***/ + + +/** + */ +double +GetEdgeLength(uint uNodeIndex1, uint uNodeIndex2, tree_t *tree) +{ + assert(NULL != tree); + assert(uNodeIndex1 < tree->m_uNodeCount && uNodeIndex2 < tree->m_uNodeCount); + if (!HasEdgeLength(uNodeIndex1, uNodeIndex2, tree)) + { + Log(&rLog, LOG_FATAL, "Missing edge length in tree %u-%u", uNodeIndex1, uNodeIndex2); + } + + if (tree->m_uNeighbor1[uNodeIndex1] == uNodeIndex2) + return tree->m_dEdgeLength1[uNodeIndex1]; + else if (tree->m_uNeighbor2[uNodeIndex1] == uNodeIndex2) + return tree->m_dEdgeLength2[uNodeIndex1]; + assert(tree->m_uNeighbor3[uNodeIndex1] == uNodeIndex2); + return tree->m_dEdgeLength3[uNodeIndex1]; +} +/*** end: GetEdgeLength ***/ + + +/** + * + */ +void +InitNode(tree_t *prTree, uint uNodeIndex) +{ + prTree->m_uNeighbor1[uNodeIndex] = NULL_NEIGHBOR; + prTree->m_uNeighbor2[uNodeIndex] = NULL_NEIGHBOR; + prTree->m_uNeighbor3[uNodeIndex] = NULL_NEIGHBOR; + prTree->m_bHasEdgeLength1[uNodeIndex] = FALSE; + prTree->m_bHasEdgeLength2[uNodeIndex] = FALSE; + prTree->m_bHasEdgeLength3[uNodeIndex] = FALSE; +#if USE_HEIGHT + prTree->m_bHasHeight[uNodeIndex] = FALSE; + prTree->m_dHeight[uNodeIndex] = dInsane; +#endif + prTree->m_dEdgeLength1[uNodeIndex] = dInsane; + prTree->m_dEdgeLength2[uNodeIndex] = dInsane; + prTree->m_dEdgeLength3[uNodeIndex] = dInsane; + + prTree->m_ptrName[uNodeIndex] = NULL; + prTree->m_Ids[uNodeIndex] = uInsane; +} +/*** end: InitNode ***/ + + +/** + * + */ +void +InitCache(uint uCacheCount, tree_t *tree) +{ + uint uNodeIndex; + + tree->m_uCacheCount = uCacheCount; + + tree->m_uNeighbor1 = (uint *) CKMALLOC(sizeof(uint) * tree->m_uCacheCount); + tree->m_uNeighbor2 = (uint *) CKMALLOC(sizeof(uint) * tree->m_uCacheCount); + tree->m_uNeighbor3 = (uint *) CKMALLOC(sizeof(uint) * tree->m_uCacheCount); + + tree->m_Ids = (uint *) CKMALLOC(sizeof(uint) * tree->m_uCacheCount); + + tree->m_dEdgeLength1 = (double *) CKMALLOC(sizeof(double) * tree->m_uCacheCount); + tree->m_dEdgeLength2 = (double *) CKMALLOC(sizeof(double) * tree->m_uCacheCount); + tree->m_dEdgeLength3 = (double *) CKMALLOC(sizeof(double) * tree->m_uCacheCount); +#if USE_HEIGHT + tree->m_dHeight = (double *) CKMALLOC(sizeof(double) * tree->m_uCacheCount); + tree->m_bHasHeight = (bool *) CKMALLOC(sizeof(bool) * tree->m_uCacheCount); +#endif + tree->m_bHasEdgeLength1 = (bool *) CKMALLOC(sizeof(bool) * tree->m_uCacheCount); + tree->m_bHasEdgeLength2 = (bool *) CKMALLOC(sizeof(bool) * tree->m_uCacheCount); + tree->m_bHasEdgeLength3 = (bool *) CKMALLOC(sizeof(bool) * tree->m_uCacheCount); + + tree->m_ptrName = (char **) CKMALLOC(sizeof(char *) * tree->m_uCacheCount); + + for (uNodeIndex = 0; uNodeIndex < tree->m_uNodeCount; ++uNodeIndex) { + InitNode(tree, uNodeIndex); + } +} +/*** end: InitCache ***/ + + + + +/** + * + * @note Replacing Tree::Clear but no freeing of memory! Just setting + * everything to 0/NULL + */ +void +TreeZero(tree_t *tree) +{ + assert(NULL != tree); + tree->m_uNodeCount = 0; + tree->m_uCacheCount = 0; + + tree->m_uNeighbor1 = NULL; + tree->m_uNeighbor2 = NULL; + tree->m_uNeighbor3 = NULL; + + tree->m_dEdgeLength1 = NULL; + tree->m_dEdgeLength2 = NULL; + tree->m_dEdgeLength3 = NULL; + +#if USE_HEIGHT + tree->m_dHeight = NULL; + tree->m_bHasHeight = NULL; +#endif + tree->m_bHasEdgeLength1 = NULL; + tree->m_bHasEdgeLength2 = NULL; + tree->m_bHasEdgeLength3 = NULL; + + tree->m_ptrName = NULL; + tree->m_Ids = NULL; + + tree->m_bRooted = FALSE; + tree->m_uRootNodeIndex = 0; +} +/* end: TreeZero */ + + + +/** + * + */ +void +TreeToFileNodeRooted(tree_t *tree, uint uNodeIndex, FILE *fp) +{ + bool bGroup; + + assert(IsRooted(tree)); + assert(NULL != tree); + bGroup = !IsLeaf(uNodeIndex, tree) || IsRoot(uNodeIndex, tree); + + if (bGroup) + fprintf(fp, "(\n"); + + + if (IsLeaf(uNodeIndex, tree)) { + /* File.PutString(GetName(uNodeIndex)); */ + fprintf(fp, "%s", tree->m_ptrName[uNodeIndex]); + } else { + TreeToFileNodeRooted(tree, GetLeft(uNodeIndex, tree), fp); + fprintf(fp, ",\n"); + TreeToFileNodeRooted(tree, GetRight(uNodeIndex, tree), fp); + } + + if (bGroup) + fprintf(fp, ")"); + + if (!IsRoot(uNodeIndex, tree)) { + uint uParent = GetParent(uNodeIndex, tree); + if (HasEdgeLength(uNodeIndex, uParent, tree)) + fprintf(fp, ":%g", GetEdgeLength(uNodeIndex, uParent, tree)); + } + fprintf(fp, "\n"); +} +/*** end: TreeToFileNodeRooted ***/ + + +/** + * + * + */ +void +TreeValidate(tree_t *tree) +{ + uint uNodeIndex; + assert(NULL != tree); + for (uNodeIndex = 0; uNodeIndex < tree->m_uNodeCount; ++uNodeIndex) { + ValidateNode(uNodeIndex, tree); + } + /* FIXME: maybe set negative length to zero? What impact would + * that have? */ +} +/*** end TreeValidate ***/ + + + +/** + * + * + */ +void +ValidateNode(uint uNodeIndex, tree_t *tree) +{ + uint uNeighborCount; + uint n1, n2, n3; + assert(NULL != tree); + + if (uNodeIndex >= tree->m_uNodeCount) + Log(&rLog, LOG_FATAL, "ValidateNode(%u), %u nodes", uNodeIndex, tree->m_uNodeCount); + + uNeighborCount = GetNeighborCount(uNodeIndex, tree); + + + if (2 == uNeighborCount) { + if (!tree->m_bRooted) { + Log(&rLog, LOG_FATAL, "Tree::ValidateNode: Node %u has two neighbors, tree is not rooted", + uNodeIndex); + } + if (uNodeIndex != tree->m_uRootNodeIndex) { + Log(&rLog, LOG_FATAL, "Tree::ValidateNode: Node %u has two neighbors, but not root node=%u", + uNodeIndex, tree->m_uRootNodeIndex); + } + } + + n1 = tree->m_uNeighbor1[uNodeIndex]; + n2 = tree->m_uNeighbor2[uNodeIndex]; + n3 = tree->m_uNeighbor3[uNodeIndex]; + + if (NULL_NEIGHBOR == n2 && NULL_NEIGHBOR != n3) { + Log(&rLog, LOG_FATAL, "Tree::ValidateNode, n2=null, n3!=null", uNodeIndex); + } + if (NULL_NEIGHBOR == n3 && NULL_NEIGHBOR != n2) { + Log(&rLog, LOG_FATAL, "Tree::ValidateNode, n3=null, n2!=null", uNodeIndex); + } + + if (n1 != NULL_NEIGHBOR) + AssertAreNeighbors(uNodeIndex, n1, tree); + if (n2 != NULL_NEIGHBOR) + AssertAreNeighbors(uNodeIndex, n2, tree); + if (n3 != NULL_NEIGHBOR) + AssertAreNeighbors(uNodeIndex, n3, tree); + + + + if (n1 != NULL_NEIGHBOR && (n1 == n2 || n1 == n3)) { + Log(&rLog, LOG_FATAL, "Tree::ValidateNode, duplicate neighbors in node %u", uNodeIndex); + } + if (n2 != NULL_NEIGHBOR && (n2 == n1 || n2 == n3)) { + Log(&rLog, LOG_FATAL, "Tree::ValidateNode, duplicate neighbors in node %u", uNodeIndex); + } + if (n3 != NULL_NEIGHBOR && (n3 == n1 || n3 == n2)) { + Log(&rLog, LOG_FATAL, "Tree::ValidateNode, duplicate neighbors in node %u", uNodeIndex); + } + + + if (IsRooted(tree)) { + if (NULL_NEIGHBOR == GetParent(uNodeIndex, tree)) { + if (uNodeIndex != tree->m_uRootNodeIndex) { + Log(&rLog, LOG_FATAL, "Tree::ValiateNode(%u), no parent", uNodeIndex); + } + } else if (GetLeft(GetParent(uNodeIndex, tree), tree) != uNodeIndex && + GetRight(GetParent(uNodeIndex, tree), tree) != uNodeIndex) { + Log(&rLog, LOG_FATAL, "Tree::ValidateNode(%u), parent / child mismatch", uNodeIndex); + } + } +} +/*** end: ValidateNode ***/ + + +/** + * + * + */ +void +AssertAreNeighbors(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree) +{ + bool Has12, Has21; + assert(NULL != tree); + + if (uNodeIndex1 >= tree->m_uNodeCount || uNodeIndex2 >= tree->m_uNodeCount) + Log(&rLog, LOG_FATAL, "AssertAreNeighbors(%u,%u), are %u nodes", + uNodeIndex1, uNodeIndex2, tree->m_uNodeCount); + + if (tree->m_uNeighbor1[uNodeIndex1] != uNodeIndex2 && + tree->m_uNeighbor2[uNodeIndex1] != uNodeIndex2 && + tree->m_uNeighbor3[uNodeIndex1] != uNodeIndex2) { + Log(&rLog, LOG_FATAL, "AssertAreNeighbors(%u,%u) failed", uNodeIndex1, uNodeIndex2); + } + + + if (tree->m_uNeighbor1[uNodeIndex2] != uNodeIndex1 && + tree->m_uNeighbor2[uNodeIndex2] != uNodeIndex1 && + tree->m_uNeighbor3[uNodeIndex2] != uNodeIndex1) { + Log(&rLog, LOG_FATAL, "AssertAreNeighbors(%u,%u) failed", uNodeIndex1, uNodeIndex2); + } + + + Has12 = HasEdgeLength(uNodeIndex1, uNodeIndex2, tree); + Has21 = HasEdgeLength(uNodeIndex2, uNodeIndex1, tree); + if (Has12 != Has21) { + HasEdgeLength(uNodeIndex1, uNodeIndex2, tree); + HasEdgeLength(uNodeIndex2, uNodeIndex1, tree); + Log(&rLog, LOG_ERROR, "HasEdgeLength(%u, %u)=%c HasEdgeLength(%u, %u)=%c\n", + uNodeIndex1, + uNodeIndex2, + Has12 ? 'T' : 'F', + uNodeIndex2, + uNodeIndex1, + Has21 ? 'T' : 'F'); + Log(&rLog, LOG_FATAL, "Tree::AssertAreNeighbors, HasEdgeLength not symmetric"); + } + + + if (Has12) { + double d12 = GetEdgeLength(uNodeIndex1, uNodeIndex2, tree); + double d21 = GetEdgeLength(uNodeIndex2, uNodeIndex1, tree); + if (d12 != d21) { + Log(&rLog, LOG_FATAL, "Tree::AssertAreNeighbors, Edge length disagrees %u-%u=%.3g, %u-%u=%.3g", + uNodeIndex1, uNodeIndex2, d12, + uNodeIndex2, uNodeIndex1, d21); + } + } +} +/*** end: AssertAreNeighbors ***/ + + + +/** + * + * @note see phyfromfile.cpp in Muscle3.7. Tree has to be a pointer to + * an already allocated tree structure. + * + * return non-Zero on failure + * + * leafids will not be set here (FIXME:CHECK if true) + */ +int +MuscleTreeFromFile(tree_t *tree, char *ftree) +{ + double dEdgeLength; + bool bEdgeLength; + char szToken[16]; + NEWICK_TOKEN_TYPE NTT; + unsigned uThirdNode; + FILE *fp = NULL; + + assert(tree!=NULL); + assert(ftree!=NULL); + + if (NULL == (fp=fopen(ftree, "r"))) { + Log(&rLog, LOG_ERROR, "Couldn't open tree-file '%s' for reading. Skipping", ftree); + return -1; + } + + /* Assume rooted. + * If we discover that it is unrooted, will convert on the fly. + */ + TreeCreateRooted(tree); + + bEdgeLength = GetGroupFromFile(fp, 0, &dEdgeLength, tree); + + + /* Next token should be either ';' for rooted tree or ',' for + * unrooted. + */ + NTT = GetToken(fp, szToken, sizeof(szToken)); + + /* If rooted, all done. */ + if (NTT_Semicolon == NTT) { + if (bEdgeLength) + Log(&rLog, LOG_WARN, " *** Warning *** edge length on root group in Newick file %s\n", ftree); + TreeValidate(tree); + fclose(fp); + return 0; + } + + if (NTT_Comma != NTT) + Log(&rLog, LOG_FATAL, "Tree::FromFile, expected ';' or ',', got '%s'", szToken); + + uThirdNode = UnrootFromFile(tree); + bEdgeLength = GetGroupFromFile(fp, uThirdNode, &dEdgeLength, tree); + if (bEdgeLength) + SetEdgeLength(0, uThirdNode, dEdgeLength, tree); + TreeValidate(tree); + + fclose(fp); + return 0; +} +/*** end MuscleTreeFromFile ***/ + + + +/** + * + */ +void +ExpandCache(tree_t *tree) +{ + const uint uNodeCount = 100; + uint uNewCacheCount; + uint *uNewNeighbor1, *uNewNeighbor2, *uNewNeighbor3; + uint *uNewIds; + double *dNewEdgeLength1, *dNewEdgeLength2, *dNewEdgeLength3; +#if USE_HEIGHT + double *dNewHeight; + bool *bNewHasHeight; +#endif + bool *bNewHasEdgeLength1, *bNewHasEdgeLength2, *bNewHasEdgeLength3; + char **ptrNewName; + + assert(NULL != tree); + uNewCacheCount = tree->m_uCacheCount + uNodeCount; + uNewNeighbor1 = (uint *) CKMALLOC( + uNewCacheCount * sizeof(uint)); + uNewNeighbor2 = (uint *) CKMALLOC( + uNewCacheCount * sizeof(uint)); + uNewNeighbor3 = (uint *) CKMALLOC( + uNewCacheCount * sizeof(uint)); + + uNewIds = (uint *) CKCALLOC( + uNewCacheCount, sizeof(uint)); + + dNewEdgeLength1 = (double *) CKMALLOC( + uNewCacheCount * sizeof(double)); + dNewEdgeLength2 = (double *) CKMALLOC( + uNewCacheCount * sizeof(double)); + dNewEdgeLength3 = (double *) CKMALLOC( + uNewCacheCount * sizeof(double)); +#if USE_HEIGHT + dNewHeight = (double *) CKMALLOC( + uNewCacheCount * sizeof(double)); + bNewHasHeight = (bool *) CKMALLOC( + uNewCacheCount * sizeof(bool)); +#endif + + bNewHasEdgeLength1 = (bool *) CKMALLOC( + uNewCacheCount * sizeof(bool)); + bNewHasEdgeLength2 = (bool *) CKMALLOC( + uNewCacheCount * sizeof(bool)); + bNewHasEdgeLength3 = (bool *) CKMALLOC( + uNewCacheCount * sizeof(bool)); + ptrNewName = (char **) CKCALLOC(uNewCacheCount, sizeof(char*)); + + if (tree->m_uCacheCount > 0) { + uint uUnsignedBytes, uEdgeBytes; + uint uBoolBytes, uNameBytes; + + uUnsignedBytes = tree->m_uCacheCount*sizeof(uint); + + memcpy(uNewNeighbor1, tree->m_uNeighbor1, uUnsignedBytes); + memcpy(uNewNeighbor2, tree->m_uNeighbor2, uUnsignedBytes); + memcpy(uNewNeighbor3, tree->m_uNeighbor3, uUnsignedBytes); + + memcpy(uNewIds, tree->m_Ids, uUnsignedBytes); + + uEdgeBytes = tree->m_uCacheCount*sizeof(double); + memcpy(dNewEdgeLength1, tree->m_dEdgeLength1, uEdgeBytes); + memcpy(dNewEdgeLength2, tree->m_dEdgeLength2, uEdgeBytes); + memcpy(dNewEdgeLength3, tree->m_dEdgeLength3, uEdgeBytes); +#if USE_HEIGHT + memcpy(dNewHeight, tree->m_dHeight, uEdgeBytes); +#endif + + uBoolBytes = tree->m_uCacheCount*sizeof(bool); + memcpy(bNewHasEdgeLength1, tree->m_bHasEdgeLength1, uBoolBytes); + memcpy(bNewHasEdgeLength2, tree->m_bHasEdgeLength2, uBoolBytes); + memcpy(bNewHasEdgeLength3, tree->m_bHasEdgeLength3, uBoolBytes); +#if USE_HEIGHT + memcpy(bNewHasHeight, tree->m_bHasHeight, uBoolBytes); +#endif + uNameBytes = tree->m_uCacheCount*sizeof(char *); + memcpy(ptrNewName, tree->m_ptrName, uNameBytes); + + /* similiar to FreeMuscleTree + */ + + /* IsLeaf needs m_uNodeCount and all m_uNeighbor's + * so free first + */ +#if 0 + for (i=0; im_uNodeCount; i++) { + if (IsLeaf(i, tree)) { +#ifndef NDEBUG + if (NULL==tree->m_ptrName[i]) { + Log(&rLog, LOG_WARN, "FIXME tree->m_ptrName[%d] is already NULL", i); + } +#endif + CKFREE(tree->m_ptrName[i]); + } + } +#endif + CKFREE(tree->m_ptrName); + + CKFREE(tree->m_uNeighbor1); + CKFREE(tree->m_uNeighbor2); + CKFREE(tree->m_uNeighbor3); + + CKFREE(tree->m_Ids); + + CKFREE(tree->m_dEdgeLength1); + CKFREE(tree->m_dEdgeLength2); + CKFREE(tree->m_dEdgeLength3); + + CKFREE(tree->m_bHasEdgeLength1); + CKFREE(tree->m_bHasEdgeLength2); + CKFREE(tree->m_bHasEdgeLength3); +#if USE_HEIGHT + CKFREE(tree->m_bHasHeight); + CKFREE(tree->m_dHeight); +#endif + } + + tree->m_uCacheCount = uNewCacheCount; + tree->m_uNeighbor1 = uNewNeighbor1; + tree->m_uNeighbor2 = uNewNeighbor2; + tree->m_uNeighbor3 = uNewNeighbor3; + tree->m_Ids = uNewIds; + tree->m_dEdgeLength1 = dNewEdgeLength1; + tree->m_dEdgeLength2 = dNewEdgeLength2; + tree->m_dEdgeLength3 = dNewEdgeLength3; + +#ifdef USE_HEIGHT + tree->m_dHeight = dNewHeight; + tree->m_bHasHeight = bNewHasHeight; +#endif + tree->m_bHasEdgeLength1 = bNewHasEdgeLength1; + tree->m_bHasEdgeLength2 = bNewHasEdgeLength2; + tree->m_bHasEdgeLength3 = bNewHasEdgeLength3; + + tree->m_ptrName = ptrNewName; + +} +/*** end: ExpandCache ***/ + + + +/** + * + * Tree must be pointer to an already allocated tree structure + * + */ +void +TreeCreateRooted(tree_t *tree) +{ + TreeZero(tree); + ExpandCache(tree); + tree->m_uNodeCount = 1; + + tree->m_uNeighbor1[0] = NULL_NEIGHBOR; + tree->m_uNeighbor2[0] = NULL_NEIGHBOR; + tree->m_uNeighbor3[0] = NULL_NEIGHBOR; + + tree->m_bHasEdgeLength1[0] = FALSE; + tree->m_bHasEdgeLength2[0] = FALSE; + tree->m_bHasEdgeLength3[0] = FALSE; +#if USE_HEIGHT + tree->m_bHasHeight[0] = FALSE; +#endif + + tree->m_uRootNodeIndex = 0; + tree->m_bRooted = TRUE; + +#ifndef NDEBUG + TreeValidate(tree); +#endif +} +/*** end: TreeCreateRooted ***/ + + +/** + * + */ +uint +UnrootFromFile(tree_t *tree) +{ + uint uThirdNode; +#if TRACE + Log("Before unroot:\n"); + LogMe(); +#endif + + if (!tree->m_bRooted) + Log(&rLog, LOG_FATAL, "Tree::Unroot, not rooted"); + + /* Convention: root node is always node zero */ + assert(IsRoot(0, tree)); + assert(NULL_NEIGHBOR == tree->m_uNeighbor1[0]); + + uThirdNode = tree->m_uNodeCount++; + + tree->m_uNeighbor1[0] = uThirdNode; + tree->m_uNeighbor1[uThirdNode] = 0; + + tree->m_uNeighbor2[uThirdNode] = NULL_NEIGHBOR; + tree->m_uNeighbor3[uThirdNode] = NULL_NEIGHBOR; + + tree->m_dEdgeLength1[0] = 0; + tree->m_dEdgeLength1[uThirdNode] = 0; + tree->m_bHasEdgeLength1[uThirdNode] = TRUE; + + tree->m_bRooted = FALSE; + +#if TRACE + Log("After unroot:\n"); + LogMe(); +#endif + + return uThirdNode; +} +/*** end: UnrootFromFile ***/ + + + +/** + * + * + */ +bool +GetGroupFromFile(FILE *fp, uint uNodeIndex, double *ptrdEdgeLength, tree_t *tree) +{ + char szToken[1024]; + NEWICK_TOKEN_TYPE NTT = GetToken(fp, szToken, sizeof(szToken)); + bool bRightLength; + bool bEof; + char c; + + /* Group is either leaf name or (left, right). */ + if (NTT_String == NTT) { + SetLeafName(uNodeIndex, szToken, tree); +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "Group is leaf '%s'", szToken); +#endif + } else if (NTT_Lparen == NTT) { + const unsigned uLeft = AppendBranch(tree, uNodeIndex); + const unsigned uRight = uLeft + 1; + double dEdgeLength; + bool bLeftLength = GetGroupFromFile(fp, uLeft, &dEdgeLength, tree); + + /* Left sub-group... + */ +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "%s", "Got '(', group is compound, expect left sub-group"); + + if (bLeftLength) { + Log(&rLog, LOG_FORCED_DEBUG, "Edge length for left sub-group: %.3g", dEdgeLength); + } else { + Log(&rLog, LOG_FORCED_DEBUG, "%s", "No edge length for left sub-group"); + } +#endif + if (bLeftLength) + SetEdgeLength(uNodeIndex, uLeft, dEdgeLength, tree); + + /* ... then comma ... + */ +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "%s", "Expect comma"); +#endif + NTT = GetToken(fp, szToken, sizeof(szToken)); + if (NTT_Comma != NTT) + Log(&rLog, LOG_FATAL, "Tree::GetGroupFromFile, expected ',', got '%s'", szToken); + + /* ...then right sub-group... + */ +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "%s", "Expect right sub-group"); +#endif + bRightLength = GetGroupFromFile(fp, uRight, &dEdgeLength, tree); + if (bRightLength) + SetEdgeLength(uNodeIndex, uRight, dEdgeLength, tree); + +#if TRACE + if (bRightLength) + Log(&rLog, LOG_FORCED_DEBUG, "Edge length for right sub-group: %.3g", dEdgeLength); + else + Log(&rLog, LOG_FORCED_DEBUG, "%s", "No edge length for right sub-group"); +#endif + + /* ... then closing parenthesis. + */ +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "%s", "Expect closing parenthesis (or comma if > 2-ary)"); +#endif + NTT = GetToken(fp, szToken, sizeof(szToken)); + if (NTT_Rparen == NTT) + ; + else if (NTT_Comma == NTT) { + if (ungetc(',', fp)==EOF) + Log(&rLog, LOG_FATAL, "%s" "ungetc failed"); + return FALSE; + } else + Log(&rLog, LOG_FATAL, "Tree::GetGroupFromFile, expected ')' or ',', got '%s'", szToken); + } else { + Log(&rLog, LOG_FATAL, "Tree::GetGroupFromFile, expected '(' or leaf name, got '%s'", + szToken); + } + + /* Group may optionally be followed by edge length. + */ + bEof = FileSkipWhiteX(fp); + if (bEof) + return FALSE; + if ((c = fgetc(fp))==EOF) /* GetCharX */ + Log(&rLog, LOG_FATAL, "%s", "fgetc reached end of file"); +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "Character following group, could be colon, is '%c'", c); +#endif + if (':' == c) { + NTT = GetToken(fp, szToken, sizeof(szToken)); + if (NTT_String != NTT) + Log(&rLog, LOG_FATAL, "Tree::GetGroupFromFile, expected edge length, got '%s'", szToken); + *ptrdEdgeLength = atof(szToken); + return TRUE; + } + if (ungetc(c, fp)==EOF) + Log(&rLog, LOG_FATAL, "%s" "ungetc failed"); + + return FALSE; +} +/*** end: GetGroupFromFile ***/ + + + + +/** + * + */ +void +FileSkipWhite(FILE *fp) +{ + bool bEof = FileSkipWhiteX(fp); + if (bEof) + Log(&rLog, LOG_FATAL, "%s", "End-of-file skipping white space"); +} +/*** end: FileSkipWhite ***/ + + + + +/** + * + */ +bool +FileSkipWhiteX(FILE *fp) +{ + for (;;) { + int c; + bool bEof; + + /* GetChar */ + if ((c = fgetc(fp))==EOF) { + bEof = TRUE; + } else { + bEof = FALSE; + } + + if (bEof) + return TRUE; + if (!isspace(c)) { + if (ungetc(c, fp)==EOF) + Log(&rLog, LOG_FATAL, "%s" "ungetc failed"); + break; + } + } + return FALSE; +} +/*** end: FileSkipWhiteX ***/ + + + + +/** + * + */ +NEWICK_TOKEN_TYPE +GetToken(FILE *fp, char szToken[], uint uBytes) +{ + char c; + unsigned uBytesCopied = 0; + NEWICK_TOKEN_TYPE TT; + + /* Skip leading white space */ + FileSkipWhite(fp); + + if ((c = fgetc(fp))==EOF) /* GetCharX */ + Log(&rLog, LOG_FATAL, "%s", "fgetc reached end of file"); + + /* In case a single-character token */ + szToken[0] = c; + szToken[1] = 0; + + switch (c) { + + case '(': + return NTT_Lparen; + + case ')': + return NTT_Rparen; + + case ':': + return NTT_Colon; + + case ';': + return NTT_Semicolon; + + case ',': + return NTT_Comma; + + case '\'': + TT = NTT_SingleQuotedString; + if ((c = fgetc(fp))==EOF) /* GetCharX */ + Log(&rLog, LOG_FATAL, "%s", "fgetc reached end of file"); + break; + + case '"': + TT = NTT_DoubleQuotedString; + if ((c = fgetc(fp))==EOF) /* GetCharX */ + Log(&rLog, LOG_FATAL, "%s", "fgetc reached end of file"); + break; + + case '[': + TT = NTT_Comment; + break; + + default: + TT = NTT_String; + break; + } + + for (;;) + { + bool bEof; + if (TT != NTT_Comment) { + if (uBytesCopied < uBytes - 2) { + szToken[uBytesCopied++] = c; + szToken[uBytesCopied] = 0; + } else { + Log(&rLog, LOG_FATAL, "Tree::GetToken: input buffer too small, token so far='%s'", szToken); + } + } + c = fgetc(fp); /* GetChar */ + bEof = (c==EOF ? TRUE : FALSE); + if (bEof) + return TT; + + switch (TT) { + + case NTT_String: + if (0 != strchr("():;,", c)) { + if (ungetc(c, fp)==EOF) + Log(&rLog, LOG_FATAL, "%s" "ungetc failed"); + return NTT_String; + } + if (isspace(c)) + return NTT_String; + break; + + case NTT_SingleQuotedString: + if ('\'' == c) + return NTT_String; + break; + + case NTT_DoubleQuotedString: + if ('"' == c) + return NTT_String; + break; + + case NTT_Comment: + if (']' == c) + return GetToken(fp, szToken, uBytes); + break; + + default: + Log(&rLog, LOG_FATAL, "Tree::GetToken, invalid TT=%u", TT); + } + } +} +/*** end: GetToken ***/ + + + +/*** SetLeafName + * + */ +void +SetLeafName(unsigned uNodeIndex, const char *ptrName, tree_t *tree) +{ + assert(uNodeIndex < tree->m_uNodeCount); + assert(IsLeaf(uNodeIndex, tree)); + free(tree->m_ptrName[uNodeIndex]); + /*LOG_DEBUG("Setting tree->m_ptrName[uNodeIndex=%d] to %s", uNodeIndex, ptrName);*/ + tree->m_ptrName[uNodeIndex] = CkStrdup(ptrName); +} +/*** end: SetLeafName ***/ + + + + +/** + * + * Append a new branch. This adds two new nodes and joins them to an + * existing leaf node. Return value is k, new nodes have indexes k and + * k+1 respectively. + * + */ +uint +AppendBranch(tree_t *tree, uint uExistingLeafIndex) +{ + uint uNewLeaf1; + uint uNewLeaf2; + + assert(tree!=NULL); + if (0 == tree->m_uNodeCount) { + Log(&rLog, LOG_FATAL, "%s(): %s", __FUNCTION__, "tree has not been created"); + } + assert(NULL_NEIGHBOR == tree->m_uNeighbor2[uExistingLeafIndex]); + assert(NULL_NEIGHBOR == tree->m_uNeighbor3[uExistingLeafIndex]); + assert(uExistingLeafIndex < tree->m_uNodeCount); +#ifndef NDEBUG + if (!IsLeaf(uExistingLeafIndex, tree)) { + Log(&rLog, LOG_FATAL, "AppendBranch(%u): not leaf", uExistingLeafIndex); + } +#endif + + if (tree->m_uNodeCount >= tree->m_uCacheCount - 2) { + ExpandCache(tree); + } + uNewLeaf1 = tree->m_uNodeCount; + uNewLeaf2 = tree->m_uNodeCount + 1; + + tree->m_uNodeCount += 2; + + tree->m_uNeighbor2[uExistingLeafIndex] = uNewLeaf1; + tree->m_uNeighbor3[uExistingLeafIndex] = uNewLeaf2; + + tree->m_uNeighbor1[uNewLeaf1] = uExistingLeafIndex; + tree->m_uNeighbor1[uNewLeaf2] = uExistingLeafIndex; + + tree->m_uNeighbor2[uNewLeaf1] = NULL_NEIGHBOR; + tree->m_uNeighbor2[uNewLeaf2] = NULL_NEIGHBOR; + + tree->m_uNeighbor3[uNewLeaf1] = NULL_NEIGHBOR; + tree->m_uNeighbor3[uNewLeaf2] = NULL_NEIGHBOR; + + tree->m_dEdgeLength2[uExistingLeafIndex] = 0; + tree->m_dEdgeLength3[uExistingLeafIndex] = 0; + + tree->m_dEdgeLength1[uNewLeaf1] = 0; + tree->m_dEdgeLength2[uNewLeaf1] = 0; + tree->m_dEdgeLength3[uNewLeaf1] = 0; + + tree->m_dEdgeLength1[uNewLeaf2] = 0; + tree->m_dEdgeLength2[uNewLeaf2] = 0; + tree->m_dEdgeLength3[uNewLeaf2] = 0; + + tree->m_bHasEdgeLength1[uNewLeaf1] = FALSE; + tree->m_bHasEdgeLength2[uNewLeaf1] = FALSE; + tree->m_bHasEdgeLength3[uNewLeaf1] = FALSE; + + tree->m_bHasEdgeLength1[uNewLeaf2] = FALSE; + tree->m_bHasEdgeLength2[uNewLeaf2] = FALSE; + tree->m_bHasEdgeLength3[uNewLeaf2] = FALSE; + +#if USE_HEIGHT + tree->m_bHasHeight[uNewLeaf1] = FALSE; + tree->m_bHasHeight[uNewLeaf2] = FALSE; +#endif + tree->m_Ids[uNewLeaf1] = uInsane; + tree->m_Ids[uNewLeaf2] = uInsane; + + return uNewLeaf1; +} +/*** end: AppendBranch ***/ + + +/** + * + * + */ +void +SetEdgeLength(uint uNodeIndex1, uint uNodeIndex2, + double dLength, tree_t *tree) +{ + assert(uNodeIndex1 < tree->m_uNodeCount && uNodeIndex2 < tree->m_uNodeCount); + assert(IsEdge(uNodeIndex1, uNodeIndex2, tree)); + + if (tree->m_uNeighbor1[uNodeIndex1] == uNodeIndex2) { + tree->m_dEdgeLength1[uNodeIndex1] = dLength; + tree->m_bHasEdgeLength1[uNodeIndex1] = TRUE; + } else if (tree->m_uNeighbor2[uNodeIndex1] == uNodeIndex2) { + tree->m_dEdgeLength2[uNodeIndex1] = dLength; + tree->m_bHasEdgeLength2[uNodeIndex1] = TRUE; + + } else { + assert(tree->m_uNeighbor3[uNodeIndex1] == uNodeIndex2); + tree->m_dEdgeLength3[uNodeIndex1] = dLength; + tree->m_bHasEdgeLength3[uNodeIndex1] = TRUE; + } + + if (tree->m_uNeighbor1[uNodeIndex2] == uNodeIndex1) { + tree->m_dEdgeLength1[uNodeIndex2] = dLength; + tree->m_bHasEdgeLength1[uNodeIndex2] = TRUE; + } else if (tree->m_uNeighbor2[uNodeIndex2] == uNodeIndex1) { + tree->m_dEdgeLength2[uNodeIndex2] = dLength; + tree->m_bHasEdgeLength2[uNodeIndex2] = TRUE; + } else { + assert(tree->m_uNeighbor3[uNodeIndex2] == uNodeIndex1); + tree->m_dEdgeLength3[uNodeIndex2] = dLength; + tree->m_bHasEdgeLength3[uNodeIndex2] = TRUE; + } +} +/*** end: SetEdgeLength ***/ + + + +/** + * + * Debug output + * + * LogMe in phy.cpp + * + */ +void +LogTree(tree_t *tree, FILE *fp) +{ + uint uNodeIndex; + uint n1, n2, n3; + char *ptrName; + + fprintf(fp, "This is a tree with %u nodes, which is ", tree->m_uNodeCount); + + if (IsRooted(tree)) { + fprintf(fp, "rooted:\n"); + fprintf(fp, "Index Parnt LengthP Left LengthL Right LengthR Id Name\n"); + fprintf(fp, "----- ----- ------- ---- ------- ----- ------- ----- ----\n"); + + } else { + fprintf(fp, "unrooted;\n"); + fprintf(fp, "Index Nbr_1 Length1 Nbr_2 Length2 Nbr_3 Length3 Id Name\n"); + fprintf(fp, "----- ----- ------- ----- ------- ----- ------- ----- ----\n"); + } + + for (uNodeIndex = 0; uNodeIndex < tree->m_uNodeCount; ++uNodeIndex) { + fprintf(fp, "%5u ", uNodeIndex); + n1 = tree->m_uNeighbor1[uNodeIndex]; + n2 = tree->m_uNeighbor2[uNodeIndex]; + n3 = tree->m_uNeighbor3[uNodeIndex]; + + if (NULL_NEIGHBOR != n1) { + fprintf(fp, "%5u ", n1); + if (tree->m_bHasEdgeLength1[uNodeIndex]) + fprintf(fp, "%7.3g ", tree->m_dEdgeLength1[uNodeIndex]); + else + fprintf(fp, " * "); + } else { + fprintf(fp, " "); + } + + if (NULL_NEIGHBOR != n2) { + fprintf(fp, "%5u ", n2); + if (tree->m_bHasEdgeLength2[uNodeIndex]) + fprintf(fp, "%7.3g ", tree->m_dEdgeLength2[uNodeIndex]); + else + fprintf(fp, " * "); + } else { + fprintf(fp, " "); + } + + if (NULL_NEIGHBOR != n3) { + fprintf(fp, "%5u ", n3); + if (tree->m_bHasEdgeLength3[uNodeIndex]) + fprintf(fp, "%7.3g ", tree->m_dEdgeLength3[uNodeIndex]); + else + fprintf(fp, " * "); + } else { + fprintf(fp, " "); + } + + if (tree->m_Ids != 0 && IsLeaf(uNodeIndex, tree)) { + unsigned uId = tree->m_Ids[uNodeIndex]; + if (uId == uInsane) + fprintf(fp, " *"); + else + fprintf(fp, "%5u", uId); + } else { + fprintf(fp, " "); + } + + if (tree->m_bRooted && uNodeIndex == tree->m_uRootNodeIndex) + fprintf(fp, " [ROOT] "); + ptrName = tree->m_ptrName[uNodeIndex]; + if (ptrName != 0) + fprintf(fp, " %s", ptrName); + + fprintf(fp, "\n"); + } +} +/*** end: LogTree ***/ + + + +/** + * + * replaces m_uLeafCount + */ +uint +GetLeafCount(tree_t *tree) +{ + assert(tree!=NULL); + + return (tree->m_uNodeCount+1)/2; +} +/*** GetLeafCount ***/ + + + +/** + * + */ +uint +GetNodeCount(tree_t *tree) +{ + assert(tree!=NULL); + + return 2*(GetLeafCount(tree)) - 1; +} +/*** end: GetNodeCount ***/ + + +/** + * + */ +uint +GetNeighbor(uint uNodeIndex, uint uNeighborSubscript, tree_t *prTree) +{ + assert(uNodeIndex < prTree->m_uNodeCount); + switch (uNeighborSubscript) + { + case 0: + return prTree->m_uNeighbor1[uNodeIndex]; + case 1: + return prTree->m_uNeighbor2[uNodeIndex]; + case 2: + return prTree->m_uNeighbor3[uNodeIndex]; + } + Log(&rLog, LOG_FATAL, "Internal error in %s: sub=%u", __FUNCTION__, uNeighborSubscript); + return NULL_NEIGHBOR; +} +/*** end: GetNeighbor ***/ + + + + + +/** + * + */ +void +SetLeafId(tree_t *tree, uint uNodeIndex, uint uId) +{ + assert(uNodeIndex < tree->m_uNodeCount); + assert(IsLeaf(uNodeIndex, tree)); + tree->m_Ids[uNodeIndex] = uId; +} +/*** end: SetLeafId ***/ + + +/** + * + */ +uint +GetRootNodeIndex(tree_t *tree) +{ + assert(NULL!=tree); + return tree->m_uRootNodeIndex; +} +/*** end: GetRootNodeIndex ***/ + + + +/** + * @note avoid usage if you want to iterate over all indices, because + * this will be slow + * + */ +uint +LeafIndexToNodeIndex(uint uLeafIndex, tree_t *prTree) { + uint uLeafCount = 0; + unsigned uNodeCount = GetNodeCount(prTree); + uint uNodeIndex; + + for (uNodeIndex = 0; uNodeIndex < uNodeCount; uNodeIndex++) { + if (IsLeaf(uNodeIndex, prTree)) { + if (uLeafCount == uLeafIndex) { + return uNodeIndex; + } else { + uLeafCount++; + } + } + } + Log(&rLog, LOG_FATAL, "Internal error: node index out of range"); + return 0; +} +/*** end: LeafIndexToNodeIndex ***/ + + + + +/** + * @brief Append a (source) tree to a (dest) tree to a given node + * which will be replaced. All other nodes in that tree will stay the + * same. + * + * @param[out] prDstTree + * The tree to append to + * @param[in] uDstTreeReplaceNodeIndex + * Dest tree node to which source tree will be appended + * @param[in] prSrcTree + * The tree to append + * + * @note No nodes inside prDstTree will change except + * uDstTreeReplaceNodeIndex + * + * + * @warning: Function won't check or touch the m_Ids/leaf-indices! + * That means if you want to join two trees with leaf indices 1-10 and + * 1-10 your m_Ids/leaf-indices won't be unique anymore and the + * association between your sequences and the tree are broken. Make + * sure m_Ids are unique before calling me. + * + * The easiest would have been to do this by recursively calling + * AppendBranch() (after adding uSrcTreeNodeIndex as extra argument to + * this function). But recursion is evil. Yet another version would be + * to setup all the data and call MuscleTreeCreate() to create a third + * tree, which seems complicated and wasteful. The approach taken here + * is the following: increase dest tree memory, copy over each src + * tree node data and update the indices and counters. This is tricky + * and has a lot of potential for bugs if tree interface is changed + * (and even if it isn't). + * + */ +void +AppendTree(tree_t *prDstTree, uint uDstTreeReplaceNodeIndex, tree_t *prSrcTree) +{ + uint uSrcTreeNodeIndex; + uint uOrgDstTreeNodeCount; + + assert(NULL!=prDstTree); + assert(NULL!=prSrcTree); + assert(uDstTreeReplaceNodeIndex < prDstTree->m_uNodeCount); + assert(IsLeaf(uDstTreeReplaceNodeIndex, prDstTree)); + assert(IsRooted(prDstTree) && IsRooted(prSrcTree)); + + + uOrgDstTreeNodeCount = prDstTree->m_uNodeCount; + + + /* increase dest tree memory + */ + while (prDstTree->m_uCacheCount + < + (GetNodeCount(prDstTree) + GetNodeCount(prSrcTree))) { + ExpandCache(prDstTree); + } + + + /* copy all src tree nodes + * + */ + for (uSrcTreeNodeIndex=0; + uSrcTreeNodeIndexm_uNodeCount; + + /* distinguish 4 cases for src nodes to copy: + * + * 1. src node is the only node, i.e. root & leaf + * + * 2. src node is root: set only left & right, but not parent + * and just replace the given dest index + * + * 3. src node is leaf: set only parent + * + * 4. src node is internal node: update all three neighbours + * + * FIXME: this is messy. Is there a cleaner way to do this by + * merging all cases? + * + */ + if (IsRoot(uSrcTreeNodeIndex, prSrcTree) && IsLeaf(uSrcTreeNodeIndex, prSrcTree)) { + /* special case: if this is the only member in + * tree, i.e. it's root and leaf. Copy leaf name and leaf + * id. No neighbours to update + */ + + /* free dst node name if set */ + if (NULL != prDstTree->m_ptrName[uDstTreeReplaceNodeIndex]) { + CKFREE(prDstTree->m_ptrName[uDstTreeReplaceNodeIndex]); + } + + prDstTree->m_ptrName[uDstTreeReplaceNodeIndex] = + CkStrdup(GetLeafName(uSrcTreeNodeIndex, prSrcTree)); + + prDstTree->m_Ids[uDstTreeReplaceNodeIndex] = + prSrcTree->m_Ids[uSrcTreeNodeIndex]; + + /* no updated of uNodeCount, because we used the replace node */ + +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "Updated dst rpl node %d with the only src leaf node: parent=%d (%f)", + uDstTreeReplaceNodeIndex, + prDstTree->m_uNeighbor1[uDstTreeReplaceNodeIndex], prDstTree->m_dEdgeLength1[uDstTreeReplaceNodeIndex]); +#endif + + } else if (IsRoot(uSrcTreeNodeIndex, prSrcTree)) { + /* src node is root: replace uDstTreeReplaceNodeIndex + * (not uNewDstNodeIndex) with src root, i.e. the + * uDstTreeReplaceNodeIndex becomes an internal node now. + * + * We only have two neighbours 2 & 3 (no parent). Keep old + * parent info (neighbor 1). + */ + + /* free dst node name if set */ + if (NULL != prDstTree->m_ptrName[uDstTreeReplaceNodeIndex]) { + CKFREE(prDstTree->m_ptrName[uDstTreeReplaceNodeIndex]); + } + + prDstTree->m_uNeighbor2[uDstTreeReplaceNodeIndex] = + prSrcTree->m_uNeighbor2[uSrcTreeNodeIndex] + uOrgDstTreeNodeCount; + prDstTree->m_uNeighbor3[uDstTreeReplaceNodeIndex] = + prSrcTree->m_uNeighbor3[uSrcTreeNodeIndex] + uOrgDstTreeNodeCount; + + prDstTree->m_bHasEdgeLength2[uDstTreeReplaceNodeIndex] = + prSrcTree->m_bHasEdgeLength2[uSrcTreeNodeIndex]; + prDstTree->m_bHasEdgeLength3[uDstTreeReplaceNodeIndex] = + prSrcTree->m_bHasEdgeLength3[uSrcTreeNodeIndex]; + + prDstTree->m_dEdgeLength2[uDstTreeReplaceNodeIndex] = + prSrcTree->m_dEdgeLength2[uSrcTreeNodeIndex]; + prDstTree->m_dEdgeLength3[uDstTreeReplaceNodeIndex] = + prSrcTree->m_dEdgeLength3[uSrcTreeNodeIndex]; + + /* make Id invalid */ + prDstTree->m_Ids[uDstTreeReplaceNodeIndex] = uInsane; + + /* no updated of uNodeCount, because we used the replace node */ + +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "Updated dst rpl node %d with the src root node: (untouched) parent=%d (%f) left=%d (%f) right=%d (%f)", + uDstTreeReplaceNodeIndex, + prDstTree->m_uNeighbor1[uDstTreeReplaceNodeIndex], prDstTree->m_dEdgeLength1[uDstTreeReplaceNodeIndex], + prDstTree->m_uNeighbor2[uDstTreeReplaceNodeIndex], prDstTree->m_dEdgeLength2[uDstTreeReplaceNodeIndex], + prDstTree->m_uNeighbor3[uDstTreeReplaceNodeIndex], prDstTree->m_dEdgeLength3[uDstTreeReplaceNodeIndex]); +#endif + + } else if (IsLeaf(uSrcTreeNodeIndex, prSrcTree)) { + /* src node is a leaf, which means we only have one + * neighbour, and that is its parent, i.e. n1 + * + */ + + /* initialise/zero new node to default values + */ + InitNode(prDstTree, uNewDstNodeIndex); + + + /* update m_ptrName/leaf name + */ + prDstTree->m_ptrName[uNewDstNodeIndex] = + CkStrdup(GetLeafName(uSrcTreeNodeIndex, prSrcTree)); + + /* update parent node (beware of special case: parent was + src tree root */ + if (IsRoot(prSrcTree->m_uNeighbor1[uSrcTreeNodeIndex], prSrcTree)) { + prDstTree->m_uNeighbor1[uNewDstNodeIndex] = + uDstTreeReplaceNodeIndex; + } else { + prDstTree->m_uNeighbor1[uNewDstNodeIndex] = + prSrcTree->m_uNeighbor1[uSrcTreeNodeIndex] + uOrgDstTreeNodeCount; + } + + /* update edge length info to parent + */ + prDstTree->m_bHasEdgeLength1[uNewDstNodeIndex] = + prSrcTree->m_bHasEdgeLength1[uSrcTreeNodeIndex]; + prDstTree->m_dEdgeLength1[uNewDstNodeIndex] = + prSrcTree->m_dEdgeLength1[uSrcTreeNodeIndex]; + + /* update sequence/object id + */ + prDstTree->m_Ids[uNewDstNodeIndex] = + prSrcTree->m_Ids[uSrcTreeNodeIndex]; + + /* we used a new node so increase their count */ + prDstTree->m_uNodeCount += 1; + +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "Updated dst node %d with a src leaf node: parent=%d (%f)", + uNewDstNodeIndex, + prDstTree->m_uNeighbor1[uNewDstNodeIndex], prDstTree->m_dEdgeLength1[uNewDstNodeIndex]); +#endif + + } else { + /* src node is not root neither leaf, means we have an + * internal node. Update all neighbour info + * + */ + + /* initialise/zero node values to default values + */ + InitNode(prDstTree, uNewDstNodeIndex); + + /* update neigbours + */ + /* parent: special case if parent was src tree root */ + if (IsRoot(prSrcTree->m_uNeighbor1[uSrcTreeNodeIndex], prSrcTree)) { + prDstTree->m_uNeighbor1[uNewDstNodeIndex] = + uDstTreeReplaceNodeIndex; + } else { + prDstTree->m_uNeighbor1[uNewDstNodeIndex] = + prSrcTree->m_uNeighbor1[uSrcTreeNodeIndex] + uOrgDstTreeNodeCount; + } + /* left */ + prDstTree->m_uNeighbor2[uNewDstNodeIndex] = + prSrcTree->m_uNeighbor2[uSrcTreeNodeIndex] + uOrgDstTreeNodeCount; + /* right */ + prDstTree->m_uNeighbor3[uNewDstNodeIndex] = + prSrcTree->m_uNeighbor3[uSrcTreeNodeIndex] + uOrgDstTreeNodeCount; + + /* update edge length info + */ + /* parent */ + prDstTree->m_bHasEdgeLength1[uNewDstNodeIndex] = + prSrcTree->m_bHasEdgeLength1[uSrcTreeNodeIndex]; + prDstTree->m_dEdgeLength1[uNewDstNodeIndex] = + prSrcTree->m_dEdgeLength1[uSrcTreeNodeIndex]; + /* left */ + prDstTree->m_bHasEdgeLength2[uNewDstNodeIndex] = + prSrcTree->m_bHasEdgeLength2[uSrcTreeNodeIndex]; + prDstTree->m_dEdgeLength2[uNewDstNodeIndex] = + prSrcTree->m_dEdgeLength2[uSrcTreeNodeIndex]; + /* right */ + prDstTree->m_bHasEdgeLength3[uNewDstNodeIndex] = + prSrcTree->m_bHasEdgeLength3[uSrcTreeNodeIndex]; + prDstTree->m_dEdgeLength3[uNewDstNodeIndex] = + prSrcTree->m_dEdgeLength3[uSrcTreeNodeIndex]; + + /* we used a new node so increase their count */ + prDstTree->m_uNodeCount += 1; + +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "Updated dst node %d with an internal src node: parent=%d (%f) left=%d (%f) right=%d (%f)", + uNewDstNodeIndex, + prDstTree->m_uNeighbor1[uNewDstNodeIndex], prDstTree->m_dEdgeLength1[uNewDstNodeIndex], + prDstTree->m_uNeighbor2[uNewDstNodeIndex], prDstTree->m_dEdgeLength2[uNewDstNodeIndex], + prDstTree->m_uNeighbor3[uNewDstNodeIndex], prDstTree->m_dEdgeLength3[uNewDstNodeIndex]); +#endif + } + + } + /* end for each src tree node */ + + + /* + * m_uRootNodeIndex stays the same. + * + * No need to touch m_uCacheCount. + * + */ +#if USE_HEIGHT + Log(&rLog, LOG_FATAL, "Internal error: Height usage not implemented in %s", __FUNCTION__); +#endif + + +#ifndef NDEBUG + TreeValidate(prDstTree); +#endif + + return; +} +/*** end: AppendTree() ***/ + diff --git a/binaries/src/clustalo/src/clustal/muscle_tree.h b/binaries/src/clustalo/src/clustal/muscle_tree.h new file mode 100644 index 0000000..ff8a782 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/muscle_tree.h @@ -0,0 +1,173 @@ +/* This a mix of tree functions and data-structures from + * Bob Edgar's Muscle (version 3.7) ported to pure C. + * + * Used files: phy.cpp, tree.h, phytofile.cpp and phyfromclust.cpp + * + * Muscle's code is public domain and so is this code here. + + * From http://www.drive5.com/muscle/license.htm: + * """ + * MUSCLE is public domain software + * + * The MUSCLE software, including object and source code and + * documentation, is hereby donated to the public domain. + * + * Disclaimer of warranty + * THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, + * EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * """ + * + */ + +/* + * RCS $Id: muscle_tree.h 230 2011-04-09 15:37:50Z andreas $ + */ + + +#ifndef CLUSTALO_MUSCLE_CLUSTALO_TREE_H +#define CLUSTALO_MUSCLE_CLUSTALO_TREE_H + +#include +#include "util.h" + +#ifndef uint +/* limit use of uint (see coding_style_guideline.txt) */ +typedef unsigned int uint; +#endif + +static const uint NULL_NEIGHBOR = UINT_MAX; + +/** + * @brief guide-tree structure + * + * @note We kept the original variable names here, to make it easy to + * search through Muscle's source code. + * From phy.cpp: + * Node has 0 to 3 neighbors: + * 0 neighbors: singleton root + * 1 neighbor: leaf, neighbor is parent + * 2 neigbors: non-singleton root + * 3 neighbors: internal node (other than root) + * + * Minimal rooted tree is single node. + * Minimal unrooted tree is single edge. + * Leaf node always has nulls in neighbors 2 and 3, neighbor 1 is parent. + * When tree is rooted, neighbor 1=parent, 2=left, 3=right. + * + */ +typedef struct { + uint m_uNodeCount;/**< number of nodes */ + uint m_uCacheCount;/**< reserved memory */ + + uint *m_uNeighbor1;/**< parent node */ + uint *m_uNeighbor2;/**< left node */ + uint *m_uNeighbor3;/**< right node */ + + /* do we have edge lengths info stored (m_dEdgeLength[123]) */ + bool *m_bHasEdgeLength1; + bool *m_bHasEdgeLength2; + bool *m_bHasEdgeLength3; + + double *m_dEdgeLength1; + double *m_dEdgeLength2; + double *m_dEdgeLength3; + +#if USE_HEIGHT + /* unused in our version of the code. we might need it at some + * stage so keep it in here, but disable via USE_HEIGHT throughout + * the code */ + double *m_dHeight; + bool *m_bHasHeight; +#endif + + /** + * leaf labels. + * index range: 0 -- (m_uNodeCount+1)/2 + */ + char **m_ptrName; + + /** + * node id. + * index range: 0 -- m_uNodeCount + */ + uint *m_Ids; + + bool m_bRooted; /**< tree is rooted */ + uint m_uRootNodeIndex; +} tree_t; + + +extern void +MuscleTreeCreate(tree_t *tree, uint uLeafCount, uint uRoot, const uint *Left, + const uint *Right, const float *LeftLength, const float* RightLength, + const uint *LeafIds, char **LeafNames); + +extern void +MuscleTreeToFile(FILE *fp, tree_t *tree); + +extern int +MuscleTreeFromFile(tree_t *tree, char *ftree); + +extern void +FreeMuscleTree(tree_t *tree); + +extern void +LogTree(tree_t *tree, FILE *fp); + +extern bool +IsRooted(tree_t *tree); + +extern uint +GetNodeCount(tree_t *tree); + +extern uint +GetLeafCount(tree_t *tree); + +extern uint +FirstDepthFirstNode(tree_t *tree); + +extern uint +NextDepthFirstNode(uint nodeindex, tree_t *tree); + +extern bool +IsLeaf(uint nodeindex, tree_t *tree); + +extern void +SetLeafId(tree_t *tree, uint uNodeIndex, uint uId); + +extern uint +GetLeafId(uint nodeindex, tree_t *tree); + +extern char * +GetLeafName(unsigned uNodeIndex, tree_t *tree); + +extern uint +GetLeft(uint nodeindex, tree_t *tree); + +extern uint +GetRight(uint nodeindex, tree_t *tree); + +extern uint +GetRootNodeIndex(tree_t *tree); + +extern bool +IsRoot(uint uNodeIndex, tree_t *tree); + +extern uint +GetParent(unsigned uNodeIndex, tree_t *tree); + +extern double +GetEdgeLength(uint uNodeIndex1, uint uNodeIndex2, tree_t *tree); + +extern uint +LeafIndexToNodeIndex(uint uLeafIndex, tree_t *prTree); + +extern void +AppendTree(tree_t *prDstTree, + uint uDstTreeNodeIndex, tree_t *prSrcTree); + +extern void +TreeValidate(tree_t *tree); + +#endif diff --git a/binaries/src/clustalo/src/clustal/muscle_upgma.c b/binaries/src/clustalo/src/clustal/muscle_upgma.c new file mode 100644 index 0000000..7e4b5df --- /dev/null +++ b/binaries/src/clustalo/src/clustal/muscle_upgma.c @@ -0,0 +1,502 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/* This the fast UPGMA algorithm (O(N^2)) as implemented in Bob Edgar's + * Muscle (UPGMA2.cpp; version 3.7) ported to pure C. + * + * Muscle's code is public domain and so is this code here. + * + * From http://www.drive5.com/muscle/license.htm: + * """ + * MUSCLE is public domain software + * + * The MUSCLE software, including object and source code and + * documentation, is hereby donated to the public domain. + * + * Disclaimer of warranty + * THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, + * EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * """ + * + */ + +/* + * RCS $Id: muscle_upgma.c 230 2011-04-09 15:37:50Z andreas $ + * + * + * Notes: + * ------ + * LINKAGE become linkage_t here + * + * Replaced the the following member functions for DistCalc DC: + * DC.GetId = sequence id as int + * DC.GetName = sequence name + * DC.GetCount = matrix dim + * DC.DistRange = vector / matrix row for object i with index j +#include +#include + +#include "util.h" +#include "log.h" +#include "symmatrix.h" + +#include "muscle_tree.h" +#include "muscle_upgma.h" + +/* from distcalc.h */ +typedef float dist_t; +static const dist_t BIG_DIST = (dist_t) 1e29; +/* from muscle.h */ +static const unsigned uInsane = 8888888; + + + + +/*static inline*/ +ulong TriangleSubscript(uint uIndex1, uint uIndex2); + + + + +#define TRACE 0 + +#ifndef MIN +#define MIN(x, y) ((x) < (y) ? (x) : (y)) +#endif +#ifndef MIN +#define MAX(x, y) ((x) > (y) ? (x) : (y)) +#endif +#define AVG(x, y) (((x) + (y))/2) + +static uint g_uLeafCount; +static ulong g_ulTriangleSize; +static uint g_uInternalNodeCount; +static uint g_uInternalNodeIndex; + +/* Triangular distance matrix is g_Dist, which is allocated + * as a one-dimensional vector of length g_ulTriangleSize. + * TriangleSubscript(i,j) maps row,column=i,j to the subscript + * into this vector. + * Row / column coordinates are a bit messy. + * Initially they are leaf indexes 0..N-1. + * But each time we create a new node (=new cluster, new subtree), + * we re-use one of the two rows that become available (the children + * of the new node). This saves memory. + * We keep track of this through the g_uNodeIndex vector. + */ +static dist_t *g_Dist; + +/* Distance to nearest neighbor in row i of distance matrix. + * Subscript is distance matrix row. + */ +static dist_t *g_MinDist; + +/* Nearest neighbor to row i of distance matrix. + * Subscript is distance matrix row. + */ +static uint *g_uNearestNeighbor; + +/* Node index of row i in distance matrix. + * Node indexes are 0..N-1 for leaves, N..2N-2 for internal nodes. + * Subscript is distance matrix row. + */ +static uint *g_uNodeIndex; + +/* The following vectors are defined on internal nodes, + * subscripts are internal node index 0..N-2. + * For g_uLeft/Right, value is the node index 0 .. 2N-2 + * because a child can be internal or leaf. + */ +static uint *g_uLeft; +static uint *g_uRight; +static dist_t *g_Height; +static dist_t *g_LeftLength; +static dist_t *g_RightLength; + + +/*** CalcDistRange + * + * Imitation of DistCalc.DistRange + * + * Sets values of row (vector / matrix row) to distances for object i with index j= g_uLeafCount || uIndex2 >= g_uLeafCount) + Log(&rLog, LOG_FATAL, "TriangleSubscript(%u,%u) %u", uIndex1, uIndex2, g_uLeafCount); +#endif + if (uIndex1 >= uIndex2) + v = uIndex2 + (uIndex1*(uIndex1 - 1))/2; + else + v = uIndex1 + (uIndex2*(uIndex2 - 1))/2; + assert(v < (g_uLeafCount*(g_uLeafCount - 1))/2); + return v; +} + +#ifdef UNUSED +static void ListState() +{ + uint i, j; + Info("Dist matrix\n"); + Info(" "); + for (i = 0; i < g_uLeafCount; ++i) + { + if (uInsane == g_uNodeIndex[i]) + continue; + Info(" %5u", g_uNodeIndex[i]); + } + Info("\n"); + + for (i = 0; i < g_uLeafCount; ++i) + { + if (uInsane == g_uNodeIndex[i]) + continue; + Info("%5u ", g_uNodeIndex[i]); + for (j = 0; j < g_uLeafCount; ++j) + { + if (uInsane == g_uNodeIndex[j]) + continue; + if (i == j) + Info(" "); + else + { + ulong v = TriangleSubscript(i, j); + Info("%5.2g ", g_Dist[v]); + } + } + Info("\n"); + } + + Info("\n"); + Info(" i Node NrNb Dist\n"); + Info("----- ----- ----- --------\n"); + for (i = 0; i < g_uLeafCount; ++i) + { + if (uInsane == g_uNodeIndex[i]) + continue; + Info("%5u %5u %5u %8.3f\n", + i, + g_uNodeIndex[i], + g_uNearestNeighbor[i], + g_MinDist[i]); + } + + Info("\n"); + Info(" Node L R Height LLength RLength\n"); + Info("----- ----- ----- ------ ------- -------\n"); + for (i = 0; i <= g_uInternalNodeIndex; ++i) + Info("%5u %5u %5u %6.2g %6.2g %6.2g\n", + i, + g_uLeft[i], + g_uRight[i], + g_Height[i], + g_LeftLength[i], + g_RightLength[i]); +} +#endif +/* ifdef UNUSED */ + +/** + * @brief Creates a UPGMA in O(N^2) tree from given distmat + * + * @param[out] tree + * newly created rooted UPGMA tree + * @param[in] distmat + * distance matrix to be clustered + * @param[in] linkage + * linkage type + * @param[in] names + * leaf names, will be copied + * + * @note called UPGMA2() in Muscle3.7. + * caller has to free with FreeMuscleTree() + * + * @see FreeMuscleTree() + */ +void +MuscleUpgma2(tree_t *tree, symmatrix_t *distmat, linkage_t linkage, char **names) +{ + int i, j; + uint *Ids; + + /* only works on full symmetric matrices */ + assert (distmat->nrows==distmat->ncols); + + g_uLeafCount = distmat->ncols; + g_ulTriangleSize = (g_uLeafCount*(g_uLeafCount - 1))/2; + g_uInternalNodeCount = g_uLeafCount - 1; + + g_Dist = (dist_t *) CKMALLOC(g_ulTriangleSize * sizeof(dist_t)); + + g_uNodeIndex = (uint*) CKMALLOC(sizeof(uint) * g_uLeafCount); + g_uNearestNeighbor = (uint*) CKMALLOC(sizeof(uint) * g_uLeafCount); + g_MinDist = (dist_t *) CKMALLOC(sizeof(dist_t) * g_uLeafCount); + Ids = (uint*) CKMALLOC(sizeof(uint) * g_uLeafCount); + /* NOTE: we replaced Names with argument names */ + + /** + * left and right node indices, as well as left and right + * branch-length and height for for internal nodes + */ + g_uLeft = (uint*) CKMALLOC(sizeof(uint) * g_uInternalNodeCount); + g_uRight = (uint*) CKMALLOC(sizeof(uint) * g_uInternalNodeCount); + g_Height = (dist_t*) CKMALLOC(sizeof(dist_t) * g_uInternalNodeCount); + g_LeftLength = (dist_t*) CKMALLOC(sizeof(dist_t) * g_uInternalNodeCount); + g_RightLength = (dist_t*) CKMALLOC(sizeof(dist_t) * g_uInternalNodeCount); + + for (i = 0; i < g_uLeafCount; ++i) { + g_MinDist[i] = BIG_DIST; + g_uNodeIndex[i] = i; + g_uNearestNeighbor[i] = uInsane; + Ids[i] = i; + } + + for (i = 0; i < g_uInternalNodeCount; ++i) { + g_uLeft[i] = uInsane; + g_uRight[i] = uInsane; + g_LeftLength[i] = BIG_DIST; + g_RightLength[i] = BIG_DIST; + g_Height[i] = BIG_DIST; + } + +/* Compute initial NxN triangular distance matrix. + * Store minimum distance for each full (not triangular) row. + * Loop from 1, not 0, because "row" is 0, 1 ... i-1, + * so nothing to do when i=0. + */ + for (i = 1; i < g_uLeafCount; ++i) { + dist_t *Row = g_Dist + TriangleSubscript(i, 0); + CalcDistRange(distmat, i, Row); + for (j = 0; j < i; ++j) { + const dist_t d = Row[j]; + if (d < g_MinDist[i]) { + g_MinDist[i] = d; + g_uNearestNeighbor[i] = j; + } + if (d < g_MinDist[j]) { + g_MinDist[j] = d; + g_uNearestNeighbor[j] = i; + } + } + } + +#if TRACE + Info("Initial state:\n"); + ListState(); +#endif + + for (g_uInternalNodeIndex = 0; + g_uInternalNodeIndex < g_uLeafCount - 1; + ++g_uInternalNodeIndex) { + + dist_t dtNewMinDist = BIG_DIST; + uint uNewNearestNeighbor = uInsane; + +#if TRACE + Info("\n"); + Info("Internal node index %5u\n", g_uInternalNodeIndex); + Info("-------------------------\n"); +#endif + + /* Find nearest neighbors */ + uint Lmin = uInsane; + uint Rmin = uInsane; + dist_t dtMinDist = BIG_DIST; + for (j = 0; j < g_uLeafCount; ++j) { + dist_t d; + if (uInsane == g_uNodeIndex[j]) + continue; + + d = g_MinDist[j]; + if (d < dtMinDist) { + dtMinDist = d; + Lmin = j; + Rmin = g_uNearestNeighbor[j]; + assert(uInsane != Rmin); + assert(uInsane != g_uNodeIndex[Rmin]); + } + } + + assert(Lmin != uInsane); + assert(Rmin != uInsane); + assert(dtMinDist != BIG_DIST); + +#if TRACE + Info("Nearest neighbors Lmin %u[=%u] Rmin %u[=%u] dist %.3g\n", + Lmin, + g_uNodeIndex[Lmin], + Rmin, + g_uNodeIndex[Rmin], + dtMinDist); +#endif + + /* Compute distances to new node + * New node overwrites row currently assigned to Lmin + */ + for ( j = 0; j < g_uLeafCount; ++j) { + ulong vL, vR; + dist_t dL, dR; + dist_t dtNewDist; + + if (j == Lmin || j == Rmin) + continue; + if (uInsane == g_uNodeIndex[j]) + continue; + + vL = TriangleSubscript(Lmin, j); + vR = TriangleSubscript(Rmin, j); + dL = g_Dist[vL]; + dR = g_Dist[vR]; + dtNewDist = 0.0; + + switch (linkage) { + case LINKAGE_AVG: + dtNewDist = AVG(dL, dR); + break; + + case LINKAGE_MIN: + dtNewDist = MIN(dL, dR); + break; + + case LINKAGE_MAX: + dtNewDist = MAX(dL, dR); + break; +/* couldn't be arsed to figure out proper usage of g_dSUEFF */ +#if 0 + case LINKAGE_BIASED: + dtNewDist = g_dSUEFF*AVG(dL, dR) + (1 - g_dSUEFF)*MIN(dL, dR); + break; +#endif + default: + Log(&rLog, LOG_FATAL, "UPGMA2: Invalid LINKAGE_%u", linkage); + } + + /* Nasty special case. + * If nearest neighbor of j is Lmin or Rmin, then make the new + * node (which overwrites the row currently occupied by Lmin) + * the nearest neighbor. This situation can occur when there are + * equal distances in the matrix. If we don't make this fix, + * the nearest neighbor pointer for j would become invalid. + * (We don't need to test for == Lmin, because in that case + * the net change needed is zero due to the change in row + * numbering). + */ + if (g_uNearestNeighbor[j] == Rmin) + g_uNearestNeighbor[j] = Lmin; + +#if TRACE + Info("New dist to %u = (%u/%.3g + %u/%.3g)/2 = %.3g\n", + j, Lmin, dL, Rmin, dR, dtNewDist); +#endif + g_Dist[vL] = dtNewDist; + if (dtNewDist < dtNewMinDist) { + dtNewMinDist = dtNewDist; + uNewNearestNeighbor = j; + } + } + + assert(g_uInternalNodeIndex < g_uLeafCount - 1 || BIG_DIST != dtNewMinDist); + assert(g_uInternalNodeIndex < g_uLeafCount - 1 || uInsane != uNewNearestNeighbor); + + const ulong v = TriangleSubscript(Lmin, Rmin); + const dist_t dLR = g_Dist[v]; + const dist_t dHeightNew = dLR/2; + const uint uLeft = g_uNodeIndex[Lmin]; + const uint uRight = g_uNodeIndex[Rmin]; + const dist_t HeightLeft = + uLeft < g_uLeafCount ? 0 : g_Height[uLeft - g_uLeafCount]; + const dist_t HeightRight = + uRight < g_uLeafCount ? 0 : g_Height[uRight - g_uLeafCount]; + + g_uLeft[g_uInternalNodeIndex] = uLeft; + g_uRight[g_uInternalNodeIndex] = uRight; + g_LeftLength[g_uInternalNodeIndex] = dHeightNew - HeightLeft; + g_RightLength[g_uInternalNodeIndex] = dHeightNew - HeightRight; + g_Height[g_uInternalNodeIndex] = dHeightNew; + + /* Row for left child overwritten by row for new node */ + g_uNodeIndex[Lmin] = g_uLeafCount + g_uInternalNodeIndex; + g_uNearestNeighbor[Lmin] = uNewNearestNeighbor; + g_MinDist[Lmin] = dtNewMinDist; + + /* Delete row for right child */ + g_uNodeIndex[Rmin] = uInsane; + +#if TRACE + Info("\nInternalNodeIndex=%u Lmin=%u Rmin=%u\n", + g_uInternalNodeIndex, Lmin, Rmin); + ListState(); +#endif + } + + uint uRoot = g_uLeafCount - 2; + +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "uRoot=%d g_uLeafCount=%d g_uInternalNodeCount=%d", uRoot, g_uLeafCount, g_uInternalNodeCount); + for (i=0; i +#include +#include +#include + +/* only neededfor iNumberOfThreads */ +#include "clustal-omega.h" + +#include "ktuple_pair.h" +#include "pair_dist.h" +#include "progress.h" +#include "util.h" + + +/* Up to rev 173 we had a USE_SYM_KTUPLE switch implemented here. When active + * ktuple distances were computed twice for each pair and averaged. Idea was + * to avoid assymmetries in the pairwise scores (score(a, b) is often not the + * same as score(b, a)). Results on BAliBASE indicate that this is overkill: + * + * r92_default core columns: avg-sp=0.800656 avg-tc=0.47711 (of total 218) + * r93-mod--norm-ktuple/ core columns: avg-sp=0.800656 avg-tc=0.47711 (of total 218) + * r93-mod--sym-ktuple/ core columns: avg-sp=0.801083 avg-tc=0.476544 (of total 217) + * r93-mod--rand-ktuple-1 core columns: avg-sp=0.799289 avg-tc=0.468028 (of total 218) + * r93-mod--rand-ktuple-2 core columns: avg-sp=0.801654 avg-tc=0.47659 (of total 217) + * r93-mod--rand-ktuple-3 core columns: avg-sp=0.800234 avg-tc=0.474908 (of total 218) + * r93-mod--rand-ktuple-4 core columns: avg-sp=0.800573 avg-tc=0.476514 (of total 218) + * r93-mod--rand-ktuple-5 core columns: avg-sp=0.799679 avg-tc=0.468716 (of total 218) + * + */ + +static double +KimuraCorrection(double frac_id); + +static int +SquidIdPairDist(symmatrix_t *tmat, mseq_t *mseq, + int istart, int iend, + int jstart, int jend, + bool use_KimuraCorrection, progress_t *prProgress, + unsigned long int *ulStepNo, unsigned long int ulTotalStepNo); + +/* Taken from Muscle's msadistkimura.cpp */ +static int DAYHOFF_PAMS[]={ + 195, /* 75.0% observed d; 195 PAMs estimated = 195% estimated d */ + 196, /* 75.1% observed d; 196 PAMs estimated */ + 197, 198, 199, 200, 200, 201, 202, 203, + 204, 205, 206, 207, 208, 209, 209, 210, 211, 212, + 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, + 223, 224, 226, 227, 228, 229, 230, 231, 232, 233, + 234, 236, 237, 238, 239, 240, 241, 243, 244, 245, + 246, 248, 249, 250, /* 250 PAMs = 80.3% observed d */ + 252, 253, 254, 255, 257, 258, + 260, 261, 262, 264, 265, 267, 268, 270, 271, 273, + 274, 276, 277, 279, 281, 282, 284, 285, 287, 289, + 291, 292, 294, 296, 298, 299, 301, 303, 305, 307, + 309, 311, 313, 315, 317, 319, 321, 323, 325, 328, + 330, 332, 335, 337, 339, 342, 344, 347, 349, 352, + 354, 357, 360, 362, 365, 368, 371, 374, 377, 380, + 383, 386, 389, 393, 396, 399, 403, 407, 410, 414, + 418, 422, 426, 430, 434, 438, 442, 447, 451, 456, + 461, 466, 471, 476, 482, 487, 493, 498, 504, 511, + 517, 524, 531, 538, 545, 553, 560, 569, 577, 586, + 595, 605, 615, 626, 637, 649, 661, 675, 688, 703, + 719, 736, 754, 775, 796, 819, 845, 874, 907, 945, + /* 92.9% observed; 945 PAMs */ + 988 /* 93.0% observed; 988 PAMs */ +}; +static int DAYHOFF_TABLE_ENTRIES = sizeof(DAYHOFF_PAMS)/sizeof(DAYHOFF_PAMS[0]); + + + +/** + * + * @brief Compute Kimura corrected distance. + * + * Original Muscle documentation following: + * """ + * This is defined to be: + * log_e(1 - p - p*p/5) + * where p is the fraction of residues that differ, i.e.: + * p = (1 - fractional_conservation) + * This measure is infinite for p = 0.8541 and is considered + * unreliable for p >= 0.75 (according to the ClustalW docs). + * ClustalW uses a table lookup for values > 0.75. The following table + * was copied from the ClustalW file dayhoff.h. + * """ + * + * @note copied from Muscle's msadistkimura.cpp:KimuraDist() + * + * @warning For protein only (uses Dayhoff substitution parameters) + * + * @param[in] p + * distance, e.g. 1.0 - fractional/relative identity + * + * @return The Kimura corrected distance + * + */ +double +KimuraCorrection(double p) +{ + int table_index; + + /* Typical case: use Kimura's empirical formula */ + if (p < 0.75) + return -log(1 - p - (p*p)/5); + + /* Per ClustalW, return 10.0 for anything over 93% */ + if (p > 0.93) + return 10.0; + + /* If 0.75 >= p <= 0.93, use table lookup */ + table_index = (int) ((p - 0.75)*1000 + 0.5); + if (table_index < 0 || table_index >= DAYHOFF_TABLE_ENTRIES) + Log(&rLog, LOG_FATAL, "Internal error in %s:%s", __FILE__, __FUNCTION__); + + return DAYHOFF_PAMS[table_index] / 100.0; +} +/*** end: KimuraCorrection() ***/ + + + + +/** + * @brief Compute distances between all aligned sequence pairs using + * squid's PairwiseIdentity, which is: idents / MIN(len1, len2) + * + * @param[out] tmat + * Where to store the computed distances + * @param[in] mseq + * The aligned sequences + * @param[in] istart + * For distances [i][j] i>=istart, i=jstart, ialigned) { + Log(&rLog, LOG_ERROR, "Sequences need to be aligned (%s)", __FUNCTION__); + return -1; + } + if (SEQTYPE_PROTEIN != mseq->seqtype && TRUE == use_kimura) { + Log(&rLog, LOG_WARN, "Using Kimura distance corretion which includes Dayhoff substitution table lookup for non-protein sequences"); + } + + NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO), + "Pairwise distance calculation progress", bPrintCR); + /* estimation of total number of steps (if istart and jstart are + * both 0) + */ + /* ulTotalStepNo = iend*jend - iend*iend/2 + iend/2; + ulStepNo = 0; */ + /*LOG_DEBUG("istart=%d iend=%d jstart=%d jend=%d", istart, iend, jstart, jend);*/ + for (i=istart; iseq[i], mseq->seq[j]); + + +#ifdef HAVE_OPENMP + #pragma omp atomic +#endif + (*ulStepNo)++; + /*LOG_DEBUG("%d:%d raw dist = %f", i, j, dist);*/ + if (use_kimura) { + dist = KimuraCorrection(dist); + /*LOG_DEBUG("cor dist = %f", dist);*/ + } + SymMatrixSetValue(tmat, i, j, dist); +#ifdef HAVE_OPENMP + #pragma omp critical(squidid) +#endif + { + Log(&rLog, LOG_DEBUG, "Aligned distance for sequence pair %d:%d= %lg", + i+1, j+1, dist); + } + } + } + + return 0; +} +/*** end: SquidIdPairDist() ***/ + + + + +/** + * @brief compute or read precomputed distances for given sequences + * + * @param[out] distmat + * Distances will be written to this matrix. will be allocated here as + * well. Caller must free with FreeSymMatrix() + * @param[in] mseq + * Distances will be computed for these sequences + * @param[in] pairdist_type + * Type of pairwise distance comparison + * @param[in] fdist_in + * If not NULL, sequences will be written from this file instead of + * computing them + * @param[in] istart + * Compute distances for sequences i:j, i>=istart, inseqs. + * @param[in] jstart + * Compute distances for sequences i:j, j>=jstart, inseqs. + * @param[in] fdist_out + * If not NULL, distances will be written to this files + * + * + */ +int +PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type, + int istart, int iend, + int jstart, int jend, + char *fdist_in, char *fdist_out) +{ + int uSeqIndex; + unsigned long int ulStepNo = 0, ulTotalStepNo; /* DD: moved from SquidIdPairDist so progress bar works multithreaded */ + int iChunk, iChunkStart, iChunkEnd; + int iChunkStarts[iNumberOfThreads]; + int iChunkEnds[iNumberOfThreads]; + progress_t *prProgress = NULL; + int iSquidSuccess = 0; + bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE; + + assert(NULL!=distmat); + assert(NULL!=mseq); + assert(istartnseqs * sizeof(char*)); + for (uSeqIndex=0; uSeqIndexnseqs; uSeqIndex++) { + names[uSeqIndex] = mseq->sqinfo[uSeqIndex].name; + } + + SymMatrixPrint((*distmat), names, fdist_out); + + Log(&rLog, LOG_INFO, "Pairwise distance matrix written to %s", + fdist_out); + CKFREE(names); + } + +#if 0 +#include "distance-distrib.h" +#endif + + if (NULL != prProgress) { + ProgressDone(prProgress); + FreeProgress(&prProgress); + } + + return 0; +} +/*** end: PairDistances() ***/ + + + diff --git a/binaries/src/clustalo/src/clustal/pair_dist.h b/binaries/src/clustalo/src/clustal/pair_dist.h new file mode 100644 index 0000000..65047ef --- /dev/null +++ b/binaries/src/clustalo/src/clustal/pair_dist.h @@ -0,0 +1,42 @@ +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: pair_dist.h 193 2011-02-07 15:45:21Z andreas $ + */ + + +#ifndef CLUSTALO_PAIR_DIST_H +#define CLUSTALO_PAIR_DIST_H + +#define PAIRDIST_UNKNOWN 0 +/* k-tuple distances: Wilbur and Lipman (1983) */ +#define PAIRDIST_KTUPLE 1 +/* fractional identity between aligned sequences. denominator is + * minimum seq len (see squid:aligneval.c) */ +#define PAIRDIST_SQUIDID 2 +/* SQUIDID + Kimura correction */ +#define PAIRDIST_SQUIDID_KIMURA 3 + +#include "seq.h" +#include "symmatrix.h" + +extern int +PairDistances(symmatrix_t **distmat, mseq_t *mseq, const int pairdist_type, + const int istart, const int iend, + const int jstart, const int jend, + char *fdist_in, char *fdist_out); + +#endif + diff --git a/binaries/src/clustalo/src/clustal/progress.c b/binaries/src/clustalo/src/clustal/progress.c new file mode 100644 index 0000000..57c99f5 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/progress.c @@ -0,0 +1,177 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: progress.c 230 2011-04-09 15:37:50Z andreas $ + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include + +#include "util.h" +#include "log.h" +#include "progress.h" + +#define LOGLEVEL_THRESHOLD LOG_INFO + +/** + * @brief Allocates a new progress structure and initialises its members. + * Free with FreeProgress() + * + * @note Starts the internal stopwatch immediatly! + * + * @see FreeProgress() + * + * @param[out] pprProgress + * Pointer pointer to progress structure. Progress structure will be + * allocated here. + * @param[in] prFile + * Where to log messages to + * @param[in] pcPrefix + * What prefix to use for messages + * @param[in] bPrintCR + * If TRUE carriage return instead of newline will be printed between log messages + */ +void +NewProgress(progress_t **pprProgress, FILE *prFile, + char *pcPrefix, bool bPrintCR) +{ + assert(NULL!=pprProgress); + assert(NULL!=prFile); + assert(NULL!=pcPrefix); + + (*pprProgress) = (progress_t *) CKMALLOC(1*sizeof(progress_t)); + (*pprProgress)->prFile = prFile; + (*pprProgress)->bPrintCR = bPrintCR; + (*pprProgress)->pcPrefix = CkStrdup(pcPrefix); + strcpy((*pprProgress)->pcLastLogMsg, "\0"); + (*pprProgress)->prStopwatch = StopwatchCreate(); + StopwatchZero((*pprProgress)->prStopwatch); + StopwatchStart((*pprProgress)->prStopwatch); + + return; +} +/*** end: NewProgress() ***/ + + + +/** + * @brief Frees progress structure and its members + * + * @param[out] pprProgress + * Pointer pointer to progress structure + * + * @see NewProgress() + * + */ +void +FreeProgress(progress_t **pprProgress) +{ + (*pprProgress)->prFile = NULL; + CKFREE((*pprProgress)->pcPrefix); + StopwatchFree((*pprProgress)->prStopwatch); + + CKFREE(*pprProgress); + return; +} +/*** end: FreeProgress() ***/ + + + + +/** + * @brief Prints a progress update (and a carriage return) + * + * @param[in] prProgress + * Pointer to the progress structure + * @param[in] iStep + * Current step number + * @param[in] iTotalSteps + * Total step number + * @param[in] bForceOutput + * If percentage hasn't changed output is normally supressed + * normally. Output can be forced with this flag. + * + */ +void +ProgressLog(progress_t *prProgress, + unsigned long int iStep, unsigned long int iTotalSteps, + bool bForceOutput) +{ + char pcLogMsg[1024]; + assert(0!=iTotalSteps); + + if (rLog.iLogLevelEnabled>LOGLEVEL_THRESHOLD) { + return; + } + + (void) snprintf(pcLogMsg, sizeof(pcLogMsg), "%s: %lu %%", + prProgress->pcPrefix, (unsigned long int)(iStep/(float)iTotalSteps*100.0)); + + if (! bForceOutput) { + /* Skip logging, if we've just logged the same message */ + if (STR_EQ(pcLogMsg, prProgress->pcLastLogMsg)) { + return; + } + } + + strncpy(prProgress->pcLastLogMsg, pcLogMsg, + sizeof(prProgress->pcLastLogMsg)); + + fprintf(prProgress->prFile, "%s (%lu out of %lu)", pcLogMsg, iStep, iTotalSteps); + if (prProgress->bPrintCR) { + fprintf(prProgress->prFile, "\r"); + } else { + fprintf(prProgress->prFile, "\n"); + + } + (void) fflush(prProgress->prFile); + + return; +} +/*** end: ProgressLog() ***/ + + +/** + * @brief Finishes progress output by printing the elapsed time + * + * @param[in] prProgress + * Pointer to the progress structure + * + */ +void +ProgressDone(progress_t *prProgress) +{ + char pcBuf[1024]; + + if (rLog.iLogLevelEnabled>LOGLEVEL_THRESHOLD) { + return; + } + + (void) snprintf(pcBuf, sizeof(pcBuf), "%s done. CPU time: ", + prProgress->pcPrefix); + StopwatchStop(prProgress->prStopwatch); + StopwatchDisplay(prProgress->prFile, pcBuf, prProgress->prStopwatch); + (void) fflush(prProgress->prFile); + + return; +} +/*** end: ProgressDone() ***/ diff --git a/binaries/src/clustalo/src/clustal/progress.h b/binaries/src/clustalo/src/clustal/progress.h new file mode 100644 index 0000000..8ebca56 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/progress.h @@ -0,0 +1,50 @@ +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: progress.h 193 2011-02-07 15:45:21Z andreas $ + */ + + +#ifndef CLUSTALO_PROGRESS_H +#define CLUSTALO_PROGRESS_H + +#include "squid/stopwatch.h" + +typedef struct { + /* where to write to */ + FILE *prFile; + /* prefix printed before each step */ + char *pcPrefix; + bool bPrintCR; + char pcLastLogMsg[1024]; + Stopwatch_t *prStopwatch; +} progress_t; + + +extern void +NewProgress(progress_t **pprProgress, FILE *prFile, char *pcPrefix, bool bPrintCR); + +extern void +FreeProgress(progress_t **pprProgress); + +extern void +ProgressLog(progress_t *prProgress, + unsigned long int iStep, unsigned long int iTotalSteps, + bool bForceOutput); + +extern void +ProgressDone(progress_t *pprProgress); + +#endif diff --git a/binaries/src/clustalo/src/clustal/queue.h b/binaries/src/clustalo/src/clustal/queue.h new file mode 100644 index 0000000..7140740 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/queue.h @@ -0,0 +1,75 @@ +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: queue.h 193 2011-02-07 15:45:21Z andreas $ + * + * Functions/Macros for FIFOs/Queues + * + */ + +#ifndef CLUSTALO_QUEUE_H +#define CLUSTALO_QUEUE_H + +#include "list.h" + + + +/* FIFO/Queue as list_t, storing data pointers + * + */ + +typedef list_t queue_t; + +/* setup queue */ +#define QUEUE_INIT(prQueue, destroy_func) ListInit((prQueue), (destroy_func)) + +/* free all elements from queue */ +#define QUEUE_DESTROY(prQueue) ListDestroy((prQueue)) + +/* enqueue */ +#define QUEUE_PUSH(prQueue, data) LIST_APPEND((prQueue), (data)) + +/* dequeue */ +#define QUEUE_POP(prQueue, data) ListRemoveNext((prQueue), NULL, (data)) + +/* is queue empty ? */ +#define QUEUE_EMPTY(prQueue) (0==LIST_SIZE((prQueue))) + + + +/* Special int FIF/Queue, storing ints by copying them instead of + * keeping pointers only + */ + +typedef queue_t int_queue_t; + +/* setup queue */ +#define INT_QUEUE_INIT(prQueue) INT_LIST_INIT((prQueue)) + +/* free all elements from queue */ +#define INT_QUEUE_DESTROY(prQueue) INT_LIST_DESTROY((prQueue)) + +/* enqueue */ +#define INT_QUEUE_PUSH(prQueue, data) INT_LIST_APPEND((prQueue), (data)) + +/* dequeue */ +#define INT_QUEUE_POP(prQueue, data) IntListRemoveNext((prQueue), NULL, (data)) + +/* is queue empty ? */ +#define INT_QUEUE_EMPTY(prQueue) (0==INT_LIST_SIZE((prQueue))) + + + +#endif diff --git a/binaries/src/clustalo/src/clustal/seq.c b/binaries/src/clustalo/src/clustal/seq.c new file mode 100644 index 0000000..8b21ee8 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/seq.c @@ -0,0 +1,1185 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: seq.c 245 2011-06-15 12:38:53Z fabian $ + * + * + * Module for sequence/alignment IO and misc. + * + * This depends heavily on Sean Eddy's squid library, which is obsoleted by + * HMMER3's Easel. However, easel doesn't support that many non-aligned input + * formats. + * + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include "squid/squid.h" +#include + +#include "util.h" +#include "log.h" +#include "seq.h" + + +#define ALLOW_ONLY_PROTEIN 0 /* requested by Hamish, FS, r244 -> r245 */ + + + + +/** + * @brief Stripped down version of squid's alistat + * + * + * @param[in] prMSeq + * The alignment to analyse + * @param[in] bSampling + * For many sequences: samples from pool + * @param[in] bReportAll + * Report identities for all sequence pairs + * + * Don't have to worry about sequence case because our version of PairwiseIdentity is case insensitive + */ +void +AliStat(mseq_t *prMSeq, bool bSampling, bool bReportAll) { + + /* + * bSampling = squid's do_fast + * bReportAll = squid's allreport + */ + float **ppdIdentMx; /* identity matrix (squid: imx) */ + const int iNumSample = 1000; /* sample size (squid: nsample) */ + int iAux; + + MSA *msa; /* squid's alignment structure */ + int small, large; + int bestj, worstj; + float sum; + float worst_worst, worst_best, best_best; + float avgid; + int i, j; + int nres; /* number of residues */ + + if (bSampling && bReportAll) { + Log(&rLog, LOG_WARN, + "Cannot report all and sample at the same time. Skipping %s()", __FUNCTION__); + return; + } + if (FALSE == prMSeq->aligned) { + Log(&rLog, LOG_WARN, + "Sequences are not aligned. Skipping %s()", __FUNCTION__); + return; + } + + /* silence gcc warnings about uninitialized variables + */ + worst_worst = worst_best = best_best = 0.0; + bestj = worstj = -1; + + + /** mseq to squid msa + * + * FIXME code overlap with WriteAlignment. Make it a function and take + * code there (contains more comments) as template + * + */ + msa = MSAAlloc(prMSeq->nseqs, + /* derive alignment length from first seq */ + strlen(prMSeq->seq[0])); + for (i=0; inseqs; i++) { + int key; /* MSA struct internal index for sequence */ + char *this_name = prMSeq->sqinfo[i].name; /* prMSeq sequence name */ + char *this_seq = prMSeq->seq[i]; /* prMSeq sequence */ + SQINFO *this_sqinfo = &prMSeq->sqinfo[i]; /* prMSeq sequence name */ + + key = GKIStoreKey(msa->index, this_name); + msa->sqname[key] = sre_strdup(this_name, strlen(this_name)); + /* setting msa->sqlen[idx] and msa->aseq[idx] */ + msa->sqlen[key] = sre_strcat(&(msa->aseq[key]), msa->sqlen[key], + this_seq, strlen(this_seq)); + if (this_sqinfo->flags & SQINFO_DESC) { + MSASetSeqDescription(msa, key, this_sqinfo->desc); + } + msa->nseq++; + } + + + + nres = 0; + small = large = -1; + for (i = 0; i < msa->nseq; i++) { + int rlen; /* raw sequence length */ + rlen = DealignedLength(msa->aseq[i]); + nres += rlen; + if (small == -1 || rlen < small) small = rlen; + if (large == -1 || rlen > large) large = rlen; + } + + + if (bSampling) { + avgid = AlignmentIdentityBySampling(msa->aseq, msa->alen, + msa->nseq, iNumSample); + + } else { + float best, worst; + + /* this might be slow...could use openmp inside squid */ + MakeIdentityMx(msa->aseq, msa->nseq, &ppdIdentMx); + if (bReportAll) { + printf(" %-15s %5s %7s %-15s %7s %-15s\n", + "NAME", "LEN", "HIGH ID", "(TO)", "LOW ID", "(TO)"); + printf(" --------------- ----- ------- --------------- ------- ---------------\n"); + } + + sum = 0.0; + worst_best = 1.0; + best_best = 0.0; + worst_worst = 1.0; + for (i = 0; i < msa->nseq; i++) { + worst = 1.0; + best = 0.0; + for (j = 0; j < msa->nseq; j++) { + /* closest seq to this one = best */ + if (i != j && ppdIdentMx[i][j] > best) { + best = ppdIdentMx[i][j]; bestj = j; + } + if (ppdIdentMx[i][j] < worst) { + worst = ppdIdentMx[i][j]; worstj = j; + } + } + + if (bReportAll) { + printf("* %-15s %5d %7.1f %-15s %7.1f %-15s\n", + msa->sqname[i], DealignedLength(msa->aseq[i]), + best * 100., msa->sqname[bestj], + worst * 100., msa->sqname[worstj]); + } + if (best > best_best) best_best = best; + if (best < worst_best) worst_best = best; + if (worst < worst_worst) worst_worst = worst; + for (j = 0; j < i; j++) + sum += ppdIdentMx[i][j]; + } + avgid = sum / (float) (msa->nseq * (msa->nseq-1)/2.0); + if (bReportAll) + puts(""); + FMX2Free(ppdIdentMx); + } /* else bSampling */ + + + + /* Print output + */ + if (msa->name != NULL) + printf("Alignment name: %s\n", msa->name); + /*printf("Format: %s\n", SeqfileFormat2String(afp->format));*/ + printf("Number of sequences: %d\n", msa->nseq); + printf("Total # residues: %d\n", nres); + printf("Smallest: %d\n", small); + printf("Largest: %d\n", large); + printf("Average length: %.1f\n", (float) nres / (float) msa->nseq); + printf("Alignment length: %d\n", msa->alen); + printf("Average identity: %.2f%%\n", 100.*avgid); + + if (! bSampling) { + printf("Most related pair: %.2f%%\n", 100.*best_best); + printf("Most unrelated pair: %.2f%%\n", 100.*worst_worst); + printf("Most distant seq: %.2f%%\n", 100.*worst_best); + } + + /* + char *cs; + cs = MajorityRuleConsensus(msa->aseq, msa->nseq, msa->alen); + printf cs; + */ + + MSAFree(msa); +} +/* end of AliStat() */ + + + + + +/** + * @brief Shuffle mseq order + * + * @param[out] mseq + * mseq structure to shuffle + * + */ +void +ShuffleMSeq(mseq_t *mseq) +{ + int iSeqIndex; + int *piPermArray; + + + /* quick and dirty: create an array with permuted indices and + * swap accordingly (which amounts to shuffling twice) + */ + + PermutationArray(&piPermArray, mseq->nseqs); + + for (iSeqIndex=0; iSeqIndexnseqs; iSeqIndex++) { + SeqSwap(mseq, piPermArray[iSeqIndex], iSeqIndex); + } + + CKFREE(piPermArray); +} +/*** end: ShuffleMSeq() ***/ + + +/** + * @brief Swap two sequences in an mseq_t structure. + * + * @param[out] prMSeq + * Multiple sequence struct + * @param[in] i + * Index of first sequence + * @param[in] j + * Index of seconds sequence + * + * + */ +void +SeqSwap(mseq_t *prMSeq, int i, int j) +{ + char *pcTmp; + SQINFO rSqinfoTmp; + + assert(NULL!=prMSeq); + assert(inseqs && jnseqs); + + if (i==j) { + return; + } + + pcTmp = prMSeq->seq[i]; + prMSeq->seq[i] = prMSeq->seq[j]; + prMSeq->seq[j] = pcTmp; + + pcTmp = prMSeq->orig_seq[i]; + prMSeq->orig_seq[i] = prMSeq->orig_seq[j]; + prMSeq->orig_seq[j] = pcTmp; + + rSqinfoTmp = prMSeq->sqinfo[i]; + prMSeq->sqinfo[i] = prMSeq->sqinfo[j]; + prMSeq->sqinfo[j] = rSqinfoTmp; + + return; +} +/*** end: SeqSwap() ***/ + + + + +/** + * @brief Dealigns all sequences in mseq structure, updates the + * sequence length info and sets aligned to FALSE + * + * @param[out] mseq + * The mseq structure to dealign + * + */ +void +DealignMSeq(mseq_t *mseq) +{ + int i; /* aux */ + for (i=0; inseqs; i++) { + DealignSeq(mseq->seq[i]); + mseq->sqinfo[i].len = strlen(mseq->seq[i]); + } + mseq->aligned = FALSE; + + return; +} +/*** end: DealinMSeq() ***/ + + + +/** + * @brief debug output of sqinfo struct + * + * @param[in] sqinfo + * Squid's SQINFO struct for a certain seqeuence + * + * @note useful for debugging only + * + */ +void +LogSqInfo(SQINFO *sqinfo) +{ + + /*LOG_DEBUG("sqinfo->flags = %d", sqinfo->flags);*/ + if (sqinfo->flags & SQINFO_NAME) + Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->name = %s", sqinfo->name); + + if (sqinfo->flags & SQINFO_ID) + Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->id = %s", sqinfo->id); + + if (sqinfo->flags & SQINFO_ACC) + Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->acc = %s", sqinfo->acc); + + if (sqinfo->flags & SQINFO_DESC) + Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->desc = %s", sqinfo->desc); + + if (sqinfo->flags & SQINFO_LEN) + Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->len = %d", sqinfo->len); + + if (sqinfo->flags & SQINFO_START) + Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->start = %d", sqinfo->start); + + if (sqinfo->flags & SQINFO_STOP) + Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->stop = %d", sqinfo->stop); + + if (sqinfo->flags & SQINFO_OLEN) + Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->olen = %d", sqinfo->olen); + + if (sqinfo->flags & SQINFO_TYPE) + Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->type = %d", sqinfo->type); + + if (sqinfo->flags & SQINFO_SS) + Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->ss = %s", sqinfo->ss); + + if (sqinfo->flags & SQINFO_SA) + Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->sa = %s", sqinfo->sa); +} +/*** end: log_sqinfo ***/ + + +/** + * @brief convert int-encoded seqtype to string + * + * @param[in] seqtype int-encoded sequence type + * + * @return character pointer describing the sequence type + * + */ +const char* +SeqTypeToStr(int seqtype) +{ + switch (seqtype) { + case SEQTYPE_DNA: + return "DNA"; + case SEQTYPE_RNA: + return "RNA"; + case SEQTYPE_PROTEIN: + return "Protein"; + case SEQTYPE_UNKNOWN: + return "UNKNOWN"; + default: + Log(&rLog, LOG_FATAL, "Internal error in %s", __FUNCTION__); + } + return "Will never get here"; +} +/*** end: seqtype_to_str ***/ + + + +/** + * @brief reads sequences from file + * + * @param[out] prMSeq + * Multiple sequence struct. Must be preallocated. + * FIXME: would make more sense to allocate it here. + * @param[in] seqfile + * Sequence file name. If '-' sequence will be read from stdin. + * @param[in] seqtype + * int-encoded sequence type. Set to + * SEQTYPE_UNKNOWN for autodetect (guessed from first sequence) + * @param[in] iMaxNumSeq + * Return an error, if more than iMaxNumSeq have been read + * @param[in] iMaxSeqLen + * Return an error, if a seq longer than iMaxSeqLen has been read + * + * @return 0 on success, -1 on error + * + * @note + * - Depends heavily on squid + * - Sequence file format will be guessed + * - If supported by squid, gzipped files can be read as well. + */ +int +ReadSequences(mseq_t *prMSeq, char *seqfile, int seqtype, + int iMaxNumSeq, int iMaxSeqLen) +{ + int fmt = SQFILE_UNKNOWN; /* file format: auto detect if unknown */ + SQFILE *dbfp; /* sequence file descriptor */ + char *cur_seq; + SQINFO cur_sqinfo; + int iSeqIdx; /* sequence counter */ + int iSeqPos; /* sequence string position counter */ + + assert(NULL!=seqfile); + + + /* Try to work around inability to autodetect from a pipe or .gz: + * assume FASTA format + */ + if (SQFILE_UNKNOWN == fmt && + (Strparse("^.*\\.gz$", seqfile, 0) || strcmp(seqfile, "-") == 0)) { + fmt = SQFILE_FASTA; + } + + /* Using squid routines to read input. taken from seqstat_main.c. we don't + * know if input is aligned, so we use SeqfileOpen instead of MSAFileOpen + * etc. NOTE this also means we discard some information, e.g. when + * reading from and writing to a stockholm file, all extra MSA + * info/annotation will be lost. + * + */ + + if (NULL == (dbfp = SeqfileOpen(seqfile, fmt, NULL))) { + Log(&rLog, LOG_ERROR, "Failed to open sequence file %s for reading", seqfile); + return -1; + } + + + /* FIXME squid's ReadSeq() will exit with fatal error if format is + * unknown. This will be a problem for a GUI. Same is true for many squid + * other functions. + * + * The original squid:ReadSeq() dealigns sequences on input. We + * use a patched version. + * + */ + while (ReadSeq(dbfp, dbfp->format, + &cur_seq, + &cur_sqinfo)) { + + if (prMSeq->nseqs+1>iMaxNumSeq) { + Log(&rLog, LOG_ERROR, "Maximum number of sequences (=%d) exceeded after reading sequence '%s' from '%s'", + iMaxNumSeq, cur_sqinfo.name, seqfile); + return -1; + } + if ((int)strlen(cur_seq)>iMaxSeqLen) { + Log(&rLog, LOG_ERROR, "Sequence '%s' has %d residues and is therefore longer than allowed (max. sequence length is %d)", + cur_sqinfo.name, strlen(cur_seq), iMaxSeqLen); + return -1; + } + + /* FIXME: use modified version of AddSeq() that allows handing down SqInfo + */ + + prMSeq->seq = (char **) + CKREALLOC(prMSeq->seq, (prMSeq->nseqs+1) * sizeof(char *)); + prMSeq->seq[prMSeq->nseqs] = CkStrdup(cur_seq); + + + prMSeq->sqinfo = (SQINFO *) + CKREALLOC(prMSeq->sqinfo, (prMSeq->nseqs+1) * sizeof(SQINFO)); + SeqinfoCopy(&prMSeq->sqinfo[prMSeq->nseqs], &cur_sqinfo); + +#ifdef TRACE + Log(&rLog, LOG_FORCED_DEBUG, "seq no %d: seq = %s", prMSeq->nseqs, prMSeq->seq[prMSeq->nseqs]); + LogSqInfo(&prMSeq->sqinfo[prMSeq->nseqs]); +#endif + /* always guess type from first seq. use squid function and + * convert value + */ + if (0 == prMSeq->nseqs) { + int type = Seqtype(prMSeq->seq[prMSeq->nseqs]); + switch (type) { + case kDNA: + prMSeq->seqtype = SEQTYPE_DNA; + break; + case kRNA: + prMSeq->seqtype = SEQTYPE_RNA; + break; + case kAmino: + prMSeq->seqtype = SEQTYPE_PROTEIN; + break; + case kOtherSeq: + prMSeq->seqtype = SEQTYPE_UNKNOWN; + break; + default: + Log(&rLog, LOG_FATAL, "Internal error in %s", __FUNCTION__); + } + + /* override with given sequence type but check with + * automatically detected type and warn if necessary + */ + if (SEQTYPE_UNKNOWN != seqtype) { + if (prMSeq->seqtype != seqtype) { + Log(&rLog, LOG_WARN, "Overriding automatically determined seq-type %s to %s as requested", + SeqTypeToStr(prMSeq->seqtype), SeqTypeToStr(seqtype)); + prMSeq->seqtype = seqtype; + } + } + /* if type could not be determined and was not set return error */ + if (SEQTYPE_UNKNOWN == seqtype && SEQTYPE_UNKNOWN == prMSeq->seqtype) { + Log(&rLog, LOG_ERROR, "Couldn't guess sequence type from first sequence"); + FreeSequence(cur_seq, &cur_sqinfo); + SeqfileClose(dbfp); + return -1; + } + } + + Log(&rLog, LOG_DEBUG, "seq-no %d: type=%s name=%s len=%d seq=%s", + prMSeq->nseqs, SeqTypeToStr(prMSeq->seqtype), + prMSeq->sqinfo[prMSeq->nseqs].name, prMSeq->sqinfo[prMSeq->nseqs].len, + prMSeq->seq[prMSeq->nseqs]); + + /* FIXME IPUAC and/or case conversion? If yes see + * corresponding squid functions. Special treatment of + * Stockholm tilde-gaps for ktuple code? + */ + + prMSeq->nseqs++; + + FreeSequence(cur_seq, &cur_sqinfo); + } + SeqfileClose(dbfp); + +#if ALLOW_ONLY_PROTEIN + if (SEQTYPE_PROTEIN != prMSeq->seqtype) { + Log(&rLog, LOG_FATAL, "Sequence type is %s. %s only works on protein.", + SeqTypeToStr(prMSeq->seqtype), PACKAGE_NAME); + } +#endif + + /* Check if sequences are aligned */ + prMSeq->aligned = SeqsAreAligned(prMSeq); + + + /* keep original sequence as copy and convert "working" sequence + * + */ + prMSeq->orig_seq = (char**) CKMALLOC(prMSeq->nseqs * sizeof(char *)); + for (iSeqIdx=0; iSeqIdxnseqs; iSeqIdx++) { + + prMSeq->orig_seq[iSeqIdx] = CkStrdup(prMSeq->seq[iSeqIdx]); + + + /* convert unknown characters according to set seqtype + * be conservative, i.e. don't allow any fancy ambiguity + * characters to make sure that ktuple code etc. works. + */ + + /* first on the fly conversion between DNA and RNA + */ + if (prMSeq->seqtype==SEQTYPE_DNA) + ToDNA(prMSeq->seq[iSeqIdx]); + if (prMSeq->seqtype==SEQTYPE_RNA) + ToRNA(prMSeq->seq[iSeqIdx]); + + /* then check of each character + */ + for (iSeqPos=0; iSeqPos<(int)strlen(prMSeq->seq[iSeqIdx]); iSeqPos++) { + char *res = &(prMSeq->seq[iSeqIdx][iSeqPos]); + if (isgap(*res)) + continue; + + if (prMSeq->seqtype==SEQTYPE_PROTEIN) { + if (NULL == strchr(AMINO_ALPHABET, toupper(*res))) { + *res = AMINOACID_ANY; + } + } else if (prMSeq->seqtype==SEQTYPE_DNA) { + if (NULL == strchr(DNA_ALPHABET, toupper(*res))) { + *res = NUCLEOTIDE_ANY; + } + } else if (prMSeq->seqtype==SEQTYPE_RNA) { + if (NULL == strchr(RNA_ALPHABET, toupper(*res))) { + *res = NUCLEOTIDE_ANY; + } + } + } + } + + + prMSeq->filename = CkStrdup(seqfile); + Log(&rLog, LOG_INFO, "Read %d sequences (type: %s) from %s", + prMSeq->nseqs, SeqTypeToStr(prMSeq->seqtype), prMSeq->filename); + + return 0; +} +/*** end: ReadSequences ***/ + + +/** + * @brief allocate and initialise new mseq_t + * + * @param[out] prMSeq + * newly allocated and initialised mseq_t + * + * @note caller has to free by calling FreeMSeq() + * + * @see FreeMSeq + * + */ +void +NewMSeq(mseq_t **prMSeq) +{ + *prMSeq = (mseq_t *) CKMALLOC(1 * sizeof(mseq_t)); + + (*prMSeq)->nseqs = 0; + (*prMSeq)->seq = NULL; + (*prMSeq)->orig_seq = NULL; + (*prMSeq)->seqtype = SEQTYPE_UNKNOWN; + (*prMSeq)->sqinfo = NULL; + (*prMSeq)->filename = NULL; +} +/*** end: NewMSeq ***/ + + + +/** + * @brief copies an mseq structure + * + * @param[out] prMSeqDest_p + * Copy of mseq structure + * @param[in] prMSeqSrc + * Source mseq structure to copy + * + * @note caller has to free copy by calling FreeMSeq() + * + */ +void +CopyMSeq(mseq_t **prMSeqDest_p, mseq_t *prMSeqSrc) +{ + int i; + assert(prMSeqSrc != NULL && prMSeqDest_p != NULL); + + NewMSeq(prMSeqDest_p); + + (*prMSeqDest_p)->nseqs = prMSeqSrc->nseqs; + (*prMSeqDest_p)->seqtype = prMSeqSrc->seqtype; + if (prMSeqSrc->filename!=NULL) { + (*prMSeqDest_p)->filename = CkStrdup(prMSeqSrc->filename); + } + + (*prMSeqDest_p)->seq = (char **) + CKMALLOC((*prMSeqDest_p)->nseqs * sizeof(char *)); + (*prMSeqDest_p)->orig_seq = (char **) + CKMALLOC((*prMSeqDest_p)->nseqs * sizeof(char *)); + (*prMSeqDest_p)->sqinfo = (SQINFO *) + CKMALLOC((*prMSeqDest_p)->nseqs * sizeof(SQINFO)); + + + + for (i=0; i<(*prMSeqDest_p)->nseqs; i++) { + (*prMSeqDest_p)->seq[i] = CkStrdup(prMSeqSrc->seq[i]); + (*prMSeqDest_p)->orig_seq[i] = CkStrdup(prMSeqSrc->orig_seq[i]); + SeqinfoCopy(&(*prMSeqDest_p)->sqinfo[i], &prMSeqSrc->sqinfo[i]); + } +} +/*** end: CopyMSeq ***/ + + + +/** + * @brief + * + * @param[in] seqname + * The sequence name to search for + * @param[in] mseq + * The multiple sequence structure to search in + * + * @return -1 on failure, sequence index of matching name otherwise + * + * @warning If sequence name happens to be used twice, only the first + * one will be reported back + * + */ +int +FindSeqName(char *seqname, mseq_t *mseq) +{ + int i; /* aux */ + + assert(NULL!=mseq); + + for (i=0; inseqs; i++) { + if (STR_EQ(mseq->sqinfo[i].name, seqname)) { + return i; + } + } + + return -1; +} +/*** end: FindSeqName() ***/ + + +/** + * @brief Frees an mseq_t and it's members and zeros all members + * + * @param[in] mseq mseq_to to free + * + * @note use in conjunction with NewMSeq() + * @see new_mseq + */ +void +FreeMSeq(mseq_t **mseq) +{ + int i; + + if (NULL==(*mseq)) { + return; + } + + if ((*mseq)->filename) { + (*mseq)->filename = CKFREE((*mseq)->filename); + } + + for (i=0; i<(*mseq)->nseqs; i++) { + FreeSequence((*mseq)->seq[i], &(*mseq)->sqinfo[i]); + CKFREE((*mseq)->orig_seq[i]); + } + if ((*mseq)->seq) { + CKFREE((*mseq)->seq); + } + if ((*mseq)->orig_seq) { /* FIXME (FS): only ptr to ptr freed, actual sequences NOT freed*/ + CKFREE((*mseq)->orig_seq); + } + if ((*mseq)->sqinfo) { + CKFREE((*mseq)->sqinfo); + } + + (*mseq)->seqtype = SEQTYPE_UNKNOWN; + (*mseq)->nseqs = 0; + + CKFREE((*mseq)); +} +/*** end: FreeMSeq ***/ + + +/** + * @brief Write alignment to file. + * + * @param[in] mseq + * The mseq_t struct containing the aligned sequences + * @param[in] pcAlnOutfile + * The name of the output file + * @param[in] outfmt + * The alignment output format (defined in squid.h) + * + * @return Non-zero on error + * + * @note We create a temporary squid MSA struct in here because we never + * use it within clustal. We might be better of using the old clustal + * output routines instead. + * + */ +int +WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt) +{ + int i; /* aux */ + MSA *msa; /* squid's alignment structure */ + FILE *pfOut = NULL; + int key; /* MSA struct internal index for sequence */ + int alen; /* alignment length */ + bool use_stdout; + + assert(mseq!=NULL); + + if (MSAFILE_UNKNOWN == outfmt) { + Log(&rLog, LOG_ERROR, "Unknown output format chosen"); + return -1; + } + + if (NULL == pcAlnOutfile) { + pfOut = stdout; + use_stdout = TRUE; + } else { + use_stdout = FALSE; + if (NULL == (pfOut = fopen(pcAlnOutfile, "w"))) { + Log(&rLog, LOG_ERROR, "Could not open file %s for writing", pcAlnOutfile); + return -1; + } + } + + + /* derive alignment length from first seq */ + alen = strlen(mseq->seq[0]); + + msa = MSAAlloc(mseq->nseqs, alen); + + /* basic structure borrowed code from squid-1.9g/a2m.c:ReadA2M() + * we actually create a copy of mseq. keeping the pointers becomes + * messy when calling MSAFree() + */ + for (i=0; inseqs; i++) { + char *this_name = mseq->sqinfo[i].name; /* mseq sequence name */ + char *this_seq = mseq->seq[i]; /* mseq sequence */ + SQINFO *this_sqinfo = &mseq->sqinfo[i]; /* mseq sequence name */ + + key = GKIStoreKey(msa->index, this_name); + msa->sqname[key] = sre_strdup(this_name, strlen(this_name)); + + /* setting msa->sqlen[idx] and msa->aseq[idx] */ + msa->sqlen[key] = sre_strcat(&(msa->aseq[key]), msa->sqlen[key], + this_seq, strlen(this_seq)); + + if (this_sqinfo->flags & SQINFO_DESC) { + /* FIXME never get here ... */ + MSASetSeqDescription(msa, key, this_sqinfo->desc); + } + /* FIXME extend this by copying more stuff according to flags. + * See MSAFileRead() in msa.c and used functions there + * + * Problem is that we never parse MSA information as we use squid'sSeqFile + */ + + msa->nseq++; + } + + + /* FIXME Would like to, but can't use MSAVerifyParse(msa) here, as it + * will die on error. Need to implement our own version + */ +#if 0 + MSAVerifyParse(msa); +#endif + + /* The below is copy of MSAFileWrite() which originally only writes to stdout. + */ + + /* Be sloppy and make a2m and fasta the same. same for vienna (which is + the same). same same. can can. boleh boleh */ + if (outfmt==SQFILE_FASTA) + outfmt = MSAFILE_A2M; + if (outfmt==SQFILE_VIENNA) + outfmt = MSAFILE_VIENNA; + + switch (outfmt) { + case MSAFILE_A2M: + WriteA2M(pfOut, msa, 0); + break; + case MSAFILE_VIENNA: + WriteA2M(pfOut, msa, 1); + break; + case MSAFILE_CLUSTAL: + WriteClustal(pfOut, msa); + break; + case MSAFILE_MSF: + WriteMSF(pfOut, msa); + break; + case MSAFILE_PHYLIP: + WritePhylip(pfOut, msa); + break; + case MSAFILE_SELEX: + WriteSELEX(pfOut, msa); + break; + case MSAFILE_STOCKHOLM: + WriteStockholm(pfOut, msa); + break; + default: + Log(&rLog, LOG_FATAL, "internal error: %s", + "invalid output format should have been detected before"); + } + + if (use_stdout == FALSE) { + (void) fclose(pfOut); + Log(&rLog, LOG_INFO, + "Alignment written to %s", pcAlnOutfile); + } + MSAFree(msa); + + return 0; +} +/*** end of WriteAlignment() ***/ + + +/** + * @brief Removes all gap-characters from a sequence. + * + * @param[out] seq + * Sequence to dealign + * + * @note seq will not be reallocated + */ +void +DealignSeq(char *seq) +{ + int aln_pos; + int dealn_pos; + + assert(seq!=NULL); + + dealn_pos=0; + for (aln_pos=0; aln_pos<(int)strlen(seq); aln_pos++) { + if (! isgap(seq[aln_pos])) { + seq[dealn_pos++] = seq[aln_pos]; + } + } + seq[dealn_pos] = '\0'; + + return; +} +/*** end: DealignSeq() ***/ + + + +/** + * @brief Sort sequences by length + * + * @param[out] prMSeq + * mseq to sort by length + * @param[out] cOrder + * Sorting order. 'd' for descending, 'a' for ascending. + * + * + */ +void +SortMSeqByLength(mseq_t *prMSeq, const char cOrder) +{ + int *piSeqLen; + int *piOrder; + int iSeqIndex; + mseq_t *prMSeqCopy = NULL; + + assert('a'==cOrder || 'd'==cOrder); + + Log(&rLog, LOG_WARN, + "FIXME: This modifies sequence ordering. Might not be what user wants. Will change output order as well"); + + piSeqLen = (int *) CKMALLOC(prMSeq->nseqs * sizeof(int)); + piOrder = (int *) CKMALLOC(prMSeq->nseqs * sizeof(int)); + for (iSeqIndex=0; iSeqIndexnseqs; iSeqIndex++) { + piSeqLen[iSeqIndex] = prMSeq->sqinfo[iSeqIndex].len; + } + QSortAndTrackIndex(piOrder, piSeqLen, prMSeq->nseqs, cOrder, FALSE); + + CopyMSeq(&prMSeqCopy, prMSeq); + for (iSeqIndex=0; iSeqIndexnseqs; iSeqIndex++) { + /* copy mseq entry + */ + CKFREE(prMSeq->seq[iSeqIndex]); + prMSeq->seq[iSeqIndex] = CkStrdup(prMSeqCopy->seq[piOrder[iSeqIndex]]); + + CKFREE(prMSeq->orig_seq[iSeqIndex]); + prMSeq->orig_seq[iSeqIndex] = CkStrdup(prMSeqCopy->orig_seq[piOrder[iSeqIndex]]); + + SeqinfoCopy(&prMSeq->sqinfo[iSeqIndex], &prMSeqCopy->sqinfo[piOrder[iSeqIndex]]); + } + + CKFREE(piSeqLen); + CKFREE(piOrder); + FreeMSeq(&prMSeqCopy); + + return; +} +/*** end: SortMSeqByLength() ***/ + + + +/** + * @brief Checks if sequences in given mseq structure are aligned. By + * definition this is only true, if sequences are of the same length + * and at least one gap was found + * + * @param[in] prMSeq + * Sequences to check + * + * @return TRUE if sequences are aligned, FALSE if not + * + * + */ +bool +SeqsAreAligned(mseq_t *prMSeq) +{ + bool bGapFound, bSameLength; + int iSeqIdx; /* sequence counter */ + int iSeqPos; /* sequence string position counter */ + + /* Special case of just one sequence: + * it is arguable that a single sequence qualifies as a profile, + * however, this is what we do at the first stage of MSA anyway. + * So, if there is only 1 sequence it is a 1-profile + * and it is (defined to be) aligned (with itself). FS, r240 -> 241 + */ + if (1 == prMSeq->nseqs) { + return TRUE; + } + + + /* Check if sequences are aligned. For being aligned, the + * sequences have to be of same length (bSameLength) and at least + * one of them has to contain at least one gap (bGapFound) + */ + bGapFound = FALSE; + bSameLength = TRUE; + for (iSeqIdx=0; iSeqIdxnseqs; iSeqIdx++) { + if (FALSE == bGapFound) { + for (iSeqPos=0; + iSeqPossqinfo[iSeqIdx].len && false==bGapFound; + iSeqPos++) { + if (isgap(prMSeq->seq[iSeqIdx][iSeqPos])) { + bGapFound = TRUE; + /* skip rest of sequence */ + break; + } + } + } + + if (iSeqIdx>0) { + if (prMSeq->sqinfo[iSeqIdx].len != prMSeq->sqinfo[iSeqIdx-1].len) { + bSameLength = FALSE; + /* no need to continue search, bSameLength==FALSE is + * sufficient condition */ + break; + } + } + } +#if 0 + Log(&rLog, LOG_FORCED_DEBUG, "bSameLength=%d bGapFound=%d", bSameLength, bGapFound); +#endif + if (TRUE == bSameLength && TRUE == bGapFound) { + return TRUE; + } else { + return FALSE; + } + +} +/*** end: SeqsAreAligned() ***/ + + + +/** + * @brief Creates a new sequence entry and appends it to an existing mseq + * structure. + * + * @param[out] prMSeqDest_p + * Already existing and initialised mseq structure + * @param[in] pcSeqName + * sequence name of the sequence to add + * @param[in] pcSeqRes + * the actual sequence (residues) to add + * + * @note Don't forget to update the align and type flag if necessary! + * + * FIXME allow adding of more features + * + */ +void +AddSeq(mseq_t **prMSeqDest_p, char *pcSeqName, char *pcSeqRes) +{ + int iSeqIdx = 0; + SQINFO sqinfo; + + assert(NULL != prMSeqDest_p); + assert(NULL != pcSeqName); + assert(NULL != pcSeqRes); + + iSeqIdx = (*prMSeqDest_p)->nseqs; + + (*prMSeqDest_p)->seq = (char **) + CKREALLOC((*prMSeqDest_p)->seq, (iSeqIdx+1) * sizeof(char *)); + (*prMSeqDest_p)->orig_seq = (char **) + CKREALLOC((*prMSeqDest_p)->orig_seq, (iSeqIdx+1) * sizeof(char *)); + (*prMSeqDest_p)->sqinfo = (SQINFO *) + CKREALLOC((*prMSeqDest_p)->sqinfo, (iSeqIdx+1) * sizeof(SQINFO)); + + + (*prMSeqDest_p)->seq[iSeqIdx] = CkStrdup(pcSeqRes); + (*prMSeqDest_p)->orig_seq[iSeqIdx] = CkStrdup(pcSeqRes); + + /* should probably get ri of SqInfo altogether in the long run and just + transfer the intersting members into our own struct + */ + sqinfo.flags = 0; /* init */ + + sqinfo.len = strlen(pcSeqRes); + sqinfo.flags |= SQINFO_LEN; + + /* name is an array of SQINFO_NAMELEN length */ + strncpy(sqinfo.name, pcSeqName, SQINFO_NAMELEN-1); + sqinfo.name[SQINFO_NAMELEN-1] = '\0'; + sqinfo.flags |= SQINFO_NAME; + + SeqinfoCopy(&(*prMSeqDest_p)->sqinfo[iSeqIdx], + & sqinfo); + + (*prMSeqDest_p)->nseqs++; + + return; +} +/* end of AddSeq() */ + + + + +/** + * @brief Appends an mseq structure to an already existing one. + * filename will be left untouched. + * + * @param[in] prMSeqDest_p + * MSeq structure to which to append to + * @param[out] prMSeqToAdd + * MSeq structure which is to append + * + * + */ +void +JoinMSeqs(mseq_t **prMSeqDest_p, mseq_t *prMSeqToAdd) +{ + int iSrcSeqIndex; + int iNewNSeq; + + assert(NULL != prMSeqDest_p && NULL != (*prMSeqDest_p)); + assert(NULL != prMSeqToAdd); + + if (0 == prMSeqToAdd->nseqs) { + Log(&rLog, LOG_WARN, "Was asked to add 0 sequences"); + return; + } + + /* warn on seqtype mismatch and keep original seqtype */ + if ((*prMSeqDest_p)->seqtype != prMSeqToAdd->seqtype) { + Log(&rLog, LOG_WARN, "Joining sequences of different type"); + } + + /* leave filename as it is */ + + /* + * copy new seq/s, orig_seq/s, sqinfo/s + */ + iNewNSeq = (*prMSeqDest_p)->nseqs + prMSeqToAdd->nseqs; + + (*prMSeqDest_p)->seq = (char **) + CKREALLOC((*prMSeqDest_p)->seq, iNewNSeq * sizeof(char *)); + + (*prMSeqDest_p)->orig_seq = (char **) + CKREALLOC((*prMSeqDest_p)->orig_seq, iNewNSeq * sizeof(char *)); + + (*prMSeqDest_p)->sqinfo = (SQINFO *) + CKREALLOC((*prMSeqDest_p)->sqinfo, iNewNSeq * sizeof(SQINFO)); + + + for (iSrcSeqIndex=0; iSrcSeqIndex < prMSeqToAdd->nseqs; iSrcSeqIndex++) { + int iDstSeqIndex = (*prMSeqDest_p)->nseqs++; + + (*prMSeqDest_p)->seq[iDstSeqIndex] = + CkStrdup(prMSeqToAdd->seq[iSrcSeqIndex]); + + (*prMSeqDest_p)->orig_seq[iDstSeqIndex] = + CkStrdup(prMSeqToAdd->orig_seq[iSrcSeqIndex]); + + SeqinfoCopy(&(*prMSeqDest_p)->sqinfo[iDstSeqIndex], + & prMSeqToAdd->sqinfo[iSrcSeqIndex]); + } + + (*prMSeqDest_p)->nseqs = iNewNSeq; + + (*prMSeqDest_p)->aligned = SeqsAreAligned(*prMSeqDest_p); + + return; +} +/*** end: JoinMSeqs() ***/ diff --git a/binaries/src/clustalo/src/clustal/seq.h b/binaries/src/clustalo/src/clustal/seq.h new file mode 100644 index 0000000..af2c98a --- /dev/null +++ b/binaries/src/clustalo/src/clustal/seq.h @@ -0,0 +1,164 @@ +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: seq.h 234 2011-04-13 05:26:16Z andreas $ + */ + +#ifndef CLUSTALO_SEQ_H +#define CLUSTALO_SEQ_H + +#include "squid/squid.h" + +#include "util.h" + + +/** + * int-encoded sequence types. + * these are in sync with squid's seqtypes and only used for + * convenience here + */ +#define SEQTYPE_UNKNOWN kOtherSeq +#define SEQTYPE_DNA kDNA +#define SEQTYPE_RNA kRNA +#define SEQTYPE_PROTEIN kAmino + +/* Alphabets are defined in squid.h: AMINO_ALPHABET, DNA_ALPHABET, + * RNA_ALPHABET (all uppercase) + */ +#define AMINOACID_ANY 'X' +#define NUCLEOTIDE_ANY 'N' + +/** + * @brief structure for storing multiple sequences + * + */ +typedef struct { + int nseqs; /**< number of sequences */ + int seqtype; /**< sequence type */ + char *filename; /**< input file / source of sequences */ + bool aligned; /**< true if all seqs are same length **/ + + /** (working) sequence residues as char pointer. + * range for first index: 0--nseq-1. + * changes during alignment. + */ + char **seq; + + /** original sequence residues as char pointer. + * range for first index: 0--nseq-1. + * only set during input + */ + char **orig_seq; + + /** + * @brief Squid's sequence info structure. + * Index range: 0--nseq-1. + * + * extra data are available: + * int flags; + * + * name: + * char name[SQINFO_NAMELEN]; + * + * database identifier: + * char id[SQINFO_NAMELEN]; + * + * database accession no: + * char acc[SQINFO_NAMELEN]; + * + * description: + * char desc[SQINFO_DESCLEN]; + * + * length of this seq, incl gaps in our case!: + * int len; + * + * start position on source seq (valid range: 1..len): + * int start; + * + * end position on source seq (valid range: 1..len): + * int stop; + * + * original length of source seq: + * int olen; + * + * kRNA, kDNA, kAmino, or kOther: + * int type; + * + * secondary structure string (index range: 0..len-1): + * char *ss; + * + * percent side chain surface access (index range: 0..len-1): + * char *sa; + * + * @see squid.h + * @see LogSqInfo() + * + */ + SQINFO *sqinfo; +} mseq_t; + +extern void +AliStat(mseq_t *prMSeq, bool bSampling, bool bReportAll); + +extern void +AddSeq(mseq_t **prMSeqDest_p, char *pcSeqName, char *pcSeqRes); + +extern void +SeqSwap(mseq_t *mseq, int i, int j); + +extern void +DealignMSeq(mseq_t *mseq); + +extern const char * +SeqTypeToStr(int seqtype); + +extern int +ReadSequences(mseq_t *prMSeq_p, char *pcSeqFile, int iSeqType, + int iMaxNumSeq, int iMaxSeqLen); + +extern void +NewMSeq(mseq_t **mseq); + +extern void +FreeMSeq(mseq_t **mseq); + +extern void +CopyMSeq(mseq_t **prMSeqDest_p, mseq_t *prMSeqSrc); + +extern void +LogSqInfo(SQINFO *sqinfo); + +extern int +FindSeqName(char *seqname, mseq_t *mseq); + +extern int +WriteAlignment(mseq_t *mseq, const char *aln_outfile, int msafile_format); + +extern void +DealignSeq(char *seq); + +extern void +ShuffleMSeq(mseq_t *prMSeq); + +extern void +SortMSeqByLength(mseq_t *prMSeq, const char cOrder); + +void +JoinMSeqs(mseq_t **prMSeqDest_p, mseq_t *prMSeqToAdd); + +bool +SeqsAreAligned(mseq_t *prMSeq); + +#endif diff --git a/binaries/src/clustalo/src/clustal/symmatrix.c b/binaries/src/clustalo/src/clustal/symmatrix.c new file mode 100644 index 0000000..169ee91 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/symmatrix.c @@ -0,0 +1,496 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: symmatrix.c 230 2011-04-09 15:37:50Z andreas $ + * + * + * Functions for symmetric (square) matrices including diagonal. + * supports the notion of non-square sub-matrices of a symmetric + * matrix, i.e. where |rows|<|cols|. + * + * FIXME Allocating one big chunk of memory is probably + * much faster and also easier to maintain. + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include +#include "symmatrix.h" + + +#if 0 +#define DEBUG +#endif + +#define MAX_BUF_SIZE 65536 + +/** + * @brief Allocates symmat and its members and initialises them. Data + * will be calloced, i.e. initialised with zeros. + * + * @param[out] symmat + * newly allocated and initialised symmatrix instance + * @param[in] nrows + * number of rows + * @param[in] + * ncols number of columns + * + * @return: non-zero on error + * + * @see FreeSymMatrix() + * + * @note: symmat data will be of fake shape nrows x ncols + * + */ +int +NewSymMatrix(symmatrix_t **symmat, int nrows, int ncols) +{ + int i; /* aux */ + + assert(nrows>0 && ncols>0 && ncols>=nrows); + assert(ncols>0 && ncols>=nrows); + + (*symmat) = (symmatrix_t *) malloc(1*sizeof(symmatrix_t)); + if (NULL == (*symmat)) { + fprintf(stderr, "Couldn't allocate memory (%s|%s)\n", + __FILE__, __FUNCTION__); + return -1; + } + + (*symmat)->data = (double **) malloc(nrows * sizeof(double *)); + if (NULL == (*symmat)->data) { + fprintf(stderr, "Couldn't allocate memory (%s|%s)\n", + __FILE__, __FUNCTION__); + free(*symmat); + *symmat = NULL; + return -1; + } + for (i=0; idata[i] = (double *) calloc((ncols-i), sizeof(double)); + if (NULL == (*symmat)->data[i]) { + fprintf(stderr, "Couldn't allocate memory (%s|%s)\n", + __FILE__, __FUNCTION__); + while (0!=--i) { + free((*symmat)->data[i]); + } + free((*symmat)->data); + free(*symmat); + *symmat = NULL; + return -1; + } +#ifdef TRACE + fprintf(stderr, "DEBUG(%s|%s():%d) initialising symmat with the number of the beast\n", + __FILE__, __FUNCTION__, __LINE__); + { + int j; + for (j=0; jdata[i][j] = -666.0; + } + + } +#endif + } + + (*symmat)->nrows = nrows; + (*symmat)->ncols = ncols; + + return 0; +} +/*** end: new_symmatrix ***/ + + +/** + * @brief Sets symmat data of given index to given value + * + * @param[in] symmat + * symmatrix_t whose data is to be set + * @param[in] i + * first index + * @param[in] j + * second index + * @param[in] value + * value used to set data point + * + * @see SymMatrixGetValue() + * + * @note This is a convenience function that checks index order. + * + */ +void +SymMatrixSetValue(symmatrix_t *symmat, const int i, const int j, const double value) +{ + assert(NULL != symmat); + + if (i<=j) { + assert(i < symmat->nrows && j < symmat->ncols); + symmat->data[i][j-i] = value; + } else { + assert(j < symmat->nrows && i < symmat->ncols); + symmat->data[j][i-j] = value; + } +} +/*** end: symmatrix_setvalue ***/ + + + +/** + * @brief Returns element of symmat corresponding to given indices + * + * @param[in] symmat + * symmatrix_t of question + * @param[in] i + * index i + * @param[in] j + * index j + * + * @return requested value + * + * @see SymMatrixSetValue() + * + * @note This is a convenience function that checks index order. + */ +double +SymMatrixGetValue(symmatrix_t *symmat, const int i, const int j) +{ + assert(NULL != symmat); + + if (i<=j) { + assert(i < symmat->nrows && j < symmat->ncols); + return symmat->data[i][j-i]; + } else { + assert(j < symmat->nrows && i < symmat->ncols); + return symmat->data[j][i-j]; + } +} +/*** end: symmatrix_getvalue ***/ + + + + + +/** + * @brief Returns a pointer to an element of symmat corresponding to + * given indices + * + * @param[out] val + * Value to be set + * @param[in] symmat + * symmatrix_t of question + * @param[in] i + * index i + * @param[in] j + * index j + * + * @return pointer to value + * + * @see SymMatrixGetValue() + * + * @note This is a convenience function that checks index order. + * + */ +void +SymMatrixGetValueP(double **val, symmatrix_t *symmat, + const int i, const int j) +{ + assert(NULL != symmat); + + if (i<=j) { + assert(i < symmat->nrows && j < symmat->ncols); + *val = &(symmat->data[i][j-i]); + } else { + assert(j < symmat->nrows && i < symmat->ncols); + *val = &(symmat->data[j][i-j]); + } +} +/*** end: symmatrix_getvaluep ***/ + + +/** + * @brief Frees memory allocated by data members of symmat and symmat + * itself. + * + * @param[in] symmat + * symmatrix_t to be freed + * + * @note Use in conjunction with NewSymMatrix() + * + * @see NewSymMatrix() + * + */ +void +FreeSymMatrix(symmatrix_t **symmat) +{ + int i; + if (NULL != (*symmat)) { + if (NULL != (*symmat)->data) { + for (i=0; i<(*symmat)->nrows; i++) { + free((*symmat)->data[i]); + } + free((*symmat)->data); + } + } + free(*symmat); + *symmat = NULL; +} +/*** end: free_symmatrix ***/ + + + +/** + * @brief Print out a symmat in phylip style. Distances are printed on + * one line per sequence/object. Since we also support matrices with + * rows\nrows; i++) { + int this_len; + assert(NULL != labels[i]); + this_len = strlen(labels[i]); + if (this_len>max_label_len) + max_label_len = this_len; + } + + if (symmat->ncols==symmat->nrows) { + fprintf(fp, "%u\n", symmat->ncols); + } else { + /* this is not standard phylip, but necessary to indicate + seed matrices */ + fprintf(fp, "%u x %u\n", symmat->nrows, symmat->ncols); + } + for (i=0; inrows; i++) { + /* phylip restriction is 10 characters. we don't care here + */ + fprintf(fp, "%-*s", max_label_len, labels[i]); + /* we are lazy and do it like fastdist: write all distances + * for one seq to one line + */ + for (j=0; jncols; j++) { + fprintf(fp, " %f", SymMatrixGetValue(symmat, i, j)); + } + fprintf(fp, "%s", "\n"); + } + if (NULL != path) { + (void) fclose(fp); + } else { + (void) fflush(fp); + } +} +/*** end: SymMatrixPrint ***/ + + + +/** + * + * @brief Read a distance matrix in phylip format + * + * @param[in] pcFileIn + * distance matrix filename + * @param[out] prSymMat_p + * the symmatrix_t. will be allocated here. + * @return: + * non-zero on error + * + * @note: + * FIXME untested code + */ +int +SymMatrixRead(char *pcFileIn, symmatrix_t **prSymMat_p) +{ + FILE *prFilePointer; + char *buf; + /* number of parsed sequences */ + int iNParsedSeq = 0; + /* number of parsed distances per sequence */ + int iNParsedDists = 0; + /* total number of sequences/objects */ + int iTotalNSeq = 0; + int iRetCode = 0; + + assert(NULL!=pcFileIn); + + /* FIXME: test correctness and implement label checking */ + fprintf(stderr, "WARNING: Reading of distance matrix from file not thoroughly tested!\n"); + fprintf(stderr, "WARNING: Assuming same order of sequences in sequence file and distance matrix file (matching of labels not implemented)\n"); + + if (NULL == (buf = (char *) malloc(MAX_BUF_SIZE * sizeof(char)))) { + fprintf(stderr, "ERROR: couldn't allocate memory at %s:%s:%d\n", + __FILE__, __FUNCTION__, __LINE__); + return -1; + } + + if (NULL == (prFilePointer = fopen(pcFileIn, "r"))) { + fprintf(stderr, "ERROR: Couldn't open %s for reading\n", pcFileIn); + free(buf); + return -1; + } + + /* get number of sequences from first line and allocate memory for + * distance matrix + * + */ + if (NULL == fgets(buf, MAX_BUF_SIZE, prFilePointer) ) { + fprintf(stderr, "Couldn't read first line from %s\n", pcFileIn); + iRetCode = -1; + goto closefile_and_freebuf; + } + if (strlen(buf)==MAX_BUF_SIZE-1) { + fprintf(stderr, "%s\n", "Looks like I couldn't read complete line. Wrong format (or too small MAX_BUF_SIZE)"); + iRetCode = -1; + goto closefile_and_freebuf; + } + if (sscanf(buf, "%d", &iTotalNSeq)!=1) { + fprintf(stderr, "ERROR: couldn't parse number of sequences from first line of %s\n", pcFileIn); + iRetCode = -1; + goto closefile_and_freebuf; + } + +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "iTotalNSeq parsed from %s is %d\n", pcFileIn, iTotalNSeq); +#endif + + if (NewSymMatrix(prSymMat_p, iTotalNSeq, iTotalNSeq)) { + fprintf(stderr, "FATAL %s", "Memory allocation for distance matrix failed"); + iRetCode = -1; + goto closefile_and_freebuf; + } + + + /* parse file line by line + * + */ + while (NULL != fgets(buf, MAX_BUF_SIZE, prFilePointer)) { + char *szToken; + int is_newseq; + + if (MAX_BUF_SIZE-1 == strlen(buf)) { + fprintf(stderr, "%s\n", "Looks like I couldn't read complete line. Wrong format (or too small MAX_BUF_SIZE)"); + iRetCode = -1; + goto closefile_and_freebuf; + } + +#ifdef DEBUG + Log(&rLog, LOG_FORCED_DEBUG, "Got line: %s\n", buf); +#endif + + /* new sequence label at beginning of line? + */ + if (isblank(buf[0])) { + is_newseq = 0; + } else { + is_newseq = 1; + } + + /* tokenise line and treat new sequence specially + */ + szToken = strtok(buf, " \t"); + if (is_newseq==1) { + iNParsedSeq++; + iNParsedDists=0; + + /* if format is lower dimensional matrix then first + * sequence has no distances but might have newline + * character at it's end. + */ + while (isspace(szToken[strlen(szToken)-1])) { + szToken[strlen(szToken)-1]='\0'; + } + /* FIXME save label? */ + szToken = strtok(NULL, " \t"); + } + /* from here on it's only parsing of distances */ + while (szToken != NULL) { + double dist; + iNParsedDists++; + + /* only parse what's needed */ + if (iNParsedDists!=iNParsedSeq) { + /* parse and store distance + */ + if (sscanf(szToken, "%lf", &dist)!=1) { + fprintf(stderr, "Couldn't parse float from entry '%s'\n", szToken); + iRetCode = -1; + goto closefile_and_freebuf; + } +#if TRACE + Log(&rLog, LOG_FORCED_DEBUG, "Parsed distance %d for seq %d = %f\n", iNParsedDists-1, iNParsedSeq-1, dist); +#endif + SymMatrixSetValue(*prSymMat_p, iNParsedSeq-1, iNParsedDists-1, dist); + SymMatrixSetValue(*prSymMat_p, iNParsedDists-1, iNParsedSeq-1, dist); + } + szToken = strtok(NULL, " \t"); + } + } + + if (iTotalNSeq!=iNParsedSeq) { + fprintf(stderr, "expected %d seqs, but only parsed %d\n", iTotalNSeq, iNParsedSeq); + iRetCode = -1; + goto closefile_and_freebuf; + } +#if TRACE + for (i=0; i +#include +#include + +#include "util.h" +#include "log.h" +#include "muscle_upgma.h" +#include "tree.h" + +/** + * + * @brief Creates a UPGMA guide tree. This is a frontend function to + * the ported Muscle UPGMA code (). + * + * @param[out] tree + * created upgma tree. will be allocated here. use FreeMuscleTree() + * to free + * @param[in] labels + * pointer to nseq sequence names + * @param[in] distmat + * distance matrix + * @param[in] ftree + * optional: if non-NULL, tree will be written to this files + * + * @see FreeMuscleTree() + * @see MuscleUpgma2() + * + */ +void +GuideTreeUpgma(tree_t **tree, char **labels, + symmatrix_t *distmat, char *ftree) +{ + linkage_t linkage = LINKAGE_AVG; + FILE *fp = NULL; + + if (NULL != ftree) { + if (NULL == (fp=fopen(ftree, "w"))) { + Log(&rLog, LOG_ERROR, "Couldn't open tree-file '%s' for writing. Skipping", ftree); + } + /* fp NULL is handled later */ + } + + (*tree) = (tree_t *) CKMALLOC(1 * sizeof(tree_t)); + MuscleUpgma2((*tree), distmat, linkage, labels); + + if (rLog.iLogLevelEnabled <= LOG_DEBUG) { + Log(&rLog, LOG_DEBUG, "tree logging..."); + LogTree((*tree), LogGetFP(&rLog, LOG_DEBUG)); + } + + if (NULL != fp) { + MuscleTreeToFile(fp, (*tree)); + Log(&rLog, LOG_INFO, "Guide tree written to %s", ftree); + fclose(fp); + } +} +/*** end: guidetree_upgma ***/ + + + +/** + * + * @brief + * + * @param[out] tree + * created upgma tree. will be allocated here. use FreeMuscleTree() + * to free + * @param[in] mseq + * @param[in] ftree + * + * @return non-zero on error + * + */ +int +GuideTreeFromFile(tree_t **tree, mseq_t *mseq, char *ftree) +{ + int iNodeCount; + int iNodeIndex; + + (*tree) = (tree_t *) CKMALLOC(1 * sizeof(tree_t)); + if (MuscleTreeFromFile((*tree), ftree)!=0) { + Log(&rLog, LOG_ERROR, "%s", "MuscleTreeFromFile failed"); + return -1; + } + + /* Make sure tree is rooted */ + if (!IsRooted((*tree))) { + Log(&rLog, LOG_ERROR, "User tree must be rooted"); + return -1; + } + + if ((int)GetLeafCount((*tree)) != mseq->nseqs) { + Log(&rLog, LOG_ERROR, "User tree does not match input sequences"); + return -1; + } + + /* compare tree labels and sequence names and set leaf-ids */ + iNodeCount = GetNodeCount((*tree)); + for (iNodeIndex = 0; iNodeIndex < iNodeCount; ++iNodeIndex) { + char *LeafName; + int iSeqIndex; + + if (!IsLeaf(iNodeIndex, (*tree))) + continue; + LeafName = GetLeafName(iNodeIndex, (*tree)); + + if ((iSeqIndex=FindSeqName(LeafName, mseq))==-1) { + Log(&rLog, LOG_ERROR, "Label '%s' in tree could not be found in sequence names", LeafName); + return -1; + } + + SetLeafId((*tree), iNodeIndex, iSeqIndex); + } + + if (rLog.iLogLevelEnabled <= LOG_DEBUG) { + Log(&rLog, LOG_DEBUG, "tree logging..."); + LogTree((*tree), LogGetFP(&rLog, LOG_DEBUG)); + } + + return 0; +} +/*** end: GuideTreeFromFile() ***/ + + + +/** + * + * @brief Depth first traversal of tree, i.e. leaf nodes (sequences) + * will be visited first. Order can be used to guide progressive + * alignment order. + * + * @param[out] piOrderLR_p + * order in which left/right nodes (profiles) are to be aligned. + * allocated here; caller must free. + * @param[in] tree + * The tree to traverse; has to be rooted + * @param[in] mseq + * corresponding multiple sequence structure + * + */ +void +TraverseTree(int **piOrderLR_p, + tree_t *tree, mseq_t *mseq) +{ + int tree_nodeindex = 0; + int order_index = 0; + + assert(NULL!=tree); + assert(NULL!=mseq); + assert(IsRooted(tree)); + + /* allocate memory for node/profile alignment order; + * for every node allocate DIFF_NODE (3) int (1 left, 1 right, 1 parent) + */ + *piOrderLR_p = (int *)CKCALLOC(DIFF_NODE * GetNodeCount(tree), sizeof(int)); + + /* Log(&rLog, LOG_FORCED_DEBUG, "print tree->m_iNodeCount=%d", tree->m_iNodeCount); */ + + + tree_nodeindex = FirstDepthFirstNode(tree); + /*LOG_DEBUG("Starting with treenodeindex = %d", tree_nodeindex);*/ + + order_index = 0; + + do { + if (IsLeaf(tree_nodeindex, tree)) { + int leafid = GetLeafId(tree_nodeindex, tree); + if (leafid >= mseq->nseqs) + Log(&rLog, LOG_FATAL, "Sequence index out of range during tree traversal (leafid=%d nseqs=%d)", + leafid, mseq->nseqs); + + /* this is a leaf node, + * indicate this by registering same leafid for left/right + */ + + (*piOrderLR_p)[DIFF_NODE*order_index+LEFT_NODE] = leafid; + (*piOrderLR_p)[DIFF_NODE*order_index+RGHT_NODE] = leafid; + (*piOrderLR_p)[DIFF_NODE*order_index+PRNT_NODE] = tree_nodeindex; + + Log(&rLog, LOG_DEBUG, "Tree traversal: Visited leaf-node %d (leaf-id %d = Seq '%s')", + tree_nodeindex, leafid, mseq->sqinfo[leafid].name); + + } else { + int merge_nodeindex; + int left; + int right; + + merge_nodeindex = tree_nodeindex; + left = GetLeft(tree_nodeindex, tree); + right = GetRight(tree_nodeindex, tree); + + /* this is not a leaf node but a merge node, + * register left node (even) and right node (odd) + */ + (*piOrderLR_p)[DIFF_NODE*order_index+LEFT_NODE] = left; + (*piOrderLR_p)[DIFF_NODE*order_index+RGHT_NODE] = right; + (*piOrderLR_p)[DIFF_NODE*order_index+PRNT_NODE] = merge_nodeindex; + + Log(&rLog, LOG_DEBUG, "Tree traversal: Visited non-leaf node %d with siblings %d (L) and %d (R)", + merge_nodeindex, left, right); + } + tree_nodeindex = NextDepthFirstNode(tree_nodeindex, tree); + + order_index++; + + } while (NULL_NEIGHBOR != tree_nodeindex); + + return; +} +/*** end: TraverseTree ***/ diff --git a/binaries/src/clustalo/src/clustal/tree.h b/binaries/src/clustalo/src/clustal/tree.h new file mode 100644 index 0000000..cc85990 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/tree.h @@ -0,0 +1,40 @@ +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: tree.h 193 2011-02-07 15:45:21Z andreas $ + */ + +#ifndef CLUSTALO_TREE_H +#define CLUSTALO_TREE_H + +#include "symmatrix.h" +#include "muscle_tree.h" +#include "seq.h" + +enum {LEFT_NODE = 0, RGHT_NODE, PRNT_NODE, DIFF_NODE}; + +extern void +GuideTreeUpgma(tree_t **tree, + char **labels, symmatrix_t *tmat, char *ftree); + +extern int +GuideTreeFromFile(tree_t **tree, + mseq_t *mseq, char *ftree); + +extern void +TraverseTree(int **piOrderLR_p, + tree_t *tree, mseq_t *mseq); + +#endif diff --git a/binaries/src/clustalo/src/clustal/util.c b/binaries/src/clustalo/src/clustal/util.c new file mode 100644 index 0000000..f3e0d89 --- /dev/null +++ b/binaries/src/clustalo/src/clustal/util.c @@ -0,0 +1,505 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: util.c 235 2011-04-13 14:13:19Z andreas $ + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include + +#include "log.h" +#include "util.h" + + + + +/* struct for QSortAndTrackIndex and SortAndTrackIndexCmp[Asc|Desc] */ +typedef struct { + int piIndex; + int piValue; +} sortwithindex_t; + + + + +/** + * @brief Copy of squid's FileExists(). Copied here to make squid independent. + */ +int +CheckIfFileExists(char *pcFilename) +{ + FILE *prFile; + if ((prFile = fopen(pcFilename, "r"))) { + fclose(prFile); + return TRUE; + } + return FALSE; +} +/* end of CheckIfFileExists */ + + +/** + * @brief Allocates memory (malloc) + * + * @param[in] bytes + * bytes to allocated + * @param[in] function + * calling function name + * @param[in] line + * calling function line + * + * @return void pointer to the newly allocated memory + * + * @note use provided macro CKMALLOC() which automatically adds + * function name and line number + * + */ +void * +CkMalloc(size_t bytes, const char *function, const int line) +{ + void *ret; + + if(NULL == (ret = malloc(bytes * sizeof(char)))) { + Log(&rLog, LOG_FATAL, "Out of memory (requested from %s:%d)\n", function, line); + } + + return ret; +} +/*** end: ckmalloc ***/ + + + +/** + * @brief Allocates memory (calloc). Memory will be + * set to zero. + * + * @param[in] count + * Allocate space for count objects + * @param[in] size + * Objects are of this size + * @param[in] function + * calling function name + * @param[in] line + * calling function line + * + * @return void pointer to the newly allocated and zeroed memory (calloc). + * + * @note use provided macro CKCALLOC() which automatically adds + * function name and line number + * + * + */ +void * +CkCalloc(size_t count, size_t size, const char *function, const int line) +{ + void *ret; + + if(NULL == (ret = calloc(count, size))) { + Log(&rLog, LOG_FATAL, "Out of memory (requested from %s:%d)\n", + function, line); + exit(EXIT_FAILURE); + } + + return ret; +} +/*** end: CkCalloc ***/ + + +/** +* @brief Reallocates memory + * + * @param[in] ptr + * Pointer to memory to be reallocated + * @param[in] bytes + * bytes to allocated + * @param[in] function + * calling function name + * @param[in] line + * calling function line + * + * @return void pointer to the newly allocated memory + * + * @note use provided macro CKREALLOC() which automatically adds + * function name and line number + * + */ +void * +CkRealloc(void *ptr, size_t bytes, const char *function, const int line) +{ + void *ret=NULL; + + if(NULL == (ret = realloc(ptr, bytes))) { + Log(&rLog, LOG_FATAL, "FATAL: Out of memory (requested from %s:%d)\n", + function, line); + } + + return ret; +} +/*** end: ckrealloc ***/ + + + +/** + * + * @brief Frees memory + * + * @param[in] ptr + * Pointer to memory to be freed + * @param[in] function + * calling function name + * @param[in] line + * calling function line + * + * @return void pointer to the now zeroed memory + * + * @note use provided macro CKFREE() + * + */ +void * +CkFree(void *ptr, const char *function, const int line) +{ + if (ptr == NULL) { + Log(&rLog, LOG_WARN, "Bad call to CkFree from %s:%d (pointer was NULL)\n", function, line); + } else { + free(ptr); + ptr = NULL; + } + return ptr; +} +/*** end: CkFree ***/ + + + + +/** + * @brief safe version of strdup + * + * @param[in] src + * String to copy from + * + * @return copy of string + * + * @note src is not allowed to be NULL. + * + */ +char * +CkStrdup(const char *src) +{ + char *cp; + assert(NULL!=src); + + /*cp = strdup(src); always makes trouble... */ + cp = (char *) CKMALLOC(strlen(src) +1); + strcpy(cp, src); + + return cp; +} +/*** end: CkStrdup ***/ + + + + +/** + * @brief Creates an int array of size len with len-1 random but unique + * integers with values 0--len-1. This is "a modified version of + * Fisher-Yates known as Durstenfeld-Fisher-Yates or + * Knuth-Fisher-Yates". See + * http://stackoverflow.com/questions/196017/unique-random-numbers-in-o1 + * + * @param[in] perm + * The permutation array. Has to be preallocated + * @param[out] len + * Length of the permutation array + * + */ +void +PermutationArray(int **perm, const int len) +{ + int max, i; + + assert(len>0); + + srand((unsigned int) time(0)); + (*perm) = (int *) CKMALLOC(len * sizeof(int)); + max = len-1; + for (i=0; i=0) { + int tmp, randno; + /* randno = addrand((unsigned long) len); / returns 0--n-1 */ + randno = (rand()%len); + + /* swap */ + tmp = (*perm)[randno]; + (*perm)[randno] = (*perm)[max]; + (*perm)[max] = tmp; + + max--; + } + return; +} +/*** end: PermutationArray() ***/ + + + +/** + * @brief Creates an array filled with random, but unique ints of + * given range. Implementation of the Floyd algorithm. See + * http://stackoverflow.com/questions/1608181/unique-random-numbers-in-an-integer-array-in-the-c-programming-language + * Assuming M is the length of the desired array and N is the numeric + * range: "This approach has the complexity of about O(M) (depends on + * the search structure used), so it is better suitable when M << N. + * This approach keeps track of already generated random numbers, so + * it requires extra memory. However, the beauty of it is that it does + * not make any of those horrendous "trial and error" iterations, + * trying to find an unused random number. This algorithm is + * guaranteed to generate one unique random number after each single + * call to the random number generator." + * + * @warning This won't work if max_value<=array_len. Only use for + * cases where array_len<piValue; + const int ib = (const int) b_t->piValue; + return ia - ib; +} +/*** end: SortAndTrackIndexCmpAsc ***/ + + + + +/** + * @brief Compare two sortwithindex_t pointers and return the + * difference between the int value of the 2nd sortwithindex_t and the + * 1st. Used for descending sort order in QSortWithIndexes() + * + * @see SortAndTrackIndexCmpDesc() and QSortAndTrackIndex() + */ +int +SortAndTrackIndexCmpDesc(const void *a, const void *b) +{ + const sortwithindex_t *a_t = (const sortwithindex_t *)a; + const sortwithindex_t *b_t = (const sortwithindex_t *)b; + + const int ia = (const int) a_t->piValue; + const int ib = (const int) b_t->piValue; + return ib - ia; +} +/*** end: SortAndTrackIndexCmpDesc ***/ + + + + +/** + * @brief Sort a given int array in ascending or descending order, + * while keeping track of the element order. + * + * @param[out] piSortedIndices + * Will contain the indices of the sorted elements. Has to be preallocated. + * @param[out] piArrayToSort + * Array with values to sort. Will only be overwritten if + * bOverwriteArrayToSort it true. + * @param[in] iArrayLen + * Number of elements in piArrayToSort. + * @param[in] cOrder + * Sort order. 'a' for ascending, 'd' for descending. + * @param[in] bOverwriteArrayToSort + * If false do not overwrite the array to sort. + * + */ +void +QSortAndTrackIndex(int *piSortedIndices, int *piArrayToSort, + const int iArrayLen, const char cOrder, + const bool bOverwriteArrayToSort) +{ + int iCtr; /**< aux */ + + sortwithindex_t *prSort; + + + assert(NULL!=piSortedIndices); + assert(iArrayLen>0); + assert(NULL!=piArrayToSort); + assert('a'==cOrder || 'd'==cOrder); + + prSort = (sortwithindex_t *) CKMALLOC(iArrayLen * sizeof(sortwithindex_t)); + + for (iCtr=0; iCtr +#include +#include +#include +#include + +#ifndef CLUSTALO_UTIL_H +#define CLUSTALO_UTIL_H + + +#define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__) +#define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__) +#define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__) +#define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__)) + +#ifndef MAX +#define MAX(a,b) ((a)>(b)?(a):(b)) +#endif +#ifndef MIN +#define MIN(a,b) ((a)<(b)?(a):(b)) +#endif + +/* STR_EQ: strings are equal, case sensitive */ +#define STR_EQ(a,b) (strcmp((a),(b)) == 0) +/* STR_NC_EQ: strings are equal, ignoring case */ +#define STR_NC_EQ(a,b) (strcasecmp((a),(b)) == 0) + + +/* type boolean and false and true defined in stdbool.h */ +#ifndef TRUE +#define TRUE true +#endif +#ifndef FALSE +#define FALSE false +#endif + +/* clashes with hhalign +#define FAIL -1 +#define OK 0 +*/ + + + +/* don't use the following directly; use macros provided above instead + */ +void *CkMalloc(size_t size, const char *function, const int line); +void *CkCalloc(size_t count, size_t size, const char *function, const int line); +void *CkRealloc(void *ptr, size_t bytes, const char *function, const int line); +void *CkFree(void *ptr, const char *function, const int line); +char *CkStrdup(const char *s); +void PermutationArray(int **array, const int len); +void RandomUniqueIntArray(int *array, const int array_len, const int max_value); +int IntCmp(const void *a, const void *b); +bool FileIsWritable(char *pcFileName); +void QSortAndTrackIndex(int *piSortedIndices, int *piArrayToSort, + const int uArrayLen, const char cOrder, const bool bOverwriteArrayToSort); + +#endif diff --git a/binaries/src/clustalo/src/clustal/weights.c b/binaries/src/clustalo/src/clustal/weights.c new file mode 100644 index 0000000..fa37d6b --- /dev/null +++ b/binaries/src/clustalo/src/clustal/weights.c @@ -0,0 +1,337 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/* Module for deriving sequence weights from a tree. Largely based on + * Bob Edgar's Muscle (mainly clwwt.cpp; version 3.7). Ported to pure + * C. Most functions where apparently based on Clustal 1.8 anyway. + * + * Muscle's code is public domain and so is this code here. + * + * From http://www.drive5.com/muscle/license.htm: + * """ + * MUSCLE is public domain software + * + * The MUSCLE software, including object and source code and + * documentation, is hereby donated to the public domain. + * + * Disclaimer of warranty + * THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, + * EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED + * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + * """ + * + */ + +/* + * RCS $Id: weights.c 231 2011-04-09 17:13:06Z andreas $ + */ + +/* + * Documentation from Muscle + * + * """ + * Compute weights by the CLUSTALW method. + * Thompson, Higgins and Gibson (1994), CABIOS (10) 19-29; + * see also CLUSTALW paper. + * + * Weights are computed from the edge lengths of a rooted tree. + * + * Define the strength of an edge to be its length divided by the number + * of leaves under that edge. The weight of a sequence is then the sum + * of edge strengths on the path from the root to the leaf. + * + * Example. + * + * 0.2 + * -----A 0.1 + * -x ------- B 0.7 + * --------y ----------- C + * 0.3 ----------z + * 0.4 -------------- D + * 0.8 + * + * Edge Length Leaves Strength + * ---- ----- ------ -------- + * xy 0.3 3 0.1 + * xA 0.2 1 0.2 + * yz 0.4 2 0.2 + * yB 0.1 1 0.1 + * zC 0.7 1 0.7 + * zD 0.8 1 0.8 + * + * Leaf Path Strengths Weight + * ---- ---- --------- ------ + * A xA 0.2 0.2 + * B xy-yB 0.1 + 0.1 0.2 + * C xy-yz-zC 0.1 + 0.2 + 0.7 1.0 + * D xy-yz-zD 0.1 + 0.2 + 0.8 1.1 + * """ + * + */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include "log.h" +#include "muscle_tree.h" +#include "weights.h" + + +/* + #undef DEBUG +*/ + + +/** + * @brief FIXME + * + * @param[out] puLeavesUnderNode + * FIXME + * @param[in] prTree + * FIXME + * @param[in] uNodeIndex + * FIXME + * + * @return The return value + * + * @note see Muscle3.7:clwwt.cpp + * + */ +uint +CountLeaves(uint *puLeavesUnderNode, tree_t *prTree, uint uNodeIndex) +{ + uint uLeft; + uint uRight; + uint uRightCount; + uint uLeftCount; + uint uCount; + + + if (IsLeaf(uNodeIndex, prTree)) { + puLeavesUnderNode[uNodeIndex] = 1; + return 1; + } + + uLeft = GetLeft(uNodeIndex, prTree); + uRight = GetRight(uNodeIndex, prTree); + uRightCount = CountLeaves(puLeavesUnderNode, prTree, uRight); + uLeftCount = CountLeaves(puLeavesUnderNode, prTree, uLeft); + uCount = uRightCount + uLeftCount; + + puLeavesUnderNode[uNodeIndex] = uCount; + + return uCount; +} +/*** end: CountLeaves() ***/ + + + + +/** + * @brief Normalise values in a double array to values between 0 and 1. + * + * @param[out] p + * double array with n elements + * @param[in] n + * number of elements in p + * + * @note From Muscle3.7: intmath.cpp:Normalize() + * + */ +void +Normalise(double *p, uint n) { + unsigned i; + double dSum = 0.0; + for (i = 0; i < n; ++i) { + dSum += p[i]; + } + if (0.0 == dSum) { + Log(&rLog, LOG_FATAL, "Normalise, sum=0"); + } + for (i = 0; i < n; ++i) { + p[i] /= dSum; + } +} +/*** end: Normalise() ***/ + + + +/** + * @brief Calculate "Clustal" weights from a tree. + * + * FIXME see doc in muscle:clwwt.cpp + * + * @param[out] pdWeights_p + * Will contain a weight for each leaf/sequence. Allocated here. User + * has to free + * @param[in] prTree + * Tree to derive weights from + * + * @return 0 on success, non-zero otherwise + * + * @note Largely copied from Muscle3.7: clwwt.cpp:CalcClustalWWeights() + * + * @warning FIXME Not sure if Muscle routines are most efficient here. + * Couldn't we do all this while traversing the tree and thereby safe + * time? + * + */ +int +CalcClustalWeights(double **pdWeights_p, tree_t *prTree) +{ + int i; /* aux */ + uint uLeafCount; + uint uNodeCount; + uint *puLeavesUnderNode; + uint uLeavesUnderRoot; + uint uRootNodeIndex; + double *pdStrengths; + uint uNodeIndex; + bool bLogWeights = FALSE; /* verbose output of weights */ + + + assert(NULL != pdWeights_p); + assert(NULL != prTree); + + if (rLog.iLogLevelEnabled <= LOG_DEBUG) { + bLogWeights = TRUE; + } + + uLeafCount = GetLeafCount(prTree); + uNodeCount = GetNodeCount(prTree); + + + (*pdWeights_p) = (double *) CKMALLOC(uNodeCount * sizeof(double)); + + if (0 == uLeafCount) { + return 0; + } else if (1 == uLeafCount) { + (*pdWeights_p)[0] = 1.0; + return 0; + } else if (2 == uLeafCount) { + (*pdWeights_p)[0] = 0.5; + (*pdWeights_p)[1] = 0.5; + return 0; + } + + if (!IsRooted(prTree)) { + Log(&rLog, LOG_ERROR, "Tree must be rooted to get weights"); + CKFREE(pdWeights_p); + return -1; + } + + +#ifdef TRACE + Log(&rLog, LOG_FORCED_DEBUG, "%s", "Weights follow"); + fprintf(stderr, "Node Leaves Length Strength\n"); + fprintf(stderr, "---- ------ -------- --------\n"); + /* 1234 123456 12345678 12345678 */ +#endif + + uRootNodeIndex = GetRootNodeIndex(prTree); + puLeavesUnderNode = (uint *) CKCALLOC(uNodeCount, sizeof(uint)); + + uLeavesUnderRoot = CountLeaves(puLeavesUnderNode, prTree, uRootNodeIndex); + if (uLeavesUnderRoot != uLeafCount) { + Log(&rLog, LOG_FATAL, "Internal error, root count %u %u", + uLeavesUnderRoot, uLeafCount); + } +#if 0 + for (uNodeIndex=0; uNodeIndex%u(%g)", uNode, pdStrengths[uNode]); + } + } + /* AW: no idea what this is, but it's done like this in Muscle */ + if (dWeight < 0.0001) { +#ifdef TRACE + fprintf(stderr, "zero->one"); +#endif + dWeight = 1.0; + } + + /* @note: the only difference to the muscle code is here: we + * use the input index for storing weights, instead of the + * tree leaf index + */ + (*pdWeights_p)[GetLeafId(uLeafNodeIndex, prTree)] = dWeight; + if (bLogWeights){ + fprintf(stderr, " = %g\n", dWeight); + } + } + +#if 0 + for (i=0; i + +/* Include clustal-omega's header. That's all you need + * + * If you developing in C++, use the following instead: + * extern "C" { + * #include "clustal-omega.h" + * } + */ +#include "clustal-omega.h" + + +int +main(int argc, char **argv) +{ + /* the multiple sequence structure */ + mseq_t *prMSeq = NULL; + /* for openmp: number of threads to use */ + int iThreads = 1; + /* alignment options to use */ + opts_t rAlnOpts; + /* an input file */ + char *pcSeqInfile; + int iAux; + + /* use LOGLEVEL_QUIET to make Clustal shut up */ + iVerbosityLevel = LOGLEVEL_INFO; + + SetDefaultAlnOpts(&rAlnOpts); + + InitClustalOmega(iThreads); + + /* Get sequence input file name from command line + */ + if (argc!=2) { + Fatal("Need sequence file as argument"); + } + pcSeqInfile = argv[1]; + + /* Read sequence file + */ + NewMSeq(&prMSeq); + if (ReadSequences(prMSeq, pcSeqInfile, + SEQTYPE_UNKNOWN, + INT_MAX, INT_MAX)) { + Fatal("Reading sequence file '%s' failed", pcSeqInfile); + } + + /* Dump some info about the sequences + */ + for (iAux=0; iAuxnseqs; iAux++) { + Info(LOGLEVEL_INFO, + "Sequence no %d has the following name: %s", + iAux, prMSeq->sqinfo[iAux].name); + Info(LOGLEVEL_INFO, + "Sequence no %d has the following residues: %s", + iAux, prMSeq->seq[iAux]); + /* more info can be found in prMSeq->sqinfo[iAux] */ + } + + + /* Align the sequences without a profile (NULL) + */ + if (Align(prMSeq, NULL, & rAlnOpts)) { + Fatal("A fatal error happended during the alignment process"); + } + + + /* Output of final alignment to stdout (NULL) as aligned fasta/a2m + */ + if (WriteAlignment(prMSeq, NULL, MSAFILE_A2M)) { + Fatal("Could not save alignment"); + } + + FreeMSeq(&prMSeq); + + Info(LOGLEVEL_INFO, "Successfull program exit"); + + return EXIT_SUCCESS; +} +/*** end of main() ***/ diff --git a/binaries/src/clustalo/src/config.h.in b/binaries/src/clustalo/src/config.h.in new file mode 100644 index 0000000..1603f2c --- /dev/null +++ b/binaries/src/clustalo/src/config.h.in @@ -0,0 +1,244 @@ +/* src/config.h.in. Generated from configure.ac by autoheader. */ + +/* Define if building universal (internal helper macro) */ +#undef AC_APPLE_UNIVERSAL_BUILD + +/* Let all files know they are being used inside Clustal Omega */ +#undef CLUSTALO + +/* This is a CYGWIN system */ +#undef CYGWIN + +/* This is a Darwin system */ +#undef DARWIN + +/* Define to 1 if you have the header file. */ +#undef HAVE_ARGTABLE2_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_ASSERT_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_CTYPE_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_DLFCN_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_FLOAT_H + +/* Define to 1 if you have the `fseek64' function. */ +#undef HAVE_FSEEK64 + +/* Define to 1 if you have the `fseeko' function. */ +#undef HAVE_FSEEKO + +/* Define to 1 if you have the `fseeko64' function. */ +#undef HAVE_FSEEKO64 + +/* Define to 1 if you have the `ftell64' function. */ +#undef HAVE_FTELL64 + +/* Define to 1 if you have the `ftello' function. */ +#undef HAVE_FTELLO + +/* Define to 1 if you have the `ftello64' function. */ +#undef HAVE_FTELLO64 + +/* Define to 1 if you have the header file. */ +#undef HAVE_INTTYPES_H + +/* Define to 1 if you have the `argtable2' library (-largtable2). */ +#undef HAVE_LIBARGTABLE2 + +/* Define to 1 if you have the `m' library (-lm). */ +#undef HAVE_LIBM + +/* Define to 1 if you have the header file. */ +#undef HAVE_LIMITS_H + +/* Has log2() */ +#undef HAVE_LOG2 + +/* Define to 1 if you have the header file. */ +#undef HAVE_MATH_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_MEMORY_H + +/* Define to 1 if you have the `ntohl' function. */ +#undef HAVE_NTOHL + +/* Define to 1 if you have the `ntohs' function. */ +#undef HAVE_NTOHS + +/* Define to 1 if you have the `ntonl' function. */ +#undef HAVE_NTONL + +/* Define to 1 if you have the `ntons' function. */ +#undef HAVE_NTONS + +/* Defined if OpenMP should and can be used */ +#undef HAVE_OPENMP + +/* Define to 1 if you have the header file. */ +#undef HAVE_STDARG_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STDINT_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STDIO_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STDLIB_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STRINGS_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_STRING_H + +/* Define to 1 if you have the `stroul' function. */ +#undef HAVE_STROUL + +/* Define to 1 if you have the `strtoull' function. */ +#undef HAVE_STRTOULL + +/* Define to 1 if you have the header file. */ +#undef HAVE_SYS_STAT_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_SYS_TYPES_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_TIME_H + +/* Define to 1 if you have the header file. */ +#undef HAVE_UNISTD_H + +/* This is a LINUX system */ +#undef LINUX + +/* Define to the sub-directory in which libtool stores uninstalled libraries. + */ +#undef LT_OBJDIR + +/* This is a MinGW system */ +#undef MINGW + +/* No-debug Mode */ +#undef NDEBUG + +/* Some strange OS */ +#undef OTHEROS + +/* Name of package */ +#undef PACKAGE + +/* Define to the address where bug reports for this package should be sent. */ +#undef PACKAGE_BUGREPORT + +/* The package code name */ +#undef PACKAGE_CODENAME + +/* Define to the full name of this package. */ +#undef PACKAGE_NAME + +/* Define to the full name and version of this package. */ +#undef PACKAGE_STRING + +/* Define to the one symbol short name of this package. */ +#undef PACKAGE_TARNAME + +/* Define to the version of this package. */ +#undef PACKAGE_VERSION + +/* The size of `fpos_t', as computed by sizeof. */ +#undef SIZEOF_FPOS_T + +/* The size of `unsigned int', as computed by sizeof. */ +#undef SIZEOF_UNSIGNED_INT + +/* The size of `unsigned long', as computed by sizeof. */ +#undef SIZEOF_UNSIGNED_LONG + +/* The size of `unsigned long long', as computed by sizeof. */ +#undef SIZEOF_UNSIGNED_LONG_LONG + +/* The size of `unsigned short', as computed by sizeof. */ +#undef SIZEOF_UNSIGNED_SHORT + +/* This is a Solaris system */ +#undef SOLARIS + +/* This is a BSD system */ +#undef SOMEBSD + +/* Define to 1 if you have the ANSI C header files. */ +#undef STDC_HEADERS + +/* Enable extensions on AIX 3, Interix. */ +#ifndef _ALL_SOURCE +# undef _ALL_SOURCE +#endif +/* Enable GNU extensions on systems that have them. */ +#ifndef _GNU_SOURCE +# undef _GNU_SOURCE +#endif +/* Enable threading extensions on Solaris. */ +#ifndef _POSIX_PTHREAD_SEMANTICS +# undef _POSIX_PTHREAD_SEMANTICS +#endif +/* Enable extensions on HP NonStop. */ +#ifndef _TANDEM_SOURCE +# undef _TANDEM_SOURCE +#endif +/* Enable general extensions on Solaris. */ +#ifndef __EXTENSIONS__ +# undef __EXTENSIONS__ +#endif + + +/* Version number of package */ +#undef VERSION + +/* Define if using the dmalloc debugging malloc package */ +#undef WITH_DMALLOC + +/* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most + significant byte first (like Motorola and SPARC, unlike Intel). */ +#if defined AC_APPLE_UNIVERSAL_BUILD +# if defined __BIG_ENDIAN__ +# define WORDS_BIGENDIAN 1 +# endif +#else +# ifndef WORDS_BIGENDIAN +# undef WORDS_BIGENDIAN +# endif +#endif + +/* Define to 1 if on MINIX. */ +#undef _MINIX + +/* Define to 2 if the system does not provide POSIX.1 features except with + this defined. */ +#undef _POSIX_1_SOURCE + +/* Define to 1 if you need to in order for `stat' and other things to work. */ +#undef _POSIX_SOURCE + +/* Define to empty if `const' does not conform to ANSI C. */ +#undef const + +/* Define to `__inline__' or `__inline' if that's what the C compiler + calls it, or to nothing if 'inline' is not supported under any name. */ +#ifndef __cplusplus +#undef inline +#endif + +/* Define to `long int' if does not define. */ +#undef off_t + +/* Define to `unsigned int' if does not define. */ +#undef size_t diff --git a/binaries/src/clustalo/src/hhalign/Makefile.am b/binaries/src/clustalo/src/hhalign/Makefile.am new file mode 100644 index 0000000..e54211b --- /dev/null +++ b/binaries/src/clustalo/src/hhalign/Makefile.am @@ -0,0 +1,26 @@ +# Some useful automake documentation: +# http://www.openismus.com/documents/linux/automake/automake.shtml +# http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html + +#SUBDIRS = +#EXTRA_DIST = +# LDADD = foofiles/libfoo.a + +AM_CXXFLAGS = -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 @OPENMP_CXXFLAGS@ @AM_CXXFLAGS@ + +noinst_LTLIBRARIES = libhhalign.la + +libhhalign_la_SOURCES = hhalign.cpp hhalign.h \ + hash-C.h hash.h hhdecl-C.h hhfunc-C.h hhfunc.h \ + hhmatrices-C.h hhutil-C.h \ + hhalignment-C.h hhalignment.h \ + hhfullalignment-C.h hhfullalignment.h \ + hhhalfalignment-C.h hhhalfalignment.h \ + hhhit-C.h hhhit.h hhhitlist-C.h hhhitlist.h \ + hhhmm-C.h hhhmm.h \ + util-C.h list-C.h list.h \ + general.h + +library_includedir=$(includedir)/clustalo/hhalign + +library_include_HEADERS = general.h hhfunc.h diff --git a/binaries/src/clustalo/src/hhalign/Makefile.in b/binaries/src/clustalo/src/hhalign/Makefile.in new file mode 100644 index 0000000..36d5b55 --- /dev/null +++ b/binaries/src/clustalo/src/hhalign/Makefile.in @@ -0,0 +1,510 @@ +# Makefile.in generated by automake 1.10.2 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, +# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + +@SET_MAKE@ + 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export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/binaries/src/clustalo/src/hhalign/general.h b/binaries/src/clustalo/src/hhalign/general.h new file mode 100644 index 0000000..b8a4a22 --- /dev/null +++ b/binaries/src/clustalo/src/hhalign/general.h @@ -0,0 +1,101 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: general.h 247 2011-06-16 11:41:15Z fabian $ + */ + + +#ifndef GENERAL_H +#define GENERAL_H + + +#include "../clustal/log.h" + +/* +***** Omega definitions************************************ + FS, 2010-02-19 +*/ +enum {NO = 0, YES}; +enum {BASE10 = 10}; +enum {AMINOACIDS = 20, STATE_TRANSITIONS = 7}; +enum {MAXWORD = 100, MAXLEN = 10000}; +enum {OVER_ALLOCATE = 2}; +enum {FAILURE = -1, OK}; +enum {RETURN_OK = 0, RETURN_FROM_MAC, RETURN_FROM_VITERBI, RETURN_FROM_PRINT_ALI, RETURN_FROM_RNP, RETURN_UNKNOWN}; +enum {REALLY_BIG_MEMORY_MB = 64000}; +enum {F_OFFSET = 1}; +enum {INTERN_ALN_2_HMM = 0, READ_ALN_2_HMM, READ_HMM_2_HMM, INTERN_HMM_2_HMM}; +#define UNITY 1.00 + +/*#define MIN(a,b) ((a)<(b)?(a):(b))*/ + + +/* parameters passed from Clustal-Omega to hhalign; FS, r240 -> */ +typedef struct { + + int iMacRamMB; /* dedicated amount of RAM for Maximum Accuracy (in MB) */ + +} hhalign_para; + +typedef struct { + /***public***/ + int n_display; + char **sname; + char **seq; + int ncons; + int nfirst; + int nss_dssp; + int nsa_dssp; + int nss_pred; + int nss_conf; + int L; + int N_in; + int N_filtered; + float *Neff_M; + float *Neff_I; + float *Neff_D; + float Neff_HMM; + char *longname; + char name[511]; + char file[511]; + char fam[511]; + char sfam[511]; + char fold[511]; + char cl[511]; + float lamda; + float mu; + /***private***/ + float **f; + float **g; + float **p; + float **tr; + float **linTr; + char trans_lin; + char *ss_dssp; + char *sa_dssp; + char *ss_pred; + char *ss_conf; + char *Xcons; + float pav[20]; + float pnul[20]; + int *l; + +} hmm_light; + + +#endif + diff --git a/binaries/src/clustalo/src/hhalign/hash-C.h b/binaries/src/clustalo/src/hhalign/hash-C.h new file mode 100644 index 0000000..24b7815 --- /dev/null +++ b/binaries/src/clustalo/src/hhalign/hash-C.h @@ -0,0 +1,594 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: hash-C.h 143 2010-10-14 13:11:14Z andreas $ + */ + +// hash.C +// Class for Hash data structure +// * works in the same way as a hash in Perl +// * keys are strings of type char* +// * data elements are of type Typ +// * objects have to be declared with maximal size, e.g. Hash hash1(10000) (num_slots should not be a power of 2) +// * works also if maximal size is exceeded, but gets slower by a factor ~num_keys/num_slots + +/* + * RCS $Id: hash-C.h 143 2010-10-14 13:11:14Z andreas $ + */ + +#ifndef HASH +#define HASH + +#ifndef MAIN +#include // cin, cout, cerr +#include // printf +#include // exit +#include // strcmp, strstr +#include // sqrt, pow +#include // INT_MIN +#include // FLT_MIN +#include // islower, isdigit etc +#include // clock +#include // perror() +using std::cout; +using std::cerr; +using std::endl; +using std::ios; +using std::ifstream; +using std::ofstream; +#endif + +#ifndef JLIST +#define JLIST +#include "list.h" // List +#include "list-C.h" ////////////////////////////////// DEBUG +#endif + +#include "hash.h" + + + +////////////////////////////////////////////////////////////////////////////// +////////////////////// Methods of class Hash ///////////////////////////////// +////////////////////////////////////////////////////////////////////////////// + +////////////////////////////////////////////////////////////////////////////// +// Private Methods + + +////////////////////////////////////////////////////////////////////////////// +// Constructor and Destructor of Hash +////////////////////////////////////////////////////////////////////////////// +// Constructor of class Hash +////////////////////////////////////////////////////////////////////////////// +template +Hash::Hash() +{ + num_keys=0; max_len=0; prev=curr=num_slots = 0; slot=NULL; +} + +template +Hash::Hash(int nslots) +{ + num_keys=0; max_len=0; prev=curr=num_slots = nslots; + slot = new Slot*[num_slots]; //Create array of num_slots slots + for (int i=0; i(0); +} + +template +Hash::Hash(int nslots, Typ f) +{ + num_keys=0; max_len=0; prev=curr=num_slots = nslots; + slot = new Slot*[num_slots]; //Create array of num_slots slots + for (int i=0; i +Hash::~Hash() +{ + RemoveAll(); + delete[] slot; slot = NULL; +} + + +//////////////////////////////////////////////////////////////////////////////////////////// +// Hash function +//////////////////////////////////////////////////////////////////////////////////////////// +template +inline unsigned int Hash::HashValue(char* key) //returns the hash value for key + { + // Calculate a hash value by the division method: + // Transform key into a natural number k = sum ( key[i]*128^(L-i) ) and calculate i= k % num_slots. + // Since calculating k would lead to an overflow, i is calculated iteratively + // and at each iteration the part divisible by num_slots is subtracted, i.e. (% num_slots is taken). + if (key==NULL) {printf("Warning from hash.C: key=NULL\n"); return 0;} + unsigned int i=0; // Start of iteration: k is zero + char* c = key; + while(*c) i = ((i<<7) + *(c++)) % num_slots; + key_len = c - key; + // cerr<<" Hash value for \'"< +void Hash::New(int nslots, Typ f) +{ + fail=f; + RemoveAll(); + delete[] slot; slot = NULL; + num_keys=0; max_len=0; prev=curr=num_slots = nslots; + slot = new Slot*[num_slots]; //Create array of num_slots slots + for (int i=0; i +Typ Hash::Show(char* key) +{ + Slot* pslot; + int i = HashValue(key); + + pslot = slot[i]; + if (!pslot) return fail; + pslot->Reset(); + do{ + if(!strcmp(pslot->ReadNext().key,key)) return pslot->ReadCurrent().data; + } while(!pslot->End()); + return fail; +} + +//////////////////////////////////////////////////////////////////////////////////////////// +// Add/replace key/data pair to hash and return address of data element +//////////////////////////////////////////////////////////////////////////////////////////// +template +Typ* Hash::Add(char* key, Typ data) +{ + Pair* pairp; + Slot* pslot; + int i = HashValue(key); + + pslot = slot[i]; + if (!pslot) { num_keys++; KeyLen(); slot[i]=new(Slot); return slot[i]->Push(key_len,key,data);} + pslot->Reset(); + do + { + pairp = pslot->ReadNextAddress(); + if(!strcmp(pairp->key,key)) + { + pairp->data=data; + pslot->Overwrite(*pairp); + return &(pairp->data); + } + } while(!pslot->End()); + num_keys++; + KeyLen(); + return pslot->Push(key_len,key,data); +} + + + +//////////////////////////////////////////////////////////////////////////////////////////// +// Add key to hash and return address of data element. +// If key exists leave data element unchanged, else set it to 'fail'. +//////////////////////////////////////////////////////////////////////////////////////////// +template +Typ* Hash::Add(char* key) +{ + Slot* pslot; + int i = HashValue(key); + + pslot = slot[i]; + if (!pslot) { num_keys++; KeyLen(); slot[i]=new(Slot); return slot[i]->Push(key_len,key,fail);} + pslot->Reset(); + do + { + if(!strcmp(pslot->ReadNext().key,key)) + { + return &((pslot->ReadCurrentAddress())->data); + } + } while(!pslot->End()); + num_keys++; + KeyLen(); + return pslot->Push(key_len,key,fail); +} + + +///////////////////////////////////////////////////////////////////////////////////////////// +// Remove key from hash and return data element for key ('fail' if key does not exist) +///////////////////////////////////////////////////////////////////////////////////////////// +template +Typ Hash::Remove(char* key) +{ + Slot* pslot; + int i = HashValue(key); + + pslot = slot[i]; + if (!pslot) return fail; + pslot->Reset(); + do + { + if(!strcmp(pslot->ReadNext().key,key)) + { + num_keys--; + pslot->Delete(); + // if key was the only element in pslot then delete whole list + if (pslot->Size()==0) {delete pslot; pslot = NULL;slot[i]=0;} + return pslot->ReadCurrent().data; + } + } while(!pslot->End()); + return fail; +} + + +////////////////////////////////////////////////////////////////////////////// +// Remove all keys from hash; +////////////////////////////////////////////////////////////////////////////// +template +void Hash::RemoveAll() +{ + for(int i=0; i +Typ Hash::ReadNext() +{ + Pair* pairp; + Slot* pslot; + + if (curr>=num_slots) {return fail;} + pslot = slot[curr]; // current list is never empty, except when current=num_slots + pairp = pslot->ReadNextAddress(); + if (pslot->End()) { + prev=curr; + do // move on to next non-empty list + { + if (++curr>=num_slots) return pairp->data; + pslot = slot[curr]; + } while (!pslot); + pslot->Reset(); + } + return pairp->data; +} + +////////////////////////////////////////////////////////////////////////////// +// Write next key into variable key and return data. Return 'fail' data and empty key if at end +// Attention: 'key' must have memory of at least char[MaxLen()+1] allocated! +////////////////////////////////////////////////////////////////////////////// +template +Typ Hash::ReadNext(char* key) +{ + Pair* pairp; + Slot* pslot; + + if (curr>=num_slots) {*key='\0'; return fail;} + pslot = slot[curr]; // current list is never empty, except when current=num_slots + pairp = pslot->ReadNextAddress(); + strcpy(key,pairp->key); + if (pslot->End()) { + prev=curr; + do // move on to next non-empty list + { + if (++curr>=num_slots) return pairp->data; + pslot = slot[curr]; + } while (!pslot); + pslot->Reset(); + } + return pairp->data; +} + + + +////////////////////////////////////////////////////////////////////////////// +// Return data of current key +////////////////////////////////////////////////////////////////////////////// +template +Typ Hash::ReadCurrent() +{ + Pair* pairp; + Slot* pslot; + + curr=prev; + if (curr>=num_slots) {return fail;} + pslot = slot[curr]; // current list is never empty, except when current=num_slots + pairp = &(pslot->ReadCurrent()); + if (pslot->End()) { + do // move on to next non-empty list + { + if (++curr>=num_slots) return pairp->data; + pslot = slot[curr]; + } while (!pslot); + pslot->Reset(); + } + return pairp->data; +} + +////////////////////////////////////////////////////////////////////////////// +// Write key last read into variable key and return data +// Attention: 'key' must have memory of at least char[MaxLen()+1] allocated! +////////////////////////////////////////////////////////////////////////////// +template +Typ Hash::ReadCurrent(char* key) +{ + Pair* pairp; + Slot* pslot; + + curr=prev; + if (curr>=num_slots) {*key='\0'; return fail;} + pslot = slot[curr]; // current list is never empty, except when current=num_slots + pairp = &(pslot->ReadCurrent()); + strcpy(key,pairp->key); + if (pslot->End()) { + do // move on to next non-empty list + { + if (++curr>=num_slots) return pairp->data; + pslot = slot[curr]; + } while (!pslot); + pslot->Reset(); + } + return pairp->data; +} + +////////////////////////////////////////////////////////////////////////////// +// Remove current key, return data, and advance to next key (after Reset() remove first element) +////////////////////////////////////////////////////////////////////////////// +template +Typ Hash::RemoveCurrent() +{ + Pair* pairp; + Slot* pslot; + curr=prev; + + if (curr>=num_slots) {return fail;} + pslot = slot[curr]; // current list is never empty, except when current=num_slots + pairp = &(pslot->Delete()); + num_keys--; + // if key was the only element in pslot then delete whole list + if (pslot->Size()==0) {delete pslot; pslot = NULL; slot[curr]=0;} + if (!pslot || pslot->End()) { + do // move on to next non-empty list + { + if (++curr>=num_slots) {prev=curr; return pairp->data;} + pslot = slot[curr]; + } while (!pslot); + pslot->Reset(); + } + prev=curr; + return pairp->data; +} + +////////////////////////////////////////////////////////////////////////////// +// Remove current key, return data, copy current key into key, and advance to next key +// (After Reset() remove first element) +// Attention: 'key' must have memory of at least char[MaxLen()+1] allocated! +////////////////////////////////////////////////////////////////////////////// +template +Typ Hash::RemoveCurrent(char* key) +{ + Pair* pairp; + Slot* pslot; + + curr=prev; + if (curr>=num_slots) {*key='\0'; return fail;} + pslot = slot[curr]; // current list is never empty, except when current=num_slots + pairp = &(pslot->Delete()); + strcpy(key,pairp->key); + num_keys--; + // if key was the only element in pslot then delete whole list + if (pslot->Size()==0) {delete pslot; pslot = NULL; slot[curr]=0;} + if (!pslot || pslot->End()) { + do // move on to next non-empty list + { + if (++curr>=num_slots) {prev=curr; return pairp->data;} + pslot = slot[curr]; + } while (!pslot); + pslot->Reset(); + } + prev=curr; + return pairp->data; +} + + + +////////////////////////////////////////////////////////////////////////////// +// Reset current position to beginning of hash +////////////////////////////////////////////////////////////////////////////// +template +void Hash::Reset() + { + curr=-1; + Slot* pslot; + do + { + curr++; + if (curr>=num_slots) {prev=curr; return;} + pslot = slot[curr]; + } while (!pslot); + pslot->Reset(); + prev=curr; + return; + } + + +///////////////////////////////////////////////////////////////////////////////////////////// +// Methods that return usefull information about the data stored in Hash: + + +//////////////////////////////////////////////////////////////////////////////////////////// +// Returns 1 if the hash contains key, 0 otherwise +//////////////////////////////////////////////////////////////////////////////////////////// +template +int Hash::Contains(char* key) +{ + Slot* pslot; + int i = HashValue(key); + + pslot = slot[i]; + if (!pslot) return 0; + pslot->Reset(); + do{ + if(!strcmp(pslot->ReadNext().key,key)) return 1; + } while(!pslot->End()); + return 0; +} + +///////////////////////////////////////////////////////////////////////////////////////////// +//print out list of keys and data +///////////////////////////////////////////////////////////////////////////////////////////// +template +void Hash::Print() +{ + char key[MaxLen()+1]; + + cout<<"\nPrint hash:\n"; + Reset(); + while(!End()) + cout<"< +void Hash::DebugPrint() +{ + Pair* pairp; + Slot* pslot; + + cout<<"\n"; + cout<<"Debug-print hash:"; + for(int i=0; iReset(); + while(!pslot->End()) + { + pairp = pslot->ReadNextAddress(); + cout<<" "<key<<"->"<data; + } + } + } + cout<<"\n\n"; + return; +} + + + +#endif /* HASH */ + + + +//////////////////////////////////////////////////////////////////////////////// +// Main program: test class Hash +//////////////////////////////////////////////////////////////////////////////// +// int main() +// { +// Hash ihash(5); +// char* key=new char[128]; +// int data; + +// ihash.Fail(1000); +// ihash.Add("So many monsters",36); +// ihash.Add("So many chickens",25); + +// // cerr<<"Address of ihash(\"So many monsters\") is "<"<"<"< +class Pair +{ +public: + char* key; //hash key + Typ data; //data for key + Pair() {} + Pair(char* k, Typ& d) {key = new char[strlen(k)+1]; strcpy(key,k); data=d;} + Pair(int& l, char* k, Typ& d) {key = new char[l+1]; strcpy(key,k); data=d;} +}; + + +//////////////////////////////////////////////////////////////////////////////////////////// +// Declaration of Slot, a list of key/data pairs +//////////////////////////////////////////////////////////////////////////////////////////// + +template +class Slot : public List< Pair > +{ +public: + //Destructor of Slot deletes whole list TOGETHER WITH THE KEY STRINGS + ~Slot() {this->Reset(); while (!this->End()) delete[] this->Pop().key; } + + // Push key/data pair onto slot list and return address of data element + // Attention: l must be at least length of key + inline Typ* Push(int& l, char* key, Typ& data) + { + Pair pair(l,key,data); //create a pair with key/data + return &(List >::Push(pair)->data); + } +}; + + +//////////////////////////////////////////////////////////////////////////////////////////// +// Declaration of Hash, an array of slots, i.e. pointers to lists of key/data +//////////////////////////////////////////////////////////////////////////////////////////// + +template +class Hash +{ +private: + int num_slots; //number of slots in slot[]. num_slots is set with the constructor + int curr; //index of current slot + int prev; //index of slot from previous ReadNext() + int num_keys; //total number of keys in hash + int max_len; //length of longest key in hash + int key_len; //length of key in argument + Typ fail; + + Slot** slot; //each slot[i] (i(0)); + + // Update maximum key length and caculate key_len; + inline void KeyLen() {if(key_len>max_len) max_len=key_len; return;} + + +//////////////////////////////////////////////////////////////////////////////////////////// +// Methods that work with a key supplied as an argument + + // Return data element for key. Returns 'fail' if key does not exist + Typ Show(char* key); + inline Typ operator[](char* key) {return Show(key);} + + // Add/replace key/data pair to hash and return address of data element for key + Typ* Add(char* key, Typ data); + + // Add key to hash and return address of data element. If key exists leave data element unchanged, else set it to 'fail'. + Typ* Add(char* key); + inline Typ* operator()(char* key) {return Add(key);} + + // Remove key from hash and return data element for key ('fail' if key does not exist) + Typ Remove(char* key); + + // Remove all keys from hash + void RemoveAll(); + + +/////////////////////////////////////////////////////////////////////////////////////////// +// Methods that work with an internal "current key": +// It is set to the first key by Reset() and moves to the next key with ReadNext or RemoveCurrent +// Note:the methods above (e.g. Store, Show, [], Add, (), etc. DO NOT CHANGE the current key + + // Return data of next key. Return 'fail' data and empty key if at end + Typ ReadNext(); + + // Write next key into variable key and return data. Return 'fail' data and empty key if at end + // Attention: 'key' must have memory of at least char[MaxLen()+1] allocated! + Typ ReadNext(char* key); + + // Return data of current key + Typ ReadCurrent(); + + // Write key last read into variable key and return data + // Attention: 'key' must have memory of at least char[MaxLen()+1] allocated! + Typ ReadCurrent(char* key); + + // Remove current key, return data and advance to next key + Typ RemoveCurrent(); + + // Remove current key, return data, copy current key into key, and advance to next key + // (After Reset() remove first element) + // Attention: 'key' must have memory of at least char[MaxLen()+1] allocated! + Typ RemoveCurrent(char* key); + + // Reset readout of keys to beginning of hash + void Reset(); + + // Returns 1 if the current key has arrived at the end, 0 otherwise + int End() {return (curr>=num_slots);} + + + +/////////////////////////////////////////////////////////////////////////////////////////// +// Methods that return usefull information about the data stored in Hash: + + // Returns 1 if the hash contains key, 0 otherwise + int Contains(char* key); + + // Return number of slots + int Size() {return num_keys;} + + // Return length of longest key INCLUDING DELETED KEYS (excluding \0) + int MaxLen() {return max_len;} + + //print out list of keys and data + void Print(); + + //Print out hash with internal representation as array + void DebugPrint(); +}; + diff --git a/binaries/src/clustalo/src/hhalign/hhalign.cpp b/binaries/src/clustalo/src/hhalign/hhalign.cpp new file mode 100644 index 0000000..c2f7329 --- /dev/null +++ b/binaries/src/clustalo/src/hhalign/hhalign.cpp @@ -0,0 +1,1375 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: hhalign.cpp 250 2011-06-17 13:06:20Z fabian $ + */ + +/* hhalign.C: + * Align a multiple alignment to an alignment or HMM + * Print out aligned input sequences in a3m format + * Compile: g++ hhalign.C -o hhalign -I/usr/include/ -L/usr/lib -lpng -lz -O3 -fno-strict-aliasing + * Compile with efence: g++ hhalign.C -o hhalign -I/usr/include/ -lefence -L/usr/lib -lpng -lz -O -g + * + * Error codes: 0: ok 1: file format error 2: file access error + * 3: memory error 4: internal numeric error + * 5: command line error + */ +#undef PNG /* include options for making png files? + (will need the png library) */ +#define MAIN +#include // cin, cout, cerr +#include // ofstream, ifstream +#include // strcmp, strstr +#include // printf +#include // exit +#include // sqrt, pow +#include // INT_MIN +#include // FLT_MIN +#include // clock +#include // islower, isdigit etc + +using std::cout; +using std::cerr; +using std::endl; +using std::ios; +using std::ifstream; +using std::ofstream; + +int iAux_GLOBAL; + +#include "general.h" +#include "util-C.h" /* imax, fmax, iround, iceil, ifloor, strint, strscn, + strcut, substr, uprstr, uprchr, Basename etc. */ +#include "list-C.h" // list data structure +#include "hash-C.h" // hash data structure + +#include "hhdecl-C.h" // Constants, global variables, struct Parameters +#include "hhutil-C.h" /* MatchChr, InsertChr, aa2i, i2aa, log2, + fast_log2, WriteToScreen, */ +#include "hhmatrices-C.h" // BLOSUM50, GONNET, HSDM +#include "hhhmm.h" // class HMM +#include "hhhit.h" // class Hit +#include "hhalignment.h" // class Alignment +#include "hhhalfalignment.h" // class HalfAlignment +#include "hhfullalignment.h" // class FullAlignment +#include "hhhitlist.h" // class Hit +#include "hhhmm-C.h" // class HMM +#include "hhalignment-C.h" // class Alignment +#include "hhhit-C.h" // class Hit +#include "hhhalfalignment-C.h" // class HalfAlignment +#include "hhfullalignment-C.h" // class FullAlignment +#include "hhhitlist-C.h" // class HitList +#include "hhfunc-C.h" // some functions common to hh programs + +#ifdef PNG +#include "pngwriter.h" //PNGWriter (http://pngwriter.sourceforge.net/) +#include "pngwriter.cc" //PNGWriter (http://pngwriter.sourceforge.net/) +#endif + +//////////////////////////////////////////////////////////////////////// +// Global variables +//////////////////////////////////////////////////////////////////////// +HMM *q; // Create query HMM with maximum of MAXRES match states +HMM *t; /* Create template HMM with maximum of MAXRES + match states */ +Alignment *qali; /* (query alignment might be needed outside of hhfunc.C + for -a option) */ +Hit hit; // Ceate new hit object pointed at by hit +HitList hitlist; /* list of hits with one Hit object for each + pairwise comparison done */ +char aliindices[256]; /* hash containing indices of all alignments + which to show in dot plot */ +char* dmapfile=NULL; /* where to write the coordinates for the HTML map file + (to click the alignments) */ +char* alitabfile=NULL; // where to write pairs of aligned residues +char* strucfile=NULL; // where to read structure scores +char* pngfile=NULL; // pointer to pngfile +char* tcfile=NULL; // TCoffee output file name +float probmin_tc=0.05; /* 5% minimum posterior probability for printing + pairs of residues for TCoffee */ + +int dotW=10; // average score of dot plot over window [i-W..i+W] +float dotthr=0.5; // score threshold for dot plot +int dotscale=600; // size scale of dotplot +char dotali=0; // show no alignments in dotplot +float dotsat=0.3; // saturation of grid and alignments in dot plot +float pself=0.001; // maximum p-value of 2nd and following self-alignments +int Nstochali=0; // # of stochastically traced alignments in dot plot +float** Pstruc=NULL; /* structure matrix which can be multiplied to prob + ratios from aa column comparisons in Forward() */ +float** Sstruc=NULL; /* structure matrix which can be added to log odds + from aa column comparisons in Forward() */ + + + + + +//////////////////////////////////////////////////////////////////////////// +// Help functions +//////////////////////////////////////////////////////////////////////////// +/** + * @brief general help function, not accessible in Clustal-Omega + */ +#if 0 +void +help() +{ + printf("\n"); + printf("HHalign %s\n",VERSION_AND_DATE); + printf("Align a query alignment/HMM to a template alignment/HMM by HMM-HMM alignment\n"); + printf("If only one alignment/HMM is given it is compared to itself and the best\n"); + printf("off-diagonal alignment plus all further non-overlapping alignments above \n"); + printf("significance threshold are shown.\n"); + printf("%s",REFERENCE); + printf("%s",COPYRIGHT); + printf("\n"); + printf("Usage: %s -i query [-t template] [options] \n",program_name); + printf(" -i input query alignment (fasta/a2m/a3m) or HMM file (.hhm)\n"); + printf(" -t input template alignment (fasta/a2m/a3m) or HMM file (.hhm)\n"); +#ifdef PNG + printf(" -png write dotplot into PNG-file (default=none) \n"); +#endif + printf("\n"); + printf("Output options: \n"); + printf(" -o write output alignment to file\n"); + printf(" -ofas write alignments in FASTA, A2M (-oa2m) or A3M (-oa3m) format \n"); + printf(" -a write query alignment in a3m format to file (default=none)\n"); + printf(" -aa append query alignment in a3m format to file (default=none)\n"); + printf(" -atab write alignment as a table (with posteriors) to file (default=none)\n"); + printf(" -v verbose mode: 0:no screen output 1:only warings 2: verbose\n"); + printf(" -seq [1,inf[ max. number of query/template sequences displayed (def=%i) \n",par.nseqdis); + printf(" -nocons don't show consensus sequence in alignments (default=show) \n"); + printf(" -nopred don't show predicted 2ndary structure in alignments (default=show) \n"); + printf(" -nodssp don't show DSSP 2ndary structure in alignments (default=show) \n"); + printf(" -aliw int number of columns per line in alignment list (def=%i)\n",par.aliwidth); + printf(" -P for self-comparison: max p-value of alignments (def=%.2g\n",pself); + printf(" -p minimum probability in summary and alignment list (def=%G) \n",par.p); + printf(" -E maximum E-value in summary and alignment list (def=%G) \n",par.E); + printf(" -Z maximum number of lines in summary hit list (def=%i) \n",par.Z); + printf(" -z minimum number of lines in summary hit list (def=%i) \n",par.z); + printf(" -B maximum number of alignments in alignment list (def=%i) \n",par.B); + printf(" -b minimum number of alignments in alignment list (def=%i) \n",par.b); + printf(" -rank int specify rank of alignment to write with -a or -aa option (default=1)\n"); + printf("\n"); +#ifdef PNG + printf("Dotplot options:\n"); + printf(" -dwin average score in dotplot over window [i-W..i+W] (def=%i) \n",dotW); + printf(" -dthr score threshold for dotplot (default=%.2f) \n",dotthr); + printf(" -dsca if value <= 20: size of dot plot unit box in pixels \n"); + printf(" if value > 20: maximum dot plot size in pixels (default=%i) \n",dotscale); + printf(" -dali show alignments with indices in in dot plot \n"); + printf(" = ... or = all \n"); + printf("\n"); +#endif + printf("Filter input alignment (options can be combined): \n"); + printf(" -id [0,100] maximum pairwise sequence identity (%%) (def=%i) \n",par.max_seqid); + printf(" -diff [0,inf[ filter most diverse set of sequences, keeping at least this \n"); + printf(" many sequences in each block of >50 columns (def=%i)\n",par.Ndiff); + printf(" -cov [0,100] minimum coverage with query (%%) (def=%i) \n",par.coverage); + printf(" -qid [0,100] minimum sequence identity with query (%%) (def=%i) \n",par.qid); + printf(" -qsc [0,100] minimum score per column with query (def=%.1f)\n",par.qsc); +// printf(" -csc [0,100] minimum score per column with core alignment (def=%-.2f)\n",par.coresc); +// printf(" -qscc [0,100] minimum score per column of core sequence with query (def=%-.2f)\n",par.qsc_core); + printf("\n"); + printf("Input alignment format: \n"); + printf(" -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert;\n"); + printf(" '-' = Delete; '.' = gaps aligned to inserts (may be omitted) \n"); + printf(" -M first use FASTA: columns with residue in 1st sequence are match states\n"); + printf(" -M [0,100] use FASTA: columns with fewer than X%% gaps are match states \n"); + printf("\n"); + printf("HMM-HMM alignment options: \n"); + printf(" -glob/-loc global or local alignment mode (def=local) \n"); + printf(" -alt show up to this number of alternative alignments (def=%i) \n",par.altali); + printf(" -vit use Viterbi algorithm for alignment instead of MAC algorithm \n"); + printf(" -mac use Maximum Accuracy (MAC) alignment (default) \n"); + printf(" -mact [0,1[ posterior probability threshold for MAC alignment (def=%.3f) \n",par.mact); + printf(" A threshold value of 0.0 yields global alignments.\n"); + printf(" -sto use global stochastic sampling algorithm to sample this many alignments\n"); + printf(" -excl exclude query positions from the alignment, e.g. '1-33,97-168'\n"); + printf(" -shift [-1,1] score offset (def=%-.3f) \n",par.shift); + printf(" -corr [0,1] weight of term for pair correlations (def=%.2f) \n",par.corr); + printf(" -ssm 0-4 0:no ss scoring [default=%i] \n",par.ssm); + printf(" 1:ss scoring after alignment \n"); + printf(" 2:ss scoring during alignment \n"); + printf(" -ssw [0,1] weight of ss score (def=%-.2f) \n",par.ssw); + printf("\n"); + printf(" -def read default options from ./.hhdefaults or /.hhdefault. \n"); + printf("\n"); + printf("Example: %s -i T0187.a3m -t d1hz4a_.hhm -png T0187pdb.png \n",program_name); + cout< for self-comparison: max p-value of alignments (def=%.2g\n",pself); + printf(" -p minimum probability in summary and alignment list (def=%G) \n",par.p); + printf(" -E maximum E-value in summary and alignment list (def=%G) \n",par.E); + printf(" -Z maximum number of lines in summary hit list (def=%i) \n",par.Z); + printf(" -z minimum number of lines in summary hit list (def=%i) \n",par.z); + printf(" -B maximum number of alignments in alignment list (def=%i) \n",par.B); + printf(" -b minimum number of alignments in alignment list (def=%i) \n",par.b); + printf(" -rank int specify rank of alignment to write with -a or -aa option (def=1)\n"); + printf(" -tc write a TCoffee library file for the pairwise comparison \n"); + printf(" -tct [0,100] min. probobability of residue pairs for TCoffee (def=%i%%)\n",iround(100*probmin_tc)); + printf("\n"); +#ifdef PNG + printf("Dotplot options:\n"); + printf(" -dwin int average score in dotplot over window [i-W..i+W] (def=%i) \n",dotW); + printf(" -dthr float score threshold for dotplot (default=%.2f) \n",dotthr); + printf(" -dsca int size of dot plot box in pixels (default=%i) \n",dotscale); + printf(" -dali show alignments with indices in in dot plot\n"); + printf(" = ... or = all \n"); + printf(" -dmap print list of coordinates in png plot \n"); +#endif +} +#endif + +/** + * @brief help hit HMM options, not accessible in Clustal-Omega + */ +#if 0 +void +help_hmm() +{ + printf("\n"); + printf("Options to filter input alignment (options can be combined): \n"); + printf(" -id [0,100] maximum pairwise sequence identity (%%) (def=%i) \n",par.max_seqid); + printf(" -diff [0,inf[ filter most diverse set of sequences, keeping at least this \n"); + printf(" many sequences in each block of >50 columns (def=%i)\n",par.Ndiff); + printf(" -cov [0,100] minimum coverage with query (%%) (def=%i) \n",par.coverage); + printf(" -qid [0,100] minimum sequence identity with query (%%) (def=%i) \n",par.qid); + printf(" -qsc [0,100] minimum score per column with query (def=%.1f)\n",par.qsc); +// printf(" -csc [0,100] minimum score per column with core alignment (def=%-.2f)\n",par.coresc); +// printf(" -qscc [0,100] minimum score per column of core sequence with query (def=%-.2f)\n",par.qsc_core); + printf(" \n"); + printf("HMM-building options: \n"); + printf(" -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert;\n"); + printf(" '-' = Delete; '.' = gaps aligned to inserts (may be omitted) \n"); + printf(" -M first use FASTA: columns with residue in 1st sequence are match states\n"); + printf(" -M [0,100] use FASTA: columns with fewer than X%% gaps are match states \n"); + printf(" -tags do NOT neutralize His-, C-myc-, FLAG-tags, and \n"); + printf(" trypsin recognition sequence to background distribution \n"); + printf(" \n"); + printf("Pseudocount options: \n"); + printf(" -Gonnet use the Gonnet substitution matrix (default) \n"); + printf(" -Blosum50 use the Blosum50 substitution matrix \n"); + printf(" -Blosum62 use the Blosum62 substitution matrix \n"); + printf(" -HSDM use the structure-derived HSDM substitution matrix \n"); + printf(" -pcm 0-3 Pseudocount mode (default=%-i) \n",par.pcm); + printf(" tau = substitution matrix pseudocount admixture \n"); + printf(" 0: no pseudo counts: tau = 0 \n"); + printf(" 1: constant tau = a \n"); + printf(" 2: divergence-dependent: tau = a/(1 + ((Neff-1)/b)^c) \n"); + printf(" Neff=( (Neff_q^d+Neff_t^d)/2 )^(1/d) \n"); + printf(" Neff_q = av number of different AAs per column in query \n"); + printf(" 3: column-specific: tau = \'2\' * (Neff(i)/Neff)^(w*Neff/20)\n"); + printf(" -pca [0,1] set a (overall admixture) (def=%-.1f) \n",par.pca); + printf(" -pcb [1,inf[ set b (threshold for Neff) (def=%-.1f) \n",par.pcb); + printf(" -pcc [0,3] set c (extinction exponent for tau(Neff)) (def=%-.1f) \n",par.pcc); + printf(" -pcw [0,3] set w (weight of pos-specificity for pcs) (def=%-.1f) \n",par.pcw); +} +#endif + +/** + * @brief help with gap handling, not accessible in Clustal-Omega + */ +#if 0 +void +help_gap() +{ + printf("\n"); + printf("Gap cost options: \n"); + printf(" -gapb [0,inf[ transition pseudocount admixture (def=%-.2f) \n",par.gapb); + printf(" -gapd [0,inf[ Transition pseudocount admixture for opening gap (default=%-.2f)\n",par.gapd); + printf(" -gape [0,1.5] Transition pseudocount admixture for extending gap (def=%-.1f)\n",par.gape); + printf(" -gapf ]0,inf] factor for increasing/reducing the gap open penalty for deletes (def=%-.2f)\n",par.gapf); + printf(" -gapg ]0,inf] factor for increasing/reducing the gap open penalty for deletes (def=%-.2f)\n",par.gapg); + printf(" -gaph ]0,inf] factor for increasing/reducing the gap extension penalty for deletes(def=%-.2f)\n",par.gaph); + printf(" -gapi ]0,inf] factor for increasing/reducing the gap extension penalty for inserts(def=%-.2f)\n",par.gapi); + printf(" -egq [0,inf[ penalty (bits) for end gaps aligned to query residues (def=%-.2f)\n",par.egq); + printf(" -egt [0,inf[ penalty (bits) for end gaps aligned to template residues (def=%-.2f)\n",par.egt); +} +#endif + +/** + * @brief help with alignment options, not accessible in Clustal-Omega + */ +#if 0 +void +help_ali() +{ + printf("\n"); + printf("Alignment options: \n"); + printf(" -glob/-loc global or local alignment mode (def=global) \n"); + printf(" -mac use Maximum Accuracy (MAC) alignment instead of Viterbi\n"); + printf(" -mact [0,1] posterior prob threshold for MAC alignment (def=%.3f) \n",par.mact); + printf(" -sto use global stochastic sampling algorithm to sample this many alignments\n"); + printf(" -sc amino acid score (tja: template HMM at column j) (def=%i)\n",par.columnscore); + printf(" 0 = log2 Sum(tja*qia/pa) (pa: aa background frequencies) \n"); + printf(" 1 = log2 Sum(tja*qia/pqa) (pqa = 1/2*(pa+ta) ) \n"); + printf(" 2 = log2 Sum(tja*qia/ta) (ta: av. aa freqs in template) \n"); + printf(" 3 = log2 Sum(tja*qia/qa) (qa: av. aa freqs in query) \n"); + printf(" -corr [0,1] weight of term for pair correlations (def=%.2f) \n",par.corr); + printf(" -shift [-1,1] score offset (def=%-.3f) \n",par.shift); + printf(" -r repeat identification: multiple hits not treated as independent\n"); + printf(" -ssm 0-2 0:no ss scoring [default=%i] \n",par.ssm); + printf(" 1:ss scoring after alignment \n"); + printf(" 2:ss scoring during alignment \n"); + printf(" -ssw [0,1] weight of ss score compared to column score (def=%-.2f) \n",par.ssw); + printf(" -ssa [0,1] ss confusion matrix = (1-ssa)*I + ssa*psipred-confusion-matrix [def=%-.2f)\n",par.ssa); +} +#endif + +/** + * @brief general help menu, not accessible in Clustal-Omega + */ +#if 0 +void +help_all() +{ + help(); + help_out(); + help_hmm(); + help_gap(); + help_ali(); + printf("\n"); + printf("Default options can be specified in './.hhdefaults' or '~/.hhdefaults'\n"); +} +#endif + +///////////////////////////////////////////////////////////////////////////// +//// Processing input options from command line and .hhdefaults file +///////////////////////////////////////////////////////////////////////////// +/** + * @brief process arguments from commandline, not accessible from Clustal-Omega + */ +#if 0 +void +ProcessArguments(int argc, char** argv) +{ + //Processing command line input + for (int i=1; i=4) cout<=argc || argv[i][0]=='-') + {help(); cerr<=argc || argv[i][0]=='-') + {help(); cerr<=argc) + {help(); cerr<=argc || argv[i][0]=='-') + {help() ; cerr<=argc || argv[i][0]=='-') + {help() ; cerr<=argc || argv[i][0]=='-') + {help() ; cerr<=argc || argv[i][0]=='-') + {help() ; cerr<=argc || argv[i][0]=='-') + {help() ; cerr<=argc || argv[i][0]=='-') + {help() ; cerr<=argc || argv[i][0]=='-') + {help() ; cerr<=argc || argv[i][0]=='-') + {help() ; cerr<=argc || argv[i][0]=='-') + {help() ; cerr<=argc) + {help(); cerr<=argc || argv[i][0]=='-') + {help(); cerr<=argc || argv[i][0]=='-') + {help(); cerr<=argc || argv[i][0]=='-') + {help() ; cerr<=argc) {help(); exit(0);} + if (!strcmp(argv[i],"out")) {help_out(); exit(0);} + if (!strcmp(argv[i],"hmm")) {help_hmm(); exit(0);} + if (!strcmp(argv[i],"gap")) {help_gap(); exit(0);} + if (!strcmp(argv[i],"ali")) {help_ali(); exit(0);} + if (!strcmp(argv[i],"all")) {help_all(); exit(0);} + else {help(); exit(0);} + } + else if (!strcmp(argv[i],"-excl")) + { + if (++i>=argc) {help(); exit(4);} + par.exclstr = new(char[strlen(argv[i])+1]); + strcpy(par.exclstr,argv[i]); + } + else if (!strcmp(argv[i],"-v") && (i=argc) + {help(); cerr<0.3 && par.mact<0.301) {par.mact=0;} } + else if (!strncmp(argv[i],"-loc",3)) par.loc=1; + else if (!strncmp(argv[i],"-alt",4) && (i='0' && argv[i][0]<='9') {par.Mgaps=atoi(argv[i]); par.M=2;} + else cerr<=4) cout<1 && !strcmp(argv[i],"-v0")) v=0; + else if (argc>1 && !strcmp(argv[i],"-v1")) v=1; + else if (argc>2 && !strcmp(argv[i],"-v")) v=atoi(argv[i+1]); + } + + // Read .hhdefaults file? + if (par.readdefaultsfile) + { + // Process default otpions from .hhconfig file + ReadDefaultsFile(argc_conf,argv_conf); + ProcessArguments(argc_conf,argv_conf); + } +#endif + /* Process command line options + (they override defaults from .hhdefaults file) */ +#ifndef CLUSTALO_NOFILE + ProcessArguments(argc,argv); +#endif + + +#ifdef CLUSTALO + int iAuxLen1 = strlen(ppcFirstProf[0]); + int iAuxLen2 = strlen(ppcSecndProf[0]); + if ( (0 == iAuxLen1) || (0 == iAuxLen2) ){ /* problem with empty profiles, FS, r249 -> r250 */ + sprintf(zcError, "%s:%s:%d: strlen(prof1)=%d, strlen(prof2)=%d -- Nothing to align!\n", + __FUNCTION__, __FILE__, __LINE__, iAuxLen1, iAuxLen2); + iRetVal = RETURN_UNKNOWN; + /* Note: at this stage cannot do 'goto this_is_the_end;' + because would cross initialisation of several variables */ + return iRetVal; + } + par.maxResLen = iAuxLen1 > iAuxLen2 ? iAuxLen1 : iAuxLen2; + const int ciGoodMeasureSeq = 10; + par.maxResLen += ciGoodMeasureSeq; + par.maxColCnt = iAuxLen1 + iAuxLen2 + ciGoodMeasureSeq; + //par.max_seqid=iFirstCnt+iSecndCnt+3; /* -id */ + par.max_seqid=DEFAULT_FILTER; /* -id */ + par.loc=0; par.mact=0; /* -glob */ + par.nseqdis=iFirstCnt+iSecndCnt; /* -seq */ + par.showcons=0; /* -nocons */ + par.showdssp=0; /* -nodssp */ + par.Mgaps=100; /* -M */ + par.M=2; /* -M */ + par.pdWg1=pdWeightsL; /* tree wg */ + par.pdWg2=pdWeightsR; /* tree wg */ + v = 0; /* -v0 */ + /* NOTE: *qali declared globally but only created here, + pass in number of sequences to get rid of statically + defined MAXSEQ (FS) + */ + Alignment qali(iFirstCnt+iSecndCnt); + HMM q(iFirstCnt+iSecndCnt); + HMM t(iFirstCnt+iSecndCnt); +#endif + + +#ifndef CLUSTALO_NOFILE + // Check command line input and default values + if (!*par.infile) + {help(); cerr<0.300) + if (v>=1) fprintf(stderr,"REMARK: in -mac -global mode -mact is forced to 0\n"); + par.mact=0; + // par.loc=1; // global forward-backward algorithm seems to work fine! use it in place of local version. + } + + // Get rootname (no directory path, no extension) and extension of infile + RemoveExtension(q.file,par.infile); + RemoveExtension(t.file,par.tfile); /* FS, NOFILE2 (commented out) */ + Extension(inext,par.infile); + Extension(text,par.tfile); /*FS, NOFILE2 (commented out) */ + + // Check option compatibilities + if (par.nseqdis>MAXSEQDIS-3-par.showcons) par.nseqdis=MAXSEQDIS-3-par.showcons; //3 reserved for secondary structure + if (par.aliwidth<20) par.aliwidth=20; + if (par.pca<0.001) par.pca=0.001; // to avoid log(0) + if (par.b>par.B) par.B=par.b; + if (par.z>par.Z) par.Z=par.z; + if (par.hitrank>0) par.altali=0; + + // Input parameters + if (v>=3) + { + cout<<"query file : "< r229 */ + int qL, tL; + if (iFirstCnt > 0) { + qL = strlen(ppcFirstProf[0]); + } + else { + qL = prHMM->L; + } + if (iSecndCnt > 0) { + tL = strlen(ppcSecndProf[0]); + } + else { + tL = prHMM->L; + } + + + // const float MEMSPACE_DYNPROG = 512*1024*1024; + /* determine amount of memory available for MAC on command-line; FS, r240 -> r241 */ + const float MEMSPACE_DYNPROG = (double)1024*1024*rHhalignPara.iMacRamMB; + // longest allowable length of database HMM + int Lmaxmem=(int)((float)MEMSPACE_DYNPROG/qL/6/8); + if (par.forward==2 && tL+2>=Lmaxmem) { + if (v>=1) + cerr<<"WARNING: Not sufficient memory to realign with MAC algorithm. Using Viterbi algorithm."< r229 */ + par.pca = par.pcaV; + par.pcb = par.pcbV; + par.pcc = par.pccV; + par.pcw = par.pcwV; + + par.gapb = par.gapbV; + par.gapd = par.gapdV; + par.gape = par.gapeV; + par.gapf = par.gapfV; + par.gapg = par.gapgV; + par.gaph = par.gaphV; + par.gapi = par.gapiV; + + } + + + // Read input file (HMM, HHM, or alignment format), and add pseudocounts etc. + q.cQT = 'q'; + if (OK != ReadAndPrepare(INTERN_ALN_2_HMM, + ppcFirstProf, iFirstCnt, prHMM, + pcPrealigned1, pcRepresent1, pdWeightsL, + (char*)(""), q, &qali)) { + sprintf(zcError, "%s:%s:%d: Problem Reading/Preparing q-profile (len=%d)\n", + __FUNCTION__, __FILE__, __LINE__, qL); + iRetVal = RETURN_FROM_RNP; + goto this_is_the_end; + } + // Set query columns in His-tags etc to Null model distribution + if (par.notags) q.NeutralizeTags(); + + // Do self-comparison? + if (0 /* !*par.tfile // FS, 2010-03-10 */) + { + // Deep-copy q into t + t = q; + + // Find overlapping alternative alignments + hit.self=1; + } + // Read template alignment/HMM t and add pseudocounts + else + { + char infile[] = ""; + /* Read input file (HMM, HHM, or alignment format), + and add pseudocounts etc. */ + t.cQT = 't'; + if (OK != ReadAndPrepare(INTERN_ALN_2_HMM, + ppcSecndProf, iSecndCnt, prHMM, + pcPrealigned2, pcRepresent2, pdWeightsR, + infile, t)) { + sprintf(zcError, "%s:%s:%d: Problem Reading/Preparing t-profile (len=%d)\n", + __FUNCTION__, __FILE__, __LINE__, tL); + iRetVal = RETURN_FROM_RNP; + goto this_is_the_end; + } + } + + // Factor Null model into HMM t + t.IncludeNullModelInHMM(q,t); + + /* switch at this stage is ineffectual as log/lin already decided in RnP(). + FS, r228 -> r229 */ + /*const float MEMSPACE_DYNPROG = 512*1024*1024; + // longest allowable length of database HMM + int Lmaxmem=(int)((float)MEMSPACE_DYNPROG/q.L/6/8); + if (par.forward==2 && t.L+2>=Lmaxmem) + { + if (v>=1) + cerr<<"WARNING: Not sufficient memory to realign with MAC algorithm. Using Viterbi algorithm."<=1 || Nstochali) + hit.AllocateForwardMatrix(q.L+2,t.L+2); + if (par.forward==2) + hit.AllocateBackwardMatrix(q.L+2,t.L+2); + +#ifndef CLUSTALO_NOFILE + // Read structure file for Forward() function? + if (strucfile && par.wstruc>0) + { + float PMIN=1E-20; + Pstruc = new(float*[q.L+2]); + for (int i=0; i=2) printf("Reading structure matrix from standard input ... (for UNIX use ^D for 'end-of-file')\n"); + } + for (int i=1; i<=q.L; i++) + { + for (int j=1; j<=t.L; j++) + { + float f; + if (fscanf(strucf,"%f",&f) <=0 ) + { + fprintf(stderr,"Error: too few numbers in file %s while reading line %i, column %i\n",strucfile,i,j); + exit(1); + } + if (par.wstruc==1) + Pstruc[i][j]=fmax(f,PMIN); + else + Pstruc[i][j]=fmax(pow(f,par.wstruc),PMIN); +// printf("%10.2E ",f); + Sstruc[i][j] = par.wstruc * log2(f); + } +// printf("\n"); + } + fclose(strucf); + } /* (strucfile && par.wstruc>0) */ +#endif + + /* Do (self-)comparison, store results if score>SMIN, + and try next best alignment */ + /* FIXME very ambigous and possibly faulty if-else */ + if (v>=2) { + if (par.forward==2) { + printf("Using maximum accuracy (MAC) alignment algorithm ...\n"); + } + else if (par.forward==0) { + printf("Using Viterbi algorithm ...\n"); + } + else if (par.forward==1) { + printf("Using stochastic sampling algorithm ...\n"); + } + else { + printf("\nWhat alignment algorithm are we using??\n"); + } + } + + + for (hit.irep=1; hit.irep<=imax(par.hitrank,par.altali); hit.irep++) + { + if (par.forward==0) + { + // generate Viterbi alignment + hit.Viterbi(q,t,Sstruc); + hit.Backtrace(q,t); + } + else if (par.forward==1) + { + // generate a single stochastically sampled alignment + hit.Forward(q,t,Pstruc); + srand( time(NULL) ); // initialize random generator + hit.StochasticBacktrace(q,t); + hitlist.Push(hit); /* insert hit at beginning of list + (last repeats first!) */ + (hit.irep)++; + break; + } + else if (par.forward==2) + { + // generate forward alignment + if (OK != hit.Forward(q,t,Pstruc)){ + fprintf(stderr, "%s:%s:%d: cannot complete hit.Forward\n", + __FUNCTION__, __FILE__, __LINE__); + iRetVal = RETURN_FROM_MAC; /* spot double overflow in Forward(). FS, r241 -> r243 */ + goto this_is_the_end; + } + if (OK != hit.Backward(q,t)){ + fprintf(stderr, "%s:%s:%d: cannot complete hit.backward\n", + __FUNCTION__, __FILE__, __LINE__); + iRetVal = RETURN_FROM_MAC; /* spot double overflow in hit.Backward(). FS, r241 -> r243 */ + goto this_is_the_end; + } + hit.MACAlignment(q,t); + if ((isnan(hit.score)) || (isnan(hit.Pforward))){ + printf("nan after MAC\n"); + } + hit.BacktraceMAC(q,t); + if ((isnan(hit.score)) || (isnan(hit.Pforward))){ + printf("nan after backtrace\n"); + } + } /* use MAC algorithm */ + // printf ("%-12.12s %-12.12s irep=%-2i score=%6.2f hit.Pvalt=%.2g\n",hit.name,hit.fam,hit.irep,hit.score,hit.Pvalt); + *dScore_p = hit.score; + + if (hit.irep<=par.hitrank || hit.score>SMIN || (hit.Pvalt0 )) + hitlist.Push(hit); // insert hit at beginning of list (last repeats first!) and do next alignment + else + { + if (hit.irep==1) hitlist.Push(hit); // first hit will be inserted into hitlist anyway, even if not significant + hit = hitlist.ReadLast(); // last alignment was not significant => read last (significant) hit from list + break; + /* FIXME: memory leak during normal alignment: both push'es above are not freed: + * valgrind --leak-check=full --show-reachable=yes ./src/clustalo -i ~/void/protein.fa -o /dev/null -v + ==9506== 1,456 bytes in 1 blocks are still reachable in loss record 4 of 5 + ==9506== at 0x4C2726C: operator new(unsigned long) (vg_replace_malloc.c:230) + ==9506== by 0x4618C5: List::Push(Hit) (list-C.h:134) + ==9506== by 0x45E87A: hhalign (hhalign.cpp:914) + ==9506== by 0x413F8C: HhalignWrapper (hhalign_wrapper.c:405) + ==9506== by 0x41A7B5: MyMain (mymain.c:676) + ==9506== by 0x4031A6: main (main.cpp:37) + ==9506== + ==9506== + ==9506== 4,442 (4,368 direct, 74 indirect) bytes in 3 blocks are definitely lost in loss record 5 of 5 + ==9506== at 0x4C2726C: operator new(unsigned long) (vg_replace_malloc.c:230) + ==9506== by 0x4618C5: List::Push(Hit) (list-C.h:134) + ==9506== by 0x45E7C0: hhalign (hhalign.cpp:911) + ==9506== by 0x413F8C: HhalignWrapper (hhalign_wrapper.c:405) + ==9506== by 0x41A7B5: MyMain (mymain.c:676) + ==9506== by 0x4031A6: main (main.cpp:37) + */ + } + } /* 1 <= hit.irep <= imax(par.hitrank,par.altali) */ + Nali = hit.irep; + + +#ifndef CLUSTALO_NOFILE + // Write posterior probability matrix as TCoffee library file + if (tcfile) + { + if (v>=2) printf("Writing TCoffee library file to %s\n",tcfile); + int i,j; + FILE* tcf=NULL; + if (strcmp(tcfile,"stdout")) tcf = fopen(tcfile, "w"); else tcf = stdout; + if (!tcf) OpenFileError(tcfile); + fprintf(tcf,"! TC_LIB_FORMAT_01\n"); + fprintf(tcf,"%i\n",2); // two sequences in library file + fprintf(tcf,"%s %i %s\n",q.name,q.L,q.seq[q.nfirst]+1); + fprintf(tcf,"%s %i %s\n",hit.name,hit.L,hit.seq[hit.nfirst]+1); + fprintf(tcf,"#1 2\n"); + for (i=1; i<=q.L; i++) // print all pairs (i,j) with probability above PROBTCMIN + for (j=1; j<=t.L; j++) + if (hit.B_MM[i][j]>probmin_tc) + fprintf(tcf,"%5i %5i %5i\n",i,j,iround(100.0*hit.B_MM[i][j])); + for (int step=hit.nsteps; step>=1; step--) // print all pairs on MAC alignment which were not yet printed + { + i=hit.i[step]; j=hit.j[step]; + // printf("%5i %5i %5i %i\n",i,j,iround(100.0*hit.B_MM[i][j]),hit.states[step]); + if (hit.states[step]>=MM && hit.B_MM[i][j]<=probmin_tc) + fprintf(tcf,"%5i %5i %5i\n",i,j,iround(100.0*hit.B_MM[i][j])); + } + + + fprintf(tcf,"! SEQ_1_TO_N\n"); + fclose(tcf); + // for (i=1; i<=q.L; i++) + // { + // double sum=0.0; + // for (j=1; j<=t.L; j++) sum+=hit.B_MM[i][j]; + // printf("i=%-3i sum=%7.4f\n",i,sum); + // } + // printf("\n"); + } /* if (tcfile) */ + + // Write last alignment into alitabfile + if (alitabfile) + { + FILE* alitabf=NULL; + if (strcmp(alitabfile,"stdout")) alitabf = fopen(alitabfile, "w"); else alitabf = stdout; + if (!alitabf) OpenFileError(alitabfile); + if (par.forward==2) + { + fprintf(alitabf," i j score SS probab\n"); + for (int step=hit.nsteps; step>=1; step--) + if (hit.states[step]>=MM) + fprintf(alitabf,"%5i %5i %6.2f %6.2f %7.4f\n",hit.i[step],hit.j[step],hit.S[step],hit.S_ss[step],hit.P_posterior[step]); + } + else + { + fprintf(alitabf," i j score SS\n"); + for (int step=hit.nsteps; step>=1; step--) + if (hit.states[step]>=MM) + fprintf(alitabf,"%5i %5i %6.2f %6.2f\n",hit.i[step],hit.j[step],hit.S[step],hit.S_ss[step]); + } + fclose(alitabf); + } /* if (alitabfile) */ +#endif + + // Do Stochastic backtracing? + if (par.forward==1) + for (int i=1; i=2) { + cout<<"Printing alignments in " << + (par.outformat==1? "FASTA" : par.outformat==2?"A2M" :"A3M") << + " format to "< r243 */ + goto this_is_the_end; + } + } /* if (*par.pairwisealisfile) */ + +#ifndef CLUSTALO_NOFILE + // Print hit list and alignments + if (*par.outfile) + { + hitlist.PrintHitList(q, par.outfile); + hitlist.PrintAlignments( +#ifdef CLUSTALO + ppcFirstProf, ppcSecndProf, +#endif + q, par.outfile); + if (v>=2) { + WriteToScreen(par.outfile,1000); //write only hit list to screen + } + } +#endif + + + /////////////////////////////////////////////////////////////////////// +#ifndef CLUSTALO_NOFILE + // Show results for hit with rank par.hitrank + if (par.hitrank==0) hit=hitlist.Read(1); else hit=hitlist.Read(par.hitrank); + + // Generate output alignment or HMM file? + if (*par.alnfile || *par.psifile || *par.hhmfile) + { + if (par.append==0) + { + if (v>=2 && *par.alnfile) printf("Merging template to query alignment and writing resulting alignment in A3M format to %s...\n",par.alnfile); + if (v>=2 && *par.psifile) printf("Merging template to query alignment and writing resulting alignment in PSI format to %s...\n",par.psifile); + } + else + { + if (v>=2 && *par.alnfile) printf("Merging template to query alignment and appending template alignment in A3M format to %s...\n",par.alnfile); + if (v>=2 && *par.psifile) printf("Merging template to query alignment and appending template alignment in PSI format to %s...\n",par.psifile); + } + + // Read query alignment into Qali + Alignment Qali; // output A3M generated by merging A3M alignments for significant hits to the query alignment + char qa3mfile[NAMELEN]; + RemoveExtension(qa3mfile,par.infile); // directory?? + strcat(qa3mfile,".a3m"); + FILE* qa3mf=fopen(qa3mfile,"r"); + if (!qa3mf) OpenFileError(qa3mfile); + Qali.Read(qa3mf,qa3mfile); + fclose(qa3mf); + + // Align query with template in master-slave mode + Qali.MergeMasterSlave(hit,par.tfile); /*FS, NOFILE2 (commented out) */ + + // Write output A3M alignment? + if (*par.alnfile) { + Qali.WriteToFile(par.alnfile,"a3m"); + } + + if (*par.psifile) + { + /* Convert ASCII to int (0-20),throw out all insert states, + record their number in I[k][i] */ + Qali.Compress("merged A3M file"); + + // Write output PSI-BLAST-formatted alignment? + Qali.WriteToFile(par.psifile,"psi"); + } + } /* if (*par.alnfile || *par.psifile || *par.hhmfile) */ +#endif /* NOFILE2 */ + ////////////////////////////////////////////////////////////////////////// + + + + + // double log2Pvalue; + // if (par.ssm && (par.ssm1 || par.ssm2)) + // { + // log2Pvalue=hit.logPval/0.693147181+0.45*(4.0*par.ssw/0.15-hit.score_ss); + // if (v>=2) + // printf("Aligned %s with %s:\nApproximate P-value INCLUDING SS SCORE = %7.2g\n",q.name,t.name,pow(2.0,log2Pvalue)); + // } else { + // if (v>=2) + // printf("Aligned %s with %s:\nApproximate P-value (without SS score) = %7.2g\n",q.name,t.name,hit.Pval); + // } + + if (v>=2) + { + if (par.hitrank==0) + printf("Aligned %s with %s: Score = %-7.2f P-value = %-7.2g\n", + q.name,t.name,hit.score,hit.Pval); + else + printf("Aligned %s with %s (rank %i): Score = %-7.2f P-value = %-7.2g\n", + q.name,t.name,par.hitrank,hit.score,hit.Pval); + } + + + this_is_the_end: + + // Delete memory for dynamic programming matrix + hit.DeleteBacktraceMatrix(q.L+2); + if (par.forward>=1 || Nstochali) + hit.DeleteForwardMatrix(q.L+2); + if (par.forward==2) + hit.DeleteBackwardMatrix(q.L+2); + /* if (Pstruc) { + for (int i=0; i0) + { + for (int i=0; i=2) printf("Done\n"); + } +#endif + + //qali.ClobberGlobal(); + hit.ClobberGlobal(); + if (iFirstCnt > 0){ + q.ClobberGlobal(); + } + if (iSecndCnt > 0){ + t.ClobberGlobal(); + } + hitlist.ClobberGlobal(); + + return iRetVal; + +} /* this is the end of hhalign() //end main */ + +////////////////////////////////////////////////////////////////////////////// +// END OF MAIN +////////////////////////////////////////////////////////////////////////////// + +/* + * EOF hhalign.C + */ + diff --git a/binaries/src/clustalo/src/hhalign/hhalign.h b/binaries/src/clustalo/src/hhalign/hhalign.h new file mode 100644 index 0000000..34ac78e --- /dev/null +++ b/binaries/src/clustalo/src/hhalign/hhalign.h @@ -0,0 +1,30 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: hhalign.h 241 2011-05-04 14:37:17Z fabian $ + */ + + +extern int +hhalign(char **ppcFirstProf, int iFirstCnt, double *pdWeightsL, + char **ppcSecndProf, int iSecndCnt, double *pdWeightsR, + double *dScore_p, hmm_light *prHMM, + char *pcPrealigned1, char *pcRepresent1, + char *pcPrealigned2, char *pcRepresent2, + hhalign_para rHhalignPara, + int iFlag, + char zcAux[], char zcError[]); diff --git a/binaries/src/clustalo/src/hhalign/hhalignment-C.h b/binaries/src/clustalo/src/hhalign/hhalignment-C.h new file mode 100644 index 0000000..c89aa45 --- /dev/null +++ b/binaries/src/clustalo/src/hhalign/hhalignment-C.h @@ -0,0 +1,3028 @@ +/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ + +/********************************************************************* + * Clustal Omega - Multiple sequence alignment + * + * Copyright (C) 2010 University College Dublin + * + * Clustal-Omega is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; either version 2 of the + * License, or (at your option) any later version. + * + * This file is part of Clustal-Omega. + * + ********************************************************************/ + +/* + * RCS $Id: hhalignment-C.h 236 2011-04-14 11:30:04Z fabian $ + */ + + +/* + * Changelog: Michael Remmert made changes to hhalign stand-alone code + * FS implemented some of the changes on 2010-10-28 -> MR1 + * + * Note: MR seems to have changed all [aijk]++ to ++[aijk], + * FS did not do that on 2010-10-28 + */ + +// hhalignment.C + +////////////////////////////////////////////////////////////////////////////// +//// Class Alignment +////////////////////////////////////////////////////////////////////////////// + +// hhalignment.C + +#ifndef MAIN +#define MAIN +#include // cin, cout, cerr +#include // ofstream, ifstream +#include // printf +using std::cout; +using std::cerr; +using std::endl; +using std::ios; +using std::ifstream; +using std::ofstream; +#include // exit +#include // strcmp, strstr +#include // sqrt, pow +#include // INT_MIN +#include // FLT_MIN +#include // clock +#include // islower, isdigit etc +#include "util-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc. +#include "list.h" // list data structure +#include "hash.h" // hash data structure +#include "hhdecl-C.h" +#include "hhutil-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc. +#include "hhhmm.h" +#endif + + +enum {KEEP_NOT = 0, KEEP_CONDITIONALLY, KEEP_ALWAYS}; + +////////////////////////////////////////////////////////////////////////////// +// Class Alignment +////////////////////////////////////////////////////////////////////////////// + + +////////////////////////////////////////////////////////////////////////////// +// Object constructor +////////////////////////////////////////////////////////////////////////////// +Alignment::Alignment(int maxseq, int maxres) +{ + + //printf(">>>>>>>>%s:%s:%d: maxseq=%d, maxres=%d\n", __FUNCTION__, __FILE__, __LINE__, maxseq, maxres); /* (FS) */ + longname = new(char[DESCLEN]); + sname = new(char*[maxseq+2]); /* MR1 */ + seq = new(char*[maxseq+2]); /* MR1 */ + l = new(int[maxres]); + X = new(char*[maxseq+2]); /* MR1 */ + I = new(short unsigned int*[maxseq+2]); /* MR1 */ + keep = new(char[maxseq+2]); /* MR1 */ + display = new(char[maxseq+2]); /* MR1 */ + wg = new(float[maxseq+2]); /* MR1 */ + nseqs = new(int[maxres+2]); /* MR1 */ + N_in=L=0; + nres=NULL; // number of residues per sequence k + first=NULL; // first residue in sequence k + last=NULL; // last residue in sequence k + ksort=NULL; // sequence indices sorted by descending nres[k] + name[0]='\0'; // no name defined yet + longname[0]='\0'; // no name defined yet + fam[0]='\0'; // no name defined yet + file[0]='\0'; // no name defined yet + readCommentLine = '0'; /* MR1 */ +} + +////////////////////////////////////////////////////////////////////////////// +// Object destructor +////////////////////////////////////////////////////////////////////////////// +Alignment::~Alignment() +{ + delete[] longname; longname = NULL; + for(int k=0; k') //line contains sequence name + { + if (k>=MAXSEQ-1) + { + if (v>=1 && k>=MAXSEQ) + cerr<=0) //if this is at least the second name line + { + if (strlen(cur_seq)==0) + { + cerr<ss_dssp",8)) { + if (kss_dssp<0) {display[k]=2; n_display++; keep[k]=KEEP_NOT; kss_dssp=k; N_ss++;} else {skip_sequence=1; k--; continue;} + } + else if (!strncmp(line,">sa_dssp",8)) { + if (ksa_dssp<0) {display[k]=KEEP_ALWAYS; n_display++; keep[k]=KEEP_NOT; ksa_dssp=k; N_ss++;} else {skip_sequence=1; k--; continue;} + } + else if (!strncmp(line,">ss_pred",8)) { + if (kss_pred<0) {display[k]=KEEP_ALWAYS; n_display++; keep[k]=KEEP_NOT; kss_pred=k; N_ss++;} else {skip_sequence=1; k--; continue;} + } + else if (!strncmp(line,">ss_conf",8)) { + if (kss_conf<0) {display[k]=KEEP_ALWAYS; n_display++; keep[k]=KEEP_NOT; kss_conf=k; N_ss++;} else {skip_sequence=1; k--; continue;} + } + else if (!strncmp(line,">ss_",4) || !strncmp(line,">sa_",4)) { + display[k]=KEEP_ALWAYS; n_display++; keep[k]=KEEP_NOT; N_ss++; + } + else if (!strncmp(line,">aa_",4)) { // ignore sequences beginning with ">aa_" + skip_sequence=1; k--; continue; + } + //store first real seq + else if (kfirst<0) + { + char word[NAMELEN]; + strwrd(word,line); // Copies first word in ptr to str + if (strstr(word,"_consensus")) + {display[k]=2; keep[k]=0; n_display++; kfirst=k;} /* MR1 */ + else + {display[k]=keep[k]=KEEP_ALWAYS; n_display++; kfirst=k;} + } + //store all sequences + else if (par.mark==0) {display[k]=keep[k]=KEEP_CONDITIONALLY; n_display++;} + //store sequences up to nseqdis + else if (line[1]=='@'&& n_display-N_ss=4) printf("Reading seq %-16.16s k=%3i n_displ=%3i display[k]=%i keep[k]=%i\n",cur_name,k,n_display,display[k],keep[k]); + sname[k] = new(char[strlen(cur_name)+1]); + if (!sname[k]) {MemoryError("array for sequence names");} + strcpy(sname[k],cur_name); + } // end if(line contains sequence name) + + else if (line[0]=='#') // Commentary line? + { + // #PF01367.9 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; PDB 1taq, 1bgx (T:271-174), 1taq (271-174) + if (name[0]) continue; // if already name defined: skip commentary line + char *ptr1, *ptr2; + ptr1=strscn_(line+1); // set ptr1 to first non-whitespace character after '#' -> AC number + strncpy(longname,ptr1,DESCLEN-1); // copy whole commentary line after '# ' into longname + longname[DESCLEN-1]='\0'; + strtr(longname,""," "); + ptr2=strcut_(ptr1); // cut after AC number and set ptr2 to first non-whitespace character after AC number + // strcpy(fam,ptr1); // copy AC number to fam + // if (!strncmp(fam,"PF",2)) strcut_(fam,'.'); // if PFAM identifier contains '.' cut it off + // strcut_(ptr2); // cut after first word ... + strcpy(name,ptr1); // ... and copy first word into name + readCommentLine = '1'; /* MR1 */ + } + + //line contains sequence residues or SS information and does not belong to a >aa_ sequence + else if (!skip_sequence) + { + if (v>=4) cout<'\0' && l=0) // ignore white-space characters ' ', \t and \n (aa2i()==-1) + {cur_seq[l]=line[h]; l++;} + else if (aa2i(line[h])==-2 && v) + cerr<'\0' && l=0 && ss2i(line[h])<=7) + {cur_seq[l]=ss2ss(line[h]); l++;} + else if (v) + cerr<'\0' && l=0) + cur_seq[l++]=line[h]; + else if (v) + cerr<'\0' && l=0 && ss2i(line[h])<=3) + {cur_seq[l]=ss2ss(line[h]); l++;} + else if (v) + cerr<'\0' && l='0' && line[h]<='9')) + {cur_seq[l]=line[h]; l++;} + else if (v) + cerr<sa_pred etc + { + while (h'\0' && l='0' && line[h]<='9') || (line[h]>='A' && line[h]<='B')) + {cur_seq[l]=line[h]; l++;} + else if (v) + cerr<=/*MAXCOL*/par.maxColCnt-1) + { + cerr<=0) //if at least one sequence was read in + { + seq[k]=new(char[strlen(cur_seq)+2]); + if (!seq[k]) MemoryError("array for input sequences"); + X[k]=new(char[strlen(cur_seq)+2]); + if (!X[k]) MemoryError("array for input sequences"); + I[k]=new(short unsigned int[strlen(cur_seq)+2]); + if (!I[k]) MemoryError("array for input sequences"); + strcpy(seq[k],cur_seq); + } + else + {cerr< extract from first sequence + { + char* ptr; + // strtr(sname[kfirst],"~"," "); // 'transpose': replaces the tilde with a blanc everywhere in sname[kfirst] + strncpy(longname,sname[kfirst],DESCLEN-1); // longname is name of first sequence + longname[DESCLEN-1]='\0'; + strncpy(name,sname[kfirst],NAMELEN-1); // Shortname is first word of longname... + name[NAMELEN-1]='\0'; + ptr = strcut(name); // ...until first white-space character + if (ptr && islower(ptr[0]) && ptr[1]=='.' && isdigit(ptr[2])) //Scop family code present as second word? + { + lwrstr(name); // Transform upper case to lower case + strcut(ptr); // Non-white-space characters until next white-space character.. + strcpy(fam,ptr); // ...are the SCOP familiy code + } + else if (name[0]=='P' && name[1]=='F' && isdigit(name[2]) && isdigit(name[3]) ) //Pfam code + { + strcpy(fam,name); // set family name = Pfam code + } + } + + + + delete[] cur_seq; cur_seq = NULL; + + // Checking for warning messages + if (v==0) return; + if (v>=2) cout<<"Read "<=3) cout<<"Query sequence for alignment has number "< WARNING */ + /* points to next character in seq[k] to be written */ + /*static short unsigned int h[MAXSEQ];*/ + /*short*/ unsigned int *h = NULL; /* short may lead to overflow for long alignments, FS, r235 -> r236 */ + + h = new(/*short*/ unsigned int[N_in+2]); /* short -> overflow, FS, r235 -> r236 */ + float *percent_gaps = NULL; /* FS, 2010-Nov */ + char *match_state = NULL; /* FS, 2010-Nov */ + + + // Initialize + for (k=0;k=3) + { + if (par.M==1) + cout<<"Using match state assignment by capital letters (a2m format)\n"; + else if (par.M==2) cout<<"Using percentage-rule match state assignment\n"; + else if (par.M==3) cout<<"Using residues of first sequence as match states\n"; + } + + // Create matrices X and I with amino acids represented by integer numbers + switch(par.M) + { + + ///////////////////////////////////////////////////////////////////////// + /* a2m/a3m format: match states capital case, + inserts lower case, delete states '-', inserted gaps '.' + The confidence values for ss prediction are interpreted as follows: + 0-9:match states(!) '-' :match state '.':insert */ + case 1: + default: + + // Warn if alignment is ment to be -M first or -M NN instead of A2M/A3M + if (v>=2 && strchr(seq[kfirst],'-') ) // Seed/query sequence contains a gap ... + { + for (k=1; kss_dssp, >ss_pred, >ss_conf, >aa_... sequences + { + while((c=seq[k][l++])) // assign residue to c at same time + { + if (c>='a' && c<='z') I[k][i-1]++;//insert state = lower case character + else if (c!='.') //match state = upper case character + { + X[k][i]=aa2i(c); + I[k][i]=0; + i++; + } + } + } + else if (k==kss_dssp || k==kss_pred) // does alignment contain sequence of secondary structure states? + { + while((c=seq[k][l++])) // assign residue to c at same time + if (c!='.' && !(c>='a' && c<='z')) X[k][i++]=ss2i(c); //match state = upper case character + } + else if (k==ksa_dssp) // does alignment contain sequence of prediction confidence values? + { + while((c=seq[k][l++])) // assign residue to c at same time + if (c!='.' && !(c>='a' && c<='z')) X[k][i++]=sa2i(c); //match state = upper case character + } + else if (k==kss_conf) // does alignment contain sequence of prediction confidence values? + { + while((c=seq[k][l++])) // assign residue to c at same time + if (c!='.') X[k][i++]=cf2i(c); //match state = 0-9 or '-' + } + else if (k==kfirst) // does alignment contain sequence of prediction confidence values? + { + while((c=seq[k][l++])) // assign residue to c at same time + if (c!='.') + { + X[k][i]=aa2i(c); + I[k][i]=0; + ++i; + } + } + else continue; + i--; + if (L!=i && L!=/*MAXRES*/par.maxResLen-2 && !unequal_lengths) unequal_lengths=k; //sequences have different lengths + L=imin(L,i); + } + if (unequal_lengths) break; + + //Replace GAP with ENDGAP for all end gaps /* MR1 */ + for (k=0; k=1 && X[k][i]==GAP; i--) X[k][i]=ENDGAP; /* MR1 */ + } + + for (i=1; i<=L; i++) this->l[i]=i; //assign column indices to match states + if (L<=0) + { + cout<<"\nError: Alignment in "< option"<=2) + { + printf("WARNING: Number of match columns too large. Only first %i match columns will be kept!\n",L); + break; + } + if (v>=2) cout<<"Alignment in "<=1 && X[k][i]==GAP; i--) X[k][i]=ENDGAP; /* MR1 */ + } + + // Add up percentage of gaps + for (l=1; l<=L; l++) + { + float res=0; + float gap=0; + for (k=0; k< N_in; k++){ + if (keep[k]){ + if ( X[k][l]=4) cout<<"percent gaps["<=100, + make slightly bigger than 100% -- to be sure to be sure */ +#define DEFAULT_MGAPS 100.0 /* Soeding's default is 50, omega default prior to telomere logic was 100 + FIXME: this used to be par.Mgaps, + in a later version re-introduce par.Mgaps to keep this value flexible */ +#define TELOMER_LENGTH 10 /* this parameter must be > 0 (unless DEFAULT_MGAPS=100), + if it is too big (L/2) then telomere logic has no effect, + don't think it should be changed (much) */ +#define TELOMER_FRACTION 0.10 + //#define HMM_MIN_LENGTH 0.923 +#define HMM_MIN_LENGTH 0.950 +#define FORTRAN_OFFSET 1 + double dDefaultMgaps; + dDefaultMgaps = DEFAULT_MGAPS; + +#if TELOMERE_LOGIC /* turn telomere logic on (1) or off (0) */ + int iTelomereLength; + +#if TELOMERE_DYNAMIC /* keep telomere length 'dynamic' */ + iTelomereLength = TELOMER_LENGTH > (int)(L*TELOMER_FRACTION) ? TELOMER_LENGTH : (int)(L*TELOMER_FRACTION); +#else + iTelomereLength = TELOMER_LENGTH; +#endif /* this was dynamic telomere */ +#endif /* this was telomere logic */ + + /* if HMMs get too small (much smaller than profile length L) + then one is liable to get a back-tracking error. + So we should ensure that the DEFAULT_MGAPS parameter does NOT + shrink the HMM too much. + take percentage-gap vector, sort it, and fix dDefaultMgaps, + such that at least (HMM_MIN_LENGTH)*(L) are left + */ +#if MGAP_LOGIC /* try to adapt Mgaps to size of final HMM */ + { + float *pfPercentGaps = NULL; + if (NULL == (pfPercentGaps = (float *)malloc((L+1)*sizeof(float)))){ + printf("%s:%s:%d: could not malloc %d float for sorted percent-gaps\n", + __FUNCTION__, __FILE__, __LINE__, L+1); + dDefaultMgaps = DEFAULT_MGAPS; + } + else { + for (l = 0; l < L; l++) { + pfPercentGaps[l] = percent_gaps[l+FORTRAN_OFFSET]; + } + qsort(pfPercentGaps, L, sizeof(float), CompFltAsc); + + dDefaultMgaps = pfPercentGaps[(int)(HMM_MIN_LENGTH*L)]; + if (dDefaultMgaps < DEFAULT_MGAPS){ + //printf("Mgaps = %f <- %f\n", DEFAULT_MGAPS, dDefaultMgaps); + dDefaultMgaps = DEFAULT_MGAPS; + } + else { + //printf("Mgaps = %f\n", dDefaultMgaps); + } + + free(pfPercentGaps); pfPercentGaps = NULL; + } + } +#endif /* tried to adapt Mgaps to size of final HMM */ + + // Throw out insert states and keep only match states + i=0; + for (k=0; k=/*MAXRES*/par.maxResLen-2) { + if (v>=1) + printf("WARNING: Number of match columns too large. Only first %i match columns will be kept!\n",i); + break; + } + i++; + this->l[i]=l; + for (k=0; k=2) cout<<"Alignment in "<=3) printf("Length of first seq = %i\n",L); + // Check for sequences with unequal lengths + for (k=1; k match state + for (l=1; l<=L; l++) + if (isalpha(seq[kfirst][l])) match_state[l]=1; else match_state[l]=0; + // Throw out insert states and keep only match states + for (k=0; k=/*MAXRES*/par.maxResLen-2) { + if (v>=1) + printf("WARNING: Number of match columns too large. Only first %i match columns will be kept!\n",i); + break; + } + i++; + this->l[i]=l; + for (k=0; k=1 && X[k][i]==GAP; i--) X[k][i]=ENDGAP; /* MR1 */ + } + + if (v>=2) cout<<"Alignment in "<=2 && !par.cons) + { + for (i=1; i<=L; i++) + if (X[kfirst][i]==GAP) + { + printf("NOTE: Use the '-cons' option to calculate a consensus sequence as first sequence of the alignment.\n"); + break; + } + } + /* MR1 + //Replace GAP with ENDGAP for all end gaps + for (k=0; k=1 && X[k][i]==GAP; i--) X[k][i]=ENDGAP; + }*/ + + // DEBUG + if (v>=4) + for (k=0; k"<9) cout<<"X"; else cout<