+++ /dev/null
-# 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 *</ {print $2}' $(find src/ -name \*.[ch] -or -name \*.cpp) | grep -v argtable2.h | sort -u | tr -d '<>'
-
-# 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 "${python_config}" != "yes"; then
-# AC_MSG_ERROR("Could not run python-config.")
-# fi
-# PYTHON_CFLAGS=`python-config --cflags`
-# PYTHON_LDFLAGS=`python-config --ldflags`
-# AC_DEFINE([PYTHON_ENABLED], [1], [define for python usage])
-#fi
-#AC_SUBST(PYTHON_CFLAGS)
-#AC_SUBST(PYTHON_LDFLAGS)
-
-
-# --- SSE support
-# "One instruction to do the same operation on 4 packed elements simultaneously."
-#
-# http://www.codeproject.com/KB/recipes/sseintro.aspx?msg=568491
-# http://www.drdobbs.com/go-parallel/blog/archives/2010/03/getting_amazing.html
-# http://software.intel.com/file/1000
-#
-# AC_MSG_CHECKING(for SSE in current arch/CFLAGS)
-# AC_LINK_IFELSE([
-# AC_LANG_PROGRAM([[
-# #include <xmmintrin.h>
-# __m128 testfunc(float *a, float *b) {
-# return _mm_add_ps(_mm_loadu_ps(a), _mm_loadu_ps(b));
-# }
-# ]])],
-# [has_sse=yes], [has_sse=no]
-# )
-# AC_MSG_RESULT($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 <sys/stat.h>],[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
git://source.jalview.org / jabaws.git / blobdiff