From: Fábio Madeira Date: Mon, 10 Apr 2017 09:47:50 +0000 (+0100) Subject: JWS-112 Bumping version of ClustalW (src, binaries and windows) to version 2.1. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7c6018cf87e67d7ac21f5230284ef2162a19320f;p=jabaws.git JWS-112 Bumping version of ClustalW (src, binaries and windows) to version 2.1. --- diff --git a/binaries/src/clustalw/COPYING b/binaries/src/clustalw/COPYING new file mode 100644 index 0000000..94a9ed0 --- /dev/null +++ b/binaries/src/clustalw/COPYING @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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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. But first, please read +. diff --git a/binaries/src/clustalw/COPYING.LESSER b/binaries/src/clustalw/COPYING.LESSER new file mode 100644 index 0000000..65c5ca8 --- /dev/null +++ b/binaries/src/clustalw/COPYING.LESSER @@ -0,0 +1,165 @@ + GNU LESSER GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + + This version of the GNU Lesser General Public License incorporates +the terms and conditions of version 3 of the GNU General Public +License, supplemented by the additional permissions listed below. + + 0. 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The particular version of the Library +with which the Combined Work was made is also called the "Linked +Version". + + The "Minimal Corresponding Source" for a Combined Work means the +Corresponding Source for the Combined Work, excluding any source code +for portions of the Combined Work that, considered in isolation, are +based on the Application, and not on the Linked Version. + + The "Corresponding Application Code" for a Combined Work means the +object code and/or source code for the Application, including any data +and utility programs needed for reproducing the Combined Work from the +Application, but excluding the System Libraries of the Combined Work. + + 1. Exception to Section 3 of the GNU GPL. + + You may convey a covered work under sections 3 and 4 of this License +without being bound by section 3 of the GNU GPL. + + 2. Conveying Modified Versions. + + If you modify a copy of the Library, and, in your modifications, a +facility refers to a function or data to be supplied by an Application +that uses the facility (other than as an argument passed when the +facility is invoked), then you may convey a copy of the modified +version: + + a) under this License, provided that you make a good faith effort to + ensure that, in the event an Application does not supply the + function or data, the facility still operates, and performs + whatever part of its purpose remains meaningful, or + + b) under the GNU GPL, with none of the additional permissions of + this License applicable to that copy. + + 3. Object Code Incorporating Material from Library Header Files. + + The object code form of an Application may incorporate material from +a header file that is part of the Library. You may convey such object +code under terms of your choice, provided that, if the incorporated +material is not limited to numerical parameters, data structure +layouts and accessors, or small macros, inline functions and templates +(ten or fewer lines in length), you do both of the following: + + a) Give prominent notice with each copy of the object code that the + Library is used in it and that the Library and its use are + covered by this License. + + b) Accompany the object code with a copy of the GNU GPL and this license + document. + + 4. Combined Works. + + You may convey a Combined Work under terms of your choice that, +taken together, effectively do not restrict modification of the +portions of the Library contained in the Combined Work and reverse +engineering for debugging such modifications, if you also do each of +the following: + + a) Give prominent notice with each copy of the Combined Work that + the Library is used in it and that the Library and its use are + covered by this License. + + b) Accompany the Combined Work with a copy of the GNU GPL and this license + document. + + c) For a Combined Work that displays copyright notices during + execution, include the copyright notice for the Library among + these notices, as well as a reference directing the user to the + copies of the GNU GPL and this license document. + + d) Do one of the following: + + 0) Convey the Minimal Corresponding Source under the terms of this + License, and the Corresponding Application Code in a form + suitable for, and under terms that permit, the user to + recombine or relink the Application with a modified version of + the Linked Version to produce a modified Combined Work, in the + manner specified by section 6 of the GNU GPL for conveying + Corresponding Source. + + 1) Use a suitable shared library mechanism for linking with the + Library. A suitable mechanism is one that (a) uses at run time + a copy of the Library already present on the user's computer + system, and (b) will operate properly with a modified version + of the Library that is interface-compatible with the Linked + Version. + + e) Provide Installation Information, but only if you would otherwise + be required to provide such information under section 6 of the + GNU GPL, and only to the extent that such information is + necessary to install and execute a modified version of the + Combined Work produced by recombining or relinking the + Application with a modified version of the Linked Version. (If + you use option 4d0, the Installation Information must accompany + the Minimal Corresponding Source and Corresponding Application + Code. If you use option 4d1, you must provide the Installation + Information in the manner specified by section 6 of the GNU GPL + for conveying Corresponding Source.) + + 5. Combined Libraries. + + You may place library facilities that are a work based on the +Library side by side in a single library together with other library +facilities that are not Applications and are not covered by this +License, and convey such a combined library under terms of your +choice, if you do both of the following: + + a) Accompany the combined library with a copy of the same work based + on the Library, uncombined with any other library facilities, + conveyed under the terms of this License. + + b) Give prominent notice with the combined library that part of it + is a work based on the Library, and explaining where to find the + accompanying uncombined form of the same work. + + 6. Revised Versions of the GNU Lesser General Public License. + + The Free Software Foundation may publish revised and/or new versions +of the GNU Lesser General Public License from time to time. Such new +versions will be similar in spirit to the present version, but may +differ in detail to address new problems or concerns. + + Each version is given a distinguishing version number. If the +Library as you received it specifies that a certain numbered version +of the GNU Lesser General Public License "or any later version" +applies to it, you have the option of following the terms and +conditions either of that published version or of any later version +published by the Free Software Foundation. If the Library as you +received it does not specify a version number of the GNU Lesser +General Public License, you may choose any version of the GNU Lesser +General Public License ever published by the Free Software Foundation. + + If the Library as you received it specifies that a proxy can decide +whether future versions of the GNU Lesser General Public License shall +apply, that proxy's public statement of acceptance of any version is +permanent authorization for you to choose that version for the +Library. diff --git a/binaries/src/clustalw/Makefile b/binaries/src/clustalw/Makefile index 356a514..a0a4ce8 100644 --- a/binaries/src/clustalw/Makefile +++ b/binaries/src/clustalw/Makefile @@ -1,8 +1,9 @@ -# Makefile.in generated by automake 1.10.2 from Makefile.am. +# Makefile.in generated by automake 1.11.1 from Makefile.am. # Makefile. Generated from Makefile.in by configure. # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, -# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +# 2003, 2004, 2005, 2006, 2007, 2008, 2009 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. @@ -20,8 +21,9 @@ # http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html pkgdatadir = $(datadir)/clustalw -pkglibdir = $(libdir)/clustalw pkgincludedir = $(includedir)/clustalw +pkglibdir = $(libdir)/clustalw +pkglibexecdir = $(libexecdir)/clustalw am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd install_sh_DATA = $(install_sh) -c -m 644 install_sh_PROGRAM = $(install_sh) -c @@ -50,6 +52,7 @@ am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \ mkinstalldirs = $(install_sh) -d CONFIG_HEADER = $(top_builddir)/src/config.h CONFIG_CLEAN_FILES = +CONFIG_CLEAN_VPATH_FILES = SOURCES = DIST_SOURCES = RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \ @@ -61,6 +64,9 @@ RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \ ps-recursive uninstall-recursive RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \ distclean-recursive maintainer-clean-recursive +AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \ + $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \ + distdir dist dist-all distcheck ETAGS = etags CTAGS = ctags DIST_SUBDIRS = $(SUBDIRS) @@ -68,24 +74,49 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) distdir = $(PACKAGE)-$(VERSION) top_distdir = $(distdir) am__remove_distdir = \ - { test ! -d $(distdir) \ - || { find $(distdir) -type d ! -perm -200 -exec chmod u+w {} ';' \ - && rm -fr $(distdir); }; } + { test ! -d "$(distdir)" \ + || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \ + && rm -fr "$(distdir)"; }; } +am__relativize = \ + dir0=`pwd`; \ + sed_first='s,^\([^/]*\)/.*$$,\1,'; \ + sed_rest='s,^[^/]*/*,,'; \ + sed_last='s,^.*/\([^/]*\)$$,\1,'; \ + sed_butlast='s,/*[^/]*$$,,'; \ + while test -n "$$dir1"; do \ + first=`echo "$$dir1" | sed -e "$$sed_first"`; \ + if test "$$first" != "."; then \ + if test "$$first" = ".."; then \ + dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \ + dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \ + else \ + first2=`echo "$$dir2" | sed -e "$$sed_first"`; \ + if test "$$first2" = "$$first"; then \ + dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \ + else \ + dir2="../$$dir2"; \ + fi; \ + dir0="$$dir0"/"$$first"; \ + fi; \ + fi; \ + dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \ + done; \ + reldir="$$dir2" DIST_ARCHIVES = $(distdir).tar.gz GZIP_ENV = --best distuninstallcheck_listfiles = find . -type f -print distcleancheck_listfiles = find . -type f -print -ACLOCAL = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run aclocal-1.10 -AMTAR = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run tar -AUTOCONF = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoconf -AUTOHEADER = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoheader -AUTOMAKE = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run automake-1.10 +ACLOCAL = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run aclocal-1.11 +AMTAR = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run tar +AUTOCONF = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoconf +AUTOHEADER = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoheader +AUTOMAKE = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run automake-1.11 AWK = gawk CC = gcc CCDEPMODE = depmode=gcc3 CFLAGS = -g -O2 CLUSTALW_NAME = ClustalW -CLUSTALW_VERSION = 2.0.12 +CLUSTALW_VERSION = 2.1 CPPFLAGS = CXX = g++ CXXCPP = g++ -E @@ -109,25 +140,26 @@ LDFLAGS = LIBOBJS = LIBS = LTLIBOBJS = -MAKEINFO = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run makeinfo +MAKEINFO = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run makeinfo MKDIR_P = /bin/mkdir -p OBJEXT = o PACKAGE = clustalw PACKAGE_BUGREPORT = clustalw@ucd.ie PACKAGE_NAME = clustalw -PACKAGE_STRING = clustalw 2.0.12 +PACKAGE_STRING = clustalw 2.1 PACKAGE_TARNAME = clustalw -PACKAGE_VERSION = 2.0.12 +PACKAGE_URL = +PACKAGE_VERSION = 2.1 PATH_SEPARATOR = : RANLIB = ranlib SET_MAKE = SHELL = /bin/sh STRIP = -VERSION = 2.0.12 -abs_builddir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw -abs_srcdir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw -abs_top_builddir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw -abs_top_srcdir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw +VERSION = 2.1 +abs_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw +abs_srcdir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw +abs_top_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw +abs_top_srcdir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw ac_ct_CC = gcc ac_ct_CXX = g++ am__include = include @@ -155,7 +187,7 @@ host_vendor = unknown htmldir = ${docdir} includedir = ${prefix}/include infodir = ${datarootdir}/info -install_sh = $(SHELL) /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/install-sh +install_sh = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/install-sh libdir = ${exec_prefix}/lib libexecdir = ${exec_prefix}/libexec localedir = ${datarootdir}/locale @@ -193,15 +225,15 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps) @for dep in $?; do \ case '$(am__configure_deps)' in \ *$$dep*) \ - echo ' cd $(srcdir) && $(AUTOMAKE) --foreign '; \ - cd $(srcdir) && $(AUTOMAKE) --foreign \ + echo ' cd $(srcdir) && $(AUTOMAKE) --foreign'; \ + $(am__cd) $(srcdir) && $(AUTOMAKE) --foreign \ && exit 0; \ exit 1;; \ esac; \ done; \ - echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \ - cd $(top_srcdir) && \ - $(AUTOMAKE) --foreign Makefile + echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \ + $(am__cd) $(top_srcdir) && \ + $(AUTOMAKE) --foreign Makefile .PRECIOUS: Makefile Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status @case '$?' in \ @@ -217,9 +249,10 @@ $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENC $(SHELL) ./config.status --recheck $(top_srcdir)/configure: $(am__configure_deps) - cd $(srcdir) && $(AUTOCONF) + $(am__cd) $(srcdir) && $(AUTOCONF) $(ACLOCAL_M4): $(am__aclocal_m4_deps) - cd $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS) + $(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS) +$(am__aclocal_m4_deps): # This directory's subdirectories are mostly independent; you can cd # into them and run `make' without going through this Makefile. @@ -228,7 +261,7 @@ $(ACLOCAL_M4): $(am__aclocal_m4_deps) # (which will cause the Makefiles to be regenerated when you run `make'); # (2) otherwise, pass the desired values on the `make' command line. $(RECURSIVE_TARGETS): - @failcom='exit 1'; \ + @fail= failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -245,7 +278,7 @@ $(RECURSIVE_TARGETS): else \ local_target="$$target"; \ fi; \ - (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ + ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ || eval $$failcom; \ done; \ if test "$$dot_seen" = "no"; then \ @@ -253,7 +286,7 @@ $(RECURSIVE_TARGETS): fi; test -z "$$fail" $(RECURSIVE_CLEAN_TARGETS): - @failcom='exit 1'; \ + @fail= failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -279,16 +312,16 @@ $(RECURSIVE_CLEAN_TARGETS): else \ local_target="$$target"; \ fi; \ - (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ + ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ || eval $$failcom; \ done && test -z "$$fail" tags-recursive: list='$(SUBDIRS)'; for subdir in $$list; do \ - test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \ + test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \ done ctags-recursive: list='$(SUBDIRS)'; for subdir in $$list; do \ - test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \ + test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \ done ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES) @@ -303,7 +336,7 @@ tags: TAGS TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ $(TAGS_FILES) $(LISP) - tags=; \ + set x; \ here=`pwd`; \ if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \ include_option=--etags-include; \ @@ -315,7 +348,7 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ list='$(SUBDIRS)'; for subdir in $$list; do \ if test "$$subdir" = .; then :; else \ test ! -f $$subdir/TAGS || \ - tags="$$tags $$include_option=$$here/$$subdir/TAGS"; \ + set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \ fi; \ done; \ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ @@ -324,36 +357,41 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ done | \ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ END { if (nonempty) { for (i in files) print i; }; }'`; \ - if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \ + shift; \ + if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \ test -n "$$unique" || unique=$$empty_fix; \ - $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ - $$tags $$unique; \ + if test $$# -gt 0; then \ + $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ + "$$@" $$unique; \ + else \ + $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ + $$unique; \ + fi; \ fi ctags: CTAGS CTAGS: ctags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ $(TAGS_FILES) $(LISP) - tags=; \ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ unique=`for i in $$list; do \ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ done | \ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ END { if (nonempty) { for (i in files) print i; }; }'`; \ - test -z "$(CTAGS_ARGS)$$tags$$unique" \ + test -z "$(CTAGS_ARGS)$$unique" \ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \ - $$tags $$unique + $$unique GTAGS: here=`$(am__cd) $(top_builddir) && pwd` \ - && cd $(top_srcdir) \ - && gtags -i $(GTAGS_ARGS) $$here + && $(am__cd) $(top_srcdir) \ + && gtags -i $(GTAGS_ARGS) "$$here" distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags distdir: $(DISTFILES) $(am__remove_distdir) - test -d $(distdir) || mkdir $(distdir) + test -d "$(distdir)" || mkdir "$(distdir)" @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ list='$(DISTFILES)'; \ @@ -369,38 +407,55 @@ distdir: $(DISTFILES) if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \ if test -d $$d/$$file; then \ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \ + if test -d "$(distdir)/$$file"; then \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ + fi; \ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \ - cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \ + cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ fi; \ - cp -pR $$d/$$file $(distdir)$$dir || exit 1; \ + cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \ else \ - test -f $(distdir)/$$file \ - || cp -p $$d/$$file $(distdir)/$$file \ + test -f "$(distdir)/$$file" \ + || cp -p $$d/$$file "$(distdir)/$$file" \ || exit 1; \ fi; \ done - list='$(DIST_SUBDIRS)'; for subdir in $$list; do \ + @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \ if test "$$subdir" = .; then :; else \ test -d "$(distdir)/$$subdir" \ || $(MKDIR_P) "$(distdir)/$$subdir" \ || exit 1; \ - distdir=`$(am__cd) $(distdir) && pwd`; \ - top_distdir=`$(am__cd) $(top_distdir) && pwd`; \ - (cd $$subdir && \ + fi; \ + done + @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \ + if test "$$subdir" = .; then :; else \ + dir1=$$subdir; dir2="$(distdir)/$$subdir"; \ + $(am__relativize); \ + new_distdir=$$reldir; \ + dir1=$$subdir; dir2="$(top_distdir)"; \ + $(am__relativize); \ + new_top_distdir=$$reldir; \ + echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \ + echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \ + ($(am__cd) $$subdir && \ $(MAKE) $(AM_MAKEFLAGS) \ - top_distdir="$$top_distdir" \ - distdir="$$distdir/$$subdir" \ + top_distdir="$$new_top_distdir" \ + distdir="$$new_distdir" \ am__remove_distdir=: \ am__skip_length_check=: \ + am__skip_mode_fix=: \ distdir) \ || exit 1; \ fi; \ done - -find $(distdir) -type d ! -perm -777 -exec chmod a+rwx {} \; -o \ + -test -n "$(am__skip_mode_fix)" \ + || find "$(distdir)" -type d ! -perm -755 \ + -exec chmod u+rwx,go+rx {} \; -o \ ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \ ! -type d ! -perm -400 -exec chmod a+r {} \; -o \ ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \ - || chmod -R a+r $(distdir) + || chmod -R a+r "$(distdir)" dist-gzip: distdir tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz $(am__remove_distdir) @@ -413,6 +468,10 @@ dist-lzma: distdir tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma $(am__remove_distdir) +dist-xz: distdir + tardir=$(distdir) && $(am__tar) | xz -c >$(distdir).tar.xz + $(am__remove_distdir) + dist-tarZ: distdir tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z $(am__remove_distdir) @@ -436,15 +495,17 @@ dist dist-all: distdir distcheck: dist case '$(DIST_ARCHIVES)' in \ *.tar.gz*) \ - GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(am__untar) ;;\ + GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\ *.tar.bz2*) \ - bunzip2 -c $(distdir).tar.bz2 | $(am__untar) ;;\ + bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\ *.tar.lzma*) \ - unlzma -c $(distdir).tar.lzma | $(am__untar) ;;\ + lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\ + *.tar.xz*) \ + xz -dc $(distdir).tar.xz | $(am__untar) ;;\ *.tar.Z*) \ uncompress -c $(distdir).tar.Z | $(am__untar) ;;\ *.shar.gz*) \ - GZIP=$(GZIP_ENV) gunzip -c $(distdir).shar.gz | unshar ;;\ + GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\ *.zip*) \ unzip $(distdir).zip ;;\ esac @@ -452,9 +513,11 @@ distcheck: dist mkdir $(distdir)/_build mkdir $(distdir)/_inst chmod a-w $(distdir) + test -d $(distdir)/_build || exit 0; \ dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \ && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \ - && cd $(distdir)/_build \ + && am__cwd=`pwd` \ + && $(am__cd) $(distdir)/_build \ && ../configure --srcdir=.. --prefix="$$dc_install_base" \ $(DISTCHECK_CONFIGURE_FLAGS) \ && $(MAKE) $(AM_MAKEFLAGS) \ @@ -476,13 +539,15 @@ distcheck: dist && rm -rf "$$dc_destdir" \ && $(MAKE) $(AM_MAKEFLAGS) dist \ && rm -rf $(DIST_ARCHIVES) \ - && $(MAKE) $(AM_MAKEFLAGS) distcleancheck + && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \ + && cd "$$am__cwd" \ + || exit 1 $(am__remove_distdir) @(echo "$(distdir) archives ready for distribution: "; \ list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \ sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x' distuninstallcheck: - @cd $(distuninstallcheck_dir) \ + @$(am__cd) '$(distuninstallcheck_dir)' \ && test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \ || { echo "ERROR: files left after uninstall:" ; \ if test -n "$(DESTDIR)"; then \ @@ -524,6 +589,7 @@ clean-generic: distclean-generic: -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES) + -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES) maintainer-clean-generic: @echo "This command is intended for maintainers to use" @@ -543,6 +609,8 @@ dvi-am: html: html-recursive +html-am: + info: info-recursive info-am: @@ -551,18 +619,28 @@ install-data-am: install-dvi: install-dvi-recursive +install-dvi-am: + install-exec-am: install-html: install-html-recursive +install-html-am: + install-info: install-info-recursive +install-info-am: + install-man: install-pdf: install-pdf-recursive +install-pdf-am: + install-ps: install-ps-recursive +install-ps-am: + installcheck-am: maintainer-clean: maintainer-clean-recursive @@ -585,23 +663,24 @@ ps-am: uninstall-am: -.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) install-am \ - install-strip +.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \ + install-am install-strip tags-recursive .PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \ all all-am am--refresh check check-am clean clean-generic \ ctags ctags-recursive dist dist-all dist-bzip2 dist-gzip \ - dist-lzma dist-shar dist-tarZ dist-zip distcheck distclean \ - distclean-generic distclean-tags distcleancheck distdir \ - distuninstallcheck dvi dvi-am html html-am info info-am \ - install install-am install-data install-data-am install-dvi \ - install-dvi-am install-exec install-exec-am install-html \ - install-html-am install-info install-info-am install-man \ - install-pdf install-pdf-am install-ps install-ps-am \ - install-strip installcheck installcheck-am installdirs \ - installdirs-am maintainer-clean maintainer-clean-generic \ - mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags \ - tags-recursive uninstall uninstall-am + dist-lzma dist-shar dist-tarZ dist-xz dist-zip distcheck \ + distclean distclean-generic distclean-tags distcleancheck \ + distdir distuninstallcheck dvi dvi-am html html-am info \ + info-am install install-am install-data install-data-am \ + install-dvi install-dvi-am install-exec install-exec-am \ + install-html install-html-am install-info install-info-am \ + install-man install-pdf install-pdf-am install-ps \ + install-ps-am install-strip installcheck installcheck-am \ + installdirs installdirs-am maintainer-clean \ + maintainer-clean-generic mostlyclean mostlyclean-generic pdf \ + pdf-am ps ps-am tags tags-recursive uninstall uninstall-am + # 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. diff --git a/binaries/src/clustalw/Makefile.in b/binaries/src/clustalw/Makefile.in index fe4f9ad..fafe5d8 100644 --- a/binaries/src/clustalw/Makefile.in +++ b/binaries/src/clustalw/Makefile.in @@ -1,8 +1,9 @@ -# Makefile.in generated by automake 1.10.2 from Makefile.am. +# Makefile.in generated by automake 1.11.1 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. +# 2003, 2004, 2005, 2006, 2007, 2008, 2009 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. @@ -20,8 +21,9 @@ # http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html VPATH = @srcdir@ pkgdatadir = $(datadir)/@PACKAGE@ -pkglibdir = $(libdir)/@PACKAGE@ pkgincludedir = $(includedir)/@PACKAGE@ +pkglibdir = $(libdir)/@PACKAGE@ +pkglibexecdir = $(libexecdir)/@PACKAGE@ am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd install_sh_DATA = $(install_sh) -c -m 644 install_sh_PROGRAM = $(install_sh) -c @@ -50,6 +52,7 @@ am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \ mkinstalldirs = $(install_sh) -d CONFIG_HEADER = $(top_builddir)/src/config.h CONFIG_CLEAN_FILES = +CONFIG_CLEAN_VPATH_FILES = SOURCES = DIST_SOURCES = RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \ @@ -61,6 +64,9 @@ RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \ ps-recursive uninstall-recursive RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \ distclean-recursive maintainer-clean-recursive +AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \ + $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \ + distdir dist dist-all distcheck ETAGS = etags CTAGS = ctags DIST_SUBDIRS = $(SUBDIRS) @@ -68,9 +74,34 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) distdir = $(PACKAGE)-$(VERSION) top_distdir = $(distdir) am__remove_distdir = \ - { test ! -d $(distdir) \ - || { find $(distdir) -type d ! -perm -200 -exec chmod u+w {} ';' \ - && rm -fr $(distdir); }; } + { test ! -d "$(distdir)" \ + || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \ + && rm -fr "$(distdir)"; }; } +am__relativize = \ + dir0=`pwd`; \ + sed_first='s,^\([^/]*\)/.*$$,\1,'; \ + sed_rest='s,^[^/]*/*,,'; \ + sed_last='s,^.*/\([^/]*\)$$,\1,'; \ + sed_butlast='s,/*[^/]*$$,,'; \ + while test -n "$$dir1"; do \ + first=`echo "$$dir1" | sed -e "$$sed_first"`; \ + if test "$$first" != "."; then \ + if test "$$first" = ".."; then \ + dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \ + dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \ + else \ + first2=`echo "$$dir2" | sed -e "$$sed_first"`; \ + if test "$$first2" = "$$first"; then \ + dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \ + else \ + dir2="../$$dir2"; \ + fi; \ + dir0="$$dir0"/"$$first"; \ + fi; \ + fi; \ + dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \ + done; \ + reldir="$$dir2" DIST_ARCHIVES = $(distdir).tar.gz GZIP_ENV = --best distuninstallcheck_listfiles = find . -type f -print @@ -117,6 +148,7 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ +PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ RANLIB = @RANLIB@ @@ -193,15 +225,15 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps) @for dep in $?; do \ case '$(am__configure_deps)' in \ *$$dep*) \ - echo ' cd $(srcdir) && $(AUTOMAKE) --foreign '; \ - cd $(srcdir) && $(AUTOMAKE) --foreign \ + echo ' cd $(srcdir) && $(AUTOMAKE) --foreign'; \ + $(am__cd) $(srcdir) && $(AUTOMAKE) --foreign \ && exit 0; \ exit 1;; \ esac; \ done; \ - echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \ - cd $(top_srcdir) && \ - $(AUTOMAKE) --foreign Makefile + echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \ + $(am__cd) $(top_srcdir) && \ + $(AUTOMAKE) --foreign Makefile .PRECIOUS: Makefile Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status @case '$?' in \ @@ -217,9 +249,10 @@ $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENC $(SHELL) ./config.status --recheck $(top_srcdir)/configure: $(am__configure_deps) - cd $(srcdir) && $(AUTOCONF) + $(am__cd) $(srcdir) && $(AUTOCONF) $(ACLOCAL_M4): $(am__aclocal_m4_deps) - cd $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS) + $(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS) +$(am__aclocal_m4_deps): # This directory's subdirectories are mostly independent; you can cd # into them and run `make' without going through this Makefile. @@ -228,7 +261,7 @@ $(ACLOCAL_M4): $(am__aclocal_m4_deps) # (which will cause the Makefiles to be regenerated when you run `make'); # (2) otherwise, pass the desired values on the `make' command line. $(RECURSIVE_TARGETS): - @failcom='exit 1'; \ + @fail= failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -245,7 +278,7 @@ $(RECURSIVE_TARGETS): else \ local_target="$$target"; \ fi; \ - (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ + ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ || eval $$failcom; \ done; \ if test "$$dot_seen" = "no"; then \ @@ -253,7 +286,7 @@ $(RECURSIVE_TARGETS): fi; test -z "$$fail" $(RECURSIVE_CLEAN_TARGETS): - @failcom='exit 1'; \ + @fail= failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -279,16 +312,16 @@ $(RECURSIVE_CLEAN_TARGETS): else \ local_target="$$target"; \ fi; \ - (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ + ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ || eval $$failcom; \ done && test -z "$$fail" tags-recursive: list='$(SUBDIRS)'; for subdir in $$list; do \ - test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \ + test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \ done ctags-recursive: list='$(SUBDIRS)'; for subdir in $$list; do \ - test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \ + test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \ done ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES) @@ -303,7 +336,7 @@ tags: TAGS TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ $(TAGS_FILES) $(LISP) - tags=; \ + set x; \ here=`pwd`; \ if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \ include_option=--etags-include; \ @@ -315,7 +348,7 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ list='$(SUBDIRS)'; for subdir in $$list; do \ if test "$$subdir" = .; then :; else \ test ! -f $$subdir/TAGS || \ - tags="$$tags $$include_option=$$here/$$subdir/TAGS"; \ + set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \ fi; \ done; \ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ @@ -324,36 +357,41 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ done | \ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ END { if (nonempty) { for (i in files) print i; }; }'`; \ - if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \ + shift; \ + if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \ test -n "$$unique" || unique=$$empty_fix; \ - $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ - $$tags $$unique; \ + if test $$# -gt 0; then \ + $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ + "$$@" $$unique; \ + else \ + $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ + $$unique; \ + fi; \ fi ctags: CTAGS CTAGS: ctags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \ $(TAGS_FILES) $(LISP) - tags=; \ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ unique=`for i in $$list; do \ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ done | \ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ END { if (nonempty) { for (i in files) print i; }; }'`; \ - test -z "$(CTAGS_ARGS)$$tags$$unique" \ + test -z "$(CTAGS_ARGS)$$unique" \ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \ - $$tags $$unique + $$unique GTAGS: here=`$(am__cd) $(top_builddir) && pwd` \ - && cd $(top_srcdir) \ - && gtags -i $(GTAGS_ARGS) $$here + && $(am__cd) $(top_srcdir) \ + && gtags -i $(GTAGS_ARGS) "$$here" distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags distdir: $(DISTFILES) $(am__remove_distdir) - test -d $(distdir) || mkdir $(distdir) + test -d "$(distdir)" || mkdir "$(distdir)" @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ list='$(DISTFILES)'; \ @@ -369,38 +407,55 @@ distdir: $(DISTFILES) if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \ if test -d $$d/$$file; then \ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \ + if test -d "$(distdir)/$$file"; then \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ + fi; \ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \ - cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \ + cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ fi; \ - cp -pR $$d/$$file $(distdir)$$dir || exit 1; \ + cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \ else \ - test -f $(distdir)/$$file \ - || cp -p $$d/$$file $(distdir)/$$file \ + test -f "$(distdir)/$$file" \ + || cp -p $$d/$$file "$(distdir)/$$file" \ || exit 1; \ fi; \ done - list='$(DIST_SUBDIRS)'; for subdir in $$list; do \ + @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \ if test "$$subdir" = .; then :; else \ test -d "$(distdir)/$$subdir" \ || $(MKDIR_P) "$(distdir)/$$subdir" \ || exit 1; \ - distdir=`$(am__cd) $(distdir) && pwd`; \ - top_distdir=`$(am__cd) $(top_distdir) && pwd`; \ - (cd $$subdir && \ + fi; \ + done + @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \ + if test "$$subdir" = .; then :; else \ + dir1=$$subdir; dir2="$(distdir)/$$subdir"; \ + $(am__relativize); \ + new_distdir=$$reldir; \ + dir1=$$subdir; dir2="$(top_distdir)"; \ + $(am__relativize); \ + new_top_distdir=$$reldir; \ + echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \ + echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \ + ($(am__cd) $$subdir && \ $(MAKE) $(AM_MAKEFLAGS) \ - top_distdir="$$top_distdir" \ - distdir="$$distdir/$$subdir" \ + top_distdir="$$new_top_distdir" \ + distdir="$$new_distdir" \ am__remove_distdir=: \ am__skip_length_check=: \ + am__skip_mode_fix=: \ distdir) \ || exit 1; \ fi; \ done - -find $(distdir) -type d ! -perm -777 -exec chmod a+rwx {} \; -o \ + -test -n "$(am__skip_mode_fix)" \ + || find "$(distdir)" -type d ! -perm -755 \ + -exec chmod u+rwx,go+rx {} \; -o \ ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \ ! -type d ! -perm -400 -exec chmod a+r {} \; -o \ ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \ - || chmod -R a+r $(distdir) + || chmod -R a+r "$(distdir)" dist-gzip: distdir tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz $(am__remove_distdir) @@ -413,6 +468,10 @@ dist-lzma: distdir tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma $(am__remove_distdir) +dist-xz: distdir + tardir=$(distdir) && $(am__tar) | xz -c >$(distdir).tar.xz + $(am__remove_distdir) + dist-tarZ: distdir tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z $(am__remove_distdir) @@ -436,15 +495,17 @@ dist dist-all: distdir distcheck: dist case '$(DIST_ARCHIVES)' in \ *.tar.gz*) \ - GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(am__untar) ;;\ + GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\ *.tar.bz2*) \ - bunzip2 -c $(distdir).tar.bz2 | $(am__untar) ;;\ + bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\ *.tar.lzma*) \ - unlzma -c $(distdir).tar.lzma | $(am__untar) ;;\ + lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\ + *.tar.xz*) \ + xz -dc $(distdir).tar.xz | $(am__untar) ;;\ *.tar.Z*) \ uncompress -c $(distdir).tar.Z | $(am__untar) ;;\ *.shar.gz*) \ - GZIP=$(GZIP_ENV) gunzip -c $(distdir).shar.gz | unshar ;;\ + GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\ *.zip*) \ unzip $(distdir).zip ;;\ esac @@ -452,9 +513,11 @@ distcheck: dist mkdir $(distdir)/_build mkdir $(distdir)/_inst chmod a-w $(distdir) + test -d $(distdir)/_build || exit 0; \ dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \ && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \ - && cd $(distdir)/_build \ + && am__cwd=`pwd` \ + && $(am__cd) $(distdir)/_build \ && ../configure --srcdir=.. --prefix="$$dc_install_base" \ $(DISTCHECK_CONFIGURE_FLAGS) \ && $(MAKE) $(AM_MAKEFLAGS) \ @@ -476,13 +539,15 @@ distcheck: dist && rm -rf "$$dc_destdir" \ && $(MAKE) $(AM_MAKEFLAGS) dist \ && rm -rf $(DIST_ARCHIVES) \ - && $(MAKE) $(AM_MAKEFLAGS) distcleancheck + && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \ + && cd "$$am__cwd" \ + || exit 1 $(am__remove_distdir) @(echo "$(distdir) archives ready for distribution: "; \ list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \ sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x' distuninstallcheck: - @cd $(distuninstallcheck_dir) \ + @$(am__cd) '$(distuninstallcheck_dir)' \ && test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \ || { echo "ERROR: files left after uninstall:" ; \ if test -n "$(DESTDIR)"; then \ @@ -524,6 +589,7 @@ clean-generic: distclean-generic: -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES) + -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES) maintainer-clean-generic: @echo "This command is intended for maintainers to use" @@ -543,6 +609,8 @@ dvi-am: html: html-recursive +html-am: + info: info-recursive info-am: @@ -551,18 +619,28 @@ install-data-am: install-dvi: install-dvi-recursive +install-dvi-am: + install-exec-am: install-html: install-html-recursive +install-html-am: + install-info: install-info-recursive +install-info-am: + install-man: install-pdf: install-pdf-recursive +install-pdf-am: + install-ps: install-ps-recursive +install-ps-am: + installcheck-am: maintainer-clean: maintainer-clean-recursive @@ -585,23 +663,24 @@ ps-am: uninstall-am: -.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) install-am \ - install-strip +.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \ + install-am install-strip tags-recursive .PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \ all all-am am--refresh check check-am clean clean-generic \ ctags ctags-recursive dist dist-all dist-bzip2 dist-gzip \ - dist-lzma dist-shar dist-tarZ dist-zip distcheck distclean \ - distclean-generic distclean-tags distcleancheck distdir \ - distuninstallcheck dvi dvi-am html html-am info info-am \ - install install-am install-data install-data-am install-dvi \ - install-dvi-am install-exec install-exec-am install-html \ - install-html-am install-info install-info-am install-man \ - install-pdf install-pdf-am install-ps install-ps-am \ - install-strip installcheck installcheck-am installdirs \ - installdirs-am maintainer-clean maintainer-clean-generic \ - mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags \ - tags-recursive uninstall uninstall-am + dist-lzma dist-shar dist-tarZ dist-xz dist-zip distcheck \ + distclean distclean-generic distclean-tags distcleancheck \ + distdir distuninstallcheck dvi dvi-am html html-am info \ + info-am install install-am install-data install-data-am \ + install-dvi install-dvi-am install-exec install-exec-am \ + install-html install-html-am install-info install-info-am \ + install-man install-pdf install-pdf-am install-ps \ + install-ps-am install-strip installcheck installcheck-am \ + installdirs installdirs-am maintainer-clean \ + maintainer-clean-generic mostlyclean mostlyclean-generic pdf \ + pdf-am ps ps-am tags tags-recursive uninstall uninstall-am + # 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. diff --git a/binaries/src/clustalw/aclocal.m4 b/binaries/src/clustalw/aclocal.m4 index bdf7327..93e43cd 100644 --- a/binaries/src/clustalw/aclocal.m4 +++ b/binaries/src/clustalw/aclocal.m4 @@ -1,7 +1,7 @@ -# generated automatically by aclocal 1.10.2 -*- Autoconf -*- +# generated automatically by aclocal 1.11.1 -*- Autoconf -*- # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, -# 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +# 2005, 2006, 2007, 2008, 2009 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. @@ -13,8 +13,8 @@ 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. +m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.65],, +[m4_warning([this file was generated for autoconf 2.65. You have another version of autoconf. It may work, but is not guaranteed to. If you have problems, you may need to regenerate the build system entirely. To do so, use the procedure documented by the package, typically `autoreconf'.])]) @@ -31,10 +31,10 @@ To do so, use the procedure documented by the package, typically `autoreconf'.]) # generated from the m4 files accompanying Automake X.Y. # (This private macro should not be called outside this file.) AC_DEFUN([AM_AUTOMAKE_VERSION], -[am__api_version='1.10' +[am__api_version='1.11' dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to dnl require some minimum version. Point them to the right macro. -m4_if([$1], [1.10.2], [], +m4_if([$1], [1.11.1], [], [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl ]) @@ -50,7 +50,7 @@ m4_define([_AM_AUTOCONF_VERSION], []) # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced. # This function is AC_REQUIREd by AM_INIT_AUTOMAKE. AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION], -[AM_AUTOMAKE_VERSION([1.10.2])dnl +[AM_AUTOMAKE_VERSION([1.11.1])dnl m4_ifndef([AC_AUTOCONF_VERSION], [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))]) @@ -110,14 +110,14 @@ am_aux_dir=`cd $ac_aux_dir && pwd` # AM_CONDITIONAL -*- Autoconf -*- -# Copyright (C) 1997, 2000, 2001, 2003, 2004, 2005, 2006 +# Copyright (C) 1997, 2000, 2001, 2003, 2004, 2005, 2006, 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. -# serial 8 +# serial 9 # AM_CONDITIONAL(NAME, SHELL-CONDITION) # ------------------------------------- @@ -130,6 +130,7 @@ AC_SUBST([$1_TRUE])dnl AC_SUBST([$1_FALSE])dnl _AM_SUBST_NOTMAKE([$1_TRUE])dnl _AM_SUBST_NOTMAKE([$1_FALSE])dnl +m4_define([_AM_COND_VALUE_$1], [$2])dnl if $2; then $1_TRUE= $1_FALSE='#' @@ -143,14 +144,14 @@ AC_CONFIG_COMMANDS_PRE( Usually this means the macro was only invoked conditionally.]]) fi])]) -# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006 +# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2009 # 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. -# serial 9 +# serial 10 # There are a few dirty hacks below to avoid letting `AC_PROG_CC' be # written in clear, in which case automake, when reading aclocal.m4, @@ -207,6 +208,16 @@ AC_CACHE_CHECK([dependency style of $depcc], if test "$am_compiler_list" = ""; then am_compiler_list=`sed -n ['s/^#*\([a-zA-Z0-9]*\))$/\1/p'] < ./depcomp` fi + am__universal=false + m4_case([$1], [CC], + [case " $depcc " in #( + *\ -arch\ *\ -arch\ *) am__universal=true ;; + esac], + [CXX], + [case " $depcc " in #( + *\ -arch\ *\ -arch\ *) am__universal=true ;; + esac]) + 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 @@ -224,7 +235,17 @@ AC_CACHE_CHECK([dependency style of $depcc], done echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf + # 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. Also, some Intel + # versions had trouble with output in subdirs + am__obj=sub/conftest.${OBJEXT-o} + am__minus_obj="-o $am__obj" case $depmode in + gcc) + # This depmode causes a compiler race in universal mode. + test "$am__universal" = false || continue + ;; nosideeffect) # after this tag, mechanisms are not by side-effect, so they'll # only be used when explicitly requested @@ -234,19 +255,23 @@ AC_CACHE_CHECK([dependency style of $depcc], break fi ;; + msvisualcpp | msvcmsys) + # This compiler won't grok `-c -o', but also, the minuso test has + # not run yet. These depmodes are late enough in the game, and + # so weak that their functioning should not be impacted. + am__obj=conftest.${OBJEXT-o} + am__minus_obj= + ;; 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} \ + source=sub/conftest.c object=$am__obj \ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \ - $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \ + $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \ >/dev/null 2>conftest.err && grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 && grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 && - grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 && + grep $am__obj sub/conftest.Po > /dev/null 2>&1 && ${MAKE-make} -s -f confmf > /dev/null 2>&1; then # icc doesn't choke on unknown options, it will just issue warnings # or remarks (even with -Werror). So we grep stderr for any message @@ -396,13 +421,13 @@ AU_DEFUN([AM_CONFIG_HEADER], [AC_CONFIG_HEADERS($@)]) # Do all the work for Automake. -*- Autoconf -*- # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, -# 2005, 2006, 2008 Free Software Foundation, Inc. +# 2005, 2006, 2008, 2009 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. -# serial 13 +# serial 16 # This macro actually does too much. Some checks are only needed if # your package does certain things. But this isn't really a big deal. @@ -419,7 +444,7 @@ AU_DEFUN([AM_CONFIG_HEADER], [AC_CONFIG_HEADERS($@)]) # arguments mandatory, and then we can depend on a new Autoconf # release and drop the old call support. AC_DEFUN([AM_INIT_AUTOMAKE], -[AC_PREREQ([2.60])dnl +[AC_PREREQ([2.62])dnl dnl Autoconf wants to disallow AM_ names. We explicitly allow dnl the ones we care about. m4_pattern_allow([^AM_[A-Z]+FLAGS$])dnl @@ -470,8 +495,8 @@ AM_MISSING_PROG(AUTOCONF, autoconf) AM_MISSING_PROG(AUTOMAKE, automake-${am__api_version}) AM_MISSING_PROG(AUTOHEADER, autoheader) AM_MISSING_PROG(MAKEINFO, makeinfo) -AM_PROG_INSTALL_SH -AM_PROG_INSTALL_STRIP +AC_REQUIRE([AM_PROG_INSTALL_SH])dnl +AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl AC_REQUIRE([AM_PROG_MKDIR_P])dnl # We need awk for the "check" target. The system "awk" is bad on # some platforms. @@ -479,24 +504,37 @@ AC_REQUIRE([AC_PROG_AWK])dnl AC_REQUIRE([AC_PROG_MAKE_SET])dnl AC_REQUIRE([AM_SET_LEADING_DOT])dnl _AM_IF_OPTION([tar-ustar], [_AM_PROG_TAR([ustar])], - [_AM_IF_OPTION([tar-pax], [_AM_PROG_TAR([pax])], - [_AM_PROG_TAR([v7])])]) + [_AM_IF_OPTION([tar-pax], [_AM_PROG_TAR([pax])], + [_AM_PROG_TAR([v7])])]) _AM_IF_OPTION([no-dependencies],, [AC_PROVIDE_IFELSE([AC_PROG_CC], - [_AM_DEPENDENCIES(CC)], - [define([AC_PROG_CC], - defn([AC_PROG_CC])[_AM_DEPENDENCIES(CC)])])dnl + [_AM_DEPENDENCIES(CC)], + [define([AC_PROG_CC], + defn([AC_PROG_CC])[_AM_DEPENDENCIES(CC)])])dnl AC_PROVIDE_IFELSE([AC_PROG_CXX], - [_AM_DEPENDENCIES(CXX)], - [define([AC_PROG_CXX], - defn([AC_PROG_CXX])[_AM_DEPENDENCIES(CXX)])])dnl + [_AM_DEPENDENCIES(CXX)], + [define([AC_PROG_CXX], + defn([AC_PROG_CXX])[_AM_DEPENDENCIES(CXX)])])dnl AC_PROVIDE_IFELSE([AC_PROG_OBJC], - [_AM_DEPENDENCIES(OBJC)], - [define([AC_PROG_OBJC], - defn([AC_PROG_OBJC])[_AM_DEPENDENCIES(OBJC)])])dnl + [_AM_DEPENDENCIES(OBJC)], + [define([AC_PROG_OBJC], + defn([AC_PROG_OBJC])[_AM_DEPENDENCIES(OBJC)])])dnl ]) +_AM_IF_OPTION([silent-rules], [AC_REQUIRE([AM_SILENT_RULES])])dnl +dnl The `parallel-tests' driver may need to know about EXEEXT, so add the +dnl `am__EXEEXT' conditional if _AM_COMPILER_EXEEXT was seen. This macro +dnl is hooked onto _AC_COMPILER_EXEEXT early, see below. +AC_CONFIG_COMMANDS_PRE(dnl +[m4_provide_if([_AM_COMPILER_EXEEXT], + [AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl ]) +dnl Hook into `_AC_COMPILER_EXEEXT' early to learn its expansion. Do not +dnl add the conditional right here, as _AC_COMPILER_EXEEXT may be further +dnl mangled by Autoconf and run in a shell conditional statement. +m4_define([_AC_COMPILER_EXEEXT], +m4_defn([_AC_COMPILER_EXEEXT])[m4_provide([_AM_COMPILER_EXEEXT])]) + # When config.status generates a header, we must update the stamp-h file. # This file resides in the same directory as the config header @@ -519,7 +557,7 @@ for _am_header in $config_headers :; do done echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count]) -# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc. +# Copyright (C) 2001, 2003, 2005, 2008 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, @@ -530,7 +568,14 @@ echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_co # Define $install_sh. AC_DEFUN([AM_PROG_INSTALL_SH], [AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl -install_sh=${install_sh-"\$(SHELL) $am_aux_dir/install-sh"} +if test x"${install_sh}" != xset; then + case $am_aux_dir in + *\ * | *\ *) + install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;; + *) + install_sh="\${SHELL} $am_aux_dir/install-sh" + esac +fi AC_SUBST(install_sh)]) # Copyright (C) 2003, 2005 Free Software Foundation, Inc. @@ -556,13 +601,13 @@ AC_SUBST([am__leading_dot])]) # Check to see how 'make' treats includes. -*- Autoconf -*- -# Copyright (C) 2001, 2002, 2003, 2005 Free Software Foundation, Inc. +# Copyright (C) 2001, 2002, 2003, 2005, 2009 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. -# serial 3 +# serial 4 # AM_MAKE_INCLUDE() # ----------------- @@ -571,7 +616,7 @@ AC_DEFUN([AM_MAKE_INCLUDE], [am_make=${MAKE-make} cat > confinc << 'END' am__doit: - @echo done + @echo this is the am__doit target .PHONY: am__doit END # If we don't find an include directive, just comment out the code. @@ -581,24 +626,24 @@ 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 "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then - am__include=include - am__quote= - _am_result=GNU -fi +# Ignore all kinds of additional output from `make'. +case `$am_make -s -f confmf 2> /dev/null` in #( +*the\ am__doit\ target*) + am__include=include + am__quote= + _am_result=GNU + ;; +esac # 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 + case `$am_make -s -f confmf 2> /dev/null` in #( + *the\ am__doit\ target*) + am__include=.include + am__quote="\"" + _am_result=BSD + ;; + esac fi AC_SUBST([am__include]) AC_SUBST([am__quote]) @@ -608,14 +653,14 @@ rm -f confinc confmf # Fake the existence of programs that GNU maintainers use. -*- Autoconf -*- -# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005 +# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005, 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. -# serial 5 +# serial 6 # AM_MISSING_PROG(NAME, PROGRAM) # ------------------------------ @@ -632,7 +677,14 @@ AC_SUBST($1)]) AC_DEFUN([AM_MISSING_HAS_RUN], [AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl AC_REQUIRE_AUX_FILE([missing])dnl -test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing" +if test x"${MISSING+set}" != xset; then + case $am_aux_dir in + *\ * | *\ *) + MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;; + *) + MISSING="\${SHELL} $am_aux_dir/missing" ;; + esac +fi # Use eval to expand $SHELL if eval "$MISSING --run true"; then am_missing_run="$MISSING --run " @@ -703,14 +755,14 @@ AC_DEFUN([_AM_IF_OPTION], # Check to make sure that the build environment is sane. -*- Autoconf -*- -# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005 +# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005, 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. -# serial 4 +# serial 5 # AM_SANITY_CHECK # --------------- @@ -719,16 +771,29 @@ AC_DEFUN([AM_SANITY_CHECK], # Just in case sleep 1 echo timestamp > conftest.file +# Reject unsafe characters in $srcdir or the absolute working directory +# name. Accept space and tab only in the latter. +am_lf=' +' +case `pwd` in + *[[\\\"\#\$\&\'\`$am_lf]]*) + AC_MSG_ERROR([unsafe absolute working directory name]);; +esac +case $srcdir in + *[[\\\"\#\$\&\'\`$am_lf\ \ ]]*) + AC_MSG_ERROR([unsafe srcdir value: `$srcdir']);; +esac + # Do `set' in a subshell so we don't clobber the current shell's # arguments. Must try -L first in case configure is actually a # symlink; some systems play weird games with the mod time of symlinks # (eg FreeBSD returns the mod time of the symlink's containing # directory). if ( - set X `ls -Lt $srcdir/configure conftest.file 2> /dev/null` + set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null` if test "$[*]" = "X"; then # -L didn't work. - set X `ls -t $srcdir/configure conftest.file` + set X `ls -t "$srcdir/configure" conftest.file` fi rm -f conftest.file if test "$[*]" != "X $srcdir/configure conftest.file" \ @@ -781,18 +846,25 @@ fi INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s" AC_SUBST([INSTALL_STRIP_PROGRAM])]) -# Copyright (C) 2006 Free Software Foundation, Inc. +# Copyright (C) 2006, 2008 Free Software Foundation, Inc. # # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. +# serial 2 + # _AM_SUBST_NOTMAKE(VARIABLE) # --------------------------- # Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in. # This macro is traced by Automake. AC_DEFUN([_AM_SUBST_NOTMAKE]) +# AM_SUBST_NOTMAKE(VARIABLE) +# --------------------------- +# Public sister of _AM_SUBST_NOTMAKE. +AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)]) + # Check how to create a tarball. -*- Autoconf -*- # Copyright (C) 2004, 2005 Free Software Foundation, Inc. diff --git a/binaries/src/clustalw/clustalw_help b/binaries/src/clustalw/clustalw_help index 25c5483..5c2c251 100644 --- a/binaries/src/clustalw/clustalw_help +++ b/binaries/src/clustalw/clustalw_help @@ -1,7 +1,7 @@ - CLUSTAL 2.0.12 Multiple Sequence Alignments + CLUSTAL 2.1 Multiple Sequence Alignments @@ -44,7 +44,7 @@ -STATS=file :Log some alignents statistics to file ->> HELP 1 << General help for CLUSTAL W (2.0.12) +>> HELP 1 << General help for CLUSTAL W (2.1) Clustal W is a general purpose multiple alignment program for DNA or proteins. @@ -273,7 +273,7 @@ meaningful. >> HELP 5 << Help for output format options. -Six output formats are offered. You can choose any (or all 6 if you wish). +Several output formats are offered. You can choose any (or all 6 if you wish). CLUSTAL format output is a self explanatory alignment format. It shows the sequences aligned in blocks. It can be read in again at a later date to @@ -284,6 +284,9 @@ GCG output can be used by any of the GCG programs that can work on multiple alignments (e.g. PRETTY, PROFILEMAKE, PLOTALIGN). It is the same as the GCG .msf format files (multiple sequence file); new in version 7 of GCG. +Fasta output cis widely used because of it's simplicity. Each sequence name is +preceeded by a '>'-sign. The sequence itself is printed out in the following lines + PHYLIP format output can be used for input to the PHYLIP package of Joe Felsenstein. This is an extremely widely used package for doing every imaginable form of phylogenetic analysis (MUCH more than the the modest intro- @@ -587,7 +590,7 @@ the minimum score over the whole matrix. -TYPE= :PROTEIN or DNA sequences -NEGATIVE :protein alignment with negative values in matrix -OUTFILE= :sequence alignment file name --OUTPUT= :GCG, GDE, PHYLIP, PIR or NEXUS +-OUTPUT= :CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTA -OUTORDER= :INPUT or ALIGNED -CASE :LOWER or UPPER (for GDE output only) -SEQNOS= :OFF or ON (for Clustal output only) diff --git a/binaries/src/clustalw/config.guess b/binaries/src/clustalw/config.guess index f32079a..e3a2116 100644 --- a/binaries/src/clustalw/config.guess +++ b/binaries/src/clustalw/config.guess @@ -1,10 +1,10 @@ #! /bin/sh # Attempt to guess a canonical system name. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, -# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 +# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 # Free Software Foundation, Inc. -timestamp='2008-01-23' +timestamp='2009-06-10' # 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 @@ -170,7 +170,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in arm*|i386|m68k|ns32k|sh3*|sparc|vax) eval $set_cc_for_build if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ - | grep __ELF__ >/dev/null + | grep -q __ELF__ then # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). # Return netbsd for either. FIX? @@ -324,6 +324,9 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in case `/usr/bin/uname -p` in sparc) echo sparc-icl-nx7; exit ;; esac ;; + s390x:SunOS:*:*) + echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; sun4H:SunOS:5.*:*) echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; @@ -331,7 +334,20 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in 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/[^.]*//'` + eval $set_cc_for_build + SUN_ARCH="i386" + # If there is a compiler, see if it is configured for 64-bit objects. + # Note that the Sun cc does not turn __LP64__ into 1 like gcc does. + # This test works for both compilers. + if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then + if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + SUN_ARCH="x86_64" + fi + fi + echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:6*:*) # According to config.sub, this is the proper way to canonicalize @@ -640,7 +656,7 @@ EOF # => hppa64-hp-hpux11.23 if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | - grep __LP64__ >/dev/null + grep -q __LP64__ then HP_ARCH="hppa2.0w" else @@ -796,7 +812,7 @@ EOF x86) echo i586-pc-interix${UNAME_RELEASE} exit ;; - EM64T | authenticamd) + EM64T | authenticamd | genuineintel) echo x86_64-unknown-interix${UNAME_RELEASE} exit ;; IA64) @@ -806,6 +822,9 @@ EOF [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) echo i${UNAME_MACHINE}-pc-mks exit ;; + 8664:Windows_NT:*) + echo x86_64-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 @@ -866,40 +885,17 @@ EOF m68*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; - mips:Linux:*:*) + mips:Linux:*:* | mips64:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU - #undef mips - #undef mipsel + #undef ${UNAME_MACHINE} + #undef ${UNAME_MACHINE}el #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) - CPU=mipsel + CPU=${UNAME_MACHINE}el #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 + CPU=${UNAME_MACHINE} #else CPU= #endif @@ -931,10 +927,13 @@ EOF EV67) UNAME_MACHINE=alphaev67 ;; EV68*) UNAME_MACHINE=alphaev68 ;; esac - objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null + objdump --private-headers /bin/sh | grep -q ld.so.1 if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} exit ;; + padre:Linux:*:*) + echo sparc-unknown-linux-gnu + exit ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in @@ -982,17 +981,6 @@ EOF 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 @@ -1058,7 +1046,7 @@ EOF i*86:syllable:*:*) echo ${UNAME_MACHINE}-pc-syllable exit ;; - i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*) + i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*) echo i386-unknown-lynxos${UNAME_RELEASE} exit ;; i*86:*DOS:*:*) @@ -1102,8 +1090,11 @@ EOF 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 + # the processor, so we play safe by assuming i586. + # Note: whatever this is, it MUST be the same as what config.sub + # prints for the "djgpp" host, or else GDB configury will decide that + # this is a cross-build. + echo i586-pc-msdosdjgpp exit ;; Intel:Mach:3*:*) echo i386-pc-mach3 @@ -1141,6 +1132,16 @@ EOF 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4; exit; } ;; + NCR*:*:4.2:* | MPRAS*:*:4.2:*) + OS_REL='.3' + 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; } + /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ + && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) echo m68k-unknown-lynxos${UNAME_RELEASE} exit ;; @@ -1153,7 +1154,7 @@ EOF rs6000:LynxOS:2.*:*) echo rs6000-unknown-lynxos${UNAME_RELEASE} exit ;; - PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) + PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*) echo powerpc-unknown-lynxos${UNAME_RELEASE} exit ;; SM[BE]S:UNIX_SV:*:*) @@ -1216,6 +1217,9 @@ EOF BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit ;; + BePC:Haiku:*:*) # Haiku running on Intel PC compatible. + echo i586-pc-haiku + exit ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit ;; @@ -1324,6 +1328,9 @@ EOF i*86:rdos:*:*) echo ${UNAME_MACHINE}-pc-rdos exit ;; + i*86:AROS:*:*) + echo ${UNAME_MACHINE}-pc-aros + exit ;; esac #echo '(No uname command or uname output not recognized.)' 1>&2 diff --git a/binaries/src/clustalw/config.log b/binaries/src/clustalw/config.log new file mode 100644 index 0000000..e1bdd03 --- /dev/null +++ b/binaries/src/clustalw/config.log @@ -0,0 +1,643 @@ +This file contains any messages produced by compilers while +running configure, to aid debugging if configure makes a mistake. + +It was created by clustalw configure 2.1, which was +generated by GNU Autoconf 2.65. Invocation command line was + + $ ./configure + +## --------- ## +## Platform. ## +## --------- ## + +hostname = ningal.cluster.lifesci.dundee.ac.uk +uname -m = x86_64 +uname -r = 2.6.32-642.6.1.el6.x86_64 +uname -s = Linux +uname -v = #1 SMP Wed Oct 5 00:36:12 UTC 2016 + +/usr/bin/uname -p = unknown +/bin/uname -X = unknown + +/bin/arch = x86_64 +/usr/bin/arch -k = unknown +/usr/convex/getsysinfo = unknown +/usr/bin/hostinfo = unknown +/bin/machine = unknown +/usr/bin/oslevel = unknown +/bin/universe = unknown + +PATH: /gridware/sge/bin/lx-amd64 +PATH: /homes/fmmarquesmadeira/.local/anaconda/envs/python3/bin +PATH: /gridware/sge/bin/lx-amd64 +PATH: /usr/lib64/qt-3.3/bin +PATH: /usr/local/bin +PATH: /bin +PATH: /usr/bin +PATH: /usr/local/sbin +PATH: /usr/sbin +PATH: /sbin +PATH: /opt/dell/srvadmin/bin +PATH: /homes/fmmarquesmadeira/.local/anaconda/bin +PATH: /homes/fmmarquesmadeira/.local/bin/stamp4.4.2/bin/linux +PATH: /homes/fmmarquesmadeira/.local/bin/mustang3.2.2/bin +PATH: /homes/fmmarquesmadeira/.local/bin/mafft7.273/bin +PATH: /homes/fmmarquesmadeira/.local/bin/foldx_Linux/bin +PATH: /homes/fmmarquesmadeira/NOBACK/lib/oxbench_1_3//bin +PATH: /homes/fmmarquesmadeira/.local/bin/Intellij/bin + + +## ----------- ## +## Core tests. ## +## ----------- ## + +configure:2211: checking build system type +configure:2225: result: x86_64-unknown-linux-gnu +configure:2245: checking host system type +configure:2258: result: x86_64-unknown-linux-gnu +configure:2278: checking target system type +configure:2291: result: x86_64-unknown-linux-gnu +configure:2377: checking for a BSD-compatible install +configure:2445: result: /usr/bin/install -c +configure:2456: checking whether build environment is sane +configure:2506: result: yes +configure:2647: checking for a thread-safe mkdir -p +configure:2686: result: /bin/mkdir -p +configure:2699: checking for gawk +configure:2715: found /bin/gawk +configure:2726: result: gawk +configure:2737: checking whether make sets $(MAKE) +configure:2759: result: yes +configure:2840: checking whether make sets $(MAKE) +configure:2862: result: yes +configure:2922: checking for gcc +configure:2938: found /usr/bin/gcc +configure:2949: result: gcc +configure:3178: checking for C compiler version +configure:3187: gcc --version >&5 +gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17) +Copyright (C) 2010 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. + +configure:3198: $? = 0 +configure:3187: gcc -v >&5 +Using built-in specs. +Target: x86_64-redhat-linux +Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux +Thread model: posix +gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC) +configure:3198: $? = 0 +configure:3187: gcc -V >&5 +gcc: '-V' option must have argument +configure:3198: $? = 1 +configure:3187: gcc -qversion >&5 +gcc: unrecognized option '-qversion' +gcc: no input files +configure:3198: $? = 1 +configure:3218: checking whether the C compiler works +configure:3240: gcc conftest.c >&5 +configure:3244: $? = 0 +configure:3293: result: yes +configure:3296: checking for C compiler default output file name +configure:3298: result: a.out +configure:3304: checking for suffix of executables +configure:3311: gcc -o conftest conftest.c >&5 +configure:3315: $? = 0 +configure:3337: result: +configure:3359: checking whether we are cross compiling +configure:3367: gcc -o conftest conftest.c >&5 +configure:3371: $? = 0 +configure:3378: ./conftest +configure:3382: $? = 0 +configure:3397: result: no +configure:3402: checking for suffix of object files +configure:3424: gcc -c conftest.c >&5 +configure:3428: $? = 0 +configure:3449: result: o +configure:3453: checking whether we are using the GNU C compiler +configure:3472: gcc -c conftest.c >&5 +configure:3472: $? = 0 +configure:3481: result: yes +configure:3490: checking whether gcc accepts -g +configure:3510: gcc -c -g conftest.c >&5 +configure:3510: $? = 0 +configure:3551: result: yes +configure:3568: checking for gcc option to accept ISO C89 +configure:3632: gcc -c -g -O2 conftest.c >&5 +configure:3632: $? = 0 +configure:3645: result: none needed +configure:3676: checking for style of include used by make +configure:3704: result: GNU +configure:3729: checking dependency style of gcc +configure:3839: result: gcc3 +configure:3912: checking for g++ +configure:3928: found /usr/bin/g++ +configure:3939: result: g++ +configure:3966: checking for C++ compiler version +configure:3975: g++ --version >&5 +g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17) +Copyright (C) 2010 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. + +configure:3986: $? = 0 +configure:3975: g++ -v >&5 +Using built-in specs. +Target: x86_64-redhat-linux +Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux +Thread model: posix +gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC) +configure:3986: $? = 0 +configure:3975: g++ -V >&5 +g++: '-V' option must have argument +configure:3986: $? = 1 +configure:3975: g++ -qversion >&5 +g++: unrecognized option '-qversion' +g++: no input files +configure:3986: $? = 1 +configure:3990: checking whether we are using the GNU C++ compiler +configure:4009: g++ -c conftest.cpp >&5 +configure:4009: $? = 0 +configure:4018: result: yes +configure:4027: checking whether g++ accepts -g +configure:4047: g++ -c -g conftest.cpp >&5 +configure:4047: $? = 0 +configure:4088: result: yes +configure:4113: checking dependency style of g++ +configure:4223: result: gcc3 +configure:4284: checking for ranlib +configure:4300: found /usr/bin/ranlib +configure:4311: result: ranlib +configure:4353: checking how to run the C++ preprocessor +configure:4380: g++ -E conftest.cpp +configure:4380: $? = 0 +configure:4394: g++ -E conftest.cpp +conftest.cpp:12:28: error: ac_nonexistent.h: No such file or directory +configure:4394: $? = 1 +configure: failed program was: +| /* confdefs.h */ +| #define PACKAGE_NAME "clustalw" +| #define PACKAGE_TARNAME "clustalw" +| #define PACKAGE_VERSION "2.1" +| #define PACKAGE_STRING "clustalw 2.1" +| #define PACKAGE_BUGREPORT "clustalw@ucd.ie" +| #define PACKAGE_URL "" +| #define OS_UNIX 1 +| #define PACKAGE "clustalw" +| #define VERSION "2.1" +| /* end confdefs.h. */ +| #include +configure:4419: result: g++ -E +configure:4439: g++ -E conftest.cpp +configure:4439: $? = 0 +configure:4453: g++ -E conftest.cpp +conftest.cpp:12:28: error: ac_nonexistent.h: No such file or directory +configure:4453: $? = 1 +configure: failed program was: +| /* confdefs.h */ +| #define PACKAGE_NAME "clustalw" +| #define PACKAGE_TARNAME "clustalw" +| #define PACKAGE_VERSION "2.1" +| #define PACKAGE_STRING "clustalw 2.1" +| #define PACKAGE_BUGREPORT "clustalw@ucd.ie" +| #define PACKAGE_URL "" +| #define OS_UNIX 1 +| #define PACKAGE "clustalw" +| #define VERSION "2.1" +| /* end confdefs.h. */ +| #include +configure:4482: checking for grep that handles long lines and -e +configure:4540: result: /bin/grep +configure:4545: checking for egrep +configure:4607: result: /bin/grep -E +configure:4612: checking for ANSI C header files +configure:4632: g++ -c -g -O2 conftest.cpp >&5 +configure:4632: $? = 0 +configure:4705: g++ -o conftest -g -O2 conftest.cpp >&5 +configure:4705: $? = 0 +configure:4705: ./conftest +configure:4705: $? = 0 +configure:4716: result: yes +configure:4732: checking for sys/types.h +configure:4732: g++ -c -g -O2 conftest.cpp >&5 +configure:4732: $? = 0 +configure:4732: result: yes +configure:4732: checking for sys/stat.h +configure:4732: g++ -c -g -O2 conftest.cpp >&5 +configure:4732: $? = 0 +configure:4732: result: yes +configure:4732: checking for stdlib.h +configure:4732: g++ -c -g -O2 conftest.cpp >&5 +configure:4732: $? = 0 +configure:4732: result: yes +configure:4732: checking for string.h +configure:4732: g++ -c -g -O2 conftest.cpp >&5 +configure:4732: $? = 0 +configure:4732: result: yes +configure:4732: checking for memory.h +configure:4732: g++ -c -g -O2 conftest.cpp >&5 +configure:4732: $? = 0 +configure:4732: result: yes +configure:4732: checking for strings.h +configure:4732: g++ -c -g -O2 conftest.cpp >&5 +configure:4732: $? = 0 +configure:4732: result: yes +configure:4732: checking for inttypes.h +configure:4732: g++ -c -g -O2 conftest.cpp >&5 +configure:4732: $? = 0 +configure:4732: result: yes +configure:4732: checking for stdint.h +configure:4732: g++ -c -g -O2 conftest.cpp >&5 +configure:4732: $? = 0 +configure:4732: result: yes +configure:4732: checking for unistd.h +configure:4732: g++ -c -g -O2 conftest.cpp >&5 +configure:4732: $? = 0 +configure:4732: result: yes +configure:4745: checking for stdbool.h that conforms to C99 +configure:4830: g++ -c -g -O2 conftest.cpp >&5 +configure:4830: $? = 0 +configure:4837: result: yes +configure:4839: checking for _Bool +configure:4839: g++ -c -g -O2 conftest.cpp >&5 +conftest.cpp: In function 'int main()': +conftest.cpp:58: error: '_Bool' was not declared in this scope +configure:4839: $? = 1 +configure: failed program was: +| /* confdefs.h */ +| #define PACKAGE_NAME "clustalw" +| #define PACKAGE_TARNAME "clustalw" +| #define PACKAGE_VERSION "2.1" +| #define PACKAGE_STRING "clustalw 2.1" +| #define PACKAGE_BUGREPORT "clustalw@ucd.ie" +| #define PACKAGE_URL "" +| #define OS_UNIX 1 +| #define PACKAGE "clustalw" +| #define VERSION "2.1" +| #define STDC_HEADERS 1 +| #define HAVE_SYS_TYPES_H 1 +| #define HAVE_SYS_STAT_H 1 +| #define HAVE_STDLIB_H 1 +| #define HAVE_STRING_H 1 +| #define HAVE_MEMORY_H 1 +| #define HAVE_STRINGS_H 1 +| #define HAVE_INTTYPES_H 1 +| #define HAVE_STDINT_H 1 +| #define HAVE_UNISTD_H 1 +| /* end confdefs.h. */ +| #include +| #ifdef HAVE_SYS_TYPES_H +| # include +| #endif +| #ifdef HAVE_SYS_STAT_H +| # include +| #endif +| #ifdef STDC_HEADERS +| # include +| # include +| #else +| # ifdef HAVE_STDLIB_H +| # include +| # endif +| #endif +| #ifdef HAVE_STRING_H +| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H +| # include +| # endif +| # include +| #endif +| #ifdef HAVE_STRINGS_H +| # include +| #endif +| #ifdef HAVE_INTTYPES_H +| # include +| #endif +| #ifdef HAVE_STDINT_H +| # include +| #endif +| #ifdef HAVE_UNISTD_H +| # include +| #endif +| int +| main () +| { +| if (sizeof (_Bool)) +| return 0; +| ; +| return 0; +| } +configure:4839: result: no +configure:4855: checking for an ANSI C-conforming const +configure:4920: g++ -c -g -O2 conftest.cpp >&5 +configure:4920: $? = 0 +configure:4927: result: yes +configure:4935: checking for size_t +configure:4935: g++ -c -g -O2 conftest.cpp >&5 +configure:4935: $? = 0 +configure:4935: g++ -c -g -O2 conftest.cpp >&5 +conftest.cpp: In function 'int main()': +conftest.cpp:59: error: expected primary-expression before ')' token +configure:4935: $? = 1 +configure: failed program was: +| /* confdefs.h */ +| #define PACKAGE_NAME "clustalw" +| #define PACKAGE_TARNAME "clustalw" +| #define PACKAGE_VERSION "2.1" +| #define PACKAGE_STRING "clustalw 2.1" +| #define PACKAGE_BUGREPORT "clustalw@ucd.ie" +| #define PACKAGE_URL "" +| #define OS_UNIX 1 +| #define PACKAGE "clustalw" +| #define VERSION "2.1" +| #define STDC_HEADERS 1 +| #define HAVE_SYS_TYPES_H 1 +| #define HAVE_SYS_STAT_H 1 +| #define HAVE_STDLIB_H 1 +| #define HAVE_STRING_H 1 +| #define HAVE_MEMORY_H 1 +| #define HAVE_STRINGS_H 1 +| #define HAVE_INTTYPES_H 1 +| #define HAVE_STDINT_H 1 +| #define HAVE_UNISTD_H 1 +| #define HAVE_STDBOOL_H 1 +| /* end confdefs.h. */ +| #include +| #ifdef HAVE_SYS_TYPES_H +| # include +| #endif +| #ifdef HAVE_SYS_STAT_H +| # include +| #endif +| #ifdef STDC_HEADERS +| # include +| # include +| #else +| # ifdef HAVE_STDLIB_H +| # include +| # endif +| #endif +| #ifdef HAVE_STRING_H +| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H +| # include +| # endif +| # include +| #endif +| #ifdef HAVE_STRINGS_H +| # include +| #endif +| #ifdef HAVE_INTTYPES_H +| # include +| #endif +| #ifdef HAVE_STDINT_H +| # include +| #endif +| #ifdef HAVE_UNISTD_H +| # include +| #endif +| int +| main () +| { +| if (sizeof ((size_t))) +| return 0; +| ; +| return 0; +| } +configure:4935: result: yes +configure:4961: checking for stdlib.h +configure:4961: result: yes +configure:4971: checking for GNU libc compatible malloc +configure:4995: g++ -o conftest -g -O2 conftest.cpp >&5 +configure:4995: $? = 0 +configure:4995: ./conftest +configure:4995: $? = 0 +configure:5005: result: yes +configure:5229: creating ./config.status + +## ---------------------- ## +## Running config.status. ## +## ---------------------- ## + +This file was extended by clustalw config.status 2.1, which was +generated by GNU Autoconf 2.65. Invocation command line was + + CONFIG_FILES = + CONFIG_HEADERS = + CONFIG_LINKS = + CONFIG_COMMANDS = + $ ./config.status + +on ningal.cluster.lifesci.dundee.ac.uk + +config.status:878: creating Makefile +config.status:878: creating m4/Makefile +config.status:878: creating src/Makefile +config.status:878: creating src/clustalw_version.h +config.status:878: creating src/config.h +config.status:1050: src/config.h is unchanged +config.status:1098: executing depfiles commands + +## ---------------- ## +## Cache variables. ## +## ---------------- ## + +ac_cv_build=x86_64-unknown-linux-gnu +ac_cv_c_compiler_gnu=yes +ac_cv_c_const=yes +ac_cv_cxx_compiler_gnu=yes +ac_cv_env_CCC_set= +ac_cv_env_CCC_value= +ac_cv_env_CC_set= +ac_cv_env_CC_value= +ac_cv_env_CFLAGS_set= +ac_cv_env_CFLAGS_value= +ac_cv_env_CPPFLAGS_set= +ac_cv_env_CPPFLAGS_value= +ac_cv_env_CXXCPP_set= +ac_cv_env_CXXCPP_value= +ac_cv_env_CXXFLAGS_set= +ac_cv_env_CXXFLAGS_value= +ac_cv_env_CXX_set= +ac_cv_env_CXX_value= +ac_cv_env_LDFLAGS_set= +ac_cv_env_LDFLAGS_value= +ac_cv_env_LIBS_set= +ac_cv_env_LIBS_value= +ac_cv_env_build_alias_set= +ac_cv_env_build_alias_value= +ac_cv_env_host_alias_set= +ac_cv_env_host_alias_value= +ac_cv_env_target_alias_set= +ac_cv_env_target_alias_value= +ac_cv_func_malloc_0_nonnull=yes +ac_cv_header_inttypes_h=yes +ac_cv_header_memory_h=yes +ac_cv_header_stdbool_h=yes +ac_cv_header_stdc=yes +ac_cv_header_stdint_h=yes +ac_cv_header_stdlib_h=yes +ac_cv_header_string_h=yes +ac_cv_header_strings_h=yes +ac_cv_header_sys_stat_h=yes +ac_cv_header_sys_types_h=yes +ac_cv_header_unistd_h=yes +ac_cv_host=x86_64-unknown-linux-gnu +ac_cv_objext=o +ac_cv_path_EGREP='/bin/grep -E' +ac_cv_path_GREP=/bin/grep +ac_cv_path_install='/usr/bin/install -c' +ac_cv_path_mkdir=/bin/mkdir +ac_cv_prog_AWK=gawk +ac_cv_prog_CXXCPP='g++ -E' +ac_cv_prog_ac_ct_CC=gcc +ac_cv_prog_ac_ct_CXX=g++ +ac_cv_prog_ac_ct_RANLIB=ranlib +ac_cv_prog_cc_c89= +ac_cv_prog_cc_g=yes +ac_cv_prog_cxx_g=yes +ac_cv_prog_make_make_set=yes +ac_cv_target=x86_64-unknown-linux-gnu +ac_cv_type__Bool=no +ac_cv_type_size_t=yes +am_cv_CC_dependencies_compiler_type=gcc3 +am_cv_CXX_dependencies_compiler_type=gcc3 + +## ----------------- ## +## Output variables. ## +## ----------------- ## + +ACLOCAL='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run aclocal-1.11' +AMDEPBACKSLASH='\' +AMDEP_FALSE='#' +AMDEP_TRUE='' +AMTAR='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run tar' +AUTOCONF='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoconf' +AUTOHEADER='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoheader' +AUTOMAKE='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run automake-1.11' +AWK='gawk' +CC='gcc' +CCDEPMODE='depmode=gcc3' +CFLAGS='-g -O2' +CLUSTALW_NAME='ClustalW' +CLUSTALW_VERSION='2.1' +CPPFLAGS='' +CXX='g++' +CXXCPP='g++ -E' +CXXDEPMODE='depmode=gcc3' +CXXFLAGS='-g -O2' +CYGPATH_W='echo' +DEFS='-DHAVE_CONFIG_H' +DEPDIR='.deps' +ECHO_C='' +ECHO_N='-n' +ECHO_T='' +EGREP='/bin/grep -E' +EXEEXT='' +GREP='/bin/grep' +INSTALL_DATA='${INSTALL} -m 644' +INSTALL_PROGRAM='${INSTALL}' +INSTALL_SCRIPT='${INSTALL}' +INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' +LDFLAGS='' +LIBOBJS='' +LIBS='' +LTLIBOBJS='' +MAKEINFO='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run makeinfo' +MKDIR_P='/bin/mkdir -p' +OBJEXT='o' +PACKAGE='clustalw' +PACKAGE_BUGREPORT='clustalw@ucd.ie' +PACKAGE_NAME='clustalw' +PACKAGE_STRING='clustalw 2.1' +PACKAGE_TARNAME='clustalw' +PACKAGE_URL='' +PACKAGE_VERSION='2.1' +PATH_SEPARATOR=':' +RANLIB='ranlib' +SET_MAKE='' +SHELL='/bin/sh' +STRIP='' +VERSION='2.1' +ac_ct_CC='gcc' +ac_ct_CXX='g++' +am__EXEEXT_FALSE='' +am__EXEEXT_TRUE='#' +am__fastdepCC_FALSE='#' +am__fastdepCC_TRUE='' +am__fastdepCXX_FALSE='#' +am__fastdepCXX_TRUE='' +am__include='include' +am__isrc='' +am__leading_dot='.' +am__quote='' +am__tar='${AMTAR} chof - "$$tardir"' +am__untar='${AMTAR} xf -' +bindir='${exec_prefix}/bin' +build='x86_64-unknown-linux-gnu' +build_alias='' +build_cpu='x86_64' +build_os='linux-gnu' +build_vendor='unknown' +datadir='${datarootdir}' +datarootdir='${prefix}/share' +docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' +dvidir='${docdir}' +exec_prefix='${prefix}' +host='x86_64-unknown-linux-gnu' +host_alias='' +host_cpu='x86_64' +host_os='linux-gnu' +host_vendor='unknown' +htmldir='${docdir}' +includedir='${prefix}/include' +infodir='${datarootdir}/info' +install_sh='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/install-sh' +libdir='${exec_prefix}/lib' +libexecdir='${exec_prefix}/libexec' +localedir='${datarootdir}/locale' +localstatedir='${prefix}/var' +mandir='${datarootdir}/man' +mkdir_p='/bin/mkdir -p' +oldincludedir='/usr/include' +pdfdir='${docdir}' +prefix='/usr/local' +program_transform_name='s,x,x,' +psdir='${docdir}' +sbindir='${exec_prefix}/sbin' +sharedstatedir='${prefix}/com' +sysconfdir='${prefix}/etc' +target='x86_64-unknown-linux-gnu' +target_alias='' +target_cpu='x86_64' +target_os='linux-gnu' +target_vendor='unknown' + +## ----------- ## +## confdefs.h. ## +## ----------- ## + +/* confdefs.h */ +#define PACKAGE_NAME "clustalw" +#define PACKAGE_TARNAME "clustalw" +#define PACKAGE_VERSION "2.1" +#define PACKAGE_STRING "clustalw 2.1" +#define PACKAGE_BUGREPORT "clustalw@ucd.ie" +#define PACKAGE_URL "" +#define OS_UNIX 1 +#define PACKAGE "clustalw" +#define VERSION "2.1" +#define STDC_HEADERS 1 +#define HAVE_SYS_TYPES_H 1 +#define HAVE_SYS_STAT_H 1 +#define HAVE_STDLIB_H 1 +#define HAVE_STRING_H 1 +#define HAVE_MEMORY_H 1 +#define HAVE_STRINGS_H 1 +#define HAVE_INTTYPES_H 1 +#define HAVE_STDINT_H 1 +#define HAVE_UNISTD_H 1 +#define HAVE_STDBOOL_H 1 +#define HAVE_STDLIB_H 1 +#define HAVE_MALLOC 1 + +configure: exit 0 diff --git a/binaries/src/clustalw/config.status b/binaries/src/clustalw/config.status index 003ff2a..353ba92 100644 --- a/binaries/src/clustalw/config.status +++ b/binaries/src/clustalw/config.status @@ -7,14 +7,16 @@ debug=false ac_cs_recheck=false ac_cs_silent=false + SHELL=${CONFIG_SHELL-/bin/sh} -## --------------------- ## -## M4sh Initialization. ## -## --------------------- ## +export SHELL +## -------------------- ## +## M4sh Initialization. ## +## -------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which @@ -22,23 +24,15 @@ if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else - case `(set -o) 2>/dev/null` in - *posix*) set -o posix ;; + 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 @@ -46,7 +40,13 @@ export as_nl 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 +# Prefer a ksh shell builtin over an external printf program on Solaris, +# but without wasting forks for bash or zsh. +if test -z "$BASH_VERSION$ZSH_VERSION" \ + && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='print -r --' + as_echo_n='print -rn --' +elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='printf %s\n' as_echo_n='printf %s' else @@ -57,7 +57,7 @@ else as_echo_body='eval expr "X$1" : "X\\(.*\\)"' as_echo_n_body='eval arg=$1; - case $arg in + case $arg in #( *"$as_nl"*) expr "X$arg" : "X\\(.*\\)$as_nl"; arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; @@ -80,13 +80,6 @@ if test "${PATH_SEPARATOR+set}" != set; then } 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. Quoting is @@ -96,15 +89,15 @@ fi IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. -case $0 in +case $0 in #(( *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break -done + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break + done IFS=$as_save_IFS ;; @@ -116,12 +109,16 @@ if test "x$as_myself" = x; then fi if test ! -f "$as_myself"; then $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 - { (exit 1); exit 1; } + exit 1 fi -# Work around bugs in pre-3.0 UWIN ksh. -for as_var in ENV MAIL MAILPATH -do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var +# Unset variables that we do not need and which cause bugs (e.g. in +# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" +# suppresses any "Segmentation fault" message there. '((' could +# trigger a bug in pdksh 5.2.14. +for as_var in BASH_ENV ENV MAIL MAILPATH +do eval test x\${$as_var+set} = xset \ + && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : done PS1='$ ' PS2='> ' @@ -133,7 +130,89 @@ export LC_ALL LANGUAGE=C export LANGUAGE -# Required to use basename. +# CDPATH. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + + +# as_fn_error ERROR [LINENO LOG_FD] +# --------------------------------- +# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are +# provided, also output the error to LOG_FD, referencing LINENO. Then exit the +# script with status $?, using 1 if that was 0. +as_fn_error () +{ + as_status=$?; test $as_status -eq 0 && as_status=1 + if test "$3"; then + as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3 + fi + $as_echo "$as_me: error: $1" >&2 + as_fn_exit $as_status +} # as_fn_error + + +# as_fn_set_status STATUS +# ----------------------- +# Set $? to STATUS, without forking. +as_fn_set_status () +{ + return $1 +} # as_fn_set_status + +# as_fn_exit STATUS +# ----------------- +# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. +as_fn_exit () +{ + set +e + as_fn_set_status $1 + exit $1 +} # as_fn_exit + +# as_fn_unset VAR +# --------------- +# Portably unset VAR. +as_fn_unset () +{ + { eval $1=; unset $1;} +} +as_unset=as_fn_unset +# as_fn_append VAR VALUE +# ---------------------- +# Append the text in VALUE to the end of the definition contained in VAR. Take +# advantage of any shell optimizations that allow amortized linear growth over +# repeated appends, instead of the typical quadratic growth present in naive +# implementations. +if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : + eval 'as_fn_append () + { + eval $1+=\$2 + }' +else + as_fn_append () + { + eval $1=\$$1\$2 + } +fi # as_fn_append + +# as_fn_arith ARG... +# ------------------ +# Perform arithmetic evaluation on the ARGs, and store the result in the +# global $as_val. Take advantage of shells that can avoid forks. The arguments +# must be portable across $(()) and expr. +if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : + eval 'as_fn_arith () + { + as_val=$(( $* )) + }' +else + as_fn_arith () + { + as_val=`expr "$@" || test $? -eq 1` + } +fi # as_fn_arith + + if expr a : '\(a\)' >/dev/null 2>&1 && test "X`expr 00001 : '.*\(...\)'`" = X001; then as_expr=expr @@ -147,8 +226,12 @@ else as_basename=false fi +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi -# Name of the executable. as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ @@ -168,76 +251,25 @@ $as_echo X/"$0" | } s/.*/./; q'` -# CDPATH. -$as_unset CDPATH - - - - as_lineno_1=$LINENO - as_lineno_2=$LINENO - test "x$as_lineno_1" != "x$as_lineno_2" && - test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || { - - # Create $as_me.lineno as a copy of $as_myself, but with $LINENO - # uniformly replaced by the line number. The first 'sed' inserts a - # line-number line after each line using $LINENO; the second 'sed' - # does the real work. The second script uses 'N' to pair each - # line-number line with the line containing $LINENO, and appends - # trailing '-' during substitution so that $LINENO is not a special - # case at line end. - # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the - # scripts with optimization help from Paolo Bonzini. Blame Lee - # E. McMahon (1931-1989) for sed's syntax. :-) - sed -n ' - p - /[$]LINENO/= - ' <$as_myself | - sed ' - s/[$]LINENO.*/&-/ - t lineno - b - :lineno - N - :loop - s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/ - t loop - s/-\n.*// - ' >$as_me.lineno && - chmod +x "$as_me.lineno" || - { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2 - { (exit 1); exit 1; }; } - - # Don't try to exec as it changes $[0], causing all sort of problems - # (the dirname of $[0] is not the place where we might find the - # original and so on. Autoconf is especially sensitive to this). - . "./$as_me.lineno" - # Exit status is that of the last command. - exit -} - - -if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then - as_dirname=dirname -else - as_dirname=false -fi +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits ECHO_C= ECHO_N= ECHO_T= -case `echo -n x` in +case `echo -n x` in #((((( -n*) - case `echo 'x\c'` in + case `echo 'xy\c'` in *c*) ECHO_T=' ';; # ECHO_T is single tab character. - *) ECHO_C='\c';; + xy) ECHO_C='\c';; + *) echo `echo ksh88 bug on AIX 6.1` > /dev/null + ECHO_T=' ';; esac;; *) ECHO_N='-n';; esac -if expr a : '\(a\)' >/dev/null 2>&1 && - test "X`expr 00001 : '.*\(...\)'`" = X001; then - as_expr=expr -else - as_expr=false -fi rm -f conf$$ conf$$.exe conf$$.file if test -d conf$$.dir; then @@ -266,8 +298,56 @@ fi rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file rmdir conf$$.dir 2>/dev/null + +# as_fn_mkdir_p +# ------------- +# Create "$as_dir" as a directory, including parents if necessary. +as_fn_mkdir_p () +{ + + case $as_dir in #( + -*) as_dir=./$as_dir;; + esac + test -d "$as_dir" || eval $as_mkdir_p || { + as_dirs= + while :; do + case $as_dir in #( + *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *) as_qdir=$as_dir;; + esac + as_dirs="'$as_qdir' $as_dirs" + as_dir=`$as_dirname -- "$as_dir" || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + test -d "$as_dir" && break + done + test -z "$as_dirs" || eval "mkdir $as_dirs" + } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir" + + +} # as_fn_mkdir_p if mkdir -p . 2>/dev/null; then - as_mkdir_p=: + as_mkdir_p='mkdir -p "$as_dir"' else test -d ./-p && rmdir ./-p as_mkdir_p=false @@ -286,10 +366,10 @@ else if test -d "$1"; then test -d "$1/."; else - case $1 in + case $1 in #( -*)set "./$1";; esac; - case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in + case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #(( ???[sx]*):;;*)false;;esac;fi '\'' sh ' @@ -304,13 +384,15 @@ as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" exec 6>&1 - -# Save the log message, to keep $[0] and so on meaningful, and to +## ----------------------------------- ## +## Main body of $CONFIG_STATUS script. ## +## ----------------------------------- ## +# Save the log message, to keep $0 and so on meaningful, and to # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by clustalw $as_me 2.0.12, which was -generated by GNU Autoconf 2.63. Invocation command line was +This file was extended by clustalw $as_me 2.1, which was +generated by GNU Autoconf 2.65. Invocation command line was CONFIG_FILES = $CONFIG_FILES CONFIG_HEADERS = $CONFIG_HEADERS @@ -327,13 +409,15 @@ config_headers=" src/config.h" config_commands=" depfiles" ac_cs_usage="\ -\`$as_me' instantiates files from templates according to the -current configuration. +\`$as_me' instantiates files and other configuration actions +from templates according to the current configuration. Unless the files +and actions are specified as TAGs, all are instantiated by default. -Usage: $0 [OPTION]... [FILE]... +Usage: $0 [OPTION]... [TAG]... -h, --help print this help, then exit -V, --version print version number and configuration settings, then exit + --config print configuration, then exit -q, --quiet, --silent do not print progress messages -d, --debug don't remove temporary files @@ -352,18 +436,19 @@ $config_headers Configuration commands: $config_commands -Report bugs to ." +Report bugs to ." +ac_cs_config="" ac_cs_version="\ -clustalw config.status 2.0.12 -configured by ./configure, generated by GNU Autoconf 2.63, - with options \"\" +clustalw config.status 2.1 +configured by ./configure, generated by GNU Autoconf 2.65, + with options \"$ac_cs_config\" -Copyright (C) 2008 Free Software Foundation, Inc. +Copyright (C) 2009 Free Software Foundation, Inc. This config.status script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it." -ac_pwd='/homes/pvtroshin/workspace/clustengine/binaries/src/clustalw' +ac_pwd='/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw' srcdir='.' INSTALL='/usr/bin/install -c' MKDIR_P='/bin/mkdir -p' @@ -392,6 +477,8 @@ do ac_cs_recheck=: ;; --version | --versio | --versi | --vers | --ver | --ve | --v | -V ) $as_echo "$ac_cs_version"; exit ;; + --config | --confi | --conf | --con | --co | --c ) + $as_echo "$ac_cs_config"; exit ;; --debug | --debu | --deb | --de | --d | -d ) debug=: ;; --file | --fil | --fi | --f ) @@ -399,20 +486,19 @@ do case $ac_optarg in *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; esac - CONFIG_FILES="$CONFIG_FILES '$ac_optarg'" + as_fn_append CONFIG_FILES " '$ac_optarg'" ac_need_defaults=false;; --header | --heade | --head | --hea ) $ac_shift case $ac_optarg in *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; esac - CONFIG_HEADERS="$CONFIG_HEADERS '$ac_optarg'" + as_fn_append CONFIG_HEADERS " '$ac_optarg'" ac_need_defaults=false;; --he | --h) # Conflict between --help and --header - { $as_echo "$as_me: error: ambiguous option: $1 -Try \`$0 --help' for more information." >&2 - { (exit 1); exit 1; }; };; + as_fn_error "ambiguous option: \`$1' +Try \`$0 --help' for more information.";; --help | --hel | -h ) $as_echo "$ac_cs_usage"; exit ;; -q | -quiet | --quiet | --quie | --qui | --qu | --q \ @@ -420,11 +506,10 @@ Try \`$0 --help' for more information." >&2 ac_cs_silent=: ;; # This is an error. - -*) { $as_echo "$as_me: error: unrecognized option: $1 -Try \`$0 --help' for more information." >&2 - { (exit 1); exit 1; }; } ;; + -*) as_fn_error "unrecognized option: \`$1' +Try \`$0 --help' for more information." ;; - *) ac_config_targets="$ac_config_targets $1" + *) as_fn_append ac_config_targets " $1" ac_need_defaults=false ;; esac @@ -473,9 +558,7 @@ do "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;; "src/clustalw_version.h") CONFIG_FILES="$CONFIG_FILES src/clustalw_version.h" ;; - *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 -$as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;} - { (exit 1); exit 1; }; };; + *) as_fn_error "invalid argument: \`$ac_config_target'" "$LINENO" 5;; esac done @@ -502,7 +585,7 @@ $debug || trap 'exit_status=$? { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status ' 0 - trap '{ (exit 1); exit 1; }' 1 2 13 15 + trap 'as_fn_exit 1' 1 2 13 15 } # Create a (secure) tmp directory for tmp files. @@ -513,11 +596,7 @@ $debug || { tmp=./conf$$-$RANDOM (umask 077 && mkdir "$tmp") -} || -{ - $as_echo "$as_me: cannot create a temporary directory in ." >&2 - { (exit 1); exit 1; } -} +} || as_fn_error "cannot create a temporary directory in ." "$LINENO" 5 # Set up the scripts for CONFIG_FILES section. # No need to generate them if there are no CONFIG_FILES. @@ -525,16 +604,24 @@ $debug || if test -n "$CONFIG_FILES"; then -ac_cr=' ' +ac_cr=`echo X | tr X '\015'` +# On cygwin, bash can eat \r inside `` if the user requested igncr. +# But we know of no other shell where ac_cr would be empty at this +# point, so we can use a bashism as a fallback. +if test "x$ac_cr" = x; then + eval ac_cr=\$\'\\r\' +fi ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' /dev/null` if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then - ac_cs_awk_cr='\\r' + ac_cs_awk_cr='\r' else ac_cs_awk_cr=$ac_cr fi echo 'BEGIN {' >"$tmp/subs1.awk" && cat >>"$tmp/subs1.awk" <<\_ACAWK && +S["am__EXEEXT_FALSE"]="" +S["am__EXEEXT_TRUE"]="#" S["LTLIBOBJS"]="" S["LIBOBJS"]="" S["EGREP"]="/bin/grep -E" @@ -565,7 +652,7 @@ S["CFLAGS"]="-g -O2" S["CC"]="gcc" S["am__untar"]="${AMTAR} xf -" S["am__tar"]="${AMTAR} chof - \"$$tardir\"" -S["AMTAR"]="${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run tar" +S["AMTAR"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run tar" S["am__leading_dot"]="." S["SET_MAKE"]="" S["AWK"]="gawk" @@ -573,13 +660,13 @@ S["mkdir_p"]="/bin/mkdir -p" S["MKDIR_P"]="/bin/mkdir -p" S["INSTALL_STRIP_PROGRAM"]="$(install_sh) -c -s" S["STRIP"]="" -S["install_sh"]="$(SHELL) /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/install-sh" -S["MAKEINFO"]="${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run makeinfo" -S["AUTOHEADER"]="${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoheader" -S["AUTOMAKE"]="${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run automake-1.10" -S["AUTOCONF"]="${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoconf" -S["ACLOCAL"]="${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run aclocal-1.10" -S["VERSION"]="2.0.12" +S["install_sh"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/install-sh" +S["MAKEINFO"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run makeinfo" +S["AUTOHEADER"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoheader" +S["AUTOMAKE"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run automake-1.11" +S["AUTOCONF"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoconf" +S["ACLOCAL"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run aclocal-1.11" +S["VERSION"]="2.1" S["PACKAGE"]="clustalw" S["CYGPATH_W"]="echo" S["am__isrc"]="" @@ -587,7 +674,7 @@ S["INSTALL_DATA"]="${INSTALL} -m 644" S["INSTALL_SCRIPT"]="${INSTALL}" S["INSTALL_PROGRAM"]="${INSTALL}" S["CLUSTALW_NAME"]="ClustalW" -S["CLUSTALW_VERSION"]="2.0.12" +S["CLUSTALW_VERSION"]="2.1" S["target_os"]="linux-gnu" S["target_vendor"]="unknown" S["target_cpu"]="x86_64" @@ -630,9 +717,10 @@ S["bindir"]="${exec_prefix}/bin" S["program_transform_name"]="s,x,x," S["prefix"]="/usr/local" S["exec_prefix"]="${prefix}" +S["PACKAGE_URL"]="" S["PACKAGE_BUGREPORT"]="clustalw@ucd.ie" -S["PACKAGE_STRING"]="clustalw 2.0.12" -S["PACKAGE_VERSION"]="2.0.12" +S["PACKAGE_STRING"]="clustalw 2.1" +S["PACKAGE_VERSION"]="2.1" S["PACKAGE_TARNAME"]="clustalw" S["PACKAGE_NAME"]="clustalw" S["PATH_SEPARATOR"]=":" @@ -669,9 +757,7 @@ if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then else cat fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \ - || { { $as_echo "$as_me:$LINENO: error: could not setup config files machinery" >&5 -$as_echo "$as_me: error: could not setup config files machinery" >&2;} - { (exit 1); exit 1; }; } + || as_fn_error "could not setup config files machinery" "$LINENO" 5 fi # test -n "$CONFIG_FILES" # Set up the scripts for CONFIG_HEADERS section. @@ -682,12 +768,13 @@ cat >"$tmp/defines.awk" <<\_ACAWK || BEGIN { D["PACKAGE_NAME"]=" \"clustalw\"" D["PACKAGE_TARNAME"]=" \"clustalw\"" -D["PACKAGE_VERSION"]=" \"2.0.12\"" -D["PACKAGE_STRING"]=" \"clustalw 2.0.12\"" +D["PACKAGE_VERSION"]=" \"2.1\"" +D["PACKAGE_STRING"]=" \"clustalw 2.1\"" D["PACKAGE_BUGREPORT"]=" \"clustalw@ucd.ie\"" +D["PACKAGE_URL"]=" \"\"" D["OS_UNIX"]=" 1" D["PACKAGE"]=" \"clustalw\"" -D["VERSION"]=" \"2.0.12\"" +D["VERSION"]=" \"2.1\"" D["STDC_HEADERS"]=" 1" D["HAVE_SYS_TYPES_H"]=" 1" D["HAVE_SYS_STAT_H"]=" 1" @@ -733,9 +820,7 @@ D["HAVE_MALLOC"]=" 1" } { print } _ACAWK - { { $as_echo "$as_me:$LINENO: error: could not setup config headers machinery" >&5 -$as_echo "$as_me: error: could not setup config headers machinery" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "could not setup config headers machinery" "$LINENO" 5 fi # test -n "$CONFIG_HEADERS" @@ -748,9 +833,7 @@ do 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 $ac_tag" >&2;} - { (exit 1); exit 1; }; };; + :L* | :C*:*) as_fn_error "invalid tag \`$ac_tag'" "$LINENO" 5;; :[FH]-) ac_tag=-:-;; :[FH]*) ac_tag=$ac_tag:$ac_tag.in;; esac @@ -778,12 +861,10 @@ $as_echo "$as_me: error: invalid tag $ac_tag" >&2;} [\\/$]*) false;; *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";; esac || - { { $as_echo "$as_me:$LINENO: error: cannot find input file: $ac_f" >&5 -$as_echo "$as_me: error: cannot find input file: $ac_f" >&2;} - { (exit 1); exit 1; }; };; + as_fn_error "cannot find input file: \`$ac_f'" "$LINENO" 5;; esac case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac - ac_file_inputs="$ac_file_inputs '$ac_f'" + as_fn_append ac_file_inputs " '$ac_f'" done # Let's still pretend it is `configure' which instantiates (i.e., don't @@ -794,7 +875,7 @@ $as_echo "$as_me: error: cannot find input file: $ac_f" >&2;} `' by configure.' if test x"$ac_file" != x-; then configure_input="$ac_file. $configure_input" - { $as_echo "$as_me:$LINENO: creating $ac_file" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5 $as_echo "$as_me: creating $ac_file" >&6;} fi # Neutralize special characters interpreted by sed in replacement strings. @@ -807,9 +888,7 @@ $as_echo "$as_me: creating $ac_file" >&6;} case $ac_tag in *:-:* | *:-) cat >"$tmp/stdin" \ - || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 -$as_echo "$as_me: error: could not create $ac_file" >&2;} - { (exit 1); exit 1; }; } ;; + || as_fn_error "could not create $ac_file" "$LINENO" 5 ;; esac ;; esac @@ -837,47 +916,7 @@ $as_echo X"$ac_file" | q } s/.*/./; q'` - { as_dir="$ac_dir" - case $as_dir in #( - -*) as_dir=./$as_dir;; - esac - test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || { - as_dirs= - while :; do - case $as_dir in #( - *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( - *) as_qdir=$as_dir;; - esac - as_dirs="'$as_qdir' $as_dirs" - as_dir=`$as_dirname -- "$as_dir" || -$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$as_dir" : 'X\(//\)[^/]' \| \ - X"$as_dir" : 'X\(//\)$' \| \ - X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$as_dir" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ - s//\1/ - q - } - /^X\(\/\/\)[^/].*/{ - s//\1/ - q - } - /^X\(\/\/\)$/{ - s//\1/ - q - } - /^X\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` - test -d "$as_dir" && break - done - test -z "$as_dirs" || eval "mkdir $as_dirs" - } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5 -$as_echo "$as_me: error: cannot create directory $as_dir" >&2;} - { (exit 1); exit 1; }; }; } + as_dir="$ac_dir"; as_fn_mkdir_p ac_builddir=. case "$ac_dir" in @@ -931,7 +970,6 @@ ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix # If the template does not know about datarootdir, expand it. # FIXME: This hack should be removed a few years after 2.60. ac_datarootdir_hack=; ac_datarootdir_seen= - ac_sed_dataroot=' /datarootdir/ { p @@ -941,12 +979,11 @@ ac_sed_dataroot=' /@docdir@/p /@infodir@/p /@localedir@/p -/@mandir@/p -' +/@mandir@/p' case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in *datarootdir*) ac_datarootdir_seen=yes;; *@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*) - { $as_echo "$as_me:$LINENO: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 $as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;} ac_datarootdir_hack=' s&@datadir@&${datarootdir}&g @@ -954,7 +991,7 @@ $as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir set s&@infodir@&${datarootdir}/info&g s&@localedir@&${datarootdir}/locale&g s&@mandir@&${datarootdir}/man&g - s&\${datarootdir}&${prefix}/share&g' ;; + s&\${datarootdir}&${prefix}/share&g' ;; esac ac_sed_extra="/^[ ]*VPATH[ ]*=/{ s/:*\$(srcdir):*/:/ @@ -982,14 +1019,12 @@ s&@MKDIR_P@&$ac_MKDIR_P&;t t $ac_datarootdir_hack " eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \ - || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 -$as_echo "$as_me: error: could not create $ac_file" >&2;} - { (exit 1); exit 1; }; } + || as_fn_error "could not create $ac_file" "$LINENO" 5 test -z "$ac_datarootdir_hack$ac_datarootdir_seen" && { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } && { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } && - { $as_echo "$as_me:$LINENO: WARNING: $ac_file contains a reference to the variable \`datarootdir' + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir' which seems to be undefined. Please make sure it is defined." >&5 $as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir' which seems to be undefined. Please make sure it is defined." >&2;} @@ -999,9 +1034,7 @@ which seems to be undefined. Please make sure it is defined." >&2;} -) cat "$tmp/out" && rm -f "$tmp/out";; *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";; esac \ - || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 -$as_echo "$as_me: error: could not create $ac_file" >&2;} - { (exit 1); exit 1; }; } + || as_fn_error "could not create $ac_file" "$LINENO" 5 ;; :H) # @@ -1012,25 +1045,19 @@ $as_echo "$as_me: error: could not create $ac_file" >&2;} $as_echo "/* $configure_input */" \ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" } >"$tmp/config.h" \ - || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 -$as_echo "$as_me: error: could not create $ac_file" >&2;} - { (exit 1); exit 1; }; } + || as_fn_error "could not create $ac_file" "$LINENO" 5 if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then - { $as_echo "$as_me:$LINENO: $ac_file is unchanged" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5 $as_echo "$as_me: $ac_file is unchanged" >&6;} else rm -f "$ac_file" mv "$tmp/config.h" "$ac_file" \ - || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 -$as_echo "$as_me: error: could not create $ac_file" >&2;} - { (exit 1); exit 1; }; } + || as_fn_error "could not create $ac_file" "$LINENO" 5 fi else $as_echo "/* $configure_input */" \ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \ - || { { $as_echo "$as_me:$LINENO: error: could not create -" >&5 -$as_echo "$as_me: error: could not create -" >&2;} - { (exit 1); exit 1; }; } + || as_fn_error "could not create -" "$LINENO" 5 fi # Compute "$ac_file"'s index in $config_headers. _am_arg="$ac_file" @@ -1068,7 +1095,7 @@ $as_echo X"$_am_arg" | s/.*/./; q'`/stamp-h$_am_stamp_count ;; - :C) { $as_echo "$as_me:$LINENO: executing $ac_file commands" >&5 + :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5 $as_echo "$as_me: executing $ac_file commands" >&6;} ;; esac @@ -1163,47 +1190,7 @@ $as_echo X"$file" | q } s/.*/./; q'` - { as_dir=$dirpart/$fdir - case $as_dir in #( - -*) as_dir=./$as_dir;; - esac - test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || { - as_dirs= - while :; do - case $as_dir in #( - *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( - *) as_qdir=$as_dir;; - esac - as_dirs="'$as_qdir' $as_dirs" - as_dir=`$as_dirname -- "$as_dir" || -$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$as_dir" : 'X\(//\)[^/]' \| \ - X"$as_dir" : 'X\(//\)$' \| \ - X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$as_dir" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ - s//\1/ - q - } - /^X\(\/\/\)[^/].*/{ - s//\1/ - q - } - /^X\(\/\/\)$/{ - s//\1/ - q - } - /^X\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` - test -d "$as_dir" && break - done - test -z "$as_dirs" || eval "mkdir $as_dirs" - } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5 -$as_echo "$as_me: error: cannot create directory $as_dir" >&2;} - { (exit 1); exit 1; }; }; } + as_dir=$dirpart/$fdir; as_fn_mkdir_p # echo "creating $dirpart/$file" echo '# dummy' > "$dirpart/$file" done @@ -1215,4 +1202,4 @@ $as_echo "$as_me: error: cannot create directory $as_dir" >&2;} done # for ac_tag -{ (exit 0); exit 0; } +as_fn_exit 0 diff --git a/binaries/src/clustalw/config.sub b/binaries/src/clustalw/config.sub index 6759825..eb0389a 100644 --- a/binaries/src/clustalw/config.sub +++ b/binaries/src/clustalw/config.sub @@ -1,10 +1,10 @@ #! /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 +# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 # Free Software Foundation, Inc. -timestamp='2008-01-16' +timestamp='2009-06-11' # This file is (in principle) common to ALL GNU software. # The presence of a machine in this file suggests that SOME GNU software @@ -122,6 +122,7 @@ maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \ uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \ + kopensolaris*-gnu* | \ storm-chaos* | os2-emx* | rtmk-nova*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` @@ -152,6 +153,9 @@ case $os in os= basic_machine=$1 ;; + -bluegene*) + os=-cnk + ;; -sim | -cisco | -oki | -wec | -winbond) os= basic_machine=$1 @@ -249,13 +253,16 @@ case $basic_machine in | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | i370 | i860 | i960 | ia64 \ | ip2k | iq2000 \ + | lm32 \ | m32c | m32r | m32rle | m68000 | m68k | m88k \ - | maxq | mb | microblaze | mcore | mep \ + | maxq | mb | microblaze | mcore | mep | metag \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ - | mips64vr | mips64vrel \ + | mips64octeon | mips64octeonel \ | mips64orion | mips64orionel \ + | mips64r5900 | mips64r5900el \ + | mips64vr | mips64vrel \ | mips64vr4100 | mips64vr4100el \ | mips64vr4300 | mips64vr4300el \ | mips64vr5000 | mips64vr5000el \ @@ -268,6 +275,7 @@ case $basic_machine in | mipsisa64sr71k | mipsisa64sr71kel \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ + | moxie \ | mt \ | msp430 \ | nios | nios2 \ @@ -277,7 +285,7 @@ case $basic_machine in | 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 \ + | sh | sh[1234] | sh[24]a | sh[24]aeb | 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 \ @@ -286,7 +294,7 @@ case $basic_machine in | v850 | v850e \ | we32k \ | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \ - | z8k) + | z8k | z80) basic_machine=$basic_machine-unknown ;; m6811 | m68hc11 | m6812 | m68hc12) @@ -329,14 +337,17 @@ case $basic_machine in | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ | i*86-* | i860-* | i960-* | ia64-* \ | ip2k-* | iq2000-* \ + | lm32-* \ | m32c-* | m32r-* | m32rle-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ - | m88110-* | m88k-* | maxq-* | mcore-* \ + | m88110-* | m88k-* | maxq-* | mcore-* | metag-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ - | mips64vr-* | mips64vrel-* \ + | mips64octeon-* | mips64octeonel-* \ | mips64orion-* | mips64orionel-* \ + | mips64r5900-* | mips64r5900el-* \ + | mips64vr-* | mips64vrel-* \ | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* \ | mips64vr5000-* | mips64vr5000el-* \ @@ -358,20 +369,20 @@ case $basic_machine in | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ | pyramid-* \ | romp-* | rs6000-* \ - | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ + | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | 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-* \ + | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* | tile-* \ | tron-* \ | v850-* | v850e-* | vax-* \ | we32k-* \ | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \ | xstormy16-* | xtensa*-* \ | ymp-* \ - | z8k-*) + | z8k-* | z80-*) ;; # Recognize the basic CPU types without company name, with glob match. xtensa*) @@ -439,6 +450,10 @@ case $basic_machine in basic_machine=m68k-apollo os=-bsd ;; + aros) + basic_machine=i386-pc + os=-aros + ;; aux) basic_machine=m68k-apple os=-aux @@ -455,10 +470,18 @@ case $basic_machine in basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; + bluegene*) + basic_machine=powerpc-ibm + os=-cnk + ;; c90) basic_machine=c90-cray os=-unicos ;; + cegcc) + basic_machine=arm-unknown + os=-cegcc + ;; convex-c1) basic_machine=c1-convex os=-bsd @@ -526,6 +549,10 @@ case $basic_machine in basic_machine=m88k-motorola os=-sysv3 ;; + dicos) + basic_machine=i686-pc + os=-dicos + ;; djgpp) basic_machine=i586-pc os=-msdosdjgpp @@ -1128,6 +1155,10 @@ case $basic_machine in basic_machine=z8k-unknown os=-sim ;; + z80-*-coff) + basic_machine=z80-unknown + os=-sim + ;; none) basic_machine=none-none os=-none @@ -1166,7 +1197,7 @@ case $basic_machine in we32k) basic_machine=we32k-att ;; - sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele) + sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele) basic_machine=sh-unknown ;; sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v) @@ -1236,10 +1267,11 @@ case $os in # 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]*\ + | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\ | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \ + | -kopensolaris* \ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \ - | -aos* \ + | -aos* | -aros* \ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \ @@ -1248,7 +1280,7 @@ case $os in | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \ - | -chorusos* | -chorusrdb* \ + | -chorusos* | -chorusrdb* | -cegcc* \ | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \ | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \ | -uxpv* | -beos* | -mpeix* | -udk* \ @@ -1388,6 +1420,9 @@ case $os in -zvmoe) os=-zvmoe ;; + -dicos*) + os=-dicos + ;; -none) ;; *) @@ -1585,7 +1620,7 @@ case $basic_machine in -sunos*) vendor=sun ;; - -aix*) + -cnk*|-aix*) vendor=ibm ;; -beos*) diff --git a/binaries/src/clustalw/configure b/binaries/src/clustalw/configure index 465e0c8..2cdb992 100644 --- a/binaries/src/clustalw/configure +++ b/binaries/src/clustalw/configure @@ -1,20 +1,24 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.63 for clustalw 2.0.12. +# Generated by GNU Autoconf 2.65 for clustalw 2.1. # # Report bugs to . # +# # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, -# 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, +# Inc. +# +# # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. -## --------------------- ## -## M4sh Initialization. ## -## --------------------- ## +## -------------------- ## +## M4sh Initialization. ## +## -------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which @@ -22,23 +26,15 @@ if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else - case `(set -o) 2>/dev/null` in - *posix*) set -o posix ;; + 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 @@ -46,7 +42,13 @@ export as_nl 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 +# Prefer a ksh shell builtin over an external printf program on Solaris, +# but without wasting forks for bash or zsh. +if test -z "$BASH_VERSION$ZSH_VERSION" \ + && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='print -r --' + as_echo_n='print -rn --' +elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='printf %s\n' as_echo_n='printf %s' else @@ -57,7 +59,7 @@ else as_echo_body='eval expr "X$1" : "X\\(.*\\)"' as_echo_n_body='eval arg=$1; - case $arg in + case $arg in #( *"$as_nl"*) expr "X$arg" : "X\\(.*\\)$as_nl"; arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; @@ -80,13 +82,6 @@ if test "${PATH_SEPARATOR+set}" != set; then } 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. Quoting is @@ -96,15 +91,15 @@ fi IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. -case $0 in +case $0 in #(( *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break -done + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break + done IFS=$as_save_IFS ;; @@ -116,12 +111,16 @@ if test "x$as_myself" = x; then fi if test ! -f "$as_myself"; then $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 - { (exit 1); exit 1; } + exit 1 fi -# Work around bugs in pre-3.0 UWIN ksh. -for as_var in ENV MAIL MAILPATH -do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var +# Unset variables that we do not need and which cause bugs (e.g. in +# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" +# suppresses any "Segmentation fault" message there. '((' could +# trigger a bug in pdksh 5.2.14. +for as_var in BASH_ENV ENV MAIL MAILPATH +do eval test x\${$as_var+set} = xset \ + && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : done PS1='$ ' PS2='> ' @@ -133,330 +132,300 @@ export LC_ALL LANGUAGE=C export LANGUAGE -# Required to use basename. -if expr a : '\(a\)' >/dev/null 2>&1 && - test "X`expr 00001 : '.*\(...\)'`" = X001; then - as_expr=expr -else - as_expr=false -fi - -if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then - as_basename=basename -else - as_basename=false -fi - - -# Name of the executable. -as_me=`$as_basename -- "$0" || -$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ - X"$0" : 'X\(//\)$' \| \ - X"$0" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X/"$0" | - sed '/^.*\/\([^/][^/]*\)\/*$/{ - s//\1/ - q - } - /^X\/\(\/\/\)$/{ - s//\1/ - q - } - /^X\/\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` - # CDPATH. -$as_unset CDPATH - +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH if test "x$CONFIG_SHELL" = x; then - if (eval ":") 2>/dev/null; then - as_have_required=yes + as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then : + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which + # is contrary to our usage. Disable this feature. + alias -g '\${1+\"\$@\"}'='\"\$@\"' + setopt NO_GLOB_SUBST else - as_have_required=no + case \`(set -o) 2>/dev/null\` in #( + *posix*) : + set -o posix ;; #( + *) : + ;; +esac fi - - if test $as_have_required = yes && (eval ": -(as_func_return () { - (exit \$1) -} -as_func_success () { - as_func_return 0 -} -as_func_failure () { - as_func_return 1 -} -as_func_ret_success () { - return 0 -} -as_func_ret_failure () { - return 1 -} +" + as_required="as_fn_return () { (exit \$1); } +as_fn_success () { as_fn_return 0; } +as_fn_failure () { as_fn_return 1; } +as_fn_ret_success () { return 0; } +as_fn_ret_failure () { return 1; } exitcode=0 -if as_func_success; then - : -else - exitcode=1 - echo as_func_success failed. -fi - -if as_func_failure; then - exitcode=1 - echo as_func_failure succeeded. -fi - -if as_func_ret_success; then - : +as_fn_success || { exitcode=1; echo as_fn_success failed.; } +as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; } +as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; } +as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; } +if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then : + +else + exitcode=1; echo positional parameters were not saved. +fi +test x\$exitcode = x0 || exit 1" + as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO + as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO + eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" && + test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1 +test \$(( 1 + 1 )) = 2 || exit 1" + if (eval "$as_required") 2>/dev/null; then : + as_have_required=yes else - exitcode=1 - echo as_func_ret_success failed. -fi - -if as_func_ret_failure; then - exitcode=1 - echo as_func_ret_failure succeeded. + as_have_required=no fi + if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then : -if ( set x; as_func_ret_success y && test x = \"\$1\" ); then - : else - exitcode=1 - echo positional parameters were not saved. -fi - -test \$exitcode = 0) || { (exit 1); exit 1; } - -( - as_lineno_1=\$LINENO - as_lineno_2=\$LINENO - test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" && - test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; } -") 2> /dev/null; then - : -else - as_candidate_shells= - as_save_IFS=$IFS; IFS=$PATH_SEPARATOR + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +as_found=false for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - case $as_dir in + as_found=: + case $as_dir in #( /*) for as_base in sh bash ksh sh5; do - as_candidate_shells="$as_candidate_shells $as_dir/$as_base" + # Try only shells that exist, to save several forks. + as_shell=$as_dir/$as_base + if { test -f "$as_shell" || test -f "$as_shell.exe"; } && + { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then : + CONFIG_SHELL=$as_shell as_have_required=yes + if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then : + break 2 +fi +fi done;; esac + as_found=false done +$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } && + { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then : + CONFIG_SHELL=$SHELL as_have_required=yes +fi; } IFS=$as_save_IFS - for as_shell in $as_candidate_shells $SHELL; do - # Try only shells that exist, to save several forks. - if { test -f "$as_shell" || test -f "$as_shell.exe"; } && - { ("$as_shell") 2> /dev/null <<\_ASEOF -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then - emulate sh - NULLCMD=: - # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which - # is contrary to our usage. Disable this feature. - alias -g '${1+"$@"}'='"$@"' - setopt NO_GLOB_SUBST -else - case `(set -o) 2>/dev/null` in - *posix*) set -o posix ;; -esac - -fi - - -: -_ASEOF -}; then - CONFIG_SHELL=$as_shell - as_have_required=yes - if { "$as_shell" 2> /dev/null <<\_ASEOF -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then - emulate sh - NULLCMD=: - # Pre-4.2 versions of Zsh do 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 - - -: -(as_func_return () { - (exit $1) -} -as_func_success () { - as_func_return 0 -} -as_func_failure () { - as_func_return 1 -} -as_func_ret_success () { - return 0 -} -as_func_ret_failure () { - return 1 -} - -exitcode=0 -if as_func_success; then - : -else - exitcode=1 - echo as_func_success failed. -fi - -if as_func_failure; then - exitcode=1 - echo as_func_failure succeeded. -fi - -if as_func_ret_success; then - : -else - exitcode=1 - echo as_func_ret_success failed. -fi - -if as_func_ret_failure; then - exitcode=1 - echo as_func_ret_failure succeeded. -fi - -if ( set x; as_func_ret_success y && test x = "$1" ); then - : -else - exitcode=1 - echo positional parameters were not saved. -fi - -test $exitcode = 0) || { (exit 1); exit 1; } - -( - as_lineno_1=$LINENO - as_lineno_2=$LINENO - test "x$as_lineno_1" != "x$as_lineno_2" && - test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; } - -_ASEOF -}; then - break -fi - -fi - - done - - if test "x$CONFIG_SHELL" != x; then - for as_var in BASH_ENV ENV - do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var - done + if test "x$CONFIG_SHELL" != x; then : + # We cannot yet assume a decent shell, so we have to provide a + # neutralization value for shells without unset; and this also + # works around shells that cannot unset nonexistent variables. + BASH_ENV=/dev/null + ENV=/dev/null + (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV export CONFIG_SHELL exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"} fi - - if test $as_have_required = no; then - echo This script requires a shell more modern than all the - echo shells that I found on your system. Please install a - echo modern shell, or manually run the script under such a - echo shell if you do have one. - { (exit 1); exit 1; } + if test x$as_have_required = xno; then : + $as_echo "$0: This script requires a shell more modern than all" + $as_echo "$0: the shells that I found on your system." + if test x${ZSH_VERSION+set} = xset ; then + $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should" + $as_echo "$0: be upgraded to zsh 4.3.4 or later." + else + $as_echo "$0: Please tell bug-autoconf@gnu.org and clustalw@ucd.ie +$0: about your system, including any error possibly output +$0: before this message. Then install a modern shell, or +$0: manually run the script under such a shell if you do +$0: have one." + fi + exit 1 fi - - fi - fi +SHELL=${CONFIG_SHELL-/bin/sh} +export SHELL +# Unset more variables known to interfere with behavior of common tools. +CLICOLOR_FORCE= GREP_OPTIONS= +unset CLICOLOR_FORCE GREP_OPTIONS +## --------------------- ## +## M4sh Shell Functions. ## +## --------------------- ## +# as_fn_unset VAR +# --------------- +# Portably unset VAR. +as_fn_unset () +{ + { eval $1=; unset $1;} +} +as_unset=as_fn_unset +# as_fn_set_status STATUS +# ----------------------- +# Set $? to STATUS, without forking. +as_fn_set_status () +{ + return $1 +} # as_fn_set_status -(eval "as_func_return () { - (exit \$1) -} -as_func_success () { - as_func_return 0 -} -as_func_failure () { - as_func_return 1 -} -as_func_ret_success () { - return 0 -} -as_func_ret_failure () { - return 1 -} +# as_fn_exit STATUS +# ----------------- +# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. +as_fn_exit () +{ + set +e + as_fn_set_status $1 + exit $1 +} # as_fn_exit + +# as_fn_mkdir_p +# ------------- +# Create "$as_dir" as a directory, including parents if necessary. +as_fn_mkdir_p () +{ -exitcode=0 -if as_func_success; then - : + case $as_dir in #( + -*) as_dir=./$as_dir;; + esac + test -d "$as_dir" || eval $as_mkdir_p || { + as_dirs= + while :; do + case $as_dir in #( + *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *) as_qdir=$as_dir;; + esac + as_dirs="'$as_qdir' $as_dirs" + as_dir=`$as_dirname -- "$as_dir" || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + test -d "$as_dir" && break + done + test -z "$as_dirs" || eval "mkdir $as_dirs" + } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir" + + +} # as_fn_mkdir_p +# as_fn_append VAR VALUE +# ---------------------- +# Append the text in VALUE to the end of the definition contained in VAR. Take +# advantage of any shell optimizations that allow amortized linear growth over +# repeated appends, instead of the typical quadratic growth present in naive +# implementations. +if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : + eval 'as_fn_append () + { + eval $1+=\$2 + }' else - exitcode=1 - echo as_func_success failed. -fi + as_fn_append () + { + eval $1=\$$1\$2 + } +fi # as_fn_append + +# as_fn_arith ARG... +# ------------------ +# Perform arithmetic evaluation on the ARGs, and store the result in the +# global $as_val. Take advantage of shells that can avoid forks. The arguments +# must be portable across $(()) and expr. +if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : + eval 'as_fn_arith () + { + as_val=$(( $* )) + }' +else + as_fn_arith () + { + as_val=`expr "$@" || test $? -eq 1` + } +fi # as_fn_arith -if as_func_failure; then - exitcode=1 - echo as_func_failure succeeded. -fi -if as_func_ret_success; then - : +# as_fn_error ERROR [LINENO LOG_FD] +# --------------------------------- +# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are +# provided, also output the error to LOG_FD, referencing LINENO. Then exit the +# script with status $?, using 1 if that was 0. +as_fn_error () +{ + as_status=$?; test $as_status -eq 0 && as_status=1 + if test "$3"; then + as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3 + fi + $as_echo "$as_me: error: $1" >&2 + as_fn_exit $as_status +} # as_fn_error + +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then + as_expr=expr else - exitcode=1 - echo as_func_ret_success failed. + as_expr=false fi -if as_func_ret_failure; then - exitcode=1 - echo as_func_ret_failure succeeded. +if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false fi -if ( set x; as_func_ret_success y && test x = \"\$1\" ); then - : +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname else - exitcode=1 - echo positional parameters were not saved. + as_dirname=false fi -test \$exitcode = 0") || { - echo No shell found that supports shell functions. - echo Please tell bug-autoconf@gnu.org about your system, - echo including any error possibly output before this message. - echo This can help us improve future autoconf versions. - echo Configuration will now proceed without shell functions. -} - +as_me=`$as_basename -- "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ + s//\1/ + q + } + /^X\/\(\/\/\)$/{ + s//\1/ + q + } + /^X\/\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` +# 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_lineno_1=$LINENO - as_lineno_2=$LINENO - test "x$as_lineno_1" != "x$as_lineno_2" && - test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || { - # Create $as_me.lineno as a copy of $as_myself, but with $LINENO - # uniformly replaced by the line number. The first 'sed' inserts a - # line-number line after each line using $LINENO; the second 'sed' - # does the real work. The second script uses 'N' to pair each - # line-number line with the line containing $LINENO, and appends - # trailing '-' during substitution so that $LINENO is not a special - # case at line end. - # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the - # scripts with optimization help from Paolo Bonzini. Blame Lee - # E. McMahon (1931-1989) for sed's syntax. :-) + as_lineno_1=$LINENO as_lineno_1a=$LINENO + as_lineno_2=$LINENO as_lineno_2a=$LINENO + eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" && + test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || { + # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-) sed -n ' p /[$]LINENO/= @@ -473,8 +442,7 @@ test \$exitcode = 0") || { s/-\n.*// ' >$as_me.lineno && chmod +x "$as_me.lineno" || - { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2 - { (exit 1); exit 1; }; } + { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; } # Don't try to exec as it changes $[0], causing all sort of problems # (the dirname of $[0] is not the place where we might find the @@ -484,29 +452,18 @@ test \$exitcode = 0") || { exit } - -if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then - as_dirname=dirname -else - as_dirname=false -fi - ECHO_C= ECHO_N= ECHO_T= -case `echo -n x` in +case `echo -n x` in #((((( -n*) - case `echo 'x\c'` in + case `echo 'xy\c'` in *c*) ECHO_T=' ';; # ECHO_T is single tab character. - *) ECHO_C='\c';; + xy) ECHO_C='\c';; + *) echo `echo ksh88 bug on AIX 6.1` > /dev/null + ECHO_T=' ';; esac;; *) ECHO_N='-n';; esac -if expr a : '\(a\)' >/dev/null 2>&1 && - test "X`expr 00001 : '.*\(...\)'`" = X001; then - as_expr=expr -else - as_expr=false -fi rm -f conf$$ conf$$.exe conf$$.file if test -d conf$$.dir; then @@ -536,7 +493,7 @@ rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file rmdir conf$$.dir 2>/dev/null if mkdir -p . 2>/dev/null; then - as_mkdir_p=: + as_mkdir_p='mkdir -p "$as_dir"' else test -d ./-p && rmdir ./-p as_mkdir_p=false @@ -555,10 +512,10 @@ else if test -d "$1"; then test -d "$1/."; else - case $1 in + case $1 in #( -*)set "./$1";; esac; - case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in + case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #(( ???[sx]*):;;*)false;;esac;fi '\'' sh ' @@ -572,8 +529,8 @@ as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" - -exec 7<&0 &1 +test -n "$DJDIR" || exec 7<&0 &1 # Name of the host. # hostname on some systems (SVR3.2, Linux) returns a bogus exit status, @@ -591,14 +548,14 @@ cross_compiling=no subdirs= MFLAGS= MAKEFLAGS= -SHELL=${CONFIG_SHELL-/bin/sh} # Identity of this package. PACKAGE_NAME='clustalw' PACKAGE_TARNAME='clustalw' -PACKAGE_VERSION='2.0.12' -PACKAGE_STRING='clustalw 2.0.12' +PACKAGE_VERSION='2.1' +PACKAGE_STRING='clustalw 2.1' PACKAGE_BUGREPORT='clustalw@ucd.ie' +PACKAGE_URL='' # Factoring default headers for most tests. ac_includes_default="\ @@ -636,7 +593,9 @@ ac_includes_default="\ # include #endif" -ac_subst_vars='LTLIBOBJS +ac_subst_vars='am__EXEEXT_FALSE +am__EXEEXT_TRUE +LTLIBOBJS LIBOBJS EGREP GREP @@ -731,6 +690,7 @@ bindir program_transform_name prefix exec_prefix +PACKAGE_URL PACKAGE_BUGREPORT PACKAGE_STRING PACKAGE_VERSION @@ -864,8 +824,7 @@ do ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2 - { (exit 1); exit 1; }; } + as_fn_error "invalid feature name: $ac_useropt" ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -891,8 +850,7 @@ do ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2 - { (exit 1); exit 1; }; } + as_fn_error "invalid feature name: $ac_useropt" ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1096,8 +1054,7 @@ do ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - { $as_echo "$as_me: error: invalid package name: $ac_useropt" >&2 - { (exit 1); exit 1; }; } + as_fn_error "invalid package name: $ac_useropt" ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1113,8 +1070,7 @@ do ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - { $as_echo "$as_me: error: invalid package name: $ac_useropt" >&2 - { (exit 1); exit 1; }; } + as_fn_error "invalid package name: $ac_useropt" ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1144,17 +1100,17 @@ do | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*) x_libraries=$ac_optarg ;; - -*) { $as_echo "$as_me: error: unrecognized option: $ac_option -Try \`$0 --help' for more information." >&2 - { (exit 1); exit 1; }; } + -*) as_fn_error "unrecognized option: \`$ac_option' +Try \`$0 --help' for more information." ;; *=*) ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='` # Reject names that are not valid shell variable names. - expr "x$ac_envvar" : ".*[^_$as_cr_alnum]" >/dev/null && - { $as_echo "$as_me: error: invalid variable name: $ac_envvar" >&2 - { (exit 1); exit 1; }; } + case $ac_envvar in #( + '' | [0-9]* | *[!_$as_cr_alnum]* ) + as_fn_error "invalid variable name: \`$ac_envvar'" ;; + esac eval $ac_envvar=\$ac_optarg export $ac_envvar ;; @@ -1171,15 +1127,13 @@ done if test -n "$ac_prev"; then ac_option=--`echo $ac_prev | sed 's/_/-/g'` - { $as_echo "$as_me: error: missing argument to $ac_option" >&2 - { (exit 1); exit 1; }; } + as_fn_error "missing argument to $ac_option" fi if test -n "$ac_unrecognized_opts"; then case $enable_option_checking in no) ;; - fatal) { $as_echo "$as_me: error: unrecognized options: $ac_unrecognized_opts" >&2 - { (exit 1); exit 1; }; } ;; + fatal) as_fn_error "unrecognized options: $ac_unrecognized_opts" ;; *) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;; esac fi @@ -1202,8 +1156,7 @@ do [\\/$]* | ?:[\\/]* ) continue;; NONE | '' ) case $ac_var in *prefix ) continue;; esac;; esac - { $as_echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2 - { (exit 1); exit 1; }; } + as_fn_error "expected an absolute directory name for --$ac_var: $ac_val" done # There might be people who depend on the old broken behavior: `$host' @@ -1233,11 +1186,9 @@ test "$silent" = yes && exec 6>/dev/null ac_pwd=`pwd` && test -n "$ac_pwd" && ac_ls_di=`ls -di .` && ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` || - { $as_echo "$as_me: error: working directory cannot be determined" >&2 - { (exit 1); exit 1; }; } + as_fn_error "working directory cannot be determined" test "X$ac_ls_di" = "X$ac_pwd_ls_di" || - { $as_echo "$as_me: error: pwd does not report name of working directory" >&2 - { (exit 1); exit 1; }; } + as_fn_error "pwd does not report name of working directory" # Find the source files, if location was not specified. @@ -1276,13 +1227,11 @@ else fi if test ! -r "$srcdir/$ac_unique_file"; then test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .." - { $as_echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2 - { (exit 1); exit 1; }; } + as_fn_error "cannot find sources ($ac_unique_file) in $srcdir" fi ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work" ac_abs_confdir=`( - cd "$srcdir" && test -r "./$ac_unique_file" || { $as_echo "$as_me: error: $ac_msg" >&2 - { (exit 1); exit 1; }; } + cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error "$ac_msg" pwd)` # When building in place, set srcdir=. if test "$ac_abs_confdir" = "$ac_pwd"; then @@ -1308,7 +1257,7 @@ if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -\`configure' configures clustalw 2.0.12 to adapt to many kinds of systems. +\`configure' configures clustalw 2.1 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1379,7 +1328,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of clustalw 2.0.12:";; + short | recursive ) echo "Configuration of clustalw 2.1:";; esac cat <<\_ACEOF @@ -1401,7 +1350,7 @@ Some influential environment variables: LDFLAGS linker flags, e.g. -L if you have libraries in a nonstandard directory LIBS libraries to pass to the linker, e.g. -l - CPPFLAGS C/C++/Objective C preprocessor flags, e.g. -I if + CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I if you have headers in a nonstandard directory CXX C++ compiler command CXXFLAGS C++ compiler flags @@ -1410,85 +1359,467 @@ Some influential environment variables: Use these variables to override the choices made by `configure' or to help it to find libraries and programs with nonstandard names/locations. -Report bugs to . +Report bugs to . +_ACEOF +ac_status=$? +fi + +if test "$ac_init_help" = "recursive"; then + # If there are subdirs, report their specific --help. + for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue + test -d "$ac_dir" || + { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } || + continue + ac_builddir=. + +case "$ac_dir" in +.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;; +*) + ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'` + # A ".." for each directory in $ac_dir_suffix. + ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'` + case $ac_top_builddir_sub in + "") ac_top_builddir_sub=. ac_top_build_prefix= ;; + *) ac_top_build_prefix=$ac_top_builddir_sub/ ;; + esac ;; +esac +ac_abs_top_builddir=$ac_pwd +ac_abs_builddir=$ac_pwd$ac_dir_suffix +# for backward compatibility: +ac_top_builddir=$ac_top_build_prefix + +case $srcdir in + .) # We are building in place. + ac_srcdir=. + ac_top_srcdir=$ac_top_builddir_sub + ac_abs_top_srcdir=$ac_pwd ;; + [\\/]* | ?:[\\/]* ) # Absolute name. + ac_srcdir=$srcdir$ac_dir_suffix; + ac_top_srcdir=$srcdir + ac_abs_top_srcdir=$srcdir ;; + *) # Relative name. + ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix + ac_top_srcdir=$ac_top_build_prefix$srcdir + ac_abs_top_srcdir=$ac_pwd/$srcdir ;; +esac +ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix + + cd "$ac_dir" || { ac_status=$?; continue; } + # Check for guested configure. + if test -f "$ac_srcdir/configure.gnu"; then + echo && + $SHELL "$ac_srcdir/configure.gnu" --help=recursive + elif test -f "$ac_srcdir/configure"; then + echo && + $SHELL "$ac_srcdir/configure" --help=recursive + else + $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2 + fi || ac_status=$? + cd "$ac_pwd" || { ac_status=$?; break; } + done +fi + +test -n "$ac_init_help" && exit $ac_status +if $ac_init_version; then + cat <<\_ACEOF +clustalw configure 2.1 +generated by GNU Autoconf 2.65 + +Copyright (C) 2009 Free Software Foundation, Inc. +This configure script is free software; the Free Software Foundation +gives unlimited permission to copy, distribute and modify it. +_ACEOF + exit +fi + +## ------------------------ ## +## Autoconf initialization. ## +## ------------------------ ## + +# ac_fn_c_try_compile LINENO +# -------------------------- +# Try to compile conftest.$ac_ext, and return whether this succeeded. +ac_fn_c_try_compile () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + 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:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compile") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + grep -v '^ *+' conftest.err >conftest.er1 + cat conftest.er1 >&5 + mv -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then : + ac_retval=0 +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_retval=1 +fi + eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;} + as_fn_set_status $ac_retval + +} # ac_fn_c_try_compile + +# ac_fn_cxx_try_compile LINENO +# ---------------------------- +# Try to compile conftest.$ac_ext, and return whether this succeeded. +ac_fn_cxx_try_compile () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + 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:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compile") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + grep -v '^ *+' conftest.err >conftest.er1 + cat conftest.er1 >&5 + mv -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then : + ac_retval=0 +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_retval=1 +fi + eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;} + as_fn_set_status $ac_retval + +} # ac_fn_cxx_try_compile + +# ac_fn_cxx_try_cpp LINENO +# ------------------------ +# Try to preprocess conftest.$ac_ext, and return whether this succeeded. +ac_fn_cxx_try_cpp () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + 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:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + grep -v '^ *+' conftest.err >conftest.er1 + cat conftest.er1 >&5 + mv -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } >/dev/null && { + test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" || + test ! -s conftest.err + }; then : + ac_retval=0 +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_retval=1 +fi + eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;} + as_fn_set_status $ac_retval + +} # ac_fn_cxx_try_cpp + +# ac_fn_cxx_try_run LINENO +# ------------------------ +# Try to link conftest.$ac_ext, and return whether this succeeded. Assumes +# that executables *can* be run. +ac_fn_cxx_try_run () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + if { { ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } && { ac_try='./conftest$ac_exeext' + { { case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; }; then : + ac_retval=0 +else + $as_echo "$as_me: program exited with status $ac_status" >&5 + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_retval=$ac_status +fi + rm -rf conftest.dSYM conftest_ipa8_conftest.oo + eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;} + as_fn_set_status $ac_retval + +} # ac_fn_cxx_try_run + +# ac_fn_cxx_check_type LINENO TYPE VAR INCLUDES +# --------------------------------------------- +# Tests whether TYPE exists after having included INCLUDES, setting cache +# variable VAR accordingly. +ac_fn_cxx_check_type () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 +$as_echo_n "checking for $2... " >&6; } +if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then : + $as_echo_n "(cached) " >&6 +else + eval "$3=no" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +if (sizeof ($2)) + return 0; + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +int +main () +{ +if (sizeof (($2))) + return 0; + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + +else + eval "$3=yes" +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +eval ac_res=\$$3 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } + eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;} + +} # ac_fn_cxx_check_type + +# ac_fn_cxx_check_header_compile LINENO HEADER VAR INCLUDES +# --------------------------------------------------------- +# Tests whether HEADER exists and can be compiled using the include files in +# INCLUDES, setting the cache variable VAR accordingly. +ac_fn_cxx_check_header_compile () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 +$as_echo_n "checking for $2... " >&6; } +if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then : + $as_echo_n "(cached) " >&6 +else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +$4 +#include <$2> +_ACEOF +if ac_fn_cxx_try_compile "$LINENO"; then : + eval "$3=yes" +else + eval "$3=no" +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +eval ac_res=\$$3 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } + eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;} + +} # ac_fn_cxx_check_header_compile + +# ac_fn_cxx_check_header_mongrel LINENO HEADER VAR INCLUDES +# --------------------------------------------------------- +# Tests whether HEADER exists, giving a warning if it cannot be compiled using +# the include files in INCLUDES and setting the cache variable VAR +# accordingly. +ac_fn_cxx_check_header_mongrel () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 +$as_echo_n "checking for $2... " >&6; } +if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then : + $as_echo_n "(cached) " >&6 +fi +eval ac_res=\$$3 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +else + # Is the header compilable? +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 usability" >&5 +$as_echo_n "checking $2 usability... 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" >&6; } +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include <$2> +_ACEOF +if ac_fn_cxx_try_cpp "$LINENO"; then : + ac_header_preproc=yes +else + ac_header_preproc=no +fi +rm -f conftest.err conftest.$ac_ext +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5 +$as_echo "$ac_header_preproc" >&6; } -case "$ac_dir" in -.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;; -*) - ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'` - # A ".." for each directory in $ac_dir_suffix. - ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'` - case $ac_top_builddir_sub in - "") ac_top_builddir_sub=. ac_top_build_prefix= ;; - *) ac_top_build_prefix=$ac_top_builddir_sub/ ;; - esac ;; +# So? What about this header? +case $ac_header_compiler:$ac_header_preproc:$ac_cxx_preproc_warn_flag in #(( + yes:no: ) + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&5 +$as_echo "$as_me: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5 +$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;} + ;; + no:yes:* ) + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: present but cannot be compiled" >&5 +$as_echo "$as_me: WARNING: $2: present but cannot be compiled" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: check for missing prerequisite headers?" >&5 +$as_echo "$as_me: WARNING: $2: check for missing prerequisite headers?" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: see the Autoconf documentation" >&5 +$as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&5 +$as_echo "$as_me: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5 +$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;} +( cat <<\_ASBOX +## ------------------------------ ## +## Report this to clustalw@ucd.ie ## +## ------------------------------ ## +_ASBOX + ) | sed "s/^/$as_me: WARNING: /" >&2 + ;; esac -ac_abs_top_builddir=$ac_pwd -ac_abs_builddir=$ac_pwd$ac_dir_suffix -# for backward compatibility: -ac_top_builddir=$ac_top_build_prefix + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 +$as_echo_n "checking for $2... " >&6; } +if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then : + $as_echo_n "(cached) " >&6 +else + eval "$3=\$ac_header_compiler" +fi +eval ac_res=\$$3 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +fi + eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;} -case $srcdir in - .) # We are building in place. - ac_srcdir=. - ac_top_srcdir=$ac_top_builddir_sub - ac_abs_top_srcdir=$ac_pwd ;; - [\\/]* | ?:[\\/]* ) # Absolute name. - ac_srcdir=$srcdir$ac_dir_suffix; - ac_top_srcdir=$srcdir - ac_abs_top_srcdir=$srcdir ;; - *) # Relative name. - ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix - ac_top_srcdir=$ac_top_build_prefix$srcdir - ac_abs_top_srcdir=$ac_pwd/$srcdir ;; +} # ac_fn_cxx_check_header_mongrel + +# ac_fn_cxx_try_link LINENO +# ------------------------- +# Try to link conftest.$ac_ext, and return whether this succeeded. +ac_fn_cxx_try_link () +{ + as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + 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=$ac_try;; esac -ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_link") 2>conftest.err + ac_status=$? + if test -s conftest.err; then + grep -v '^ *+' conftest.err >conftest.er1 + cat conftest.er1 >&5 + mv -f conftest.er1 conftest.err + fi + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then : + ac_retval=0 +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 - cd "$ac_dir" || { ac_status=$?; continue; } - # Check for guested configure. - if test -f "$ac_srcdir/configure.gnu"; then - echo && - $SHELL "$ac_srcdir/configure.gnu" --help=recursive - elif test -f "$ac_srcdir/configure"; then - echo && - $SHELL "$ac_srcdir/configure" --help=recursive - else - $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2 - fi || ac_status=$? - cd "$ac_pwd" || { ac_status=$?; break; } - done + ac_retval=1 fi + # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information + # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would + # interfere with the next link command; also delete a directory that is + # left behind by Apple's compiler. We do this before executing the actions. + rm -rf conftest.dSYM conftest_ipa8_conftest.oo + eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;} + as_fn_set_status $ac_retval -test -n "$ac_init_help" && exit $ac_status -if $ac_init_version; then - cat <<\_ACEOF -clustalw configure 2.0.12 -generated by GNU Autoconf 2.63 - -Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, -2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. -This configure script is free software; the Free Software Foundation -gives unlimited permission to copy, distribute and modify it. -_ACEOF - exit -fi +} # ac_fn_cxx_try_link cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. -It was created by clustalw $as_me 2.0.12, which was -generated by GNU Autoconf 2.63. Invocation command line was +It was created by clustalw $as_me 2.1, which was +generated by GNU Autoconf 2.65. Invocation command line was $ $0 $@ @@ -1524,8 +1855,8 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - $as_echo "PATH: $as_dir" -done + $as_echo "PATH: $as_dir" + done IFS=$as_save_IFS } >&5 @@ -1562,9 +1893,9 @@ do ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;; esac case $ac_pass in - 1) ac_configure_args0="$ac_configure_args0 '$ac_arg'" ;; + 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;; 2) - ac_configure_args1="$ac_configure_args1 '$ac_arg'" + as_fn_append ac_configure_args1 " '$ac_arg'" if test $ac_must_keep_next = true; then ac_must_keep_next=false # Got value, back to normal. else @@ -1580,13 +1911,13 @@ do -* ) ac_must_keep_next=true ;; esac fi - ac_configure_args="$ac_configure_args '$ac_arg'" + as_fn_append ac_configure_args " '$ac_arg'" ;; esac done done -$as_unset ac_configure_args0 || test "${ac_configure_args0+set}" != set || { ac_configure_args0=; export ac_configure_args0; } -$as_unset ac_configure_args1 || test "${ac_configure_args1+set}" != set || { ac_configure_args1=; export ac_configure_args1; } +{ ac_configure_args0=; unset ac_configure_args0;} +{ ac_configure_args1=; unset ac_configure_args1;} # When interrupted or exit'd, cleanup temporary files, and complete # config.log. We remove comments because anyway the quotes in there @@ -1611,13 +1942,13 @@ _ASBOX case $ac_val in #( *${as_nl}*) case $ac_var in #( - *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5 + *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; esac case $ac_var in #( _ | IFS | as_nl) ;; #( BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( - *) $as_unset $ac_var ;; + *) { eval $ac_var=; unset $ac_var;} ;; esac ;; esac done @@ -1689,39 +2020,41 @@ _ASBOX exit $exit_status ' 0 for ac_signal in 1 2 13 15; do - trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal + trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal done ac_signal=0 # confdefs.h avoids OS command line length limits that DEFS can exceed. rm -f -r conftest* confdefs.h +$as_echo "/* confdefs.h */" > confdefs.h + # Predefined preprocessor variables. cat >>confdefs.h <<_ACEOF #define PACKAGE_NAME "$PACKAGE_NAME" _ACEOF - cat >>confdefs.h <<_ACEOF #define PACKAGE_TARNAME "$PACKAGE_TARNAME" _ACEOF - cat >>confdefs.h <<_ACEOF #define PACKAGE_VERSION "$PACKAGE_VERSION" _ACEOF - cat >>confdefs.h <<_ACEOF #define PACKAGE_STRING "$PACKAGE_STRING" _ACEOF - cat >>confdefs.h <<_ACEOF #define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT" _ACEOF +cat >>confdefs.h <<_ACEOF +#define PACKAGE_URL "$PACKAGE_URL" +_ACEOF + # Let the site file select an alternate cache file if it wants to. # Prefer an explicitly selected file to automatically selected ones. @@ -1739,8 +2072,8 @@ fi for ac_site_file in "$ac_site_file1" "$ac_site_file2" do test "x$ac_site_file" = xNONE && continue - if test -r "$ac_site_file"; then - { $as_echo "$as_me:$LINENO: loading site script $ac_site_file" >&5 + if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5 $as_echo "$as_me: loading site script $ac_site_file" >&6;} sed 's/^/| /' "$ac_site_file" >&5 . "$ac_site_file" @@ -1748,10 +2081,10 @@ $as_echo "$as_me: loading site script $ac_site_file" >&6;} done if test -r "$cache_file"; then - # Some versions of bash will fail to source /dev/null (special - # files actually), so we avoid doing that. - if test -f "$cache_file"; then - { $as_echo "$as_me:$LINENO: loading cache $cache_file" >&5 + # Some versions of bash will fail to source /dev/null (special files + # actually), so we avoid doing that. DJGPP emulates it as a regular file. + if test /dev/null != "$cache_file" && test -f "$cache_file"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5 $as_echo "$as_me: loading cache $cache_file" >&6;} case $cache_file in [\\/]* | ?:[\\/]* ) . "$cache_file";; @@ -1759,7 +2092,7 @@ $as_echo "$as_me: loading cache $cache_file" >&6;} esac fi else - { $as_echo "$as_me:$LINENO: creating cache $cache_file" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5 $as_echo "$as_me: creating cache $cache_file" >&6;} >$cache_file fi @@ -1774,11 +2107,11 @@ for ac_var in $ac_precious_vars; do eval ac_new_val=\$ac_env_${ac_var}_value case $ac_old_set,$ac_new_set in set,) - { $as_echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 $as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} ac_cache_corrupted=: ;; ,set) - { $as_echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5 $as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_cache_corrupted=: ;; ,);; @@ -1788,17 +2121,17 @@ $as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_old_val_w=`echo x $ac_old_val` ac_new_val_w=`echo x $ac_new_val` if test "$ac_old_val_w" != "$ac_new_val_w"; then - { $as_echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5 $as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} ac_cache_corrupted=: else - { $as_echo "$as_me:$LINENO: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 $as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;} eval $ac_var=\$ac_old_val fi - { $as_echo "$as_me:$LINENO: former value: \`$ac_old_val'" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5 $as_echo "$as_me: former value: \`$ac_old_val'" >&2;} - { $as_echo "$as_me:$LINENO: current value: \`$ac_new_val'" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5 $as_echo "$as_me: current value: \`$ac_new_val'" >&2;} fi;; esac @@ -1810,43 +2143,20 @@ $as_echo "$as_me: current value: \`$ac_new_val'" >&2;} esac case " $ac_configure_args " in *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy. - *) ac_configure_args="$ac_configure_args '$ac_arg'" ;; + *) as_fn_append ac_configure_args " '$ac_arg'" ;; esac fi done if $ac_cache_corrupted; then - { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} - { $as_echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5 $as_echo "$as_me: error: changes in the environment can compromise the build" >&2;} - { { $as_echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5 -$as_echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 fi - - - - - - - - - - - - - - - - - - - - - - - - +## -------------------- ## +## Main body of script. ## +## -------------------- ## ac_ext=c ac_cpp='$CPP $CPPFLAGS' @@ -1873,24 +2183,16 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu # AC_CANONICAL_SYSTEM will also run AC_CANONICAL_HOST and allows to use --target ac_aux_dir= for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do - if test -f "$ac_dir/install-sh"; then - ac_aux_dir=$ac_dir - ac_install_sh="$ac_aux_dir/install-sh -c" - break - elif test -f "$ac_dir/install.sh"; then - ac_aux_dir=$ac_dir - ac_install_sh="$ac_aux_dir/install.sh -c" - break - elif test -f "$ac_dir/shtool"; then - ac_aux_dir=$ac_dir - ac_install_sh="$ac_aux_dir/shtool install -c" - break - fi + for ac_t in install-sh install.sh shtool; do + if test -f "$ac_dir/$ac_t"; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/$ac_t -c" + break 2 + fi + done done if test -z "$ac_aux_dir"; then - { { $as_echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&5 -$as_echo "$as_me: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5 fi # These three variables are undocumented and unsupported, @@ -1904,35 +2206,27 @@ ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var. # 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_fn_error "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5 -{ $as_echo "$as_me:$LINENO: checking build system type" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5 $as_echo_n "checking build system type... " >&6; } -if test "${ac_cv_build+set}" = set; then +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 "$as_me: error: cannot guess build type; you must specify one" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "cannot guess build type; you must specify one" "$LINENO" 5 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 $ac_build_alias failed" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5 fi -{ $as_echo "$as_me:$LINENO: result: $ac_cv_build" >&5 +{ $as_echo "$as_me:${as_lineno-$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 "$as_me: error: invalid value of canonical build" >&2;} - { (exit 1); exit 1; }; };; +*) as_fn_error "invalid value of canonical build" "$LINENO" 5;; esac build=$ac_cv_build ac_save_IFS=$IFS; IFS='-' @@ -1948,28 +2242,24 @@ 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 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5 $as_echo_n "checking host system type... " >&6; } -if test "${ac_cv_host+set}" = set; then +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 $host_alias failed" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5 fi fi -{ $as_echo "$as_me:$LINENO: result: $ac_cv_host" >&5 +{ $as_echo "$as_me:${as_lineno-$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 "$as_me: error: invalid value of canonical host" >&2;} - { (exit 1); exit 1; }; };; +*) as_fn_error "invalid value of canonical host" "$LINENO" 5;; esac host=$ac_cv_host ac_save_IFS=$IFS; IFS='-' @@ -1985,28 +2275,24 @@ IFS=$ac_save_IFS case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac -{ $as_echo "$as_me:$LINENO: checking target system type" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking target system type" >&5 $as_echo_n "checking target system type... " >&6; } -if test "${ac_cv_target+set}" = set; then +if test "${ac_cv_target+set}" = set; then : $as_echo_n "(cached) " >&6 else if test "x$target_alias" = x; then ac_cv_target=$ac_cv_host else ac_cv_target=`$SHELL "$ac_aux_dir/config.sub" $target_alias` || - { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&5 -$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5 fi fi -{ $as_echo "$as_me:$LINENO: result: $ac_cv_target" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_target" >&5 $as_echo "$ac_cv_target" >&6; } case $ac_cv_target in *-*-*) ;; -*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical target" >&5 -$as_echo "$as_me: error: invalid value of canonical target" >&2;} - { (exit 1); exit 1; }; };; +*) as_fn_error "invalid value of canonical target" "$LINENO" 5;; esac target=$ac_cv_target ac_save_IFS=$IFS; IFS='-' @@ -2028,42 +2314,33 @@ test -n "$target_alias" && test "$program_prefix$program_suffix$program_transform_name" = \ NONENONEs,x,x, && program_prefix=${target_alias}- + # DEFINES here are going to config.h and have to be the same as in clustalx.pro #echo "host_os $host_os" case $target_os in *linux*|*solaris*|*bsd*) -cat >>confdefs.h <<\_ACEOF -#define OS_UNIX 1 -_ACEOF +$as_echo "#define OS_UNIX 1" >>confdefs.h ;; *darwin*) -cat >>confdefs.h <<\_ACEOF -#define OS_MAC 1 -_ACEOF +$as_echo "#define OS_MAC 1" >>confdefs.h -cat >>confdefs.h <<\_ACEOF -#define OS_UNIX 1 -_ACEOF +$as_echo "#define OS_UNIX 1" >>confdefs.h ;; *cygwin*|*mingw*) -cat >>confdefs.h <<\_ACEOF -#define OS_WINDOWS 1 -_ACEOF +$as_echo "#define OS_WINDOWS 1" >>confdefs.h ;; *) - { $as_echo "$as_me:$LINENO: WARNING: \"Couldn't determine target operating system. Using Unix\"" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \"Couldn't determine target operating system. Using Unix\"" >&5 $as_echo "$as_me: WARNING: \"Couldn't determine target operating system. Using Unix\"" >&2;}; -cat >>confdefs.h <<\_ACEOF -#define OS_UNIX 1 -_ACEOF +$as_echo "#define OS_UNIX 1" >>confdefs.h ;; esac @@ -2081,7 +2358,7 @@ CLUSTALW_NAME="ClustalW" # 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__api_version='1.10' +am__api_version='1.11' # Find a good install program. We prefer a C program (faster), # so one script is as good as another. But avoid the broken or @@ -2097,10 +2374,10 @@ am__api_version='1.10' # 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 +{ $as_echo "$as_me:${as_lineno-$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 "${ac_cv_path_install+set}" = set; then +if test "${ac_cv_path_install+set}" = set; then : $as_echo_n "(cached) " >&6 else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR @@ -2108,11 +2385,11 @@ 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/* | \ + # 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\\/* | \ + ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \ /usr/ucb/* ) ;; *) # OSF1 and SCO ODT 3.0 have their own names for install. @@ -2149,7 +2426,7 @@ case $as_dir/ in ;; esac -done + done IFS=$as_save_IFS rm -rf conftest.one conftest.two conftest.dir @@ -2165,7 +2442,7 @@ fi INSTALL=$ac_install_sh fi fi -{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5 $as_echo "$INSTALL" >&6; } # Use test -z because SunOS4 sh mishandles braces in ${var-val}. @@ -2176,21 +2453,34 @@ test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' -{ $as_echo "$as_me:$LINENO: checking whether build environment is sane" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5 $as_echo_n "checking whether build environment is sane... " >&6; } # Just in case sleep 1 echo timestamp > conftest.file +# Reject unsafe characters in $srcdir or the absolute working directory +# name. Accept space and tab only in the latter. +am_lf=' +' +case `pwd` in + *[\\\"\#\$\&\'\`$am_lf]*) + as_fn_error "unsafe absolute working directory name" "$LINENO" 5;; +esac +case $srcdir in + *[\\\"\#\$\&\'\`$am_lf\ \ ]*) + as_fn_error "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;; +esac + # Do `set' in a subshell so we don't clobber the current shell's # arguments. Must try -L first in case configure is actually a # symlink; some systems play weird games with the mod time of symlinks # (eg FreeBSD returns the mod time of the symlink's containing # directory). if ( - set X `ls -Lt $srcdir/configure conftest.file 2> /dev/null` + set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null` if test "$*" = "X"; then # -L didn't work. - set X `ls -t $srcdir/configure conftest.file` + set X `ls -t "$srcdir/configure" conftest.file` fi rm -f conftest.file if test "$*" != "X $srcdir/configure conftest.file" \ @@ -2200,11 +2490,8 @@ if ( # if, for instance, CONFIG_SHELL is bash and it inherits a # broken ls alias from the environment. This has actually # happened. Such a system could not be considered "sane". - { { $as_echo "$as_me:$LINENO: error: ls -t appears to fail. Make sure there is not a broken -alias in your environment" >&5 -$as_echo "$as_me: error: ls -t appears to fail. Make sure there is not a broken -alias in your environment" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "ls -t appears to fail. Make sure there is not a broken +alias in your environment" "$LINENO" 5 fi test "$2" = conftest.file @@ -2213,13 +2500,10 @@ then # Ok. : else - { { $as_echo "$as_me:$LINENO: error: newly created file is older than distributed files! -Check your system clock" >&5 -$as_echo "$as_me: error: newly created file is older than distributed files! -Check your system clock" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "newly created file is older than distributed files! +Check your system clock" "$LINENO" 5 fi -{ $as_echo "$as_me:$LINENO: result: yes" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } test "$program_prefix" != NONE && program_transform_name="s&^&$program_prefix&;$program_transform_name" @@ -2234,20 +2518,136 @@ program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"` # expand $ac_aux_dir to an absolute path am_aux_dir=`cd $ac_aux_dir && pwd` -test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing" +if test x"${MISSING+set}" != xset; then + case $am_aux_dir in + *\ * | *\ *) + MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;; + *) + MISSING="\${SHELL} $am_aux_dir/missing" ;; + esac +fi # Use eval to expand $SHELL if eval "$MISSING --run true"; then am_missing_run="$MISSING --run " else am_missing_run= - { $as_echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5 $as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;} fi -{ $as_echo "$as_me:$LINENO: checking for a thread-safe mkdir -p" >&5 +if test x"${install_sh}" != xset; then + case $am_aux_dir in + *\ * | *\ *) + install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;; + *) + install_sh="\${SHELL} $am_aux_dir/install-sh" + esac +fi + +# Installed binaries are usually stripped using `strip' when the user +# run `make install-strip'. However `strip' might not be the right +# tool to use in cross-compilation environments, therefore Automake +# will honor the `STRIP' environment variable to overrule this program. +if test "$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:${as_lineno-$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:${as_lineno-$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:${as_lineno-$LINENO}: result: $STRIP" >&5 +$as_echo "$STRIP" >&6; } +else + { $as_echo "$as_me:${as_lineno-$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:${as_lineno-$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:${as_lineno-$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:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5 +$as_echo "$ac_ct_STRIP" >&6; } +else + { $as_echo "$as_me:${as_lineno-$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:${as_lineno-$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" + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5 $as_echo_n "checking for a thread-safe mkdir -p... " >&6; } if test -z "$MKDIR_P"; then - if test "${ac_cv_path_mkdir+set}" = set; then + if test "${ac_cv_path_mkdir+set}" = set; then : $as_echo_n "(cached) " >&6 else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR @@ -2255,7 +2655,7 @@ for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_prog in mkdir gmkdir; do + for ac_prog in mkdir gmkdir; do for ac_exec_ext in '' $ac_executable_extensions; do { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #( @@ -2267,11 +2667,12 @@ do esac done done -done + done IFS=$as_save_IFS fi + test -d ./--version && rmdir ./--version if test "${ac_cv_path_mkdir+set}" = set; then MKDIR_P="$ac_cv_path_mkdir -p" else @@ -2279,11 +2680,10 @@ fi # 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 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5 $as_echo "$MKDIR_P" >&6; } mkdir_p="$MKDIR_P" @@ -2296,9 +2696,9 @@ for ac_prog in gawk mawk nawk awk do # Extract the first word of "$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 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_AWK+set}" = set; then +if test "${ac_cv_prog_AWK+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$AWK"; then @@ -2309,24 +2709,24 @@ 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 + 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 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done IFS=$as_save_IFS fi fi AWK=$ac_cv_prog_AWK if test -n "$AWK"; then - { $as_echo "$as_me:$LINENO: result: $AWK" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5 $as_echo "$AWK" >&6; } else - { $as_echo "$as_me:$LINENO: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi @@ -2334,11 +2734,11 @@ fi test -n "$AWK" && break done -{ $as_echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5 +{ $as_echo "$as_me:${as_lineno-$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 \"\${$as_var+set}\" = set"; }; then +if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then : $as_echo_n "(cached) " >&6 else cat >conftest.make <<\_ACEOF @@ -2356,11 +2756,11 @@ esac rm -f conftest.make fi if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then - { $as_echo "$as_me:$LINENO: result: yes" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } SET_MAKE= else - { $as_echo "$as_me:$LINENO: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } SET_MAKE="MAKE=${MAKE-make}" fi @@ -2380,9 +2780,7 @@ if test "`cd $srcdir && pwd`" != "`pwd`"; then am__isrc=' -I$(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 "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "source directory already configured; run \"make distclean\" there first" "$LINENO" 5 fi fi @@ -2398,7 +2796,7 @@ fi # Define the identity of the package. PACKAGE='clustalw' - VERSION='2.0.12' + VERSION='2.1' cat >>confdefs.h <<_ACEOF @@ -2426,108 +2824,6 @@ 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="$ac_cv_prog_STRIP" -fi - -fi -INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s" - # We need awk for the "check" target. The system "awk" is bad on # some platforms. # Always define AMTAR for backward compatibility. @@ -2541,11 +2837,11 @@ am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -' -{ $as_echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5 +{ $as_echo "$as_me:${as_lineno-$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 \"\${$as_var+set}\" = set"; }; then +if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then : $as_echo_n "(cached) " >&6 else cat >conftest.make <<\_ACEOF @@ -2563,11 +2859,11 @@ esac rm -f conftest.make fi if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then - { $as_echo "$as_me:$LINENO: result: yes" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } SET_MAKE= else - { $as_echo "$as_me:$LINENO: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } SET_MAKE="MAKE=${MAKE-make}" fi @@ -2583,9 +2879,9 @@ 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 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_CC+set}" = set; then +if test "${ac_cv_prog_CC+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$CC"; then @@ -2596,24 +2892,24 @@ 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 + 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 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - { $as_echo "$as_me:$LINENO: result: $CC" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 $as_echo "$CC" >&6; } else - { $as_echo "$as_me:$LINENO: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi @@ -2623,9 +2919,9 @@ if test -z "$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 +{ $as_echo "$as_me:${as_lineno-$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 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CC"; then @@ -2636,24 +2932,24 @@ 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 + 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 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done IFS=$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 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 $as_echo "$ac_ct_CC" >&6; } else - { $as_echo "$as_me:$LINENO: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi @@ -2662,7 +2958,7 @@ fi 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:${as_lineno-$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 @@ -2676,9 +2972,9 @@ 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 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_CC+set}" = set; then +if test "${ac_cv_prog_CC+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$CC"; then @@ -2689,24 +2985,24 @@ 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 + 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 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - { $as_echo "$as_me:$LINENO: result: $CC" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 $as_echo "$CC" >&6; } else - { $as_echo "$as_me:$LINENO: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi @@ -2716,9 +3012,9 @@ fi if test -z "$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 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_CC+set}" = set; then +if test "${ac_cv_prog_CC+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$CC"; then @@ -2730,18 +3026,18 @@ 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 + 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 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done IFS=$as_save_IFS if test $ac_prog_rejected = yes; then @@ -2760,10 +3056,10 @@ fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - { $as_echo "$as_me:$LINENO: result: $CC" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 $as_echo "$CC" >&6; } else - { $as_echo "$as_me:$LINENO: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi @@ -2775,9 +3071,9 @@ if test -z "$CC"; then 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 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_CC+set}" = set; then +if test "${ac_cv_prog_CC+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$CC"; then @@ -2788,24 +3084,24 @@ 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 + 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 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - { $as_echo "$as_me:$LINENO: result: $CC" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 $as_echo "$CC" >&6; } else - { $as_echo "$as_me:$LINENO: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi @@ -2819,9 +3115,9 @@ if test -z "$CC"; then 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 +{ $as_echo "$as_me:${as_lineno-$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 +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CC"; then @@ -2832,24 +3128,24 @@ 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 + 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 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done IFS=$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 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 $as_echo "$ac_ct_CC" >&6; } else - { $as_echo "$as_me:$LINENO: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi @@ -2862,7 +3158,7 @@ done 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:${as_lineno-$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 @@ -2873,57 +3169,37 @@ fi fi -test -z "$CC" && { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$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 "$as_me: error: no acceptable C compiler found in \$PATH -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; }; } +as_fn_error "no acceptable C compiler found in \$PATH +See \`config.log' for more details." "$LINENO" 5; } # Provide some information about the compiler. -$as_echo "$as_me:$LINENO: checking for C compiler version" >&5 +$as_echo "$as_me:${as_lineno-$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" +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" case "(($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 +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err ac_status=$? - $as_echo "$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); } + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + fi + rm -f conftest.er1 conftest.err + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF +cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -2939,8 +3215,8 @@ ac_clean_files="$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... " >&6; } +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5 +$as_echo_n "checking whether the C compiler works... " >&6; } ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` # The possible output files: @@ -2956,17 +3232,17 @@ do done rm -f $ac_rmfiles -if { (ac_try="$ac_link_default" +if { { ac_try="$ac_link_default" case "(($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 "$ac_try_echo") >&5 +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 (eval "$ac_link_default") 2>&5 ac_status=$? - $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; then + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; then : # Autoconf-2.13 could set the ac_cv_exeext variable to `no'. # So ignore a value of `no', otherwise this would lead to `EXEEXT = no' # in a Makefile. We should not override ac_cv_exeext if it was cached, @@ -2983,7 +3259,7 @@ do # certainly right. break;; *.* ) - if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no; + if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no; then :; else ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` fi @@ -3002,84 +3278,42 @@ 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 +if test -z "$ac_file"; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +$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:${as_lineno-$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 "$as_me: error: C compiler cannot create executables -See \`config.log' for more details." >&2;} - { (exit 77); exit 77; }; }; } +{ as_fn_set_status 77 +as_fn_error "C compiler cannot create executables +See \`config.log' for more details." "$LINENO" 5; }; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +$as_echo "yes" >&6; } fi - +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5 +$as_echo_n "checking for C compiler default output file name... " >&6; } +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5 +$as_echo "$ac_file" >&6; } ac_exeext=$ac_cv_exeext -# Check that the compiler produces executables we can run. If not, either -# the compiler is broken, or we cross compile. -{ $as_echo "$as_me:$LINENO: checking whether the C compiler works" >&5 -$as_echo_n "checking whether the C compiler works... " >&6; } -# FIXME: These cross compiler hacks should be removed for Autoconf 3.0 -# If not cross compiling, check that we can run a simple program. -if test "$cross_compiling" != yes; then - if { ac_try='./$ac_file' - { (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 $ac_status); }; }; then - cross_compiling=no - else - if test "$cross_compiling" = maybe; then - cross_compiling=yes - else - { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 -$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -{ { $as_echo "$as_me:$LINENO: error: cannot run C compiled programs. -If you meant to cross compile, use \`--host'. -See \`config.log' for more details." >&5 -$as_echo "$as_me: error: cannot run C compiled programs. -If you meant to cross compile, use \`--host'. -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; }; } - fi - fi -fi -{ $as_echo "$as_me:$LINENO: result: yes" >&5 -$as_echo "yes" >&6; } - rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out ac_clean_files=$ac_clean_files_save -# Check that the compiler produces executables we can run. If not, either -# the compiler is broken, or we cross compile. -{ $as_echo "$as_me:$LINENO: checking whether we are cross compiling" >&5 -$as_echo_n "checking whether we are cross compiling... " >&6; } -{ $as_echo "$as_me:$LINENO: result: $cross_compiling" >&5 -$as_echo "$cross_compiling" >&6; } - -{ $as_echo "$as_me:$LINENO: checking for suffix of executables" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5 $as_echo_n "checking for suffix of executables... " >&6; } -if { (ac_try="$ac_link" +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 "$ac_try_echo") >&5 +eval ac_try_echo="\"\$as_me:${as_lineno-$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); }; then + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; then : # If both `conftest.exe' and `conftest' are `present' (well, observable) # catch `conftest.exe'. For instance with Cygwin, `ls conftest' will # work properly (i.e., refer to `conftest.exe'), while it won't with @@ -3094,32 +3328,83 @@ for ac_file in conftest.exe conftest conftest.*; do esac done else - { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 + { { $as_echo "$as_me:${as_lineno-$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 "$as_me: error: cannot compute suffix of executables: cannot compile and link -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; }; } +as_fn_error "cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." "$LINENO" 5; } fi - -rm -f conftest$ac_cv_exeext -{ $as_echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 +rm -f conftest conftest$ac_cv_exeext +{ $as_echo "$as_me:${as_lineno-$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:$LINENO: checking for suffix of object files" >&5 +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +int +main () +{ +FILE *f = fopen ("conftest.out", "w"); + return ferror (f) || fclose (f) != 0; + + ; + return 0; +} +_ACEOF +ac_clean_files="$ac_clean_files conftest.out" +# Check that the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5 +$as_echo_n "checking whether we are cross compiling... " >&6; } +if test "$cross_compiling" != yes; then + { { ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } + if { ac_try='./conftest$ac_cv_exeext' + { { case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; }; then + cross_compiling=no + else + if test "$cross_compiling" = maybe; then + cross_compiling=yes + else + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error "cannot run C compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." "$LINENO" 5; } + fi + fi +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5 +$as_echo "$cross_compiling" >&6; } + +rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out +ac_clean_files=$ac_clean_files_save +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5 $as_echo_n "checking for suffix of object files... " >&6; } -if test "${ac_cv_objext+set}" = set; then +if test "${ac_cv_objext+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 + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -3131,17 +3416,17 @@ main () } _ACEOF rm -f conftest.o conftest.obj -if { (ac_try="$ac_compile" +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 "$ac_try_echo") >&5 +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 (eval "$ac_compile") 2>&5 ac_status=$? - $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); }; then + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; }; then : for ac_file in conftest.o conftest.obj conftest.*; do test -f "$ac_file" || continue; case $ac_file in @@ -3154,31 +3439,23 @@ else $as_echo "$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:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile -See \`config.log' for more details." >&5 -$as_echo "$as_me: error: cannot compute suffix of object files: cannot compile -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; }; } +as_fn_error "cannot compute suffix of object files: cannot compile +See \`config.log' for more details." "$LINENO" 5; } fi - rm -f conftest.$ac_cv_objext conftest.$ac_ext fi -{ $as_echo "$as_me:$LINENO: result: $ac_cv_objext" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5 $as_echo "$ac_cv_objext" >&6; } OBJEXT=$ac_cv_objext ac_objext=$OBJEXT -{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 +{ $as_echo "$as_me:${as_lineno-$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 +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 + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -3192,37 +3469,16 @@ main () return 0; } _ACEOF -rm -f conftest.$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.$ac_objext; then +if ac_fn_c_try_compile "$LINENO"; then : ac_compiler_gnu=yes else - $as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - - ac_compiler_gnu=no + ac_compiler_gnu=no fi - rm -f core conftest.err conftest.$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 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5 $as_echo "$ac_cv_c_compiler_gnu" >&6; } if test $ac_compiler_gnu = yes; then GCC=yes @@ -3231,20 +3487,16 @@ else fi ac_test_CFLAGS=${CFLAGS+set} ac_save_CFLAGS=$CFLAGS -{ $as_echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 +{ $as_echo "$as_me:${as_lineno-$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 +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.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -3255,75 +3507,11 @@ 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.$ac_objext; then +if ac_fn_c_try_compile "$LINENO"; 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.$ac_ext <<_ACEOF + CFLAGS="" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -3334,42 +3522,33 @@ 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.$ac_objext; then - ac_cv_prog_cc_g=yes +if ac_fn_c_try_compile "$LINENO"; 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 confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +int +main () +{ + ; + return 0; +} +_ACEOF +if ac_fn_c_try_compile "$LINENO"; then : + ac_cv_prog_cc_g=yes 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 +{ $as_echo "$as_me:${as_lineno-$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 @@ -3386,18 +3565,14 @@ else CFLAGS= fi fi -{ $as_echo "$as_me:$LINENO: checking for $CC option to accept ISO C89" >&5 +{ $as_echo "$as_me:${as_lineno-$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 +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.$ac_ext <<_ACEOF +cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include @@ -3454,32 +3629,9 @@ 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.$ac_objext; then + if ac_fn_c_try_compile "$LINENO"; 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$ac_cv_prog_cc_c89" != "xno" && break done @@ -3490,17 +3642,19 @@ fi # AC_CACHE_VAL case "x$ac_cv_prog_cc_c89" in x) - { $as_echo "$as_me:$LINENO: result: none needed" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 $as_echo "none needed" >&6; } ;; xno) - { $as_echo "$as_me:$LINENO: result: unsupported" >&5 + { $as_echo "$as_me:${as_lineno-$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 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 $as_echo "$ac_cv_prog_cc_c89" >&6; } ;; esac +if test "x$ac_cv_prog_cc_c89" != xno; then : +fi ac_ext=c ac_cpp='$CPP $CPPFLAGS' @@ -3515,44 +3669,44 @@ ac_config_commands="$ac_config_commands depfiles" am_make=${MAKE-make} cat > confinc << 'END' am__doit: - @echo done + @echo this is the am__doit target .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 +{ $as_echo "$as_me:${as_lineno-$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 +# Ignore all kinds of additional output from `make'. +case `$am_make -s -f confmf 2> /dev/null` in #( +*the\ am__doit\ target*) + am__include=include + am__quote= + _am_result=GNU + ;; +esac # Now try BSD make style include. if test "$am__include" = "#"; then echo '.include "confinc"' > confmf - if test "`$am_make -s -f confmf 2> /dev/null`" = "done"; then - am__include=.include - am__quote="\"" - _am_result=BSD - fi + case `$am_make -s -f confmf 2> /dev/null` in #( + *the\ am__doit\ target*) + am__include=.include + am__quote="\"" + _am_result=BSD + ;; + esac fi -{ $as_echo "$as_me:$LINENO: result: $_am_result" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5 $as_echo "$_am_result" >&6; } rm -f confinc confmf # Check whether --enable-dependency-tracking was given. -if test "${enable_dependency_tracking+set}" = set; then +if test "${enable_dependency_tracking+set}" = set; then : enableval=$enable_dependency_tracking; fi @@ -3572,9 +3726,9 @@ fi depcc="$CC" am_compiler_list= -{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5 +{ $as_echo "$as_me:${as_lineno-$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 +if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then @@ -3600,6 +3754,11 @@ else if test "$am_compiler_list" = ""; then am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp` fi + am__universal=false + case " $depcc " in #( + *\ -arch\ *\ -arch\ *) am__universal=true ;; + esac + 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 @@ -3617,7 +3776,17 @@ else done echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf + # 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. Also, some Intel + # versions had trouble with output in subdirs + am__obj=sub/conftest.${OBJEXT-o} + am__minus_obj="-o $am__obj" case $depmode in + gcc) + # This depmode causes a compiler race in universal mode. + test "$am__universal" = false || continue + ;; nosideeffect) # after this tag, mechanisms are not by side-effect, so they'll # only be used when explicitly requested @@ -3627,19 +3796,23 @@ else break fi ;; + msvisualcpp | msvcmsys) + # This compiler won't grok `-c -o', but also, the minuso test has + # not run yet. These depmodes are late enough in the game, and + # so weak that their functioning should not be impacted. + am__obj=conftest.${OBJEXT-o} + am__minus_obj= + ;; none) break ;; esac - # We check with `-c' and `-o' for the sake of the "dashmstdout" - # mode. It turns out that the SunPro C++ compiler does not properly - # handle `-M -o', and we need to detect this. if depmode=$depmode \ - source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \ + source=sub/conftest.c object=$am__obj \ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \ - $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \ + $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \ >/dev/null 2>conftest.err && grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 && grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 && - grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 && + grep $am__obj 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 @@ -3663,7 +3836,7 @@ else fi fi -{ $as_echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5 $as_echo "$am_cv_CC_dependencies_compiler_type" >&6; } CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type @@ -3692,9 +3865,9 @@ if test -z "$CXX"; then 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 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_CXX+set}" = set; then +if test "${ac_cv_prog_CXX+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$CXX"; then @@ -3705,24 +3878,24 @@ 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 + 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_CXX="$ac_tool_prefix$ac_prog" - $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done IFS=$as_save_IFS fi fi CXX=$ac_cv_prog_CXX if test -n "$CXX"; then - { $as_echo "$as_me:$LINENO: result: $CXX" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5 $as_echo "$CXX" >&6; } else - { $as_echo "$as_me:$LINENO: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi @@ -3736,9 +3909,9 @@ if test -z "$CXX"; then 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 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then +if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CXX"; then @@ -3749,24 +3922,24 @@ 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 + 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_CXX="$ac_prog" - $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done -done + done IFS=$as_save_IFS fi fi ac_ct_CXX=$ac_cv_prog_ac_ct_CXX if test -n "$ac_ct_CXX"; then - { $as_echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5 $as_echo "$ac_ct_CXX" >&6; } else - { $as_echo "$as_me:$LINENO: result: no" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi @@ -3779,7 +3952,7 @@ done 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:${as_lineno-$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 @@ -3790,53 +3963,36 @@ fi fi fi # Provide some information about the compiler. -$as_echo "$as_me:$LINENO: checking for C++ compiler version" >&5 +$as_echo "$as_me:${as_lineno-$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" +for ac_option in --version -v -V -qversion; do + { { ac_try="$ac_compiler $ac_option >&5" case "(($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 +eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" +$as_echo "$ac_try_echo"; } >&5 + (eval "$ac_compiler $ac_option >&5") 2>conftest.err ac_status=$? - $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 - (exit $ac_status); } + if test -s conftest.err; then + sed '10a\ +... rest of stderr output deleted ... + 10q' conftest.err >conftest.er1 + cat conftest.er1 >&5 + fi + rm -f conftest.er1 conftest.err + $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 + test $ac_status = 0; } +done -{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5 +{ $as_echo "$as_me:${as_lineno-$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_cxx_compiler_gnu+set}" = set; then +if test "${ac_cv_cxx_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 + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -3850,37 +4006,16 @@ main () return 0; } _ACEOF -rm -f conftest.$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_cxx_werror_flag" || - test ! -s conftest.err - } && test -s conftest.$ac_objext; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_compiler_gnu=yes else - $as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - - ac_compiler_gnu=no + ac_compiler_gnu=no fi - rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_cxx_compiler_gnu=$ac_compiler_gnu fi -{ $as_echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5 $as_echo "$ac_cv_cxx_compiler_gnu" >&6; } if test $ac_compiler_gnu = yes; then GXX=yes @@ -3889,20 +4024,16 @@ else fi ac_test_CXXFLAGS=${CXXFLAGS+set} ac_save_CXXFLAGS=$CXXFLAGS -{ $as_echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5 $as_echo_n "checking whether $CXX accepts -g... " >&6; } -if test "${ac_cv_prog_cxx_g+set}" = set; then +if test "${ac_cv_prog_cxx_g+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_save_cxx_werror_flag=$ac_cxx_werror_flag ac_cxx_werror_flag=yes ac_cv_prog_cxx_g=no CXXFLAGS="-g" - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -3913,35 +4044,11 @@ 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_cxx_werror_flag" || - test ! -s conftest.err - } && test -s conftest.$ac_objext; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_cv_prog_cxx_g=yes else - $as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - - CXXFLAGS="" - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + CXXFLAGS="" + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -3952,36 +4059,12 @@ main () return 0; } _ACEOF -rm -f conftest.$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_cxx_werror_flag" || - test ! -s conftest.err - } && test -s conftest.$ac_objext; then - : -else - $as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +if ac_fn_cxx_try_compile "$LINENO"; then : - ac_cxx_werror_flag=$ac_save_cxx_werror_flag +else + ac_cxx_werror_flag=$ac_save_cxx_werror_flag CXXFLAGS="-g" - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -3992,42 +4075,17 @@ 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_cxx_werror_flag" || - test ! -s conftest.err - } && test -s conftest.$ac_objext; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_cv_prog_cxx_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.$ac_ext ac_cxx_werror_flag=$ac_save_cxx_werror_flag fi -{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5 $as_echo "$ac_cv_prog_cxx_g" >&6; } if test "$ac_test_CXXFLAGS" = set; then CXXFLAGS=$ac_save_CXXFLAGS @@ -4052,9 +4110,9 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu depcc="$CXX" am_compiler_list= -{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5 $as_echo_n "checking dependency style of $depcc... " >&6; } -if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then +if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then @@ -4080,6 +4138,11 @@ else if test "$am_compiler_list" = ""; then am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp` fi + am__universal=false + case " $depcc " in #( + *\ -arch\ *\ -arch\ *) am__universal=true ;; + esac + 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 @@ -4097,7 +4160,17 @@ else done echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf + # 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. Also, some Intel + # versions had trouble with output in subdirs + am__obj=sub/conftest.${OBJEXT-o} + am__minus_obj="-o $am__obj" case $depmode in + gcc) + # This depmode causes a compiler race in universal mode. + test "$am__universal" = false || continue + ;; nosideeffect) # after this tag, mechanisms are not by side-effect, so they'll # only be used when explicitly requested @@ -4107,19 +4180,23 @@ else break fi ;; + msvisualcpp | msvcmsys) + # This compiler won't grok `-c -o', but also, the minuso test has + # not run yet. These depmodes are late enough in the game, and + # so weak that their functioning should not be impacted. + am__obj=conftest.${OBJEXT-o} + am__minus_obj= + ;; none) break ;; esac - # We check with `-c' and `-o' for the sake of the "dashmstdout" - # mode. It turns out that the SunPro C++ compiler does not properly - # handle `-M -o', and we need to detect this. if depmode=$depmode \ - source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \ + source=sub/conftest.c object=$am__obj \ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \ - $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \ + $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \ >/dev/null 2>conftest.err && grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 && grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 && - grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 && + grep $am__obj 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 @@ -4143,7 +4220,7 @@ else fi fi -{ $as_echo "$as_me:$LINENO: result: $am_cv_CXX_dependencies_compiler_type" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5 $as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; } CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type @@ -4164,9 +4241,9 @@ fi if test -n "$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 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_RANLIB+set}" = set; then +if test "${ac_cv_prog_RANLIB+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$RANLIB"; then @@ -4177,176 +4254,84 @@ 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 - -# 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 - + 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:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 + fi done + done IFS=$as_save_IFS -rm -rf conftest.one conftest.two conftest.dir +fi +fi +RANLIB=$ac_cv_prog_RANLIB +if test -n "$RANLIB"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5 +$as_echo "$RANLIB" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + fi - if test "${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 +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:${as_lineno-$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:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + break 2 fi -fi -{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5 -$as_echo "$INSTALL" >&6; } +done + done +IFS=$as_save_IFS -# 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='${INSTALL}' +fi +fi +ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB +if test -n "$ac_ct_RANLIB"; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5 +$as_echo "$ac_ct_RANLIB" >&6; } +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi -test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' + if test "x$ac_ct_RANLIB" = x; then + RANLIB=":" + else + case $cross_compiling:$ac_tool_warned in +yes:) +{ $as_echo "$as_me:${as_lineno-$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 "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' +# AC_PROG_INSTALL will generate an install target so that users may +# just type 'make install' to install the software. # use C++ compiler and linker @@ -4365,10 +4350,10 @@ 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 +{ $as_echo "$as_me:${as_lineno-$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 "${ac_cv_prog_CXXCPP+set}" = set; then + if test "${ac_cv_prog_CXXCPP+set}" = set; then : $as_echo_n "(cached) " >&6 else # Double quotes because CXXCPP needs to be expanded @@ -4383,11 +4368,7 @@ do # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __STDC__ # include @@ -4396,78 +4377,34 @@ cat >>conftest.$ac_ext <<_ACEOF #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.$ac_ext >&5 +if ac_fn_cxx_try_cpp "$LINENO"; then : +else # 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 + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF -if { (ac_try="$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$ac_cxx_werror_flag" || - test ! -s conftest.err - }; then +if ac_fn_cxx_try_cpp "$LINENO"; 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 +if $ac_preproc_ok; then : break fi @@ -4479,7 +4416,7 @@ fi else ac_cv_prog_CXXCPP=$CXXCPP fi -{ $as_echo "$as_me:$LINENO: result: $CXXCPP" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXXCPP" >&5 $as_echo "$CXXCPP" >&6; } ac_preproc_ok=false for ac_cxx_preproc_warn_flag in '' yes @@ -4490,11 +4427,7 @@ do # 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.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __STDC__ # include @@ -4503,87 +4436,40 @@ cat >>conftest.$ac_ext <<_ACEOF #endif Syntax error _ACEOF -if { (ac_try="$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.$ac_ext >&5 +if ac_fn_cxx_try_cpp "$LINENO"; then : +else # 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 + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF -if { (ac_try="$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$ac_cxx_werror_flag" || - test ! -s conftest.err - }; then +if ac_fn_cxx_try_cpp "$LINENO"; 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 - : +if $ac_preproc_ok; then : + else - { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 + { { $as_echo "$as_me:${as_lineno-$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 \"$CXXCPP\" fails sanity check -See \`config.log' for more details." >&2;} - { (exit 1); exit 1; }; }; } +as_fn_error "C++ preprocessor \"$CXXCPP\" fails sanity check +See \`config.log' for more details." "$LINENO" 5; } fi ac_ext=cpp @@ -4593,9 +4479,9 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex ac_compiler_gnu=$ac_cv_cxx_compiler_gnu -{ $as_echo "$as_me:$LINENO: checking for grep that handles long lines and -e" >&5 +{ $as_echo "$as_me:${as_lineno-$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 +if test "${ac_cv_path_GREP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -z "$GREP"; then @@ -4606,7 +4492,7 @@ 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_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 @@ -4626,7 +4512,7 @@ case `"$ac_path_GREP" --version 2>&1` in $as_echo 'GREP' >> "conftest.nl" "$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` + as_fn_arith $ac_count + 1 && ac_count=$as_val 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" @@ -4641,26 +4527,24 @@ esac $ac_path_GREP_found && break 3 done done -done + done IFS=$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; }; } + as_fn_error "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 fi else ac_cv_path_GREP=$GREP fi fi -{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_GREP" >&5 +{ $as_echo "$as_me:${as_lineno-$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 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5 $as_echo_n "checking for egrep... " >&6; } -if test "${ac_cv_path_EGREP+set}" = set; then +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 @@ -4674,7 +4558,7 @@ 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_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 @@ -4694,7 +4578,7 @@ case `"$ac_path_EGREP" --version 2>&1` in $as_echo 'EGREP' >> "conftest.nl" "$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` + as_fn_arith $ac_count + 1 && ac_count=$as_val 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" @@ -4709,12 +4593,10 @@ esac $ac_path_EGREP_found && break 3 done done -done + done IFS=$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; }; } + as_fn_error "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 fi else ac_cv_path_EGREP=$EGREP @@ -4722,21 +4604,17 @@ fi fi fi -{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_EGREP" >&5 +{ $as_echo "$as_me:${as_lineno-$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 +{ $as_echo "$as_me:${as_lineno-$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 +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 + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include @@ -4751,48 +4629,23 @@ main () return 0; } _ACEOF -rm -f conftest.$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_cxx_werror_flag" || - test ! -s conftest.err - } && test -s conftest.$ac_objext; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_cv_header_stdc=yes else - $as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - - ac_cv_header_stdc=no + ac_cv_header_stdc=no fi - rm -f core conftest.err conftest.$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 + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | - $EGREP "memchr" >/dev/null 2>&1; then - : + $EGREP "memchr" >/dev/null 2>&1; then : + else ac_cv_header_stdc=no fi @@ -4802,18 +4655,14 @@ 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 + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | - $EGREP "free" >/dev/null 2>&1; then - : + $EGREP "free" >/dev/null 2>&1; then : + else ac_cv_header_stdc=no fi @@ -4823,14 +4672,10 @@ 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 + 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 + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include @@ -4857,51 +4702,22 @@ main () return 0; } _ACEOF -rm -f conftest$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 +if ac_fn_cxx_try_run "$LINENO"; then : -( exit $ac_status ) -ac_cv_header_stdc=no +else + ac_cv_header_stdc=no fi -rm -rf conftest.dSYM -rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ + conftest.$ac_objext conftest.beam conftest.$ac_ext fi - fi fi -{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5 $as_echo "$ac_cv_header_stdc" >&6; } if test $ac_cv_header_stdc = yes; then -cat >>confdefs.h <<\_ACEOF -#define STDC_HEADERS 1 -_ACEOF +$as_echo "#define STDC_HEADERS 1" >>confdefs.h fi @@ -4909,69 +4725,14 @@ fi # Checks for typedefs, structures, and compiler characteristics. # 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_cxx_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$as_val" = x""yes; then +do : + as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +ac_fn_cxx_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default +" +eval as_val=\$$as_ac_Header + if test "x$as_val" = x""yes; then : cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF @@ -4981,16 +4742,12 @@ fi done -{ $as_echo "$as_me:$LINENO: checking for stdbool.h that conforms to C99" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for stdbool.h that conforms to C99" >&5 $as_echo_n "checking for stdbool.h that conforms to C99... " >&6; } -if test "${ac_cv_header_stdbool_h+set}" = set; then +if test "${ac_cv_header_stdbool_h+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 + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include @@ -5062,139 +4819,25 @@ main () *pq |= q; *pq |= ! q; - /* Refer to every declared value, to avoid compiler optimizations. */ - return (!a + !b + !c + !d + !e + !f + !g + !h + !i + !!j + !k + !!l - + !m + !n + !o + !p + !q + !pq); - - ; - return 0; -} -_ACEOF -rm -f conftest.$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_cxx_werror_flag" || - test ! -s conftest.err - } && test -s conftest.$ac_objext; then - ac_cv_header_stdbool_h=yes -else - $as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - - ac_cv_header_stdbool_h=no -fi - -rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext -fi -{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdbool_h" >&5 -$as_echo "$ac_cv_header_stdbool_h" >&6; } -{ $as_echo "$as_me:$LINENO: checking for _Bool" >&5 -$as_echo_n "checking for _Bool... " >&6; } -if test "${ac_cv_type__Bool+set}" = set; then - $as_echo_n "(cached) " >&6 -else - ac_cv_type__Bool=no -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF -/* end confdefs.h. */ -$ac_includes_default -int -main () -{ -if (sizeof (_Bool)) - return 0; - ; - return 0; -} -_ACEOF -rm -f conftest.$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_cxx_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. */ -$ac_includes_default -int -main () -{ -if (sizeof ((_Bool))) - return 0; + /* Refer to every declared value, to avoid compiler optimizations. */ + return (!a + !b + !c + !d + !e + !f + !g + !h + !i + !!j + !k + !!l + + !m + !n + !o + !p + !q + !pq); + ; return 0; } _ACEOF -rm -f conftest.$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_cxx_werror_flag" || - test ! -s conftest.err - } && test -s conftest.$ac_objext; then - : -else - $as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - - ac_cv_type__Bool=yes -fi - -rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +if ac_fn_cxx_try_compile "$LINENO"; then : + ac_cv_header_stdbool_h=yes else - $as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - - + ac_cv_header_stdbool_h=no fi - rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -{ $as_echo "$as_me:$LINENO: result: $ac_cv_type__Bool" >&5 -$as_echo "$ac_cv_type__Bool" >&6; } -if test "x$ac_cv_type__Bool" = x""yes; then +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdbool_h" >&5 +$as_echo "$ac_cv_header_stdbool_h" >&6; } +ac_fn_cxx_check_type "$LINENO" "_Bool" "ac_cv_type__Bool" "$ac_includes_default" +if test "x$ac_cv_type__Bool" = x""yes; then : cat >>confdefs.h <<_ACEOF #define HAVE__BOOL 1 @@ -5205,22 +4848,16 @@ fi if test $ac_cv_header_stdbool_h = yes; then -cat >>confdefs.h <<\_ACEOF -#define HAVE_STDBOOL_H 1 -_ACEOF +$as_echo "#define HAVE_STDBOOL_H 1" >>confdefs.h fi -{ $as_echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5 +{ $as_echo "$as_me:${as_lineno-$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 +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 + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int @@ -5280,140 +4917,24 @@ main () return 0; } _ACEOF -rm -f conftest.$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_cxx_werror_flag" || - test ! -s conftest.err - } && test -s conftest.$ac_objext; then +if ac_fn_cxx_try_compile "$LINENO"; then : ac_cv_c_const=yes else - $as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - - ac_cv_c_const=no + ac_cv_c_const=no fi - rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_const" >&5 +{ $as_echo "$as_me:${as_lineno-$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_cxx_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_cxx_werror_flag" || - test ! -s conftest.err - } && test -s conftest.$ac_objext; then - : -else - $as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 +$as_echo "#define const /**/" >>confdefs.h - 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.$ac_ext >&5 - - -fi +ac_fn_cxx_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default" +if test "x$ac_cv_type_size_t" = x""yes; then : -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 @@ -5435,170 +4956,27 @@ fi ac_config_headers="$ac_config_headers src/config.h" - for ac_header in stdlib.h -do -as_ac_Header=`$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_cxx_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... 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What about this header? -case $ac_header_compiler:$ac_header_preproc:$ac_cxx_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$as_val" = x""yes; then +do : + ac_fn_cxx_check_header_mongrel "$LINENO" "stdlib.h" "ac_cv_header_stdlib_h" "$ac_includes_default" +if test "x$ac_cv_header_stdlib_h" = x""yes; then : cat >>confdefs.h <<_ACEOF -#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 +#define HAVE_STDLIB_H 1 _ACEOF fi done -{ $as_echo "$as_me:$LINENO: checking for GNU libc compatible malloc" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU libc compatible malloc" >&5 $as_echo_n "checking for GNU libc compatible malloc... " >&6; } -if test "${ac_cv_func_malloc_0_nonnull+set}" = set; then +if test "${ac_cv_func_malloc_0_nonnull+set}" = set; then : $as_echo_n "(cached) " >&6 else - if test "$cross_compiling" = yes; then + if test "$cross_compiling" = yes; then : ac_cv_func_malloc_0_nonnull=no else - cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF + cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #if defined STDC_HEADERS || defined HAVE_STDLIB_H # include @@ -5614,55 +4992,24 @@ return ! malloc (0); return 0; } _ACEOF -rm -f conftest$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 $ac_status); }; }; then +if ac_fn_cxx_try_run "$LINENO"; then : ac_cv_func_malloc_0_nonnull=yes 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 $ac_status ) -ac_cv_func_malloc_0_nonnull=no + ac_cv_func_malloc_0_nonnull=no fi -rm -rf conftest.dSYM -rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ + conftest.$ac_objext conftest.beam conftest.$ac_ext fi - fi -{ $as_echo "$as_me:$LINENO: result: $ac_cv_func_malloc_0_nonnull" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_malloc_0_nonnull" >&5 $as_echo "$ac_cv_func_malloc_0_nonnull" >&6; } -if test $ac_cv_func_malloc_0_nonnull = yes; then +if test $ac_cv_func_malloc_0_nonnull = yes; then : -cat >>confdefs.h <<\_ACEOF -#define HAVE_MALLOC 1 -_ACEOF +$as_echo "#define HAVE_MALLOC 1" >>confdefs.h else - cat >>confdefs.h <<\_ACEOF -#define HAVE_MALLOC 0 -_ACEOF + $as_echo "#define HAVE_MALLOC 0" >>confdefs.h case " $LIBOBJS " in *" malloc.$ac_objext "* ) ;; @@ -5671,39 +5018,31 @@ _ACEOF esac -cat >>confdefs.h <<\_ACEOF -#define malloc rpl_malloc -_ACEOF +$as_echo "#define malloc rpl_malloc" >>confdefs.h fi - # enable hashing if requested (--with-mhash) # will set HAVE_MHASH_H only # Check whether --with-mhash was given. -if test "${with_mhash+set}" = set; then +if test "${with_mhash+set}" = set; then : withval=$with_mhash; with_mhash=$withval else with_mhash=no fi if test "$with_mhash" = "yes"; then - -{ $as_echo "$as_me:$LINENO: checking for mhash_init in -lmhash" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for mhash_init in -lmhash" >&5 $as_echo_n "checking for mhash_init in -lmhash... " >&6; } -if test "${ac_cv_lib_mhash_mhash_init+set}" = set; then +if test "${ac_cv_lib_mhash_mhash_init+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lmhash $LIBS" -cat >conftest.$ac_ext <<_ACEOF -/* confdefs.h. */ -_ACEOF -cat confdefs.h >>conftest.$ac_ext -cat >>conftest.$ac_ext <<_ACEOF +cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -5715,212 +5054,44 @@ extern "C" char mhash_init (); int main () -{ -return mhash_init (); - ; - return 0; -} -_ACEOF -rm -f conftest.$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 - ac_cv_lib_mhash_mhash_init=yes -else - $as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - - ac_cv_lib_mhash_mhash_init=no -fi - -rm -rf conftest.dSYM -rm -f core conftest.err conftest.$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: $ac_cv_lib_mhash_mhash_init" >&5 -$as_echo "$ac_cv_lib_mhash_mhash_init" >&6; } -if test "x$ac_cv_lib_mhash_mhash_init" = x""yes; then - cat >>confdefs.h <<_ACEOF -#define HAVE_LIBMHASH 1 -_ACEOF - - LIBS="-lmhash $LIBS" - -else - { { $as_echo "$as_me:$LINENO: error: mhash lib not found" >&5 -$as_echo "$as_me: error: mhash lib not found" >&2;} - { (exit 1); exit 1; }; } -fi - - -for ac_header in mhash.h -do -as_ac_Header=`$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_cxx_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_cxx_preproc_warn_flag$ac_cxx_werror_flag" || - test ! -s conftest.err - }; then - ac_header_preproc=yes +{ +return mhash_init (); + ; + return 0; +} +_ACEOF +if ac_fn_cxx_try_link "$LINENO"; then : + ac_cv_lib_mhash_mhash_init=yes else - $as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 - - ac_header_preproc=no + ac_cv_lib_mhash_mhash_init=no +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mhash_mhash_init" >&5 +$as_echo "$ac_cv_lib_mhash_mhash_init" >&6; } +if test "x$ac_cv_lib_mhash_mhash_init" = x""yes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_LIBMHASH 1 +_ACEOF -rm -f conftest.err conftest.$ac_ext -{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 -$as_echo "$ac_header_preproc" >&6; } + LIBS="-lmhash $LIBS" -# So? What about this header? -case $ac_header_compiler:$ac_header_preproc:$ac_cxx_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" + as_fn_error "mhash lib not found" "$LINENO" 5 fi -ac_res=`eval 'as_val=${'$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$as_val" = x""yes; then + for ac_header in mhash.h +do : + ac_fn_cxx_check_header_mongrel "$LINENO" "mhash.h" "ac_cv_header_mhash_h" "$ac_includes_default" +if test "x$ac_cv_header_mhash_h" = x""yes; then : cat >>confdefs.h <<_ACEOF -#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 +#define HAVE_MHASH_H 1 _ACEOF else - { { $as_echo "$as_me:$LINENO: error: mhash header not found" >&5 -$as_echo "$as_me: error: mhash header not found" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "mhash header not found" "$LINENO" 5 fi done @@ -5960,13 +5131,13 @@ _ACEOF case $ac_val in #( *${as_nl}*) case $ac_var in #( - *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5 + *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; esac case $ac_var in #( _ | IFS | as_nl) ;; #( BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( - *) $as_unset $ac_var ;; + *) { eval $ac_var=; unset $ac_var;} ;; esac ;; esac done @@ -5974,8 +5145,8 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; (set) 2>&1 | case $as_nl`(ac_space=' '; set) 2>&1` in #( *${as_nl}ac_space=\ *) - # `set' does not quote correctly, so add quotes (double-quote - # substitution turns \\\\ into \\, and sed turns \\ into \). + # `set' does not quote correctly, so add quotes: double-quote + # substitution turns \\\\ into \\, and sed turns \\ into \. sed -n \ "s/'/'\\\\''/g; s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p" @@ -5998,11 +5169,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; if diff "$cache_file" confcache >/dev/null 2>&1; then :; else if test -w "$cache_file"; then test "x$cache_file" != "x/dev/null" && - { $as_echo "$as_me:$LINENO: updating cache $cache_file" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5 $as_echo "$as_me: updating cache $cache_file" >&6;} cat confcache >$cache_file else - { $as_echo "$as_me:$LINENO: not updating unwritable cache $cache_file" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5 $as_echo "$as_me: not updating unwritable cache $cache_file" >&6;} fi fi @@ -6022,43 +5193,43 @@ for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue ac_i=`$as_echo "$ac_i" | sed "$ac_script"` # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR # will be set to the directory where LIBOBJS objects are built. - ac_libobjs="$ac_libobjs \${LIBOBJDIR}$ac_i\$U.$ac_objext" - ac_ltlibobjs="$ac_ltlibobjs \${LIBOBJDIR}$ac_i"'$U.lo' + as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext" + as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo' done LIBOBJS=$ac_libobjs LTLIBOBJS=$ac_ltlibobjs + if test -n "$EXEEXT"; then + am__EXEEXT_TRUE= + am__EXEEXT_FALSE='#' +else + am__EXEEXT_TRUE='#' + am__EXEEXT_FALSE= +fi + if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then - { { $as_echo "$as_me:$LINENO: error: conditional \"AMDEP\" was never defined. -Usually this means the macro was only invoked conditionally." >&5 -$as_echo "$as_me: error: conditional \"AMDEP\" was never defined. -Usually this means the macro was only invoked conditionally." >&2;} - { (exit 1); exit 1; }; } + as_fn_error "conditional \"AMDEP\" was never defined. +Usually this means the macro was only invoked conditionally." "$LINENO" 5 fi if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then - { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCC\" was never defined. -Usually this means the macro was only invoked conditionally." >&5 -$as_echo "$as_me: error: conditional \"am__fastdepCC\" was never defined. -Usually this means the macro was only invoked conditionally." >&2;} - { (exit 1); exit 1; }; } + as_fn_error "conditional \"am__fastdepCC\" was never defined. +Usually this means the macro was only invoked conditionally." "$LINENO" 5 fi if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then - { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCXX\" was never defined. -Usually this means the macro was only invoked conditionally." >&5 -$as_echo "$as_me: error: conditional \"am__fastdepCXX\" was never defined. -Usually this means the macro was only invoked conditionally." >&2;} - { (exit 1); exit 1; }; } + as_fn_error "conditional \"am__fastdepCXX\" was never defined. +Usually this means the macro was only invoked conditionally." "$LINENO" 5 fi : ${CONFIG_STATUS=./config.status} ac_write_fail=0 ac_clean_files_save=$ac_clean_files ac_clean_files="$ac_clean_files $CONFIG_STATUS" -{ $as_echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5 +{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5 $as_echo "$as_me: creating $CONFIG_STATUS" >&6;} -cat >$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +as_write_fail=0 +cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1 #! $SHELL # Generated by $as_me. # Run this file to recreate the current configuration. @@ -6068,17 +5239,18 @@ cat >$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 debug=false ac_cs_recheck=false ac_cs_silent=false -SHELL=\${CONFIG_SHELL-$SHELL} -_ACEOF -cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 -## --------------------- ## -## M4sh Initialization. ## -## --------------------- ## +SHELL=\${CONFIG_SHELL-$SHELL} +export SHELL +_ASEOF +cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1 +## -------------------- ## +## M4sh Initialization. ## +## -------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which @@ -6086,23 +5258,15 @@ if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else - case `(set -o) 2>/dev/null` in - *posix*) set -o posix ;; + 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 @@ -6110,7 +5274,13 @@ export as_nl 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 +# Prefer a ksh shell builtin over an external printf program on Solaris, +# but without wasting forks for bash or zsh. +if test -z "$BASH_VERSION$ZSH_VERSION" \ + && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then + as_echo='print -r --' + as_echo_n='print -rn --' +elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='printf %s\n' as_echo_n='printf %s' else @@ -6121,7 +5291,7 @@ else as_echo_body='eval expr "X$1" : "X\\(.*\\)"' as_echo_n_body='eval arg=$1; - case $arg in + case $arg in #( *"$as_nl"*) expr "X$arg" : "X\\(.*\\)$as_nl"; arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; @@ -6144,13 +5314,6 @@ if test "${PATH_SEPARATOR+set}" != set; then } 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. Quoting is @@ -6160,15 +5323,15 @@ fi IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. -case $0 in +case $0 in #(( *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break -done + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break + done IFS=$as_save_IFS ;; @@ -6180,12 +5343,16 @@ if test "x$as_myself" = x; then fi if test ! -f "$as_myself"; then $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 - { (exit 1); exit 1; } + exit 1 fi -# Work around bugs in pre-3.0 UWIN ksh. -for as_var in ENV MAIL MAILPATH -do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var +# Unset variables that we do not need and which cause bugs (e.g. in +# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" +# suppresses any "Segmentation fault" message there. '((' could +# trigger a bug in pdksh 5.2.14. +for as_var in BASH_ENV ENV MAIL MAILPATH +do eval test x\${$as_var+set} = xset \ + && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : done PS1='$ ' PS2='> ' @@ -6197,7 +5364,89 @@ export LC_ALL LANGUAGE=C export LANGUAGE -# Required to use basename. +# CDPATH. +(unset CDPATH) >/dev/null 2>&1 && unset CDPATH + + +# as_fn_error ERROR [LINENO LOG_FD] +# --------------------------------- +# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are +# provided, also output the error to LOG_FD, referencing LINENO. Then exit the +# script with status $?, using 1 if that was 0. +as_fn_error () +{ + as_status=$?; test $as_status -eq 0 && as_status=1 + if test "$3"; then + as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3 + fi + $as_echo "$as_me: error: $1" >&2 + as_fn_exit $as_status +} # as_fn_error + + +# as_fn_set_status STATUS +# ----------------------- +# Set $? to STATUS, without forking. +as_fn_set_status () +{ + return $1 +} # as_fn_set_status + +# as_fn_exit STATUS +# ----------------- +# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. +as_fn_exit () +{ + set +e + as_fn_set_status $1 + exit $1 +} # as_fn_exit + +# as_fn_unset VAR +# --------------- +# Portably unset VAR. +as_fn_unset () +{ + { eval $1=; unset $1;} +} +as_unset=as_fn_unset +# as_fn_append VAR VALUE +# ---------------------- +# Append the text in VALUE to the end of the definition contained in VAR. Take +# advantage of any shell optimizations that allow amortized linear growth over +# repeated appends, instead of the typical quadratic growth present in naive +# implementations. +if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : + eval 'as_fn_append () + { + eval $1+=\$2 + }' +else + as_fn_append () + { + eval $1=\$$1\$2 + } +fi # as_fn_append + +# as_fn_arith ARG... +# ------------------ +# Perform arithmetic evaluation on the ARGs, and store the result in the +# global $as_val. Take advantage of shells that can avoid forks. The arguments +# must be portable across $(()) and expr. +if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : + eval 'as_fn_arith () + { + as_val=$(( $* )) + }' +else + as_fn_arith () + { + as_val=`expr "$@" || test $? -eq 1` + } +fi # as_fn_arith + + if expr a : '\(a\)' >/dev/null 2>&1 && test "X`expr 00001 : '.*\(...\)'`" = X001; then as_expr=expr @@ -6211,8 +5460,12 @@ else as_basename=false fi +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi -# Name of the executable. as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ @@ -6232,76 +5485,25 @@ $as_echo X/"$0" | } s/.*/./; q'` -# CDPATH. -$as_unset CDPATH - - - - as_lineno_1=$LINENO - as_lineno_2=$LINENO - test "x$as_lineno_1" != "x$as_lineno_2" && - test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || { - - # Create $as_me.lineno as a copy of $as_myself, but with $LINENO - # uniformly replaced by the line number. The first 'sed' inserts a - # line-number line after each line using $LINENO; the second 'sed' - # does the real work. The second script uses 'N' to pair each - # line-number line with the line containing $LINENO, and appends - # trailing '-' during substitution so that $LINENO is not a special - # case at line end. - # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the - # scripts with optimization help from Paolo Bonzini. Blame Lee - # E. McMahon (1931-1989) for sed's syntax. :-) - sed -n ' - p - /[$]LINENO/= - ' <$as_myself | - sed ' - s/[$]LINENO.*/&-/ - t lineno - b - :lineno - N - :loop - s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/ - t loop - s/-\n.*// - ' >$as_me.lineno && - chmod +x "$as_me.lineno" || - { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2 - { (exit 1); exit 1; }; } - - # Don't try to exec as it changes $[0], causing all sort of problems - # (the dirname of $[0] is not the place where we might find the - # original and so on. Autoconf is especially sensitive to this). - . "./$as_me.lineno" - # Exit status is that of the last command. - exit -} - - -if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then - as_dirname=dirname -else - as_dirname=false -fi +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits ECHO_C= ECHO_N= ECHO_T= -case `echo -n x` in +case `echo -n x` in #((((( -n*) - case `echo 'x\c'` in + case `echo 'xy\c'` in *c*) ECHO_T=' ';; # ECHO_T is single tab character. - *) ECHO_C='\c';; + xy) ECHO_C='\c';; + *) echo `echo ksh88 bug on AIX 6.1` > /dev/null + ECHO_T=' ';; esac;; *) ECHO_N='-n';; esac -if expr a : '\(a\)' >/dev/null 2>&1 && - test "X`expr 00001 : '.*\(...\)'`" = X001; then - as_expr=expr -else - as_expr=false -fi rm -f conf$$ conf$$.exe conf$$.file if test -d conf$$.dir; then @@ -6330,8 +5532,56 @@ fi rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file rmdir conf$$.dir 2>/dev/null + +# as_fn_mkdir_p +# ------------- +# Create "$as_dir" as a directory, including parents if necessary. +as_fn_mkdir_p () +{ + + case $as_dir in #( + -*) as_dir=./$as_dir;; + esac + test -d "$as_dir" || eval $as_mkdir_p || { + as_dirs= + while :; do + case $as_dir in #( + *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *) as_qdir=$as_dir;; + esac + as_dirs="'$as_qdir' $as_dirs" + as_dir=`$as_dirname -- "$as_dir" || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + test -d "$as_dir" && break + done + test -z "$as_dirs" || eval "mkdir $as_dirs" + } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir" + + +} # as_fn_mkdir_p if mkdir -p . 2>/dev/null; then - as_mkdir_p=: + as_mkdir_p='mkdir -p "$as_dir"' else test -d ./-p && rmdir ./-p as_mkdir_p=false @@ -6350,10 +5600,10 @@ else if test -d "$1"; then test -d "$1/."; else - case $1 in + case $1 in #( -*)set "./$1";; esac; - case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in + case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #(( ???[sx]*):;;*)false;;esac;fi '\'' sh ' @@ -6368,13 +5618,19 @@ as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" exec 6>&1 +## ----------------------------------- ## +## Main body of $CONFIG_STATUS script. ## +## ----------------------------------- ## +_ASEOF +test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1 -# Save the log message, to keep $[0] and so on meaningful, and to +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +# Save the log message, to keep $0 and so on meaningful, and to # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by clustalw $as_me 2.0.12, which was -generated by GNU Autoconf 2.63. Invocation command line was +This file was extended by clustalw $as_me 2.1, which was +generated by GNU Autoconf 2.65. Invocation command line was CONFIG_FILES = $CONFIG_FILES CONFIG_HEADERS = $CONFIG_HEADERS @@ -6406,13 +5662,15 @@ _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 ac_cs_usage="\ -\`$as_me' instantiates files from templates according to the -current configuration. +\`$as_me' instantiates files and other configuration actions +from templates according to the current configuration. Unless the files +and actions are specified as TAGs, all are instantiated by default. -Usage: $0 [OPTION]... [FILE]... +Usage: $0 [OPTION]... [TAG]... -h, --help print this help, then exit -V, --version print version number and configuration settings, then exit + --config print configuration, then exit -q, --quiet, --silent do not print progress messages -d, --debug don't remove temporary files @@ -6431,16 +5689,17 @@ $config_headers Configuration commands: $config_commands -Report bugs to ." +Report bugs to ." _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 +ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ -clustalw config.status 2.0.12 -configured by $0, generated by GNU Autoconf 2.63, - with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\" +clustalw config.status 2.1 +configured by $0, generated by GNU Autoconf 2.65, + with options \\"\$ac_cs_config\\" -Copyright (C) 2008 Free Software Foundation, Inc. +Copyright (C) 2009 Free Software Foundation, Inc. This config.status script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it." @@ -6476,6 +5735,8 @@ do ac_cs_recheck=: ;; --version | --versio | --versi | --vers | --ver | --ve | --v | -V ) $as_echo "$ac_cs_version"; exit ;; + --config | --confi | --conf | --con | --co | --c ) + $as_echo "$ac_cs_config"; exit ;; --debug | --debu | --deb | --de | --d | -d ) debug=: ;; --file | --fil | --fi | --f ) @@ -6483,20 +5744,19 @@ do case $ac_optarg in *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; esac - CONFIG_FILES="$CONFIG_FILES '$ac_optarg'" + as_fn_append CONFIG_FILES " '$ac_optarg'" ac_need_defaults=false;; --header | --heade | --head | --hea ) $ac_shift case $ac_optarg in *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; esac - CONFIG_HEADERS="$CONFIG_HEADERS '$ac_optarg'" + as_fn_append CONFIG_HEADERS " '$ac_optarg'" ac_need_defaults=false;; --he | --h) # Conflict between --help and --header - { $as_echo "$as_me: error: ambiguous option: $1 -Try \`$0 --help' for more information." >&2 - { (exit 1); exit 1; }; };; + as_fn_error "ambiguous option: \`$1' +Try \`$0 --help' for more information.";; --help | --hel | -h ) $as_echo "$ac_cs_usage"; exit ;; -q | -quiet | --quiet | --quie | --qui | --qu | --q \ @@ -6504,11 +5764,10 @@ Try \`$0 --help' for more information." >&2 ac_cs_silent=: ;; # This is an error. - -*) { $as_echo "$as_me: error: unrecognized option: $1 -Try \`$0 --help' for more information." >&2 - { (exit 1); exit 1; }; } ;; + -*) as_fn_error "unrecognized option: \`$1' +Try \`$0 --help' for more information." ;; - *) ac_config_targets="$ac_config_targets $1" + *) as_fn_append ac_config_targets " $1" ac_need_defaults=false ;; esac @@ -6566,9 +5825,7 @@ do "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;; "src/clustalw_version.h") CONFIG_FILES="$CONFIG_FILES src/clustalw_version.h" ;; - *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 -$as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;} - { (exit 1); exit 1; }; };; + *) as_fn_error "invalid argument: \`$ac_config_target'" "$LINENO" 5;; esac done @@ -6595,7 +5852,7 @@ $debug || trap 'exit_status=$? { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status ' 0 - trap '{ (exit 1); exit 1; }' 1 2 13 15 + trap 'as_fn_exit 1' 1 2 13 15 } # Create a (secure) tmp directory for tmp files. @@ -6606,11 +5863,7 @@ $debug || { tmp=./conf$$-$RANDOM (umask 077 && mkdir "$tmp") -} || -{ - $as_echo "$as_me: cannot create a temporary directory in ." >&2 - { (exit 1); exit 1; } -} +} || as_fn_error "cannot create a temporary directory in ." "$LINENO" 5 # Set up the scripts for CONFIG_FILES section. # No need to generate them if there are no CONFIG_FILES. @@ -6618,10 +5871,16 @@ $debug || if test -n "$CONFIG_FILES"; then -ac_cr=' ' +ac_cr=`echo X | tr X '\015'` +# On cygwin, bash can eat \r inside `` if the user requested igncr. +# But we know of no other shell where ac_cr would be empty at this +# point, so we can use a bashism as a fallback. +if test "x$ac_cr" = x; then + eval ac_cr=\$\'\\r\' +fi ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' /dev/null` if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then - ac_cs_awk_cr='\\r' + ac_cs_awk_cr='\r' else ac_cs_awk_cr=$ac_cr fi @@ -6635,24 +5894,18 @@ _ACEOF echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' && echo "_ACEOF" } >conf$$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; }; } + as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5 ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'` ac_delim='%!_!# ' for ac_last_try in false false false false false :; do . ./conf$$subs.sh || - { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 -$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5 ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$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; }; } + as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5 else ac_delim="$ac_delim!$ac_delim _$ac_delim!! " fi @@ -6674,7 +5927,7 @@ s/'"$ac_delim"'$// t delim :nl h -s/\(.\{148\}\).*/\1/ +s/\(.\{148\}\)..*/\1/ t more1 s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/ p @@ -6688,7 +5941,7 @@ s/.\{148\}// t nl :delim h -s/\(.\{148\}\).*/\1/ +s/\(.\{148\}\)..*/\1/ t more2 s/["\\]/\\&/g; s/^/"/; s/$/"/ p @@ -6741,9 +5994,7 @@ if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then else cat fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \ - || { { $as_echo "$as_me:$LINENO: error: could not setup config files machinery" >&5 -$as_echo "$as_me: error: could not setup config files machinery" >&2;} - { (exit 1); exit 1; }; } + || as_fn_error "could not setup config files machinery" "$LINENO" 5 _ACEOF # VPATH may cause trouble with some makes, so we remove $(srcdir), @@ -6784,9 +6035,7 @@ for ac_last_try in false false :; do if test -z "$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; }; } + as_fn_error "could not make $CONFIG_HEADERS" "$LINENO" 5 else ac_delim="$ac_delim!$ac_delim _$ac_delim!! " fi @@ -6871,9 +6120,7 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 _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 "$as_me: error: could not setup config headers machinery" >&2;} - { (exit 1); exit 1; }; } + as_fn_error "could not setup config headers machinery" "$LINENO" 5 fi # test -n "$CONFIG_HEADERS" @@ -6886,9 +6133,7 @@ do 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 $ac_tag" >&2;} - { (exit 1); exit 1; }; };; + :L* | :C*:*) as_fn_error "invalid tag \`$ac_tag'" "$LINENO" 5;; :[FH]-) ac_tag=-:-;; :[FH]*) ac_tag=$ac_tag:$ac_tag.in;; esac @@ -6916,12 +6161,10 @@ $as_echo "$as_me: error: invalid tag $ac_tag" >&2;} [\\/$]*) false;; *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";; esac || - { { $as_echo "$as_me:$LINENO: error: cannot find input file: $ac_f" >&5 -$as_echo "$as_me: error: cannot find input file: $ac_f" >&2;} - { (exit 1); exit 1; }; };; + as_fn_error "cannot find input file: \`$ac_f'" "$LINENO" 5;; esac case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac - ac_file_inputs="$ac_file_inputs '$ac_f'" + as_fn_append ac_file_inputs " '$ac_f'" done # Let's still pretend it is `configure' which instantiates (i.e., don't @@ -6932,7 +6175,7 @@ $as_echo "$as_me: error: cannot find input file: $ac_f" >&2;} `' by configure.' if test x"$ac_file" != x-; then configure_input="$ac_file. $configure_input" - { $as_echo "$as_me:$LINENO: creating $ac_file" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5 $as_echo "$as_me: creating $ac_file" >&6;} fi # Neutralize special characters interpreted by sed in replacement strings. @@ -6945,9 +6188,7 @@ $as_echo "$as_me: creating $ac_file" >&6;} case $ac_tag in *:-:* | *:-) cat >"$tmp/stdin" \ - || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 -$as_echo "$as_me: error: could not create $ac_file" >&2;} - { (exit 1); exit 1; }; } ;; + || as_fn_error "could not create $ac_file" "$LINENO" 5 ;; esac ;; esac @@ -6975,47 +6216,7 @@ $as_echo X"$ac_file" | q } s/.*/./; q'` - { as_dir="$ac_dir" - case $as_dir in #( - -*) as_dir=./$as_dir;; - esac - test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || { - as_dirs= - while :; do - case $as_dir in #( - *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( - *) as_qdir=$as_dir;; - esac - as_dirs="'$as_qdir' $as_dirs" - as_dir=`$as_dirname -- "$as_dir" || -$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$as_dir" : 'X\(//\)[^/]' \| \ - X"$as_dir" : 'X\(//\)$' \| \ - X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$as_dir" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ - s//\1/ - q - } - /^X\(\/\/\)[^/].*/{ - s//\1/ - q - } - /^X\(\/\/\)$/{ - s//\1/ - q - } - /^X\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` - test -d "$as_dir" && break - done - test -z "$as_dirs" || eval "mkdir $as_dirs" - } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5 -$as_echo "$as_me: error: cannot create directory $as_dir" >&2;} - { (exit 1); exit 1; }; }; } + as_dir="$ac_dir"; as_fn_mkdir_p ac_builddir=. case "$ac_dir" in @@ -7072,7 +6273,6 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # If the template does not know about datarootdir, expand it. # FIXME: This hack should be removed a few years after 2.60. ac_datarootdir_hack=; ac_datarootdir_seen= - ac_sed_dataroot=' /datarootdir/ { p @@ -7082,12 +6282,11 @@ ac_sed_dataroot=' /@docdir@/p /@infodir@/p /@localedir@/p -/@mandir@/p -' +/@mandir@/p' case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in *datarootdir*) ac_datarootdir_seen=yes;; *@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*) - { $as_echo "$as_me:$LINENO: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 $as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;} _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 @@ -7097,7 +6296,7 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 s&@infodir@&$infodir&g s&@localedir@&$localedir&g s&@mandir@&$mandir&g - s&\\\${datarootdir}&$datarootdir&g' ;; + s&\\\${datarootdir}&$datarootdir&g' ;; esac _ACEOF @@ -7126,14 +6325,12 @@ s&@MKDIR_P@&$ac_MKDIR_P&;t t $ac_datarootdir_hack " eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \ - || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 -$as_echo "$as_me: error: could not create $ac_file" >&2;} - { (exit 1); exit 1; }; } + || as_fn_error "could not create $ac_file" "$LINENO" 5 test -z "$ac_datarootdir_hack$ac_datarootdir_seen" && { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } && { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } && - { $as_echo "$as_me:$LINENO: WARNING: $ac_file contains a reference to the variable \`datarootdir' + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir' which seems to be undefined. Please make sure it is defined." >&5 $as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir' which seems to be undefined. Please make sure it is defined." >&2;} @@ -7143,9 +6340,7 @@ which seems to be undefined. Please make sure it is defined." >&2;} -) cat "$tmp/out" && rm -f "$tmp/out";; *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";; esac \ - || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 -$as_echo "$as_me: error: could not create $ac_file" >&2;} - { (exit 1); exit 1; }; } + || as_fn_error "could not create $ac_file" "$LINENO" 5 ;; :H) # @@ -7156,25 +6351,19 @@ $as_echo "$as_me: error: could not create $ac_file" >&2;} $as_echo "/* $configure_input */" \ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" } >"$tmp/config.h" \ - || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 -$as_echo "$as_me: error: could not create $ac_file" >&2;} - { (exit 1); exit 1; }; } + || as_fn_error "could not create $ac_file" "$LINENO" 5 if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then - { $as_echo "$as_me:$LINENO: $ac_file is unchanged" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5 $as_echo "$as_me: $ac_file is unchanged" >&6;} else rm -f "$ac_file" mv "$tmp/config.h" "$ac_file" \ - || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 -$as_echo "$as_me: error: could not create $ac_file" >&2;} - { (exit 1); exit 1; }; } + || as_fn_error "could not create $ac_file" "$LINENO" 5 fi else $as_echo "/* $configure_input */" \ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \ - || { { $as_echo "$as_me:$LINENO: error: could not create -" >&5 -$as_echo "$as_me: error: could not create -" >&2;} - { (exit 1); exit 1; }; } + || as_fn_error "could not create -" "$LINENO" 5 fi # Compute "$ac_file"'s index in $config_headers. _am_arg="$ac_file" @@ -7212,7 +6401,7 @@ $as_echo X"$_am_arg" | s/.*/./; q'`/stamp-h$_am_stamp_count ;; - :C) { $as_echo "$as_me:$LINENO: executing $ac_file commands" >&5 + :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5 $as_echo "$as_me: executing $ac_file commands" >&6;} ;; esac @@ -7307,47 +6496,7 @@ $as_echo X"$file" | q } s/.*/./; q'` - { as_dir=$dirpart/$fdir - case $as_dir in #( - -*) as_dir=./$as_dir;; - esac - test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || { - as_dirs= - while :; do - case $as_dir in #( - *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( - *) as_qdir=$as_dir;; - esac - as_dirs="'$as_qdir' $as_dirs" - as_dir=`$as_dirname -- "$as_dir" || -$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$as_dir" : 'X\(//\)[^/]' \| \ - X"$as_dir" : 'X\(//\)$' \| \ - X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$as_dir" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ - s//\1/ - q - } - /^X\(\/\/\)[^/].*/{ - s//\1/ - q - } - /^X\(\/\/\)$/{ - s//\1/ - q - } - /^X\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` - test -d "$as_dir" && break - done - test -z "$as_dirs" || eval "mkdir $as_dirs" - } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5 -$as_echo "$as_me: error: cannot create directory $as_dir" >&2;} - { (exit 1); exit 1; }; }; } + as_dir=$dirpart/$fdir; as_fn_mkdir_p # echo "creating $dirpart/$file" echo '# dummy' > "$dirpart/$file" done @@ -7359,15 +6508,12 @@ $as_echo "$as_me: error: cannot create directory $as_dir" >&2;} done # for ac_tag -{ (exit 0); exit 0; } +as_fn_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; }; } + as_fn_error "write failure creating $CONFIG_STATUS" "$LINENO" 5 # configure is writing to config.log, and then calls config.status. @@ -7388,10 +6534,10 @@ if test "$no_create" != yes; then 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; } + $ac_cs_success || as_fn_exit $? fi if test -n "$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:${as_lineno-$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/clustalw/configure.ac b/binaries/src/clustalw/configure.ac index 02d7b54..12410d9 100644 --- a/binaries/src/clustalw/configure.ac +++ b/binaries/src/clustalw/configure.ac @@ -20,7 +20,7 @@ # after apllying any changes you will have to run # $ autoreconf # -AC_INIT([clustalw], [2.0.12], [clustalw@ucd.ie]) +AC_INIT([clustalw], [2.1], [clustalw@ucd.ie]) # # 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 diff --git a/binaries/src/clustalw/depcomp b/binaries/src/clustalw/depcomp index e5f9736..df8eea7 100644 --- a/binaries/src/clustalw/depcomp +++ b/binaries/src/clustalw/depcomp @@ -1,10 +1,10 @@ #! /bin/sh # depcomp - compile a program generating dependencies as side-effects -scriptversion=2007-03-29.01 +scriptversion=2009-04-28.21; # UTC -# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007 Free Software -# Foundation, Inc. +# 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 @@ -17,9 +17,7 @@ scriptversion=2007-03-29.01 # 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. +# 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 @@ -87,6 +85,15 @@ if test "$depmode" = dashXmstdout; then depmode=dashmstdout fi +cygpath_u="cygpath -u -f -" +if test "$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 "$depmode" in gcc3) ## gcc 3 implements dependency tracking that does exactly what @@ -192,14 +199,14 @@ sgi) ' < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \ tr ' -' ' ' >> $depfile - echo >> $depfile +' ' ' >> "$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/$/:/' \ - >> $depfile + >> "$depfile" else # The sourcefile does not contain any dependencies, so just # store a dummy comment line, to avoid errors with the Makefile @@ -328,7 +335,12 @@ hp2) 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" >> "$depfile" + sed -ne '2,${ + s/^ *// + s/ \\*$// + s/$/:/ + p + }' "$tmpdepfile" >> "$depfile" else echo "#dummy" > "$depfile" fi @@ -404,7 +416,7 @@ dashmstdout) # Remove the call to Libtool. if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do + while test "X$1" != 'X--mode=compile'; do shift done shift @@ -455,32 +467,39 @@ makedepend) "$@" || exit $? # Remove any Libtool call if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do + while test "X$1" != 'X--mode=compile'; do shift done shift fi # X makedepend shift - cleared=no - for arg in "$@"; do + 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 $object | sed 's/^.*\././'`" + obj_suffix=`echo "$object" | sed 's/^.*\././'` touch "$tmpdepfile" ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@" rm -f "$depfile" @@ -500,7 +519,7 @@ cpp) # Remove the call to Libtool. if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do + while test "X$1" != 'X--mode=compile'; do shift done shift @@ -538,13 +557,27 @@ cpp) msvisualcpp) # Important note: in order to support this mode, a compiler *must* - # always write the preprocessed file to stdout, regardless of -o, - # because we must use -o when running libtool. + # always write the preprocessed file to stdout. "$@" || 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 @@ -557,16 +590,23 @@ msvisualcpp) ;; esac done - "$@" -E | - sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile" + "$@" -E 2>/dev/null | + sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile" rm -f "$depfile" echo "$object : \\" > "$depfile" - . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" + sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" echo " " >> "$depfile" - . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile" + sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile" rm -f "$tmpdepfile" ;; +msvcmsys) + # This case exists only to let depend.m4 do its work. It works by + # looking at the text of this script. This case will never be run, + # since it is checked for above. + exit 1 + ;; + none) exec "$@" ;; @@ -585,5 +625,6 @@ exit 0 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" # End: diff --git a/binaries/src/clustalw/install-sh b/binaries/src/clustalw/install-sh index a5897de..6781b98 100644 --- a/binaries/src/clustalw/install-sh +++ b/binaries/src/clustalw/install-sh @@ -1,7 +1,7 @@ #!/bin/sh # install - install a program, script, or datafile -scriptversion=2006-12-25.00 +scriptversion=2009-04-28.21; # UTC # This originates from X11R5 (mit/util/scripts/install.sh), which was # later released in X11R6 (xc/config/util/install.sh) with the @@ -515,5 +515,6 @@ done # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" # End: diff --git a/binaries/src/clustalw/m4/Makefile b/binaries/src/clustalw/m4/Makefile index d5151cc..9a53855 100644 --- a/binaries/src/clustalw/m4/Makefile +++ b/binaries/src/clustalw/m4/Makefile @@ -1,8 +1,9 @@ -# Makefile.in generated by automake 1.10.2 from Makefile.am. +# Makefile.in generated by automake 1.11.1 from Makefile.am. # m4/Makefile. Generated from Makefile.in by configure. # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, -# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +# 2003, 2004, 2005, 2006, 2007, 2008, 2009 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. @@ -16,8 +17,9 @@ pkgdatadir = $(datadir)/clustalw -pkglibdir = $(libdir)/clustalw pkgincludedir = $(includedir)/clustalw +pkglibdir = $(libdir)/clustalw +pkglibexecdir = $(libexecdir)/clustalw am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd install_sh_DATA = $(install_sh) -c -m 644 install_sh_PROGRAM = $(install_sh) -c @@ -42,6 +44,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ mkinstalldirs = $(install_sh) -d CONFIG_HEADER = $(top_builddir)/src/config.h CONFIG_CLEAN_FILES = +CONFIG_CLEAN_VPATH_FILES = SOURCES = DIST_SOURCES = am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; @@ -49,22 +52,36 @@ am__vpath_adj = case $$p in \ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \ *) f=$$p;; \ esac; -am__strip_dir = `echo $$p | sed -e 's|^.*/||'`; +am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`; +am__install_max = 40 +am__nobase_strip_setup = \ + srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'` +am__nobase_strip = \ + for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||" +am__nobase_list = $(am__nobase_strip_setup); \ + for p in $$list; do echo "$$p $$p"; done | \ + sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \ + $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \ + if (++n[$$2] == $(am__install_max)) \ + { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \ + END { for (dir in files) print dir, files[dir] }' +am__base_list = \ + sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \ + sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g' am__installdirs = "$(DESTDIR)$(m4datadir)" -m4dataDATA_INSTALL = $(INSTALL_DATA) DATA = $(m4data_DATA) DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) -ACLOCAL = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run aclocal-1.10 -AMTAR = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run tar -AUTOCONF = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoconf -AUTOHEADER = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoheader -AUTOMAKE = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run automake-1.10 +ACLOCAL = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run aclocal-1.11 +AMTAR = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run tar +AUTOCONF = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoconf +AUTOHEADER = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoheader +AUTOMAKE = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run automake-1.11 AWK = gawk CC = gcc CCDEPMODE = depmode=gcc3 CFLAGS = -g -O2 CLUSTALW_NAME = ClustalW -CLUSTALW_VERSION = 2.0.12 +CLUSTALW_VERSION = 2.1 CPPFLAGS = CXX = g++ CXXCPP = g++ -E @@ -88,25 +105,26 @@ LDFLAGS = LIBOBJS = LIBS = LTLIBOBJS = -MAKEINFO = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run makeinfo +MAKEINFO = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run makeinfo MKDIR_P = /bin/mkdir -p OBJEXT = o PACKAGE = clustalw PACKAGE_BUGREPORT = clustalw@ucd.ie PACKAGE_NAME = clustalw -PACKAGE_STRING = clustalw 2.0.12 +PACKAGE_STRING = clustalw 2.1 PACKAGE_TARNAME = clustalw -PACKAGE_VERSION = 2.0.12 +PACKAGE_URL = +PACKAGE_VERSION = 2.1 PATH_SEPARATOR = : RANLIB = ranlib SET_MAKE = SHELL = /bin/sh STRIP = -VERSION = 2.0.12 -abs_builddir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/m4 -abs_srcdir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/m4 -abs_top_builddir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw -abs_top_srcdir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw +VERSION = 2.1 +abs_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/m4 +abs_srcdir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/m4 +abs_top_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw +abs_top_srcdir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw ac_ct_CC = gcc ac_ct_CXX = g++ am__include = include @@ -134,7 +152,7 @@ host_vendor = unknown htmldir = ${docdir} includedir = ${prefix}/include infodir = ${datarootdir}/info -install_sh = $(SHELL) /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/install-sh +install_sh = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/install-sh libdir = ${exec_prefix}/lib libexecdir = ${exec_prefix}/libexec localedir = ${datarootdir}/locale @@ -181,9 +199,9 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps) exit 1;; \ esac; \ done; \ - echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu m4/Makefile'; \ - cd $(top_srcdir) && \ - $(AUTOMAKE) --gnu m4/Makefile + echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu m4/Makefile'; \ + $(am__cd) $(top_srcdir) && \ + $(AUTOMAKE) --gnu m4/Makefile .PRECIOUS: Makefile Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status @case '$?' in \ @@ -201,23 +219,27 @@ $(top_srcdir)/configure: $(am__configure_deps) cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh $(ACLOCAL_M4): $(am__aclocal_m4_deps) cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh +$(am__aclocal_m4_deps): install-m4dataDATA: $(m4data_DATA) @$(NORMAL_INSTALL) test -z "$(m4datadir)" || $(MKDIR_P) "$(DESTDIR)$(m4datadir)" - @list='$(m4data_DATA)'; for p in $$list; do \ + @list='$(m4data_DATA)'; test -n "$(m4datadir)" || list=; \ + for p in $$list; do \ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ - f=$(am__strip_dir) \ - echo " $(m4dataDATA_INSTALL) '$$d$$p' '$(DESTDIR)$(m4datadir)/$$f'"; \ - $(m4dataDATA_INSTALL) "$$d$$p" "$(DESTDIR)$(m4datadir)/$$f"; \ + echo "$$d$$p"; \ + done | $(am__base_list) | \ + while read files; do \ + echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(m4datadir)'"; \ + $(INSTALL_DATA) $$files "$(DESTDIR)$(m4datadir)" || exit $$?; \ done uninstall-m4dataDATA: @$(NORMAL_UNINSTALL) - @list='$(m4data_DATA)'; for p in $$list; do \ - f=$(am__strip_dir) \ - echo " rm -f '$(DESTDIR)$(m4datadir)/$$f'"; \ - rm -f "$(DESTDIR)$(m4datadir)/$$f"; \ - done + @list='$(m4data_DATA)'; test -n "$(m4datadir)" || list=; \ + files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \ + test -n "$$files" || exit 0; \ + echo " ( cd '$(DESTDIR)$(m4datadir)' && rm -f" $$files ")"; \ + cd "$(DESTDIR)$(m4datadir)" && rm -f $$files tags: TAGS TAGS: @@ -241,13 +263,17 @@ distdir: $(DISTFILES) if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \ if test -d $$d/$$file; then \ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \ + if test -d "$(distdir)/$$file"; then \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ + fi; \ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \ - cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \ + cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ fi; \ - cp -pR $$d/$$file $(distdir)$$dir || exit 1; \ + cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \ else \ - test -f $(distdir)/$$file \ - || cp -p $$d/$$file $(distdir)/$$file \ + test -f "$(distdir)/$$file" \ + || cp -p $$d/$$file "$(distdir)/$$file" \ || exit 1; \ fi; \ done @@ -278,6 +304,7 @@ clean-generic: distclean-generic: -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES) + -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES) maintainer-clean-generic: @echo "This command is intended for maintainers to use" @@ -296,6 +323,8 @@ dvi-am: html: html-am +html-am: + info: info-am info-am: @@ -304,18 +333,28 @@ install-data-am: install-m4dataDATA install-dvi: install-dvi-am +install-dvi-am: + install-exec-am: install-html: install-html-am +install-html-am: + install-info: install-info-am +install-info-am: + install-man: install-pdf: install-pdf-am +install-pdf-am: + install-ps: install-ps-am +install-ps-am: + installcheck-am: maintainer-clean: maintainer-clean-am @@ -349,6 +388,7 @@ uninstall-am: uninstall-m4dataDATA maintainer-clean-generic mostlyclean mostlyclean-generic pdf \ pdf-am ps ps-am uninstall uninstall-am uninstall-m4dataDATA + # 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/clustalw/m4/Makefile.in b/binaries/src/clustalw/m4/Makefile.in index e168e43..bd5e6ef 100644 --- a/binaries/src/clustalw/m4/Makefile.in +++ b/binaries/src/clustalw/m4/Makefile.in @@ -1,8 +1,9 @@ -# Makefile.in generated by automake 1.10.2 from Makefile.am. +# Makefile.in generated by automake 1.11.1 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. +# 2003, 2004, 2005, 2006, 2007, 2008, 2009 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. @@ -16,8 +17,9 @@ VPATH = @srcdir@ pkgdatadir = $(datadir)/@PACKAGE@ -pkglibdir = $(libdir)/@PACKAGE@ pkgincludedir = $(includedir)/@PACKAGE@ +pkglibdir = $(libdir)/@PACKAGE@ +pkglibexecdir = $(libexecdir)/@PACKAGE@ am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd install_sh_DATA = $(install_sh) -c -m 644 install_sh_PROGRAM = $(install_sh) -c @@ -42,6 +44,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ mkinstalldirs = $(install_sh) -d CONFIG_HEADER = $(top_builddir)/src/config.h CONFIG_CLEAN_FILES = +CONFIG_CLEAN_VPATH_FILES = SOURCES = DIST_SOURCES = am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; @@ -49,9 +52,23 @@ am__vpath_adj = case $$p in \ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \ *) f=$$p;; \ esac; -am__strip_dir = `echo $$p | sed -e 's|^.*/||'`; +am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`; +am__install_max = 40 +am__nobase_strip_setup = \ + srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'` +am__nobase_strip = \ + for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||" +am__nobase_list = $(am__nobase_strip_setup); \ + for p in $$list; do echo "$$p $$p"; done | \ + sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \ + $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \ + if (++n[$$2] == $(am__install_max)) \ + { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \ + END { for (dir in files) print dir, files[dir] }' +am__base_list = \ + sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \ + sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g' am__installdirs = "$(DESTDIR)$(m4datadir)" -m4dataDATA_INSTALL = $(INSTALL_DATA) DATA = $(m4data_DATA) DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) ACLOCAL = @ACLOCAL@ @@ -96,6 +113,7 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ +PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ RANLIB = @RANLIB@ @@ -181,9 +199,9 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps) exit 1;; \ esac; \ done; \ - echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu m4/Makefile'; \ - cd $(top_srcdir) && \ - $(AUTOMAKE) --gnu m4/Makefile + echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu m4/Makefile'; \ + $(am__cd) $(top_srcdir) && \ + $(AUTOMAKE) --gnu m4/Makefile .PRECIOUS: Makefile Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status @case '$?' in \ @@ -201,23 +219,27 @@ $(top_srcdir)/configure: $(am__configure_deps) cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh $(ACLOCAL_M4): $(am__aclocal_m4_deps) cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh +$(am__aclocal_m4_deps): install-m4dataDATA: $(m4data_DATA) @$(NORMAL_INSTALL) test -z "$(m4datadir)" || $(MKDIR_P) "$(DESTDIR)$(m4datadir)" - @list='$(m4data_DATA)'; for p in $$list; do \ + @list='$(m4data_DATA)'; test -n "$(m4datadir)" || list=; \ + for p in $$list; do \ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ - f=$(am__strip_dir) \ - echo " $(m4dataDATA_INSTALL) '$$d$$p' '$(DESTDIR)$(m4datadir)/$$f'"; \ - $(m4dataDATA_INSTALL) "$$d$$p" "$(DESTDIR)$(m4datadir)/$$f"; \ + echo "$$d$$p"; \ + done | $(am__base_list) | \ + while read files; do \ + echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(m4datadir)'"; \ + $(INSTALL_DATA) $$files "$(DESTDIR)$(m4datadir)" || exit $$?; \ done uninstall-m4dataDATA: @$(NORMAL_UNINSTALL) - @list='$(m4data_DATA)'; for p in $$list; do \ - f=$(am__strip_dir) \ - echo " rm -f '$(DESTDIR)$(m4datadir)/$$f'"; \ - rm -f "$(DESTDIR)$(m4datadir)/$$f"; \ - done + @list='$(m4data_DATA)'; test -n "$(m4datadir)" || list=; \ + files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \ + test -n "$$files" || exit 0; \ + echo " ( cd '$(DESTDIR)$(m4datadir)' && rm -f" $$files ")"; \ + cd "$(DESTDIR)$(m4datadir)" && rm -f $$files tags: TAGS TAGS: @@ -241,13 +263,17 @@ distdir: $(DISTFILES) if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \ if test -d $$d/$$file; then \ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \ + if test -d "$(distdir)/$$file"; then \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ + fi; \ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \ - cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \ + cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ fi; \ - cp -pR $$d/$$file $(distdir)$$dir || exit 1; \ + cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \ else \ - test -f $(distdir)/$$file \ - || cp -p $$d/$$file $(distdir)/$$file \ + test -f "$(distdir)/$$file" \ + || cp -p $$d/$$file "$(distdir)/$$file" \ || exit 1; \ fi; \ done @@ -278,6 +304,7 @@ clean-generic: distclean-generic: -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES) + -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES) maintainer-clean-generic: @echo "This command is intended for maintainers to use" @@ -296,6 +323,8 @@ dvi-am: html: html-am +html-am: + info: info-am info-am: @@ -304,18 +333,28 @@ install-data-am: install-m4dataDATA install-dvi: install-dvi-am +install-dvi-am: + install-exec-am: install-html: install-html-am +install-html-am: + install-info: install-info-am +install-info-am: + install-man: install-pdf: install-pdf-am +install-pdf-am: + install-ps: install-ps-am +install-ps-am: + installcheck-am: maintainer-clean: maintainer-clean-am @@ -349,6 +388,7 @@ uninstall-am: uninstall-m4dataDATA maintainer-clean-generic mostlyclean mostlyclean-generic pdf \ pdf-am ps ps-am uninstall uninstall-am uninstall-m4dataDATA + # 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/clustalw/missing b/binaries/src/clustalw/missing index 1c8ff70..28055d2 100644 --- a/binaries/src/clustalw/missing +++ b/binaries/src/clustalw/missing @@ -1,10 +1,10 @@ #! /bin/sh # Common stub for a few missing GNU programs while installing. -scriptversion=2006-05-10.23 +scriptversion=2009-04-28.21; # UTC -# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006 -# Free Software Foundation, Inc. +# 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 @@ -18,9 +18,7 @@ scriptversion=2006-05-10.23 # 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. +# 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 @@ -89,6 +87,9 @@ Supported PROGRAM values: 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 $? ;; @@ -106,15 +107,22 @@ Send bug reports to ." 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). +# the program). This is about non-GNU programs, so use $1 not +# $program. case $1 in - lex|yacc) + lex*|yacc*) # Not GNU programs, they don't have --version. ;; - tar) + tar*) if test -n "$run"; then echo 1>&2 "ERROR: \`tar' requires --run" exit 1 @@ -138,7 +146,7 @@ esac # If it does not exist, or fails to run (possibly an outdated version), # try to emulate it. -case $1 in +case $program in aclocal*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if @@ -148,7 +156,7 @@ WARNING: \`$1' is $msg. You should only need it if touch aclocal.m4 ;; - autoconf) + autoconf*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified \`${configure_ac}'. You might want to install the @@ -157,7 +165,7 @@ WARNING: \`$1' is $msg. You should only need it if touch configure ;; - autoheader) + autoheader*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified \`acconfig.h' or \`${configure_ac}'. You might want @@ -187,7 +195,7 @@ WARNING: \`$1' is $msg. You should only need it if while read f; do touch "$f"; done ;; - autom4te) + autom4te*) echo 1>&2 "\ WARNING: \`$1' is needed, but is $msg. You might have modified some files without having the @@ -210,7 +218,7 @@ WARNING: \`$1' is needed, but is $msg. fi ;; - bison|yacc) + 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 @@ -240,7 +248,7 @@ WARNING: \`$1' $msg. You should only need it if fi ;; - lex|flex) + 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 @@ -263,7 +271,7 @@ WARNING: \`$1' is $msg. You should only need it if fi ;; - help2man) + 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 @@ -277,11 +285,11 @@ WARNING: \`$1' is $msg. You should only need it if else test -z "$file" || exec >$file echo ".ab help2man is required to generate this page" - exit 1 + exit $? fi ;; - makeinfo) + 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 @@ -310,7 +318,7 @@ WARNING: \`$1' is $msg. You should only need it if touch $file ;; - tar) + tar*) shift # We have already tried tar in the generic part. @@ -363,5 +371,6 @@ exit 0 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" # End: diff --git a/binaries/src/clustalw/src/.deps/Alignment.Po b/binaries/src/clustalw/src/.deps/Alignment.Po index 63e38bd..920594b 100644 --- a/binaries/src/clustalw/src/.deps/Alignment.Po +++ b/binaries/src/clustalw/src/.deps/Alignment.Po @@ -1,159 +1,137 @@ -Alignment.o Alignment.o: alignment/Alignment.cpp config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/bits/types.h \ - /usr/include/bits/typesizes.h /usr/include/libio.h \ - /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ - /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/sched.h /usr/include/time.h /usr/include/bits/sched.h \ - /usr/include/bits/time.h /usr/include/signal.h \ - /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ - /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ - /usr/include/sys/select.h /usr/include/bits/select.h \ - /usr/include/sys/sysmacros.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + alignment/Sequence.h alignment/../general/userparams.h \ + alignment/../general/UserParameters.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + alignment/../general/utils.h alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h alignment/../general/clustalw.h \ + alignment/../general/general.h alignment/../general/Array2D.h \ + alignment/../general/SquareMat.h alignment/../general/SymMatrix.h \ + alignment/../general/utils.h \ + alignment/../substitutionMatrix/globalmatrix.h \ + alignment/../substitutionMatrix/SubMatrix.h \ + alignment/../substitutionMatrix/../general/clustalw.h \ + alignment/../substitutionMatrix/../general/userparams.h \ + alignment/../substitutionMatrix/../general/utils.h \ + alignment/../substitutionMatrix/../general/Array2D.h \ + alignment/../general/VectorOutOfRange.h \ + alignment/../general/SequenceNotFoundException.h config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -163,9 +141,13 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: /usr/include/math.h: @@ -185,79 +167,93 @@ config.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: + +/usr/include/bits/wchar.h: /usr/include/xlocale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/include/bits/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/bits/typesizes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/libio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/include/_G_config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/gconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/bits/sys_errlist.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: /usr/include/locale.h: /usr/include/bits/locale.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/include/nl_types.h: +/usr/include/ctype.h: -/usr/include/iconv.h: +/usr/include/bits/types.h: -/usr/include/libintl.h: +/usr/include/bits/typesizes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/include/endian.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/include/bits/endian.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/include/bits/byteswap.h: -/usr/include/pthread.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/include/endian.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/include/bits/endian.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: /usr/include/sched.h: @@ -267,10 +263,6 @@ config.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -285,187 +277,127 @@ config.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/include/stdint.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/include/stdlib.h: - -/usr/include/bits/waitflags.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/include/bits/waitstatus.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -/usr/include/sys/types.h: - -/usr/include/sys/select.h: - -/usr/include/bits/select.h: - -/usr/include/sys/sysmacros.h: - -/usr/include/alloca.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +alignment/Alignment.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/include/wctype.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/include/stdlib.h: -alignment/Alignment.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/alloca.h: -alignment/Sequence.h: +/usr/include/libio.h: -alignment/../general/userparams.h: +/usr/include/_G_config.h: -alignment/../general/UserParameters.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/bits/sys_errlist.h: -alignment/../general/utils.h: +/usr/include/bits/stdio.h: -alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -475,8 +407,6 @@ alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: diff --git a/binaries/src/clustalw/src/.deps/AlignmentOutput.Po b/binaries/src/clustalw/src/.deps/AlignmentOutput.Po index 8078048..cfaf598 100644 --- a/binaries/src/clustalw/src/.deps/AlignmentOutput.Po +++ b/binaries/src/clustalw/src/.deps/AlignmentOutput.Po @@ -1,163 +1,152 @@ -AlignmentOutput.o AlignmentOutput.o: alignment/AlignmentOutput.cpp \ - config.h alignment/AlignmentOutput.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cassert \ - /usr/include/assert.h alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -167,129 +156,119 @@ alignment/AlignmentOutput.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -303,163 +282,139 @@ alignment/AlignmentOutput.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/include/wctype.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cassert: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/assert.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +alignment/Alignment.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cassert: +alignment/../general/Utility.h: -/usr/include/assert.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -alignment/Alignment.h: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/sys/types.h: -alignment/Sequence.h: +/usr/include/sys/select.h: -alignment/../general/userparams.h: +/usr/include/bits/select.h: -alignment/../general/UserParameters.h: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/sys/sysmacros.h: -alignment/../general/utils.h: +/usr/include/alloca.h: -alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -469,8 +424,6 @@ alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -485,7 +438,7 @@ alignment/../general/SquareMat.h: alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -505,7 +458,7 @@ alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: alignment/../general/utils.h: diff --git a/binaries/src/clustalw/src/.deps/AlignmentSteps.Po b/binaries/src/clustalw/src/.deps/AlignmentSteps.Po index 8d1ae06..b010eca 100644 --- a/binaries/src/clustalw/src/.deps/AlignmentSteps.Po +++ b/binaries/src/clustalw/src/.deps/AlignmentSteps.Po @@ -1,134 +1,104 @@ -AlignmentSteps.o AlignmentSteps.o: tree/AlignmentSteps.cpp config.h \ - tree/AlignmentSteps.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc +AlignmentSteps.o: tree/AlignmentSteps.cpp config.h tree/AlignmentSteps.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: diff --git a/binaries/src/clustalw/src/.deps/Clustal.Po b/binaries/src/clustalw/src/.deps/Clustal.Po index 0392e41..df48e20 100644 --- a/binaries/src/clustalw/src/.deps/Clustal.Po +++ b/binaries/src/clustalw/src/.deps/Clustal.Po @@ -1,184 +1,171 @@ -Clustal.o Clustal.o: Clustal.cpp config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/iconv.h: +/usr/include/locale.h: -/usr/include/libintl.h: +/usr/include/bits/locale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/include/bits/types.h: -/usr/include/pthread.h: +/usr/include/bits/typesizes.h: /usr/include/endian.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: + /usr/include/sched.h: /usr/include/time.h: @@ -268,10 +275,6 @@ config.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -286,167 +289,85 @@ config.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/include/stdlib.h: - -/usr/include/bits/waitflags.h: - -/usr/include/bits/waitstatus.h: - -/usr/include/sys/types.h: - -/usr/include/sys/select.h: - -/usr/include/bits/select.h: - -/usr/include/sys/sysmacros.h: - -/usr/include/alloca.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/include/wctype.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/include/bits/sys_errlist.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/stdio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: Clustal.h: @@ -456,23 +377,25 @@ general/general.h: general/Array2D.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -general/SquareMat.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -492,14 +415,36 @@ general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/sys/types.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/alloca.h: general/utils.h: general/Utility.h: +/usr/include/string.h: + /usr/include/errno.h: /usr/include/bits/errno.h: @@ -508,8 +453,6 @@ general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -524,6 +467,14 @@ general/utils.h: fileInput/FileReader.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: + fileInput/../alignment/Alignment.h: fileInput/../alignment/Sequence.h: @@ -576,11 +527,11 @@ alignment/Alignment.h: alignment/AlignmentOutput.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cassert: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cassert: /usr/include/assert.h: @@ -635,3 +586,5 @@ alignment/../substitutionMatrix/globalmatrix.h: general/ClustalWResources.h: Help.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ctime: diff --git a/binaries/src/clustalw/src/.deps/ClustalFileParser.Po b/binaries/src/clustalw/src/.deps/ClustalFileParser.Po index 0e4d6ed..b059042 100644 --- a/binaries/src/clustalw/src/.deps/ClustalFileParser.Po +++ b/binaries/src/clustalw/src/.deps/ClustalFileParser.Po @@ -1,156 +1,145 @@ -ClustalFileParser.o ClustalFileParser.o: fileInput/ClustalFileParser.cpp \ - config.h fileInput/ClustalFileParser.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - fileInput/FileParser.h fileInput/../alignment/Sequence.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - fileInput/../alignment/../general/userparams.h \ - fileInput/../alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - fileInput/../alignment/../general/utils.h \ - fileInput/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - fileInput/../alignment/../general/clustalw.h \ - fileInput/../alignment/../general/general.h \ - fileInput/../alignment/../general/Array2D.h \ - fileInput/../alignment/../general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - fileInput/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - fileInput/../alignment/../general/utils.h \ - fileInput/../general/userparams.h fileInput/InFileStream.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc +ClustalFileParser.o: fileInput/ClustalFileParser.cpp config.h \ + fileInput/ClustalFileParser.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \ + 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/usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + fileInput/../alignment/../general/clustalw.h \ + fileInput/../alignment/../general/general.h \ + fileInput/../alignment/../general/Array2D.h \ + fileInput/../alignment/../general/SquareMat.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + fileInput/../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + fileInput/../alignment/../general/utils.h \ + fileInput/../general/userparams.h fileInput/InFileStream.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h config.h: fileInput/ClustalFileParser.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -160,129 +149,119 @@ fileInput/ClustalFileParser.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/include/gconv.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/include/bits/types.h: -/usr/include/bits/sys_errlist.h: +/usr/include/bits/typesizes.h: -/usr/include/bits/stdio.h: +/usr/include/endian.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/endian.h: -/usr/include/locale.h: +/usr/include/bits/byteswap.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -296,143 +275,107 @@ fileInput/ClustalFileParser.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: +fileInput/FileParser.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: +fileInput/../alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: +fileInput/../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: +fileInput/../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -fileInput/FileParser.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -fileInput/../alignment/Sequence.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -fileInput/../alignment/../general/userparams.h: - -fileInput/../alignment/../general/UserParameters.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +fileInput/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +fileInput/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/include/wctype.h: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/sys_errlist.h: -fileInput/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -fileInput/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -442,8 +385,6 @@ fileInput/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -456,13 +397,11 @@ fileInput/../alignment/../general/Array2D.h: fileInput/../alignment/../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: fileInput/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -482,9 +421,9 @@ fileInput/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: fileInput/../alignment/../general/utils.h: @@ -492,8 +431,22 @@ fileInput/../general/userparams.h: fileInput/InFileStream.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: diff --git a/binaries/src/clustalw/src/.deps/ClustalWResources.Po b/binaries/src/clustalw/src/.deps/ClustalWResources.Po index 12de588..114443f 100644 --- a/binaries/src/clustalw/src/.deps/ClustalWResources.Po +++ b/binaries/src/clustalw/src/.deps/ClustalWResources.Po @@ -1,144 +1,130 @@ -ClustalWResources.o ClustalWResources.o: general/ClustalWResources.cpp \ - config.h general/ClustalWResources.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - general/clustalw.h general/general.h general/Array2D.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc +ClustalWResources.o: general/ClustalWResources.cpp config.h \ + general/ClustalWResources.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + 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/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + 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/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + general/clustalw.h general/general.h general/Array2D.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + general/SquareMat.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc config.h: general/ClustalWResources.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -148,129 +134,119 @@ general/ClustalWResources.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/xlocale.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: - -/usr/include/limits.h: - -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/stdlib.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/bits/waitflags.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/include/bits/waitstatus.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/endian.h: - -/usr/include/bits/endian.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/sys/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/include/bits/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/include/bits/typesizes.h: +/usr/include/wchar.h: -/usr/include/time.h: +/usr/include/stdio.h: -/usr/include/sys/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: -/usr/include/bits/select.h: +/usr/include/bits/wchar.h: -/usr/include/bits/sigset.h: +/usr/include/xlocale.h: -/usr/include/bits/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/include/sys/sysmacros.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/include/bits/pthreadtypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/include/alloca.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/libio.h: +/usr/include/locale.h: -/usr/include/_G_config.h: +/usr/include/bits/locale.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/include/gconv.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/include/bits/types.h: -/usr/include/bits/sys_errlist.h: +/usr/include/bits/typesizes.h: -/usr/include/bits/stdio.h: +/usr/include/endian.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/endian.h: -/usr/include/locale.h: +/usr/include/bits/byteswap.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -284,172 +260,138 @@ general/ClustalWResources.h: /usr/include/getopt.h: 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-/usr/include/bits/inf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: -/usr/include/bits/nan.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: -/usr/include/bits/mathdef.h: +/usr/include/libio.h: -/usr/include/bits/mathcalls.h: +/usr/include/_G_config.h: -/usr/include/bits/mathinline.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/include/bits/sys_errlist.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/bits/stdio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: diff --git a/binaries/src/clustalw/src/.deps/ClusterTree.Po b/binaries/src/clustalw/src/.deps/ClusterTree.Po index 32d7d03..ce1b9b4 100644 --- a/binaries/src/clustalw/src/.deps/ClusterTree.Po +++ b/binaries/src/clustalw/src/.deps/ClusterTree.Po @@ -1,176 +1,164 @@ -ClusterTree.o ClusterTree.o: tree/ClusterTree.cpp config.h \ - tree/ClusterTree.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -180,72 +168,92 @@ tree/ClusterTree.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: + +/usr/include/bits/wchar.h: /usr/include/xlocale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/include/bits/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/include/bits/typesizes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/libio.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/include/bits/types.h: -/usr/include/pthread.h: +/usr/include/bits/typesizes.h: /usr/include/endian.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: + /usr/include/sched.h: /usr/include/time.h: @@ -254,10 +262,6 @@ tree/ClusterTree.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -272,193 +276,143 @@ tree/ClusterTree.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: - 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +tree/../alignment/Alignment.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +tree/../alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +tree/../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +tree/../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +tree/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +tree/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/include/stdlib.h: -tree/../alignment/Alignment.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/sys/select.h: -tree/../alignment/Sequence.h: +/usr/include/bits/select.h: -tree/../alignment/../general/userparams.h: +/usr/include/bits/sigset.h: -tree/../alignment/../general/UserParameters.h: +/usr/include/sys/sysmacros.h: -tree/../alignment/../general/utils.h: +/usr/include/alloca.h: -tree/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -468,8 +422,6 @@ tree/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -484,7 +436,7 @@ tree/../alignment/../general/SquareMat.h: tree/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -504,7 +456,7 @@ tree/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: tree/../alignment/../general/utils.h: @@ -542,6 +494,6 @@ tree/dayhoff.h: tree/RandomGenerator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: diff --git a/binaries/src/clustalw/src/.deps/ClusterTreeOutput.Po b/binaries/src/clustalw/src/.deps/ClusterTreeOutput.Po index 2f920c6..21731ef 100644 --- a/binaries/src/clustalw/src/.deps/ClusterTreeOutput.Po +++ b/binaries/src/clustalw/src/.deps/ClusterTreeOutput.Po @@ -1,166 +1,156 @@ -ClusterTreeOutput.o ClusterTreeOutput.o: tree/ClusterTreeOutput.cpp \ - config.h tree/ClusterTreeOutput.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc \ - tree/../alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - tree/../alignment/Sequence.h tree/../alignment/../general/userparams.h \ - tree/../alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - tree/../alignment/../general/utils.h \ - tree/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - tree/../alignment/../general/clustalw.h \ - tree/../alignment/../general/general.h \ - tree/../alignment/../general/Array2D.h \ - tree/../alignment/../general/SquareMat.h \ - tree/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - tree/../alignment/../general/utils.h \ - tree/../alignment/../substitutionMatrix/globalmatrix.h \ - tree/../alignment/../substitutionMatrix/SubMatrix.h \ - tree/../alignment/../substitutionMatrix/../general/clustalw.h \ - tree/../alignment/../substitutionMatrix/../general/userparams.h \ - tree/../alignment/../substitutionMatrix/../general/utils.h \ - tree/../alignment/../substitutionMatrix/../general/Array2D.h \ - tree/../alignment/../general/VectorOutOfRange.h \ - tree/../alignment/../general/SequenceNotFoundException.h \ - tree/../general/clustalw.h +ClusterTreeOutput.o: tree/ClusterTreeOutput.cpp config.h \ + tree/ClusterTreeOutput.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -170,123 +160,125 @@ tree/ClusterTreeOutput.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -300,159 +292,123 @@ tree/ClusterTreeOutput.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - 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-tree/../alignment/Alignment.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +tree/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +tree/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/sys/types.h: -tree/../alignment/Sequence.h: +/usr/include/sys/select.h: -tree/../alignment/../general/userparams.h: +/usr/include/bits/select.h: -tree/../alignment/../general/UserParameters.h: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/sys/sysmacros.h: -tree/../alignment/../general/utils.h: +/usr/include/alloca.h: -tree/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -462,8 +418,6 @@ tree/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -478,7 +432,7 @@ tree/../alignment/../general/SquareMat.h: tree/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -498,7 +452,7 @@ tree/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: tree/../alignment/../general/utils.h: diff --git a/binaries/src/clustalw/src/.deps/CommandLineParser.Po b/binaries/src/clustalw/src/.deps/CommandLineParser.Po index 092b8a3..5ad7fbd 100644 --- a/binaries/src/clustalw/src/.deps/CommandLineParser.Po +++ b/binaries/src/clustalw/src/.deps/CommandLineParser.Po @@ -1,188 +1,177 @@ -CommandLineParser.o CommandLineParser.o: interface/CommandLineParser.cpp \ - config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/include/ctype.h /usr/include/bits/types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/bits/typesizes.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/include/string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/bits/sched.h /usr/include/bits/time.h \ - /usr/include/signal.h /usr/include/bits/sigset.h \ - /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ - /usr/include/unistd.h /usr/include/bits/posix_opt.h \ - /usr/include/bits/environments.h /usr/include/bits/confname.h \ - /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ - /usr/include/sys/select.h /usr/include/bits/select.h \ - /usr/include/sys/sysmacros.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc \ - interface/CommandLineParser.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - interface/../Clustal.h interface/../general/clustalw.h \ - interface/../general/general.h interface/../general/Array2D.h \ - interface/../general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - interface/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - interface/../general/utils.h interface/../general/Utility.h \ - /usr/include/errno.h /usr/include/bits/errno.h \ - /usr/include/linux/errno.h /usr/include/asm/errno.h \ - /usr/include/asm-x86_64/errno.h /usr/include/asm-generic/errno.h \ - /usr/include/asm-generic/errno-base.h interface/../general/clustalw.h \ - interface/../general/userparams.h interface/../general/UserParameters.h \ - interface/../general/utils.h interface/../fileInput/FileReader.h \ - interface/../fileInput/../alignment/Alignment.h \ - interface/../fileInput/../alignment/Sequence.h \ - interface/../fileInput/../alignment/../general/userparams.h \ - interface/../fileInput/../alignment/../general/utils.h \ - interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h \ - interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h \ - interface/../fileInput/../alignment/../substitutionMatrix/../general/clustalw.h \ - interface/../fileInput/../alignment/../substitutionMatrix/../general/userparams.h \ - interface/../fileInput/../alignment/../substitutionMatrix/../general/utils.h \ - interface/../fileInput/../alignment/../substitutionMatrix/../general/Array2D.h \ - interface/../fileInput/../alignment/../general/VectorOutOfRange.h \ - interface/../fileInput/../alignment/../general/SequenceNotFoundException.h \ - interface/../fileInput/../alignment/Sequence.h \ - interface/../fileInput/../general/userparams.h \ - interface/../fileInput/../general/utils.h \ - interface/../fileInput/FileParser.h \ - interface/../fileInput/InFileStream.h \ - interface/../fileInput/ClustalFileParser.h \ - interface/../fileInput/PearsonFileParser.h \ - interface/../fileInput/PIRFileParser.h \ - interface/../fileInput/GDEFileParser.h \ - interface/../fileInput/MSFFileParser.h \ - interface/../fileInput/RSFFileParser.h \ - interface/../fileInput/EMBLFileParser.h \ - interface/../alignment/Alignment.h \ - interface/../alignment/AlignmentOutput.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cassert \ - /usr/include/assert.h interface/../alignment/Alignment.h \ - interface/../general/clustalw.h interface/../general/userparams.h \ - interface/../general/utils.h interface/../general/debuglogObject.h \ - interface/../general/DebugLog.h interface/../general/statsObject.h \ - interface/../general/Stats.h \ - interface/../substitutionMatrix/globalmatrix.h general/Utility.h \ - general/statsObject.h +CommandLineParser.o: interface/CommandLineParser.cpp config.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/wchar.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/bits/wchar.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + 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interface/../fileInput/../alignment/../general/VectorOutOfRange.h \ + interface/../fileInput/../alignment/../general/SequenceNotFoundException.h \ + interface/../fileInput/../alignment/Sequence.h \ + interface/../fileInput/../general/userparams.h \ + interface/../fileInput/../general/utils.h \ + interface/../fileInput/FileParser.h \ + interface/../fileInput/InFileStream.h \ + interface/../fileInput/ClustalFileParser.h \ + interface/../fileInput/PearsonFileParser.h \ + interface/../fileInput/PIRFileParser.h \ + interface/../fileInput/GDEFileParser.h \ + interface/../fileInput/MSFFileParser.h \ + interface/../fileInput/RSFFileParser.h \ + interface/../fileInput/EMBLFileParser.h \ + interface/../alignment/Alignment.h \ + interface/../alignment/AlignmentOutput.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cassert \ + /usr/include/assert.h interface/../alignment/Alignment.h \ + interface/../general/clustalw.h interface/../general/userparams.h \ + interface/../general/utils.h interface/../general/debuglogObject.h \ + interface/../general/DebugLog.h interface/../general/statsObject.h \ + interface/../general/Stats.h \ + interface/../substitutionMatrix/globalmatrix.h general/Utility.h \ + general/statsObject.h config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -192,25 +181,27 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: /usr/include/ctype.h: /usr/include/bits/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: - /usr/include/bits/typesizes.h: /usr/include/endian.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + /usr/include/xlocale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: /usr/include/stdio.h: @@ -220,11 +211,7 @@ config.h: /usr/include/wchar.h: -/usr/include/bits/wchar.h: - -/usr/include/gconv.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: /usr/include/bits/stdio_lim.h: @@ -232,235 +219,175 @@ config.h: /usr/include/bits/stdio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: - -/usr/include/string.h: - 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +interface/CommandLineParser.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -interface/CommandLineParser.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: interface/../Clustal.h: @@ -472,13 +399,11 @@ interface/../general/Array2D.h: interface/../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: interface/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -498,14 +423,36 @@ interface/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/sys/types.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/alloca.h: interface/../general/utils.h: interface/../general/Utility.h: +/usr/include/string.h: + /usr/include/errno.h: /usr/include/bits/errno.h: @@ -514,8 +461,6 @@ interface/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -530,6 +475,14 @@ interface/../general/utils.h: interface/../fileInput/FileReader.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: + interface/../fileInput/../alignment/Alignment.h: interface/../fileInput/../alignment/Sequence.h: @@ -582,11 +535,11 @@ interface/../alignment/Alignment.h: interface/../alignment/AlignmentOutput.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cassert: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cassert: /usr/include/assert.h: diff --git a/binaries/src/clustalw/src/.deps/DebugLog.Po b/binaries/src/clustalw/src/.deps/DebugLog.Po index 1a717f1..aca6b24 100644 --- a/binaries/src/clustalw/src/.deps/DebugLog.Po +++ b/binaries/src/clustalw/src/.deps/DebugLog.Po @@ -1,128 +1,107 @@ -DebugLog.o DebugLog.o: general/DebugLog.cpp config.h general/DebugLog.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream config.h: general/DebugLog.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -132,129 +111,119 @@ general/DebugLog.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/bits/sys_errlist.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/include/bits/stdio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: diff --git a/binaries/src/clustalw/src/.deps/EMBLFileParser.Po b/binaries/src/clustalw/src/.deps/EMBLFileParser.Po index 35d50b6..cc3fe04 100644 --- a/binaries/src/clustalw/src/.deps/EMBLFileParser.Po +++ b/binaries/src/clustalw/src/.deps/EMBLFileParser.Po @@ -1,156 +1,145 @@ -EMBLFileParser.o EMBLFileParser.o: fileInput/EMBLFileParser.cpp config.h \ - fileInput/EMBLFileParser.h \ - 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fileInput/../alignment/../general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - fileInput/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - fileInput/../alignment/../general/utils.h \ - fileInput/../general/userparams.h fileInput/InFileStream.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc +EMBLFileParser.o: fileInput/EMBLFileParser.cpp config.h \ + fileInput/EMBLFileParser.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + 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/usr/include/bits/byteswap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + fileInput/FileParser.h fileInput/../alignment/Sequence.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + 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fileInput/../alignment/../general/utils.h \ + fileInput/../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + fileInput/../alignment/../general/clustalw.h \ + fileInput/../alignment/../general/general.h \ + fileInput/../alignment/../general/Array2D.h \ + fileInput/../alignment/../general/SquareMat.h \ + 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\ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h config.h: fileInput/EMBLFileParser.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -160,129 +149,119 @@ fileInput/EMBLFileParser.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/include/wctype.h: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/sys_errlist.h: -fileInput/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -fileInput/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -442,8 +385,6 @@ fileInput/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -456,13 +397,11 @@ fileInput/../alignment/../general/Array2D.h: fileInput/../alignment/../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: fileInput/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -482,9 +421,9 @@ fileInput/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: fileInput/../alignment/../general/utils.h: @@ -492,8 +431,22 @@ fileInput/../general/userparams.h: fileInput/InFileStream.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: diff --git a/binaries/src/clustalw/src/.deps/FastPairwiseAlign.Po b/binaries/src/clustalw/src/.deps/FastPairwiseAlign.Po index cc9e01c..384e6cc 100644 --- a/binaries/src/clustalw/src/.deps/FastPairwiseAlign.Po +++ b/binaries/src/clustalw/src/.deps/FastPairwiseAlign.Po @@ -1,148 +1,130 @@ -FastPairwiseAlign.o FastPairwiseAlign.o: pairwise/FastPairwiseAlign.cpp \ - config.h /usr/include/math.h /usr/include/features.h \ - /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ - /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ - /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ - /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ - pairwise/FastPairwiseAlign.h pairwise/PairwiseAlignBase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - pairwise/../alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - pairwise/../alignment/Sequence.h \ - pairwise/../alignment/../general/userparams.h \ - pairwise/../alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - pairwise/../alignment/../general/utils.h \ - pairwise/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - pairwise/../alignment/../general/clustalw.h \ - pairwise/../alignment/../general/general.h \ - pairwise/../alignment/../general/Array2D.h \ - pairwise/../alignment/../general/SquareMat.h \ - pairwise/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - pairwise/../alignment/../general/utils.h \ - pairwise/../alignment/../substitutionMatrix/globalmatrix.h \ - pairwise/../alignment/../substitutionMatrix/SubMatrix.h \ - pairwise/../alignment/../substitutionMatrix/../general/clustalw.h \ - pairwise/../alignment/../substitutionMatrix/../general/userparams.h \ - pairwise/../alignment/../substitutionMatrix/../general/utils.h \ - pairwise/../alignment/../substitutionMatrix/../general/Array2D.h \ - pairwise/../alignment/../general/VectorOutOfRange.h \ - pairwise/../alignment/../general/SequenceNotFoundException.h +FastPairwiseAlign.o: pairwise/FastPairwiseAlign.cpp config.h \ + /usr/include/math.h /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ + /usr/include/gnu/stubs-64.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h pairwise/FastPairwiseAlign.h \ + pairwise/PairwiseAlignBase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + pairwise/../alignment/Alignment.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + pairwise/../alignment/Sequence.h \ + pairwise/../alignment/../general/userparams.h \ + pairwise/../alignment/../general/UserParameters.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + pairwise/../alignment/../general/utils.h \ + pairwise/../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + pairwise/../alignment/../general/clustalw.h \ + pairwise/../alignment/../general/general.h \ + pairwise/../alignment/../general/Array2D.h \ + pairwise/../alignment/../general/SquareMat.h \ + pairwise/../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + pairwise/../alignment/../general/utils.h \ + pairwise/../alignment/../substitutionMatrix/globalmatrix.h \ + pairwise/../alignment/../substitutionMatrix/SubMatrix.h \ + pairwise/../alignment/../substitutionMatrix/../general/clustalw.h \ + pairwise/../alignment/../substitutionMatrix/../general/userparams.h \ + pairwise/../alignment/../substitutionMatrix/../general/utils.h \ + pairwise/../alignment/../substitutionMatrix/../general/Array2D.h \ + pairwise/../alignment/../general/VectorOutOfRange.h \ + pairwise/../alignment/../general/SequenceNotFoundException.h config.h: @@ -178,135 +160,141 @@ pairwise/FastPairwiseAlign.h: pairwise/PairwiseAlignBase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/include/bits/stdio_lim.h: 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+/usr/include/bits/types.h: -/usr/include/bits/stdio.h: +/usr/include/bits/typesizes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/endian.h: -/usr/include/locale.h: +/usr/include/bits/endian.h: -/usr/include/bits/locale.h: +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -320,149 +308,95 @@ pairwise/PairwiseAlignBase.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/include/stdint.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: - -pairwise/../alignment/Alignment.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +pairwise/../alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +pairwise/../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +pairwise/../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/include/wctype.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +pairwise/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +pairwise/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/alloca.h: -pairwise/../alignment/Sequence.h: +/usr/include/libio.h: -pairwise/../alignment/../general/userparams.h: +/usr/include/_G_config.h: -pairwise/../alignment/../general/UserParameters.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/bits/sys_errlist.h: -pairwise/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -pairwise/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -472,8 +406,6 @@ pairwise/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -488,9 +420,9 @@ pairwise/../alignment/../general/SquareMat.h: pairwise/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: pairwise/../alignment/../general/utils.h: diff --git a/binaries/src/clustalw/src/.deps/FileParser.Po b/binaries/src/clustalw/src/.deps/FileParser.Po index 6e6d88e..a7c4f01 100644 --- a/binaries/src/clustalw/src/.deps/FileParser.Po +++ b/binaries/src/clustalw/src/.deps/FileParser.Po @@ -1,143 +1,131 @@ -FileParser.o FileParser.o: fileInput/FileParser.cpp config.h \ - fileInput/FileParser.h /usr/include/ctype.h /usr/include/features.h \ - /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/include/bits/types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/bits/typesizes.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/xlocale.h \ - fileInput/../alignment/Sequence.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/include/string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - 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fileInput/../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + fileInput/../alignment/../general/utils.h \ + fileInput/../general/userparams.h fileInput/InFileStream.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h config.h: @@ -157,135 +145,137 @@ fileInput/FileParser.h: /usr/include/bits/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: - /usr/include/bits/typesizes.h: /usr/include/endian.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + /usr/include/xlocale.h: fileInput/../alignment/Sequence.h: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/include/stdlib.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/include/bits/waitflags.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/include/bits/waitstatus.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/include/sys/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/include/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/include/sys/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/include/bits/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/include/bits/sigset.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/include/bits/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/include/sys/sysmacros.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/include/bits/pthreadtypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/include/alloca.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: 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/usr/include/bits/locale.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -299,137 +289,89 @@ fileInput/../alignment/Sequence.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +fileInput/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +fileInput/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/include/wctype.h: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/sys_errlist.h: -fileInput/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -fileInput/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -439,8 +381,6 @@ fileInput/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -453,13 +393,11 @@ fileInput/../alignment/../general/Array2D.h: fileInput/../alignment/../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: fileInput/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -479,9 +417,9 @@ fileInput/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: fileInput/../alignment/../general/utils.h: @@ -489,8 +427,22 @@ fileInput/../general/userparams.h: fileInput/InFileStream.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: diff --git a/binaries/src/clustalw/src/.deps/FileReader.Po b/binaries/src/clustalw/src/.deps/FileReader.Po index 036321b..b7d60fe 100644 --- a/binaries/src/clustalw/src/.deps/FileReader.Po +++ b/binaries/src/clustalw/src/.deps/FileReader.Po @@ -1,177 +1,161 @@ -FileReader.o FileReader.o: fileInput/FileReader.cpp config.h \ - fileInput/FileReader.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - fileInput/../alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + fileInput/ClustalFileParser.h fileInput/PearsonFileParser.h \ + fileInput/PIRFileParser.h fileInput/GDEFileParser.h \ + fileInput/MSFFileParser.h fileInput/RSFFileParser.h \ + fileInput/EMBLFileParser.h config.h: fileInput/FileReader.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -181,123 +165,131 @@ fileInput/FileReader.h: /usr/include/gnu/stubs-64.h: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +fileInput/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/alloca.h: -fileInput/../alignment/Sequence.h: +/usr/include/libio.h: -fileInput/../alignment/../general/userparams.h: +/usr/include/_G_config.h: -fileInput/../alignment/../general/UserParameters.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/bits/sys_errlist.h: -fileInput/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -fileInput/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -463,8 +411,6 @@ fileInput/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -479,7 +425,7 @@ fileInput/../alignment/../general/SquareMat.h: fileInput/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -499,7 +445,7 @@ fileInput/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: fileInput/../alignment/../general/utils.h: @@ -529,11 +475,17 @@ fileInput/FileParser.h: fileInput/InFileStream.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: fileInput/ClustalFileParser.h: diff --git a/binaries/src/clustalw/src/.deps/FullPairwiseAlign.Po b/binaries/src/clustalw/src/.deps/FullPairwiseAlign.Po index 015d98c..97348a0 100644 --- a/binaries/src/clustalw/src/.deps/FullPairwiseAlign.Po +++ b/binaries/src/clustalw/src/.deps/FullPairwiseAlign.Po @@ -1,149 +1,131 @@ -FullPairwiseAlign.o FullPairwiseAlign.o: pairwise/FullPairwiseAlign.cpp \ - config.h pairwise/FullPairwiseAlign.h pairwise/PairwiseAlignBase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - pairwise/../alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - pairwise/../alignment/Sequence.h \ - pairwise/../alignment/../general/userparams.h \ - pairwise/../alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - pairwise/../alignment/../general/utils.h \ - pairwise/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - pairwise/../alignment/../general/clustalw.h \ - pairwise/../alignment/../general/general.h \ - pairwise/../alignment/../general/Array2D.h \ - pairwise/../alignment/../general/SquareMat.h \ - pairwise/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - pairwise/../alignment/../general/utils.h \ - pairwise/../alignment/../substitutionMatrix/globalmatrix.h \ - pairwise/../alignment/../substitutionMatrix/SubMatrix.h \ - pairwise/../alignment/../substitutionMatrix/../general/clustalw.h \ - pairwise/../alignment/../substitutionMatrix/../general/userparams.h \ - pairwise/../alignment/../substitutionMatrix/../general/utils.h \ - pairwise/../alignment/../substitutionMatrix/../general/Array2D.h \ - pairwise/../alignment/../general/VectorOutOfRange.h \ - pairwise/../alignment/../general/SequenceNotFoundException.h +FullPairwiseAlign.o: pairwise/FullPairwiseAlign.cpp config.h \ + pairwise/FullPairwiseAlign.h pairwise/PairwiseAlignBase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + pairwise/../alignment/Alignment.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + pairwise/../alignment/Sequence.h \ + pairwise/../alignment/../general/userparams.h \ + pairwise/../alignment/../general/UserParameters.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + pairwise/../alignment/../general/utils.h \ + pairwise/../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + pairwise/../alignment/../general/clustalw.h \ + pairwise/../alignment/../general/general.h \ + pairwise/../alignment/../general/Array2D.h \ + pairwise/../alignment/../general/SquareMat.h \ + pairwise/../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + pairwise/../alignment/../general/utils.h \ + pairwise/../alignment/../substitutionMatrix/globalmatrix.h \ + pairwise/../alignment/../substitutionMatrix/SubMatrix.h \ + pairwise/../alignment/../substitutionMatrix/../general/clustalw.h \ + pairwise/../alignment/../substitutionMatrix/../general/userparams.h \ + pairwise/../alignment/../substitutionMatrix/../general/utils.h \ + pairwise/../alignment/../substitutionMatrix/../general/Array2D.h \ + pairwise/../alignment/../general/VectorOutOfRange.h \ + pairwise/../alignment/../general/SequenceNotFoundException.h config.h: @@ -151,19 +133,15 @@ pairwise/FullPairwiseAlign.h: pairwise/PairwiseAlignBase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -173,279 +151,235 @@ pairwise/PairwiseAlignBase.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/bits/xopen_lim.h: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +pairwise/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +pairwise/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/alloca.h: -pairwise/../alignment/Sequence.h: +/usr/include/libio.h: -pairwise/../alignment/../general/userparams.h: +/usr/include/_G_config.h: -pairwise/../alignment/../general/UserParameters.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/bits/sys_errlist.h: -pairwise/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -pairwise/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -455,8 +389,6 @@ pairwise/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -471,7 +403,7 @@ pairwise/../alignment/../general/SquareMat.h: pairwise/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -491,7 +423,7 @@ pairwise/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: pairwise/../alignment/../general/utils.h: diff --git a/binaries/src/clustalw/src/.deps/GDEFileParser.Po b/binaries/src/clustalw/src/.deps/GDEFileParser.Po index be2e74d..e225ad9 100644 --- a/binaries/src/clustalw/src/.deps/GDEFileParser.Po +++ b/binaries/src/clustalw/src/.deps/GDEFileParser.Po @@ -1,156 +1,145 @@ -GDEFileParser.o GDEFileParser.o: fileInput/GDEFileParser.cpp config.h \ - fileInput/GDEFileParser.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - fileInput/../alignment/../general/utils.h \ - fileInput/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - fileInput/../alignment/../general/clustalw.h \ - fileInput/../alignment/../general/general.h \ - fileInput/../alignment/../general/Array2D.h \ - fileInput/../alignment/../general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - fileInput/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - fileInput/../alignment/../general/utils.h \ - fileInput/../general/userparams.h fileInput/InFileStream.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc +GDEFileParser.o: fileInput/GDEFileParser.cpp config.h \ + fileInput/GDEFileParser.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + 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/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + fileInput/../alignment/../general/utils.h \ + fileInput/../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + fileInput/../alignment/../general/clustalw.h \ + fileInput/../alignment/../general/general.h \ + fileInput/../alignment/../general/Array2D.h \ + fileInput/../alignment/../general/SquareMat.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + fileInput/../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + fileInput/../alignment/../general/utils.h \ + fileInput/../general/userparams.h fileInput/InFileStream.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h config.h: fileInput/GDEFileParser.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -160,129 +149,119 @@ fileInput/GDEFileParser.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: -/usr/include/string.h: - -/usr/include/xlocale.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/stdlib.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/include/bits/waitflags.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/bits/waitstatus.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/endian.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/include/bits/endian.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/include/sys/types.h: - -/usr/include/bits/types.h: +/usr/include/wchar.h: -/usr/include/bits/typesizes.h: +/usr/include/stdio.h: -/usr/include/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: -/usr/include/sys/select.h: - -/usr/include/bits/select.h: +/usr/include/bits/wchar.h: -/usr/include/bits/sigset.h: +/usr/include/xlocale.h: -/usr/include/bits/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/include/sys/sysmacros.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/include/bits/pthreadtypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/include/alloca.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/libio.h: +/usr/include/locale.h: -/usr/include/_G_config.h: +/usr/include/bits/locale.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/include/gconv.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/include/bits/types.h: -/usr/include/bits/sys_errlist.h: +/usr/include/bits/typesizes.h: -/usr/include/bits/stdio.h: +/usr/include/endian.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/endian.h: -/usr/include/locale.h: +/usr/include/bits/byteswap.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -296,143 +275,107 @@ fileInput/GDEFileParser.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - 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+/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/sys_errlist.h: -fileInput/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -fileInput/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -442,8 +385,6 @@ fileInput/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -456,13 +397,11 @@ fileInput/../alignment/../general/Array2D.h: fileInput/../alignment/../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: fileInput/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -482,9 +421,9 @@ fileInput/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: fileInput/../alignment/../general/utils.h: @@ -492,8 +431,22 @@ fileInput/../general/userparams.h: fileInput/InFileStream.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: diff --git a/binaries/src/clustalw/src/.deps/Help.Po b/binaries/src/clustalw/src/.deps/Help.Po index ce5808b..0be6ef2 100644 --- a/binaries/src/clustalw/src/.deps/Help.Po +++ b/binaries/src/clustalw/src/.deps/Help.Po @@ -1,127 +1,101 @@ -Help.o Help.o: Help.cpp config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - clustalw_version.h Help.h +Help.o: Help.cpp config.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + 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/usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + clustalw_version.h Help.h config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -131,78 +105,98 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: + /usr/include/sched.h: /usr/include/time.h: @@ -211,10 +205,6 @@ config.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -229,169 +219,75 @@ config.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/include/stdlib.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/include/bits/waitflags.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/include/bits/waitstatus.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/include/sys/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/include/sys/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/include/bits/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/include/sys/sysmacros.h: - -/usr/include/alloca.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: /usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: clustalw_version.h: diff --git a/binaries/src/clustalw/src/.deps/InFileStream.Po b/binaries/src/clustalw/src/.deps/InFileStream.Po index 9482a0a..d295f9a 100644 --- a/binaries/src/clustalw/src/.deps/InFileStream.Po +++ b/binaries/src/clustalw/src/.deps/InFileStream.Po @@ -1,125 +1,110 @@ -InFileStream.o InFileStream.o: fileInput/InFileStream.cpp config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - fileInput/InFileStream.h +InFileStream.o: fileInput/InFileStream.cpp config.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + fileInput/InFileStream.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -129,129 +114,119 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/xlocale.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/limits.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +fileInput/InFileStream.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: -fileInput/InFileStream.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: diff --git a/binaries/src/clustalw/src/.deps/InteractiveMenu.Po b/binaries/src/clustalw/src/.deps/InteractiveMenu.Po index 6b1e8aa..3b5a1b6 100644 --- a/binaries/src/clustalw/src/.deps/InteractiveMenu.Po +++ b/binaries/src/clustalw/src/.deps/InteractiveMenu.Po @@ -1,172 +1,161 @@ -InteractiveMenu.o InteractiveMenu.o: interface/InteractiveMenu.cpp \ - config.h /usr/include/stdio.h /usr/include/features.h \ - /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h /usr/include/time.h \ - /usr/include/sys/select.h /usr/include/bits/select.h \ - /usr/include/bits/sigset.h /usr/include/bits/time.h \ - /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \ - /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - interface/InteractiveMenu.h interface/../Clustal.h \ - interface/../general/clustalw.h interface/../general/general.h \ - interface/../general/Array2D.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - interface/../general/SquareMat.h interface/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - interface/../general/utils.h interface/../general/Utility.h \ - /usr/include/errno.h /usr/include/bits/errno.h \ - /usr/include/linux/errno.h /usr/include/asm/errno.h \ - /usr/include/asm-x86_64/errno.h /usr/include/asm-generic/errno.h \ - /usr/include/asm-generic/errno-base.h interface/../general/clustalw.h \ - interface/../general/userparams.h interface/../general/UserParameters.h \ - interface/../general/utils.h interface/../fileInput/FileReader.h \ - interface/../fileInput/../alignment/Alignment.h \ - interface/../fileInput/../alignment/Sequence.h \ - interface/../fileInput/../alignment/../general/userparams.h \ - interface/../fileInput/../alignment/../general/utils.h \ - interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h \ - interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h \ - interface/../fileInput/../alignment/../substitutionMatrix/../general/clustalw.h \ - interface/../fileInput/../alignment/../substitutionMatrix/../general/userparams.h \ - interface/../fileInput/../alignment/../substitutionMatrix/../general/utils.h \ - interface/../fileInput/../alignment/../substitutionMatrix/../general/Array2D.h \ - interface/../fileInput/../alignment/../general/VectorOutOfRange.h \ - interface/../fileInput/../alignment/../general/SequenceNotFoundException.h \ - interface/../fileInput/../alignment/Sequence.h \ - interface/../fileInput/../general/userparams.h \ - interface/../fileInput/../general/utils.h \ - interface/../fileInput/FileParser.h \ - interface/../fileInput/InFileStream.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc \ - interface/../fileInput/ClustalFileParser.h \ - interface/../fileInput/PearsonFileParser.h \ - interface/../fileInput/PIRFileParser.h \ - interface/../fileInput/GDEFileParser.h \ - interface/../fileInput/MSFFileParser.h \ - interface/../fileInput/RSFFileParser.h \ - interface/../fileInput/EMBLFileParser.h \ - interface/../alignment/Alignment.h \ - interface/../alignment/AlignmentOutput.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cassert \ - /usr/include/assert.h interface/../alignment/Alignment.h \ - interface/../general/clustalw.h interface/../general/userparams.h \ - interface/../general/utils.h \ - interface/../substitutionMatrix/globalmatrix.h +InteractiveMenu.o: interface/InteractiveMenu.cpp config.h \ + /usr/include/stdio.h /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ + /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/typesizes.h \ + /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + 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interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h \ + interface/../fileInput/../alignment/../substitutionMatrix/../general/clustalw.h \ + interface/../fileInput/../alignment/../substitutionMatrix/../general/userparams.h \ + interface/../fileInput/../alignment/../substitutionMatrix/../general/utils.h \ + interface/../fileInput/../alignment/../substitutionMatrix/../general/Array2D.h \ + interface/../fileInput/../alignment/../general/VectorOutOfRange.h \ + interface/../fileInput/../alignment/../general/SequenceNotFoundException.h \ + interface/../fileInput/../alignment/Sequence.h \ + interface/../fileInput/../general/userparams.h \ + interface/../fileInput/../general/utils.h \ + interface/../fileInput/FileParser.h \ + interface/../fileInput/InFileStream.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + interface/../fileInput/ClustalFileParser.h \ + interface/../fileInput/PearsonFileParser.h \ + interface/../fileInput/PIRFileParser.h \ + interface/../fileInput/GDEFileParser.h \ + interface/../fileInput/MSFFileParser.h \ + interface/../fileInput/RSFFileParser.h \ + interface/../fileInput/EMBLFileParser.h \ + interface/../alignment/Alignment.h \ + interface/../alignment/AlignmentOutput.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cassert \ + /usr/include/assert.h interface/../alignment/Alignment.h \ + interface/../general/clustalw.h interface/../general/userparams.h \ + interface/../general/utils.h \ + interface/../substitutionMatrix/globalmatrix.h config.h: @@ -182,7 +171,7 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: /usr/include/bits/types.h: @@ -194,11 +183,7 @@ config.h: /usr/include/wchar.h: -/usr/include/bits/wchar.h: - -/usr/include/gconv.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: /usr/include/bits/stdio_lim.h: @@ -206,109 +191,113 @@ config.h: /usr/include/bits/stdio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/include/endian.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/endian.h: -/usr/include/locale.h: +/usr/include/bits/byteswap.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -322,127 +311,73 @@ config.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: /usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: interface/InteractiveMenu.h: @@ -454,19 +389,23 @@ interface/../general/general.h: interface/../general/Array2D.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: interface/../general/SquareMat.h: interface/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -486,14 +425,16 @@ interface/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: interface/../general/utils.h: interface/../general/Utility.h: +/usr/include/string.h: + /usr/include/errno.h: /usr/include/bits/errno.h: @@ -502,8 +443,6 @@ interface/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -518,6 +457,14 @@ interface/../general/utils.h: interface/../fileInput/FileReader.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: + interface/../fileInput/../alignment/Alignment.h: interface/../fileInput/../alignment/Sequence.h: @@ -552,11 +499,17 @@ interface/../fileInput/FileParser.h: interface/../fileInput/InFileStream.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: interface/../fileInput/ClustalFileParser.h: @@ -576,11 +529,11 @@ interface/../alignment/Alignment.h: interface/../alignment/AlignmentOutput.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cassert: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cassert: /usr/include/assert.h: diff --git a/binaries/src/clustalw/src/.deps/InvalidCombination.Po b/binaries/src/clustalw/src/.deps/InvalidCombination.Po index 1104fc1..08ba88f 100644 --- a/binaries/src/clustalw/src/.deps/InvalidCombination.Po +++ b/binaries/src/clustalw/src/.deps/InvalidCombination.Po @@ -1,127 +1,98 @@ -InvalidCombination.o InvalidCombination.o: \ - general/InvalidCombination.cpp config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/bits/types.h \ - /usr/include/bits/typesizes.h /usr/include/libio.h \ - /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ - /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ - /usr/include/sys/select.h /usr/include/bits/select.h \ - /usr/include/sys/sysmacros.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc +InvalidCombination.o: general/InvalidCombination.cpp config.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + 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/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -131,72 +102,92 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: + +/usr/include/bits/wchar.h: /usr/include/xlocale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/include/bits/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/include/bits/typesizes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/libio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/_G_config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/include/gconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/sys_errlist.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/bits/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/iconv.h: +/usr/include/locale.h: -/usr/include/libintl.h: +/usr/include/bits/locale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/include/bits/types.h: -/usr/include/pthread.h: +/usr/include/bits/typesizes.h: /usr/include/endian.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: + /usr/include/sched.h: /usr/include/time.h: @@ -205,10 +196,6 @@ config.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -223,160 +210,62 @@ config.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/include/stdlib.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/include/bits/waitflags.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/include/bits/waitstatus.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/include/sys/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/include/sys/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/include/bits/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/include/sys/sysmacros.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/include/alloca.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: /usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: diff --git a/binaries/src/clustalw/src/.deps/Iteration.Po b/binaries/src/clustalw/src/.deps/Iteration.Po index f9a58d8..9a801c9 100644 --- a/binaries/src/clustalw/src/.deps/Iteration.Po +++ b/binaries/src/clustalw/src/.deps/Iteration.Po @@ -1,159 +1,145 @@ -Iteration.o Iteration.o: multipleAlign/Iteration.cpp config.h \ - multipleAlign/Iteration.h multipleAlign/../alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - 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multipleAlign/../alignment/../general/Array2D.h \ - multipleAlign/../alignment/../general/SquareMat.h \ - multipleAlign/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - multipleAlign/../alignment/../general/utils.h \ - multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \ - multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \ - multipleAlign/../alignment/../general/VectorOutOfRange.h \ - multipleAlign/../alignment/../general/SequenceNotFoundException.h \ - multipleAlign/../general/clustalw.h \ - multipleAlign/../alignment/ObjectiveScore.h \ - multipleAlign/../alignment/../general/clustalw.h \ - multipleAlign/../general/utils.h multipleAlign/../general/userparams.h \ - multipleAlign/../tree/TreeInterface.h \ - multipleAlign/../tree/AlignmentSteps.h \ - multipleAlign/../tree/../alignment/Alignment.h \ - multipleAlign/../tree/../general/clustalw.h \ - multipleAlign/../clustalw_version.h multipleAlign/MSA.h \ - multipleAlign/ProfileBase.h multipleAlign/../tree/AlignmentSteps.h \ - multipleAlign/ProfileAlignAlgorithm.h +Iteration.o: multipleAlign/Iteration.cpp config.h \ + multipleAlign/Iteration.h multipleAlign/../alignment/Alignment.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + 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multipleAlign/../alignment/../general/userparams.h \ + multipleAlign/../alignment/../general/UserParameters.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + 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multipleAlign/../general/userparams.h \ + multipleAlign/../tree/TreeInterface.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h \ + multipleAlign/../tree/AlignmentSteps.h \ + multipleAlign/../tree/../alignment/Alignment.h \ + multipleAlign/../tree/../general/clustalw.h \ + multipleAlign/../clustalw_version.h multipleAlign/MSA.h \ + multipleAlign/ProfileBase.h multipleAlign/../tree/AlignmentSteps.h \ + multipleAlign/ProfileAlignAlgorithm.h config.h: @@ -161,19 +147,15 @@ multipleAlign/Iteration.h: multipleAlign/../alignment/Alignment.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -183,123 +165,131 @@ multipleAlign/../alignment/Alignment.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/wchar.h: +/usr/include/locale.h: -/usr/include/bits/wchar.h: +/usr/include/bits/locale.h: -/usr/include/gconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/include/bits/sys_errlist.h: +/usr/include/ctype.h: -/usr/include/bits/stdio.h: +/usr/include/bits/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/typesizes.h: -/usr/include/locale.h: +/usr/include/endian.h: -/usr/include/bits/locale.h: +/usr/include/bits/endian.h: -/usr/include/langinfo.h: +/usr/include/bits/byteswap.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -313,147 +303,95 @@ multipleAlign/../alignment/Alignment.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/include/stdint.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +multipleAlign/../alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +multipleAlign/../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +multipleAlign/../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/include/wctype.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +multipleAlign/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +multipleAlign/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/alloca.h: -multipleAlign/../alignment/Sequence.h: +/usr/include/libio.h: -multipleAlign/../alignment/../general/userparams.h: +/usr/include/_G_config.h: -multipleAlign/../alignment/../general/UserParameters.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/bits/sys_errlist.h: -multipleAlign/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -multipleAlign/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -463,8 +401,6 @@ multipleAlign/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -479,7 +415,7 @@ multipleAlign/../alignment/../general/SquareMat.h: multipleAlign/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -499,7 +435,7 @@ multipleAlign/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: multipleAlign/../alignment/../general/utils.h: @@ -531,6 +467,14 @@ multipleAlign/../general/userparams.h: multipleAlign/../tree/TreeInterface.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: + multipleAlign/../tree/AlignmentSteps.h: multipleAlign/../tree/../alignment/Alignment.h: diff --git a/binaries/src/clustalw/src/.deps/LowScoreSegProfile.Po b/binaries/src/clustalw/src/.deps/LowScoreSegProfile.Po index adfc337..7f4d080 100644 --- a/binaries/src/clustalw/src/.deps/LowScoreSegProfile.Po +++ b/binaries/src/clustalw/src/.deps/LowScoreSegProfile.Po @@ -1,150 +1,131 @@ -LowScoreSegProfile.o LowScoreSegProfile.o: \ - multipleAlign/LowScoreSegProfile.cpp config.h \ - multipleAlign/LowScoreSegProfile.h \ - multipleAlign/../alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - 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/usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + multipleAlign/../alignment/../general/utils.h \ + multipleAlign/../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + multipleAlign/../alignment/../general/clustalw.h \ + multipleAlign/../alignment/../general/general.h \ + multipleAlign/../alignment/../general/Array2D.h \ + multipleAlign/../alignment/../general/SquareMat.h \ + multipleAlign/../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + multipleAlign/../alignment/../general/utils.h \ + multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \ + multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \ + multipleAlign/../alignment/../general/VectorOutOfRange.h \ + multipleAlign/../alignment/../general/SequenceNotFoundException.h config.h: @@ -152,19 +133,15 @@ multipleAlign/LowScoreSegProfile.h: multipleAlign/../alignment/Alignment.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -174,123 +151,131 @@ multipleAlign/../alignment/Alignment.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/xlocale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/include/stdlib.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/include/bits/waitflags.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/include/bits/waitstatus.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/include/endian.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/include/bits/endian.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/include/sys/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/include/bits/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/include/bits/typesizes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/include/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/include/sys/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/include/bits/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/include/bits/sigset.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/include/bits/time.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/wchar.h: +/usr/include/locale.h: -/usr/include/bits/wchar.h: +/usr/include/bits/locale.h: -/usr/include/gconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/include/bits/sys_errlist.h: +/usr/include/ctype.h: -/usr/include/bits/stdio.h: +/usr/include/bits/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/typesizes.h: -/usr/include/locale.h: +/usr/include/endian.h: -/usr/include/bits/locale.h: +/usr/include/bits/endian.h: + +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -304,147 +289,95 @@ multipleAlign/../alignment/Alignment.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: 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+multipleAlign/../alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +multipleAlign/../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +multipleAlign/../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/include/wctype.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +multipleAlign/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +multipleAlign/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/alloca.h: -multipleAlign/../alignment/Sequence.h: +/usr/include/libio.h: -multipleAlign/../alignment/../general/userparams.h: +/usr/include/_G_config.h: -multipleAlign/../alignment/../general/UserParameters.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/bits/sys_errlist.h: -multipleAlign/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -multipleAlign/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -454,8 +387,6 @@ multipleAlign/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -470,7 +401,7 @@ multipleAlign/../alignment/../general/SquareMat.h: multipleAlign/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -490,7 +421,7 @@ multipleAlign/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: multipleAlign/../alignment/../general/utils.h: diff --git a/binaries/src/clustalw/src/.deps/MSA.Po b/binaries/src/clustalw/src/.deps/MSA.Po index a8aade8..534ff49 100644 --- a/binaries/src/clustalw/src/.deps/MSA.Po +++ b/binaries/src/clustalw/src/.deps/MSA.Po @@ -1,170 +1,153 @@ -MSA.o MSA.o: multipleAlign/MSA.cpp config.h multipleAlign/MSA.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc config.h: multipleAlign/MSA.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -174,71 +157,37 @@ multipleAlign/MSA.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: /usr/include/bits/wchar.h: -/usr/include/gconv.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: - -/usr/include/bits/stdio_lim.h: - -/usr/include/bits/sys_errlist.h: - -/usr/include/bits/stdio.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: - -/usr/include/locale.h: - -/usr/include/bits/locale.h: - -/usr/include/langinfo.h: - -/usr/include/nl_types.h: - -/usr/include/iconv.h: +/usr/include/xlocale.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: @@ -246,18 +195,20 @@ multipleAlign/MSA.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + /usr/include/sched.h: +/usr/include/bits/types.h: + +/usr/include/bits/typesizes.h: + /usr/include/time.h: /usr/include/bits/sched.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -272,189 +223,173 @@ multipleAlign/MSA.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +multipleAlign/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +multipleAlign/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/bits/waitflags.h: -multipleAlign/ProfileBase.h: +/usr/include/bits/waitstatus.h: -multipleAlign/../alignment/Alignment.h: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/alloca.h: -multipleAlign/../alignment/Sequence.h: +/usr/include/libio.h: -multipleAlign/../alignment/../general/userparams.h: +/usr/include/_G_config.h: -multipleAlign/../alignment/../general/UserParameters.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/bits/sys_errlist.h: -multipleAlign/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -multipleAlign/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -464,8 +399,6 @@ multipleAlign/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -480,7 +413,7 @@ multipleAlign/../alignment/../general/SquareMat.h: multipleAlign/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -500,7 +433,7 @@ multipleAlign/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: multipleAlign/../alignment/../general/utils.h: @@ -534,8 +467,14 @@ multipleAlign/../general/debuglogObject.h: multipleAlign/../general/DebugLog.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: diff --git a/binaries/src/clustalw/src/.deps/MSFFileParser.Po b/binaries/src/clustalw/src/.deps/MSFFileParser.Po index 90c7519..7e2e462 100644 --- a/binaries/src/clustalw/src/.deps/MSFFileParser.Po +++ b/binaries/src/clustalw/src/.deps/MSFFileParser.Po @@ -1,156 +1,145 @@ -MSFFileParser.o MSFFileParser.o: fileInput/MSFFileParser.cpp config.h \ - fileInput/MSFFileParser.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - fileInput/FileParser.h fileInput/../alignment/Sequence.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - fileInput/../alignment/../general/userparams.h \ - fileInput/../alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - fileInput/../alignment/../general/utils.h \ - fileInput/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - fileInput/../alignment/../general/clustalw.h \ - fileInput/../alignment/../general/general.h \ - fileInput/../alignment/../general/Array2D.h \ - fileInput/../alignment/../general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - fileInput/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - fileInput/../alignment/../general/utils.h \ - fileInput/../general/userparams.h fileInput/InFileStream.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc +MSFFileParser.o: fileInput/MSFFileParser.cpp config.h \ + fileInput/MSFFileParser.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + 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/usr/include/bits/byteswap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + fileInput/FileParser.h fileInput/../alignment/Sequence.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + 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fileInput/../alignment/../general/utils.h \ + fileInput/../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + fileInput/../alignment/../general/clustalw.h \ + fileInput/../alignment/../general/general.h \ + fileInput/../alignment/../general/Array2D.h \ + fileInput/../alignment/../general/SquareMat.h \ + 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\ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h config.h: fileInput/MSFFileParser.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -160,129 +149,119 @@ fileInput/MSFFileParser.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: 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-/usr/include/stdlib.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/include/bits/waitflags.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/bits/waitstatus.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/endian.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/include/bits/endian.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/include/sys/types.h: - -/usr/include/bits/types.h: +/usr/include/wchar.h: -/usr/include/bits/typesizes.h: +/usr/include/stdio.h: -/usr/include/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: -/usr/include/sys/select.h: - -/usr/include/bits/select.h: +/usr/include/bits/wchar.h: -/usr/include/bits/sigset.h: +/usr/include/xlocale.h: -/usr/include/bits/time.h: 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-/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/libio.h: +/usr/include/locale.h: -/usr/include/_G_config.h: +/usr/include/bits/locale.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/include/gconv.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/include/bits/types.h: -/usr/include/bits/sys_errlist.h: +/usr/include/bits/typesizes.h: -/usr/include/bits/stdio.h: +/usr/include/endian.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/endian.h: -/usr/include/locale.h: +/usr/include/bits/byteswap.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -296,143 +275,107 @@ fileInput/MSFFileParser.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: +fileInput/FileParser.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: +fileInput/../alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: +fileInput/../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: +fileInput/../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -fileInput/FileParser.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -fileInput/../alignment/Sequence.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -fileInput/../alignment/../general/userparams.h: - -fileInput/../alignment/../general/UserParameters.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +fileInput/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +fileInput/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/include/wctype.h: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/sys_errlist.h: -fileInput/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -fileInput/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -442,8 +385,6 @@ fileInput/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -456,13 +397,11 @@ fileInput/../alignment/../general/Array2D.h: fileInput/../alignment/../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: fileInput/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -482,9 +421,9 @@ fileInput/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: fileInput/../alignment/../general/utils.h: @@ -492,8 +431,22 @@ fileInput/../general/userparams.h: fileInput/InFileStream.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: diff --git a/binaries/src/clustalw/src/.deps/MyersMillerProfileAlign.Po b/binaries/src/clustalw/src/.deps/MyersMillerProfileAlign.Po index 34fe947..aa17233 100644 --- a/binaries/src/clustalw/src/.deps/MyersMillerProfileAlign.Po +++ b/binaries/src/clustalw/src/.deps/MyersMillerProfileAlign.Po @@ -1,172 +1,149 @@ -MyersMillerProfileAlign.o MyersMillerProfileAlign.o: \ - multipleAlign/MyersMillerProfileAlign.cpp config.h \ - multipleAlign/MyersMillerProfileAlign.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - multipleAlign/ProfileAlignAlgorithm.h \ - multipleAlign/../alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - multipleAlign/../alignment/Sequence.h \ - multipleAlign/../alignment/../general/userparams.h \ - multipleAlign/../alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - multipleAlign/../alignment/../general/utils.h \ - multipleAlign/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - multipleAlign/../alignment/../general/clustalw.h \ - multipleAlign/../alignment/../general/general.h \ - multipleAlign/../alignment/../general/Array2D.h \ - multipleAlign/../alignment/../general/SquareMat.h \ - multipleAlign/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - multipleAlign/../alignment/../general/utils.h \ - multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \ - multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \ - multipleAlign/../alignment/../general/VectorOutOfRange.h \ - multipleAlign/../alignment/../general/SequenceNotFoundException.h \ - multipleAlign/ProfileStandard.h multipleAlign/ProfileBase.h \ - multipleAlign/ProfileWithSub.h multipleAlign/Iteration.h \ - multipleAlign/../general/clustalw.h +MyersMillerProfileAlign.o: multipleAlign/MyersMillerProfileAlign.cpp \ + config.h multipleAlign/MyersMillerProfileAlign.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + multipleAlign/ProfileAlignAlgorithm.h \ + multipleAlign/../alignment/Alignment.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +multipleAlign/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/alloca.h: -multipleAlign/../alignment/Sequence.h: +/usr/include/libio.h: -multipleAlign/../alignment/../general/userparams.h: +/usr/include/_G_config.h: -multipleAlign/../alignment/../general/UserParameters.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/bits/sys_errlist.h: -multipleAlign/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -multipleAlign/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -460,8 +393,6 @@ multipleAlign/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -476,7 +407,7 @@ multipleAlign/../alignment/../general/SquareMat.h: multipleAlign/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -496,7 +427,7 @@ multipleAlign/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: multipleAlign/../alignment/../general/utils.h: diff --git a/binaries/src/clustalw/src/.deps/NJTree.Po b/binaries/src/clustalw/src/.deps/NJTree.Po index 5e021dd..9c39822 100644 --- a/binaries/src/clustalw/src/.deps/NJTree.Po +++ b/binaries/src/clustalw/src/.deps/NJTree.Po @@ -1,137 +1,126 @@ -NJTree.o NJTree.o: tree/NJTree.cpp config.h /usr/include/math.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ - /usr/include/gnu/stubs-64.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h tree/NJTree.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - 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tree/../general/Utility.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h tree/../general/clustalw.h config.h: @@ -165,135 +154,115 @@ config.h: tree/NJTree.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: 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-/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: /usr/include/bits/wchar.h: -/usr/include/gconv.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: - -/usr/include/bits/sys_errlist.h: - -/usr/include/bits/stdio.h: +/usr/include/xlocale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/include/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: -/usr/include/nl_types.h: +/usr/include/pthread.h: -/usr/include/iconv.h: +/usr/include/endian.h: -/usr/include/libintl.h: +/usr/include/bits/endian.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/include/bits/byteswap.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/include/sched.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/include/bits/types.h: -/usr/include/pthread.h: +/usr/include/bits/typesizes.h: -/usr/include/sched.h: +/usr/include/time.h: /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -307,159 +276,143 @@ tree/NJTree.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: -/usr/include/wctype.h: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/include/bits/sys_errlist.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/include/bits/stdio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +tree/../general/clustalw.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +tree/../general/general.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +tree/../general/Array2D.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +tree/../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +tree/../general/SymMatrix.h: -tree/ClusterTreeAlgorithm.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/stdlib.h: -tree/../general/clustalw.h: +/usr/include/bits/waitflags.h: -tree/../general/general.h: +/usr/include/bits/waitstatus.h: -tree/../general/Array2D.h: +/usr/include/sys/types.h: -tree/../general/SquareMat.h: +/usr/include/sys/select.h: -tree/../general/SymMatrix.h: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/alloca.h: tree/../general/userparams.h: @@ -469,6 +422,8 @@ tree/../general/utils.h: tree/../general/Utility.h: +/usr/include/string.h: + /usr/include/errno.h: /usr/include/bits/errno.h: @@ -477,8 +432,6 @@ tree/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: diff --git a/binaries/src/clustalw/src/.deps/Node.Po b/binaries/src/clustalw/src/.deps/Node.Po index a5016eb..a847e3a 100644 --- a/binaries/src/clustalw/src/.deps/Node.Po +++ b/binaries/src/clustalw/src/.deps/Node.Po @@ -1,149 +1,136 @@ -Node.o Node.o: tree/UPGMA/Node.cpp config.h tree/UPGMA/Node.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - tree/UPGMA/upgmadata.h tree/UPGMA/../../general/VectorUtility.h \ - tree/UPGMA/../../general/debuglogObject.h \ - tree/UPGMA/../../general/DebugLog.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/include/sys/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/include/bits/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/include/bits/typesizes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/include/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/include/sys/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/include/bits/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/include/bits/sigset.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/include/bits/time.h: +/usr/include/wchar.h: -/usr/include/sys/sysmacros.h: +/usr/include/stdio.h: -/usr/include/bits/pthreadtypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: -/usr/include/alloca.h: +/usr/include/bits/wchar.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/include/xlocale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/libio.h: +/usr/include/locale.h: -/usr/include/_G_config.h: +/usr/include/bits/locale.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/include/gconv.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/include/bits/types.h: -/usr/include/bits/sys_errlist.h: +/usr/include/bits/typesizes.h: -/usr/include/bits/stdio.h: +/usr/include/endian.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/endian.h: -/usr/include/locale.h: +/usr/include/bits/byteswap.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -291,79 +282,9 @@ tree/UPGMA/Node.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: tree/UPGMA/upgmadata.h: @@ -373,59 +294,65 @@ tree/UPGMA/../../general/debuglogObject.h: tree/UPGMA/../../general/DebugLog.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: /usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/libio.h: + +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: tree/UPGMA/../../general/clustalw.h: @@ -433,17 +360,15 @@ tree/UPGMA/../../general/general.h: tree/UPGMA/../../general/Array2D.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: tree/UPGMA/../../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: tree/UPGMA/../../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -463,10 +388,30 @@ tree/UPGMA/../../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/bits/waitstatus.h: + +/usr/include/sys/types.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: diff --git a/binaries/src/clustalw/src/.deps/ObjectiveScore.Po b/binaries/src/clustalw/src/.deps/ObjectiveScore.Po index b014ef0..741c786 100644 --- a/binaries/src/clustalw/src/.deps/ObjectiveScore.Po +++ b/binaries/src/clustalw/src/.deps/ObjectiveScore.Po @@ -1,171 +1,154 @@ -ObjectiveScore.o ObjectiveScore.o: alignment/ObjectiveScore.cpp config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/bits/types.h \ - /usr/include/bits/typesizes.h /usr/include/libio.h \ - /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ - /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/sched.h /usr/include/time.h /usr/include/bits/sched.h \ - /usr/include/bits/time.h /usr/include/signal.h \ - /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ - /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ - /usr/include/sys/select.h /usr/include/bits/select.h \ - /usr/include/sys/sysmacros.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc \ - alignment/ObjectiveScore.h alignment/../general/clustalw.h \ - alignment/../general/general.h alignment/../general/Array2D.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - alignment/../general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - alignment/../substitutionMatrix/globalmatrix.h \ - alignment/../substitutionMatrix/SubMatrix.h \ - alignment/../substitutionMatrix/../general/clustalw.h \ - alignment/../substitutionMatrix/../general/userparams.h \ - alignment/../substitutionMatrix/../general/UserParameters.h \ - alignment/../substitutionMatrix/../general/utils.h \ - alignment/../substitutionMatrix/../general/Utility.h \ - /usr/include/errno.h /usr/include/bits/errno.h \ - /usr/include/linux/errno.h /usr/include/asm/errno.h \ - /usr/include/asm-x86_64/errno.h /usr/include/asm-generic/errno.h \ - /usr/include/asm-generic/errno-base.h \ - alignment/../substitutionMatrix/../general/clustalw.h \ - alignment/../substitutionMatrix/../general/general.h \ - alignment/../substitutionMatrix/../general/utils.h \ - alignment/../substitutionMatrix/../general/Array2D.h \ - alignment/Alignment.h alignment/Sequence.h \ - alignment/../general/userparams.h alignment/../general/utils.h \ - alignment/../general/VectorOutOfRange.h \ - alignment/../general/SequenceNotFoundException.h \ - alignment/../general/debuglogObject.h alignment/../general/DebugLog.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc +ObjectiveScore.o: alignment/ObjectiveScore.cpp config.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc \ + alignment/ObjectiveScore.h alignment/../general/clustalw.h \ + alignment/../general/general.h alignment/../general/Array2D.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + alignment/../general/SquareMat.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h alignment/../substitutionMatrix/globalmatrix.h \ + alignment/../substitutionMatrix/SubMatrix.h \ + alignment/../substitutionMatrix/../general/clustalw.h \ + alignment/../substitutionMatrix/../general/userparams.h \ + alignment/../substitutionMatrix/../general/UserParameters.h \ + alignment/../substitutionMatrix/../general/utils.h \ + alignment/../substitutionMatrix/../general/Utility.h \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + alignment/../substitutionMatrix/../general/clustalw.h \ + alignment/../substitutionMatrix/../general/general.h \ + alignment/../substitutionMatrix/../general/utils.h \ + alignment/../substitutionMatrix/../general/Array2D.h \ + alignment/Alignment.h alignment/Sequence.h \ + alignment/../general/userparams.h alignment/../general/utils.h \ + alignment/../general/VectorOutOfRange.h \ + alignment/../general/SequenceNotFoundException.h \ + alignment/../general/debuglogObject.h alignment/../general/DebugLog.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -175,72 +158,92 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: + +/usr/include/bits/wchar.h: /usr/include/xlocale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/include/bits/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/include/bits/typesizes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/libio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/_G_config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/include/gconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/sys_errlist.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/bits/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/iconv.h: +/usr/include/locale.h: -/usr/include/libintl.h: +/usr/include/bits/locale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/include/bits/types.h: -/usr/include/pthread.h: +/usr/include/bits/typesizes.h: /usr/include/endian.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: + /usr/include/sched.h: /usr/include/time.h: @@ -249,10 +252,6 @@ config.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -267,163 +266,65 @@ config.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: - -/usr/include/limits.h: - -/usr/include/bits/posix1_lim.h: - -/usr/include/bits/local_lim.h: - -/usr/include/linux/limits.h: - -/usr/include/bits/posix2_lim.h: - -/usr/include/bits/xopen_lim.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: - -/usr/include/stdlib.h: - -/usr/include/bits/waitflags.h: - -/usr/include/bits/waitstatus.h: - -/usr/include/sys/types.h: - -/usr/include/sys/select.h: - -/usr/include/bits/select.h: - -/usr/include/sys/sysmacros.h: - -/usr/include/alloca.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: /usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: alignment/ObjectiveScore.h: @@ -433,25 +334,27 @@ alignment/../general/general.h: alignment/../general/Array2D.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -alignment/../general/SquareMat.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +alignment/../general/SquareMat.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -471,9 +374,29 @@ alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/sys/types.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/alloca.h: alignment/../substitutionMatrix/globalmatrix.h: @@ -489,6 +412,18 @@ alignment/../substitutionMatrix/../general/utils.h: alignment/../substitutionMatrix/../general/Utility.h: +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/string.h: + /usr/include/errno.h: /usr/include/bits/errno.h: @@ -497,8 +432,6 @@ alignment/../substitutionMatrix/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -527,8 +460,14 @@ alignment/../general/debuglogObject.h: alignment/../general/DebugLog.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: diff --git a/binaries/src/clustalw/src/.deps/OutputFile.Po b/binaries/src/clustalw/src/.deps/OutputFile.Po index 2e435fc..deca3f3 100644 --- a/binaries/src/clustalw/src/.deps/OutputFile.Po +++ b/binaries/src/clustalw/src/.deps/OutputFile.Po @@ -1,151 +1,140 @@ -OutputFile.o OutputFile.o: general/OutputFile.cpp config.h \ - general/OutputFile.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - 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/usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -155,123 +144,125 @@ general/OutputFile.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: 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-/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -285,135 +276,101 @@ general/OutputFile.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/include/bits/sys_errlist.h: -/usr/include/wctype.h: +/usr/include/bits/stdio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/include/sys/sysmacros.h: -general/utils.h: +/usr/include/alloca.h: -general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -423,8 +380,6 @@ general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -435,25 +390,23 @@ general/general.h: general/Array2D.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -473,9 +426,9 @@ general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: general/userparams.h: diff --git a/binaries/src/clustalw/src/.deps/PIRFileParser.Po b/binaries/src/clustalw/src/.deps/PIRFileParser.Po index e62d5e6..1290ff0 100644 --- a/binaries/src/clustalw/src/.deps/PIRFileParser.Po +++ b/binaries/src/clustalw/src/.deps/PIRFileParser.Po @@ -1,156 +1,145 @@ -PIRFileParser.o PIRFileParser.o: fileInput/PIRFileParser.cpp config.h \ - fileInput/PIRFileParser.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - 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fileInput/../alignment/../general/userparams.h \ - fileInput/../alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - 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\ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - fileInput/../alignment/../general/utils.h \ - fileInput/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - fileInput/../alignment/../general/clustalw.h \ - fileInput/../alignment/../general/general.h \ - fileInput/../alignment/../general/Array2D.h \ - fileInput/../alignment/../general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - fileInput/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - fileInput/../alignment/../general/utils.h \ - fileInput/../general/userparams.h fileInput/InFileStream.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc +PIRFileParser.o: fileInput/PIRFileParser.cpp config.h \ + fileInput/PIRFileParser.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + 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/usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + fileInput/FileParser.h fileInput/../alignment/Sequence.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + fileInput/../alignment/../general/userparams.h \ + fileInput/../alignment/../general/UserParameters.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + fileInput/../alignment/../general/utils.h \ + fileInput/../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + fileInput/../alignment/../general/clustalw.h \ + fileInput/../alignment/../general/general.h \ + fileInput/../alignment/../general/Array2D.h \ + fileInput/../alignment/../general/SquareMat.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + fileInput/../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + fileInput/../alignment/../general/utils.h \ + fileInput/../general/userparams.h fileInput/InFileStream.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h config.h: fileInput/PIRFileParser.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -160,129 +149,119 @@ fileInput/PIRFileParser.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/include/wctype.h: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/sys_errlist.h: -fileInput/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -fileInput/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -442,8 +385,6 @@ fileInput/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -456,13 +397,11 @@ fileInput/../alignment/../general/Array2D.h: fileInput/../alignment/../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: fileInput/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -482,9 +421,9 @@ fileInput/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: fileInput/../alignment/../general/utils.h: @@ -492,8 +431,22 @@ fileInput/../general/userparams.h: fileInput/InFileStream.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: diff --git a/binaries/src/clustalw/src/.deps/PearsonFileParser.Po b/binaries/src/clustalw/src/.deps/PearsonFileParser.Po index 2d0f4cd..abc6392 100644 --- a/binaries/src/clustalw/src/.deps/PearsonFileParser.Po +++ b/binaries/src/clustalw/src/.deps/PearsonFileParser.Po @@ -1,156 +1,145 @@ -PearsonFileParser.o PearsonFileParser.o: fileInput/PearsonFileParser.cpp \ - config.h fileInput/PearsonFileParser.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - fileInput/FileParser.h fileInput/../alignment/Sequence.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - fileInput/../alignment/../general/userparams.h \ - fileInput/../alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - fileInput/../alignment/../general/utils.h \ - fileInput/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - fileInput/../alignment/../general/clustalw.h \ - fileInput/../alignment/../general/general.h \ - fileInput/../alignment/../general/Array2D.h \ - fileInput/../alignment/../general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - fileInput/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - fileInput/../alignment/../general/utils.h \ - fileInput/../general/userparams.h fileInput/InFileStream.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc +PearsonFileParser.o: fileInput/PearsonFileParser.cpp config.h \ + fileInput/PearsonFileParser.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + fileInput/FileParser.h fileInput/../alignment/Sequence.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + fileInput/../alignment/../general/userparams.h \ + fileInput/../alignment/../general/UserParameters.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + fileInput/../alignment/../general/utils.h \ + fileInput/../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + fileInput/../alignment/../general/clustalw.h \ + fileInput/../alignment/../general/general.h \ + fileInput/../alignment/../general/Array2D.h \ + fileInput/../alignment/../general/SquareMat.h \ + 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\ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h config.h: fileInput/PearsonFileParser.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -160,129 +149,119 @@ fileInput/PearsonFileParser.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -296,143 +275,107 @@ fileInput/PearsonFileParser.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: +fileInput/FileParser.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: +fileInput/../alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: +fileInput/../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: +fileInput/../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -fileInput/FileParser.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -fileInput/../alignment/Sequence.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -fileInput/../alignment/../general/userparams.h: - -fileInput/../alignment/../general/UserParameters.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +fileInput/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +fileInput/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/include/wctype.h: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/sys_errlist.h: -fileInput/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -fileInput/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -442,8 +385,6 @@ fileInput/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -456,13 +397,11 @@ fileInput/../alignment/../general/Array2D.h: fileInput/../alignment/../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: fileInput/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -482,9 +421,9 @@ fileInput/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: fileInput/../alignment/../general/utils.h: @@ -492,8 +431,22 @@ fileInput/../general/userparams.h: fileInput/InFileStream.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: diff --git a/binaries/src/clustalw/src/.deps/ProfileBase.Po b/binaries/src/clustalw/src/.deps/ProfileBase.Po index 6f405e9..2196eef 100644 --- a/binaries/src/clustalw/src/.deps/ProfileBase.Po +++ b/binaries/src/clustalw/src/.deps/ProfileBase.Po @@ -1,148 +1,130 @@ -ProfileBase.o ProfileBase.o: multipleAlign/ProfileBase.cpp config.h \ - multipleAlign/ProfileBase.h multipleAlign/../alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - multipleAlign/../alignment/Sequence.h \ - multipleAlign/../alignment/../general/userparams.h \ - multipleAlign/../alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - multipleAlign/../alignment/../general/utils.h \ - multipleAlign/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - multipleAlign/../alignment/../general/clustalw.h \ - multipleAlign/../alignment/../general/general.h \ - multipleAlign/../alignment/../general/Array2D.h \ - multipleAlign/../alignment/../general/SquareMat.h \ - multipleAlign/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - multipleAlign/../alignment/../general/utils.h \ - multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \ - multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \ - multipleAlign/../alignment/../general/VectorOutOfRange.h \ - multipleAlign/../alignment/../general/SequenceNotFoundException.h +ProfileBase.o: multipleAlign/ProfileBase.cpp config.h \ + multipleAlign/ProfileBase.h multipleAlign/../alignment/Alignment.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + 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/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + multipleAlign/../alignment/Sequence.h \ + multipleAlign/../alignment/../general/userparams.h \ + multipleAlign/../alignment/../general/UserParameters.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + multipleAlign/../alignment/../general/utils.h \ + multipleAlign/../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + multipleAlign/../alignment/../general/clustalw.h \ + multipleAlign/../alignment/../general/general.h \ + multipleAlign/../alignment/../general/Array2D.h \ + multipleAlign/../alignment/../general/SquareMat.h \ + multipleAlign/../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + multipleAlign/../alignment/../general/utils.h \ + multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \ + multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \ + multipleAlign/../alignment/../general/VectorOutOfRange.h \ + multipleAlign/../alignment/../general/SequenceNotFoundException.h config.h: @@ -150,19 +132,15 @@ multipleAlign/ProfileBase.h: multipleAlign/../alignment/Alignment.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -172,123 +150,131 @@ multipleAlign/../alignment/Alignment.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/xlocale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: 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-/usr/include/bits/typesizes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/include/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/include/sys/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/include/bits/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/include/bits/sigset.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/include/bits/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/include/sys/sysmacros.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/include/bits/pthreadtypes.h: +/usr/include/wchar.h: -/usr/include/alloca.h: +/usr/include/stdio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: 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-/usr/include/bits/sys_errlist.h: +/usr/include/ctype.h: -/usr/include/bits/stdio.h: +/usr/include/bits/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/typesizes.h: -/usr/include/locale.h: +/usr/include/endian.h: -/usr/include/bits/locale.h: +/usr/include/bits/endian.h: + +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -302,147 +288,95 @@ multipleAlign/../alignment/Alignment.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +multipleAlign/../alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +multipleAlign/../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +multipleAlign/../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/include/wctype.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +multipleAlign/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +multipleAlign/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/alloca.h: -multipleAlign/../alignment/Sequence.h: +/usr/include/libio.h: -multipleAlign/../alignment/../general/userparams.h: +/usr/include/_G_config.h: -multipleAlign/../alignment/../general/UserParameters.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/bits/sys_errlist.h: -multipleAlign/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -multipleAlign/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -452,8 +386,6 @@ multipleAlign/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -468,7 +400,7 @@ multipleAlign/../alignment/../general/SquareMat.h: multipleAlign/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -488,7 +420,7 @@ multipleAlign/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: multipleAlign/../alignment/../general/utils.h: diff --git a/binaries/src/clustalw/src/.deps/ProfileStandard.Po b/binaries/src/clustalw/src/.deps/ProfileStandard.Po index e8bed5e..c0db6ce 100644 --- a/binaries/src/clustalw/src/.deps/ProfileStandard.Po +++ b/binaries/src/clustalw/src/.deps/ProfileStandard.Po @@ -1,150 +1,131 @@ -ProfileStandard.o ProfileStandard.o: multipleAlign/ProfileStandard.cpp \ - config.h multipleAlign/ProfileStandard.h \ - multipleAlign/../alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - 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multipleAlign/../alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - multipleAlign/../alignment/../general/utils.h \ - multipleAlign/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - multipleAlign/../alignment/../general/clustalw.h \ - multipleAlign/../alignment/../general/general.h \ - multipleAlign/../alignment/../general/Array2D.h \ - multipleAlign/../alignment/../general/SquareMat.h \ - multipleAlign/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - multipleAlign/../alignment/../general/utils.h \ - multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \ - multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \ - multipleAlign/../alignment/../general/VectorOutOfRange.h \ - multipleAlign/../alignment/../general/SequenceNotFoundException.h \ - multipleAlign/ProfileBase.h +ProfileStandard.o: multipleAlign/ProfileStandard.cpp config.h \ + multipleAlign/ProfileStandard.h multipleAlign/../alignment/Alignment.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + 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/usr/include/bits/locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + multipleAlign/../alignment/Sequence.h \ + multipleAlign/../alignment/../general/userparams.h \ + multipleAlign/../alignment/../general/UserParameters.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + multipleAlign/../alignment/../general/utils.h \ + multipleAlign/../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + multipleAlign/../alignment/../general/clustalw.h \ + multipleAlign/../alignment/../general/general.h \ + multipleAlign/../alignment/../general/Array2D.h \ + multipleAlign/../alignment/../general/SquareMat.h \ + multipleAlign/../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + multipleAlign/../alignment/../general/utils.h \ + multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \ + multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \ + multipleAlign/../alignment/../general/VectorOutOfRange.h \ + multipleAlign/../alignment/../general/SequenceNotFoundException.h \ + multipleAlign/ProfileBase.h config.h: @@ -152,19 +133,15 @@ multipleAlign/ProfileStandard.h: multipleAlign/../alignment/Alignment.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -174,123 +151,131 @@ multipleAlign/../alignment/Alignment.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/include/stdlib.h: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/typesizes.h: -/usr/include/locale.h: +/usr/include/endian.h: -/usr/include/bits/locale.h: +/usr/include/bits/endian.h: + +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -304,147 +289,95 @@ multipleAlign/../alignment/Alignment.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/include/wctype.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +multipleAlign/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +multipleAlign/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/alloca.h: -multipleAlign/../alignment/Sequence.h: +/usr/include/libio.h: -multipleAlign/../alignment/../general/userparams.h: +/usr/include/_G_config.h: -multipleAlign/../alignment/../general/UserParameters.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/bits/sys_errlist.h: -multipleAlign/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -multipleAlign/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -454,8 +387,6 @@ multipleAlign/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -470,7 +401,7 @@ multipleAlign/../alignment/../general/SquareMat.h: multipleAlign/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -490,7 +421,7 @@ multipleAlign/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: multipleAlign/../alignment/../general/utils.h: diff --git a/binaries/src/clustalw/src/.deps/ProfileWithSub.Po b/binaries/src/clustalw/src/.deps/ProfileWithSub.Po index 708c641..cd6d7fe 100644 --- a/binaries/src/clustalw/src/.deps/ProfileWithSub.Po +++ b/binaries/src/clustalw/src/.deps/ProfileWithSub.Po @@ -1,150 +1,131 @@ -ProfileWithSub.o ProfileWithSub.o: multipleAlign/ProfileWithSub.cpp \ - config.h multipleAlign/ProfileWithSub.h \ - multipleAlign/../alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - multipleAlign/../alignment/Sequence.h \ - multipleAlign/../alignment/../general/userparams.h \ - multipleAlign/../alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - multipleAlign/../alignment/../general/utils.h \ - multipleAlign/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - multipleAlign/../alignment/../general/clustalw.h \ - multipleAlign/../alignment/../general/general.h \ - multipleAlign/../alignment/../general/Array2D.h \ - multipleAlign/../alignment/../general/SquareMat.h \ - multipleAlign/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - multipleAlign/../alignment/../general/utils.h \ - multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \ - multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \ - multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \ - multipleAlign/../alignment/../general/VectorOutOfRange.h \ - multipleAlign/../alignment/../general/SequenceNotFoundException.h \ - multipleAlign/ProfileBase.h +ProfileWithSub.o: multipleAlign/ProfileWithSub.cpp config.h \ + multipleAlign/ProfileWithSub.h multipleAlign/../alignment/Alignment.h \ + 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multipleAlign/../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + multipleAlign/../alignment/../general/utils.h \ + multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \ + multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \ + multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \ + multipleAlign/../alignment/../general/VectorOutOfRange.h \ + multipleAlign/../alignment/../general/SequenceNotFoundException.h \ + multipleAlign/ProfileBase.h config.h: @@ -152,19 +133,15 @@ multipleAlign/ProfileWithSub.h: multipleAlign/../alignment/Alignment.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -174,123 +151,131 @@ multipleAlign/../alignment/Alignment.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -304,147 +289,95 @@ multipleAlign/../alignment/Alignment.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: -/usr/include/stdint.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +multipleAlign/../alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +multipleAlign/../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +multipleAlign/../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/include/wctype.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +multipleAlign/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +multipleAlign/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/alloca.h: -multipleAlign/../alignment/Sequence.h: +/usr/include/libio.h: -multipleAlign/../alignment/../general/userparams.h: +/usr/include/_G_config.h: -multipleAlign/../alignment/../general/UserParameters.h: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/bits/sys_errlist.h: -multipleAlign/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -multipleAlign/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -454,8 +387,6 @@ multipleAlign/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -470,7 +401,7 @@ multipleAlign/../alignment/../general/SquareMat.h: multipleAlign/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -490,7 +421,7 @@ multipleAlign/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: multipleAlign/../alignment/../general/utils.h: diff --git a/binaries/src/clustalw/src/.deps/RSFFileParser.Po b/binaries/src/clustalw/src/.deps/RSFFileParser.Po index 1ddf251..f52b8b0 100644 --- a/binaries/src/clustalw/src/.deps/RSFFileParser.Po +++ b/binaries/src/clustalw/src/.deps/RSFFileParser.Po @@ -1,156 +1,145 @@ -RSFFileParser.o RSFFileParser.o: fileInput/RSFFileParser.cpp config.h \ - fileInput/RSFFileParser.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + fileInput/../alignment/../general/utils.h \ + fileInput/../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + fileInput/../alignment/../general/clustalw.h \ + fileInput/../alignment/../general/general.h \ + fileInput/../alignment/../general/Array2D.h \ + fileInput/../alignment/../general/SquareMat.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + fileInput/../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + fileInput/../alignment/../general/utils.h \ + fileInput/../general/userparams.h fileInput/InFileStream.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h config.h: fileInput/RSFFileParser.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -160,129 +149,119 @@ fileInput/RSFFileParser.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/include/sys/sysmacros.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/include/bits/pthreadtypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/include/alloca.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/libio.h: +/usr/include/locale.h: -/usr/include/_G_config.h: +/usr/include/bits/locale.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/include/gconv.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/include/bits/types.h: -/usr/include/bits/sys_errlist.h: +/usr/include/bits/typesizes.h: -/usr/include/bits/stdio.h: +/usr/include/endian.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/endian.h: -/usr/include/locale.h: +/usr/include/bits/byteswap.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -296,143 +275,107 @@ fileInput/RSFFileParser.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: +fileInput/FileParser.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: +fileInput/../alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: +fileInput/../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: +fileInput/../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -fileInput/FileParser.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -fileInput/../alignment/Sequence.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -fileInput/../alignment/../general/userparams.h: - -fileInput/../alignment/../general/UserParameters.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +fileInput/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +fileInput/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/include/wctype.h: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/sys_errlist.h: -fileInput/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -fileInput/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -442,8 +385,6 @@ fileInput/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -456,13 +397,11 @@ fileInput/../alignment/../general/Array2D.h: fileInput/../alignment/../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: fileInput/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -482,9 +421,9 @@ fileInput/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: fileInput/../alignment/../general/utils.h: @@ -492,8 +431,22 @@ fileInput/../general/userparams.h: fileInput/InFileStream.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: diff --git a/binaries/src/clustalw/src/.deps/RandomGenerator.Po b/binaries/src/clustalw/src/.deps/RandomGenerator.Po index 1705172..37c36b3 100644 --- a/binaries/src/clustalw/src/.deps/RandomGenerator.Po +++ b/binaries/src/clustalw/src/.deps/RandomGenerator.Po @@ -1,5 +1,5 @@ -RandomGenerator.o RandomGenerator.o: tree/RandomGenerator.cpp config.h \ - tree/RandomGenerator.h +RandomGenerator.o: tree/RandomGenerator.cpp config.h \ + tree/RandomGenerator.h config.h: diff --git a/binaries/src/clustalw/src/.deps/RootedClusterTree.Po b/binaries/src/clustalw/src/.deps/RootedClusterTree.Po index ad2d00f..70c3de0 100644 --- a/binaries/src/clustalw/src/.deps/RootedClusterTree.Po +++ b/binaries/src/clustalw/src/.deps/RootedClusterTree.Po @@ -1,166 +1,155 @@ -RootedClusterTree.o RootedClusterTree.o: \ - tree/UPGMA/RootedClusterTree.cpp config.h tree/UPGMA/RootedClusterTree.h \ - tree/UPGMA/../ClusterTree.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/bits/types.h \ - /usr/include/bits/typesizes.h /usr/include/libio.h \ - /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ - /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/sched.h /usr/include/time.h /usr/include/bits/sched.h \ - /usr/include/bits/time.h /usr/include/signal.h \ - /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ - /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ - /usr/include/sys/select.h /usr/include/bits/select.h \ - /usr/include/sys/sysmacros.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - 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tree/UPGMA/../../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + tree/UPGMA/../../alignment/../general/utils.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/userparams.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/Array2D.h \ + tree/UPGMA/../../alignment/../general/VectorOutOfRange.h \ + tree/UPGMA/../../alignment/../general/SequenceNotFoundException.h \ + tree/UPGMA/../NJTree.h tree/UPGMA/../ClusterTreeAlgorithm.h \ + tree/UPGMA/../../general/clustalw.h \ + tree/UPGMA/../../general/userparams.h tree/UPGMA/../ClusterTreeOutput.h \ + tree/UPGMA/../../general/OutputFile.h tree/UPGMA/RootedGuideTree.h \ + tree/UPGMA/Node.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/limits \ + tree/UPGMA/upgmadata.h tree/UPGMA/../../alignment/Alignment.h \ + tree/UPGMA/../AlignmentSteps.h tree/UPGMA/../../general/OutputFile.h \ + tree/UPGMA/UPGMAAlgorithm.h tree/UPGMA/../../general/clustalw.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_list.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/list.tcc \ + tree/UPGMA/RootedTreeOutput.h config.h: @@ -168,19 +157,19 @@ tree/UPGMA/RootedClusterTree.h: tree/UPGMA/../ClusterTree.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -190,72 +179,92 @@ tree/UPGMA/../ClusterTree.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: + +/usr/include/bits/wchar.h: /usr/include/xlocale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/include/bits/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/include/bits/typesizes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/libio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/_G_config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/include/gconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/sys_errlist.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/bits/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/iconv.h: +/usr/include/locale.h: -/usr/include/libintl.h: +/usr/include/bits/locale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/include/bits/types.h: -/usr/include/pthread.h: +/usr/include/bits/typesizes.h: /usr/include/endian.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: + /usr/include/sched.h: /usr/include/time.h: @@ -264,10 +273,6 @@ tree/UPGMA/../ClusterTree.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -282,193 +287,143 @@ tree/UPGMA/../ClusterTree.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/include/stdlib.h: -tree/UPGMA/../../alignment/Alignment.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/sys/select.h: -tree/UPGMA/../../alignment/Sequence.h: +/usr/include/bits/select.h: -tree/UPGMA/../../alignment/../general/userparams.h: +/usr/include/bits/sigset.h: -tree/UPGMA/../../alignment/../general/UserParameters.h: +/usr/include/sys/sysmacros.h: -tree/UPGMA/../../alignment/../general/utils.h: +/usr/include/alloca.h: -tree/UPGMA/../../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -478,8 +433,6 @@ tree/UPGMA/../../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -494,7 +447,7 @@ tree/UPGMA/../../alignment/../general/SquareMat.h: tree/UPGMA/../../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -514,7 +467,7 @@ tree/UPGMA/../../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: tree/UPGMA/../../alignment/../general/utils.h: @@ -550,6 +503,8 @@ tree/UPGMA/RootedGuideTree.h: tree/UPGMA/Node.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/limits: + tree/UPGMA/upgmadata.h: tree/UPGMA/../../alignment/Alignment.h: @@ -562,10 +517,10 @@ tree/UPGMA/UPGMAAlgorithm.h: tree/UPGMA/../../general/clustalw.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/list: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/list: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_list.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_list.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/list.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/list.tcc: tree/UPGMA/RootedTreeOutput.h: diff --git a/binaries/src/clustalw/src/.deps/RootedGuideTree.Po b/binaries/src/clustalw/src/.deps/RootedGuideTree.Po index 236c15d..8d2696d 100644 --- a/binaries/src/clustalw/src/.deps/RootedGuideTree.Po +++ b/binaries/src/clustalw/src/.deps/RootedGuideTree.Po @@ -1,166 +1,151 @@ -RootedGuideTree.o RootedGuideTree.o: tree/UPGMA/RootedGuideTree.cpp \ - config.h \ - 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/usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + tree/UPGMA/../../alignment/../general/clustalw.h \ + tree/UPGMA/../../alignment/../general/general.h \ + tree/UPGMA/../../alignment/../general/Array2D.h \ + tree/UPGMA/../../alignment/../general/SquareMat.h \ + tree/UPGMA/../../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + tree/UPGMA/../../alignment/../general/utils.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/userparams.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/Array2D.h \ + tree/UPGMA/../../alignment/../general/VectorOutOfRange.h \ + tree/UPGMA/../../alignment/../general/SequenceNotFoundException.h \ + tree/UPGMA/../../general/userparams.h config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -170,78 +155,98 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: + +/usr/include/bits/wchar.h: /usr/include/xlocale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/include/bits/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/include/bits/typesizes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/libio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/_G_config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/include/gconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/sys_errlist.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/bits/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/iconv.h: +/usr/include/locale.h: -/usr/include/libintl.h: +/usr/include/bits/locale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/include/bits/types.h: -/usr/include/pthread.h: +/usr/include/bits/typesizes.h: /usr/include/endian.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: + /usr/include/sched.h: /usr/include/time.h: @@ -250,10 +255,6 @@ config.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -268,199 +269,143 @@ config.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/include/stdint.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/include/wctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +tree/UPGMA/upgmadata.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/bits/sys_errlist.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/bits/stdio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: -tree/UPGMA/RootedGuideTree.h: +tree/UPGMA/../../alignment/Alignment.h: -tree/UPGMA/Node.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +tree/UPGMA/../../alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +tree/UPGMA/../../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +tree/UPGMA/../../alignment/../general/UserParameters.h: -tree/UPGMA/upgmadata.h: +tree/UPGMA/../../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +tree/UPGMA/../../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/include/stdlib.h: -tree/UPGMA/../../alignment/Alignment.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/sys/select.h: -tree/UPGMA/../../alignment/Sequence.h: +/usr/include/bits/select.h: -tree/UPGMA/../../alignment/../general/userparams.h: +/usr/include/bits/sigset.h: -tree/UPGMA/../../alignment/../general/UserParameters.h: +/usr/include/sys/sysmacros.h: -tree/UPGMA/../../alignment/../general/utils.h: +/usr/include/alloca.h: -tree/UPGMA/../../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -470,8 +415,6 @@ tree/UPGMA/../../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -486,7 +429,7 @@ tree/UPGMA/../../alignment/../general/SquareMat.h: tree/UPGMA/../../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -506,7 +449,7 @@ tree/UPGMA/../../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: tree/UPGMA/../../alignment/../general/utils.h: diff --git a/binaries/src/clustalw/src/.deps/RootedTreeOutput.Po b/binaries/src/clustalw/src/.deps/RootedTreeOutput.Po index 53a570a..3fdd91e 100644 --- a/binaries/src/clustalw/src/.deps/RootedTreeOutput.Po +++ b/binaries/src/clustalw/src/.deps/RootedTreeOutput.Po @@ -1,173 +1,159 @@ -RootedTreeOutput.o RootedTreeOutput.o: tree/UPGMA/RootedTreeOutput.cpp \ - config.h tree/UPGMA/RootedTreeOutput.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/bits/types.h \ - /usr/include/bits/typesizes.h /usr/include/libio.h \ - /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ - /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/sched.h /usr/include/time.h /usr/include/bits/sched.h \ - /usr/include/bits/time.h /usr/include/signal.h \ - /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ - 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\ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ - /usr/include/sys/select.h /usr/include/bits/select.h \ - /usr/include/sys/sysmacros.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - 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tree/UPGMA/../../alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - tree/UPGMA/../../alignment/Sequence.h \ - tree/UPGMA/../../alignment/../general/userparams.h \ - tree/UPGMA/../../alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - tree/UPGMA/../../alignment/../general/utils.h \ - tree/UPGMA/../../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - tree/UPGMA/../../alignment/../general/clustalw.h \ - tree/UPGMA/../../alignment/../general/general.h \ - tree/UPGMA/../../alignment/../general/Array2D.h \ - tree/UPGMA/../../alignment/../general/SquareMat.h \ - tree/UPGMA/../../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - tree/UPGMA/../../alignment/../general/utils.h \ - tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h \ - tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h \ - tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h \ - tree/UPGMA/../../alignment/../substitutionMatrix/../general/userparams.h \ - tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h \ - tree/UPGMA/../../alignment/../substitutionMatrix/../general/Array2D.h \ - tree/UPGMA/../../alignment/../general/VectorOutOfRange.h \ - tree/UPGMA/../../alignment/../general/SequenceNotFoundException.h \ - tree/UPGMA/../../general/clustalw.h +RootedTreeOutput.o: tree/UPGMA/RootedTreeOutput.cpp config.h \ + tree/UPGMA/RootedTreeOutput.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h 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tree/UPGMA/RootedGuideTree.h tree/UPGMA/Node.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/limits \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + tree/UPGMA/upgmadata.h tree/UPGMA/../../alignment/Alignment.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + tree/UPGMA/../../alignment/Sequence.h \ + tree/UPGMA/../../alignment/../general/userparams.h \ + tree/UPGMA/../../alignment/../general/UserParameters.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + tree/UPGMA/../../alignment/../general/utils.h \ + tree/UPGMA/../../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + tree/UPGMA/../../alignment/../general/clustalw.h \ + tree/UPGMA/../../alignment/../general/general.h \ + tree/UPGMA/../../alignment/../general/Array2D.h \ + tree/UPGMA/../../alignment/../general/SquareMat.h \ + tree/UPGMA/../../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + tree/UPGMA/../../alignment/../general/utils.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/userparams.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/Array2D.h \ + tree/UPGMA/../../alignment/../general/VectorOutOfRange.h \ + tree/UPGMA/../../alignment/../general/SequenceNotFoundException.h \ + tree/UPGMA/../../general/clustalw.h config.h: tree/UPGMA/RootedTreeOutput.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -177,72 +163,92 @@ tree/UPGMA/RootedTreeOutput.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: -tree/UPGMA/RootedGuideTree.h: +tree/UPGMA/../../alignment/Sequence.h: -tree/UPGMA/Node.h: +tree/UPGMA/../../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +tree/UPGMA/../../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +tree/UPGMA/../../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +tree/UPGMA/../../alignment/../general/Utility.h: -tree/UPGMA/upgmadata.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -tree/UPGMA/../../alignment/Alignment.h: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/sys/types.h: -tree/UPGMA/../../alignment/Sequence.h: +/usr/include/sys/select.h: -tree/UPGMA/../../alignment/../general/userparams.h: +/usr/include/bits/select.h: -tree/UPGMA/../../alignment/../general/UserParameters.h: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/sys/sysmacros.h: -tree/UPGMA/../../alignment/../general/utils.h: +/usr/include/alloca.h: -tree/UPGMA/../../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -471,8 +417,6 @@ tree/UPGMA/../../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -487,7 +431,7 @@ tree/UPGMA/../../alignment/../general/SquareMat.h: tree/UPGMA/../../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -507,7 +451,7 @@ tree/UPGMA/../../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: tree/UPGMA/../../alignment/../general/utils.h: diff --git a/binaries/src/clustalw/src/.deps/Sequence.Po b/binaries/src/clustalw/src/.deps/Sequence.Po index 9d20aa7..204246c 100644 --- a/binaries/src/clustalw/src/.deps/Sequence.Po +++ b/binaries/src/clustalw/src/.deps/Sequence.Po @@ -1,148 +1,135 @@ -Sequence.o Sequence.o: alignment/Sequence.cpp config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - alignment/Sequence.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - alignment/../general/userparams.h alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - alignment/../general/utils.h alignment/../general/Utility.h \ - /usr/include/errno.h /usr/include/bits/errno.h \ - /usr/include/linux/errno.h /usr/include/asm/errno.h \ - /usr/include/asm-x86_64/errno.h /usr/include/asm-generic/errno.h \ - /usr/include/asm-generic/errno-base.h alignment/../general/clustalw.h \ - alignment/../general/general.h alignment/../general/Array2D.h \ - alignment/../general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - alignment/../general/utils.h +Sequence.o: alignment/Sequence.cpp config.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/algorithm \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algo.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/include/xlocale.h /usr/include/sys/types.h \ + /usr/include/bits/types.h /usr/include/bits/typesizes.h \ + /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/bits/time.h \ + /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \ + /usr/include/alloca.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/algorithmfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_heap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + alignment/Sequence.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ + /usr/include/bits/setjmp.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + alignment/../general/userparams.h alignment/../general/UserParameters.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + alignment/../general/utils.h alignment/../general/Utility.h \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h alignment/../general/clustalw.h \ + alignment/../general/general.h alignment/../general/Array2D.h \ + alignment/../general/SquareMat.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + alignment/../general/utils.h config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/algorithm: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -152,39 +139,39 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/xlocale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algo.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: /usr/include/stdlib.h: @@ -196,6 +183,10 @@ config.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + +/usr/include/xlocale.h: + /usr/include/sys/types.h: /usr/include/bits/types.h: @@ -218,209 +209,169 @@ config.h: /usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/algorithmfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_heap.h: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/include/libio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/include/_G_config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/include/gconv.h: +alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/include/bits/sys_errlist.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/include/bits/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/include/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/include/bits/locale.h: - -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: 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+/usr/include/bits/sched.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/include/bits/setjmp.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/include/unistd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: +/usr/include/bits/posix_opt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: +/usr/include/bits/environments.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: +/usr/include/bits/confname.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: +/usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/_G_config.h: -alignment/../general/utils.h: +/usr/include/bits/stdio_lim.h: -alignment/../general/Utility.h: +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/string.h: /usr/include/errno.h: @@ -430,8 +381,6 @@ alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -444,13 +393,11 @@ alignment/../general/Array2D.h: alignment/../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -470,8 +417,8 @@ alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: alignment/../general/utils.h: diff --git a/binaries/src/clustalw/src/.deps/Stats.Po b/binaries/src/clustalw/src/.deps/Stats.Po index 9176c02..e606101 100644 --- a/binaries/src/clustalw/src/.deps/Stats.Po +++ b/binaries/src/clustalw/src/.deps/Stats.Po @@ -1,149 +1,136 @@ -Stats.o Stats.o: general/Stats.cpp config.h /usr/include/stdio.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ - /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - 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general/../alignment/../general/SequenceNotFoundException.h \ + general/Stats.h config.h: @@ -159,7 +146,7 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: /usr/include/bits/types.h: @@ -171,11 +158,7 @@ config.h: /usr/include/wchar.h: -/usr/include/bits/wchar.h: - -/usr/include/gconv.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: /usr/include/bits/stdio_lim.h: @@ -183,15 +166,15 @@ config.h: /usr/include/bits/stdio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: /usr/include/stdlib.h: @@ -203,6 +186,8 @@ config.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + /usr/include/xlocale.h: /usr/include/sys/types.h: @@ -223,215 +208,177 @@ config.h: /usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: general/../alignment/Alignment.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: general/../alignment/Sequence.h: @@ -443,6 +390,8 @@ general/../alignment/../general/utils.h: general/../alignment/../general/Utility.h: +/usr/include/string.h: + /usr/include/errno.h: /usr/include/bits/errno.h: @@ -451,8 +400,6 @@ general/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -467,7 +414,7 @@ general/../alignment/../general/SquareMat.h: general/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -487,7 +434,7 @@ general/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: general/../alignment/../general/utils.h: diff --git a/binaries/src/clustalw/src/.deps/SubMatrix.Po b/binaries/src/clustalw/src/.deps/SubMatrix.Po index 291031d..9ba682c 100644 --- a/binaries/src/clustalw/src/.deps/SubMatrix.Po +++ b/binaries/src/clustalw/src/.deps/SubMatrix.Po @@ -1,149 +1,134 @@ -SubMatrix.o SubMatrix.o: substitutionMatrix/SubMatrix.cpp config.h \ - /usr/include/stdio.h /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ - /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc \ - substitutionMatrix/SubMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - substitutionMatrix/../general/clustalw.h \ - substitutionMatrix/../general/general.h \ - substitutionMatrix/../general/Array2D.h \ - substitutionMatrix/../general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - substitutionMatrix/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - substitutionMatrix/../general/userparams.h \ - substitutionMatrix/../general/UserParameters.h \ - substitutionMatrix/../general/utils.h \ - substitutionMatrix/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - substitutionMatrix/../general/clustalw.h \ - substitutionMatrix/../general/utils.h \ - substitutionMatrix/../general/Array2D.h substitutionMatrix/matrices.h \ - substitutionMatrix/../general/InvalidCombination.cpp config.h \ - substitutionMatrix/../general/debuglogObject.h \ - substitutionMatrix/../general/DebugLog.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc +SubMatrix.o: substitutionMatrix/SubMatrix.cpp config.h \ + /usr/include/stdio.h /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ + /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/typesizes.h \ + /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h \ + /usr/include/bits/byteswap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc \ + substitutionMatrix/SubMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + substitutionMatrix/../general/clustalw.h \ + substitutionMatrix/../general/general.h \ + substitutionMatrix/../general/Array2D.h \ + substitutionMatrix/../general/SquareMat.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + substitutionMatrix/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + substitutionMatrix/../general/userparams.h \ + substitutionMatrix/../general/UserParameters.h \ + substitutionMatrix/../general/utils.h \ + substitutionMatrix/../general/Utility.h /usr/include/string.h \ + /usr/include/errno.h /usr/include/bits/errno.h \ + /usr/include/linux/errno.h /usr/include/asm/errno.h \ + /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ + substitutionMatrix/../general/clustalw.h \ + substitutionMatrix/../general/utils.h \ + substitutionMatrix/../general/Array2D.h substitutionMatrix/matrices.h \ + substitutionMatrix/../general/InvalidCombination.cpp \ + substitutionMatrix/../general/debuglogObject.h \ + substitutionMatrix/../general/DebugLog.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc config.h: @@ -159,7 +144,7 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: /usr/include/bits/types.h: @@ -171,11 +156,7 @@ config.h: /usr/include/wchar.h: -/usr/include/bits/wchar.h: - -/usr/include/gconv.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: /usr/include/bits/stdio_lim.h: @@ -183,109 +164,113 @@ config.h: /usr/include/bits/stdio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -299,137 +284,89 @@ config.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: /usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +substitutionMatrix/SubMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -substitutionMatrix/SubMatrix.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: substitutionMatrix/../general/clustalw.h: @@ -439,13 +376,11 @@ substitutionMatrix/../general/Array2D.h: substitutionMatrix/../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: substitutionMatrix/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -465,9 +400,9 @@ substitutionMatrix/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: substitutionMatrix/../general/userparams.h: @@ -477,6 +412,8 @@ substitutionMatrix/../general/utils.h: substitutionMatrix/../general/Utility.h: +/usr/include/string.h: + /usr/include/errno.h: /usr/include/bits/errno.h: @@ -485,8 +422,6 @@ substitutionMatrix/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -501,14 +436,18 @@ substitutionMatrix/matrices.h: substitutionMatrix/../general/InvalidCombination.cpp: -config.h: - substitutionMatrix/../general/debuglogObject.h: substitutionMatrix/../general/DebugLog.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: diff --git a/binaries/src/clustalw/src/.deps/SymMatrix.Po b/binaries/src/clustalw/src/.deps/SymMatrix.Po index bda14c3..8c84cfb 100644 --- a/binaries/src/clustalw/src/.deps/SymMatrix.Po +++ b/binaries/src/clustalw/src/.deps/SymMatrix.Po @@ -1,139 +1,117 @@ -SymMatrix.o SymMatrix.o: general/SymMatrix.cpp config.h \ - general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/bits/types.h \ - /usr/include/bits/typesizes.h /usr/include/libio.h \ - /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ - /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h \ - 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/usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept +SymMatrix.o: general/SymMatrix.cpp config.h general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + 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\ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h config.h: general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -143,78 +121,98 @@ general/SymMatrix.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: + +/usr/include/bits/wchar.h: /usr/include/xlocale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/include/bits/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/include/bits/typesizes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/libio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/_G_config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/include/gconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/sys_errlist.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/bits/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/iconv.h: +/usr/include/locale.h: -/usr/include/libintl.h: +/usr/include/bits/locale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/include/bits/types.h: -/usr/include/pthread.h: +/usr/include/bits/typesizes.h: /usr/include/endian.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: + /usr/include/sched.h: /usr/include/time.h: @@ -223,10 +221,6 @@ general/SymMatrix.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -241,175 +235,79 @@ general/SymMatrix.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -429,6 +327,26 @@ general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/alloca.h: diff --git a/binaries/src/clustalw/src/.deps/Tree.Po b/binaries/src/clustalw/src/.deps/Tree.Po index 16a1771..d3113ee 100644 --- a/binaries/src/clustalw/src/.deps/Tree.Po +++ b/binaries/src/clustalw/src/.deps/Tree.Po @@ -1,171 +1,160 @@ -Tree.o Tree.o: tree/Tree.cpp config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -175,72 +164,92 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: + /usr/include/sched.h: /usr/include/time.h: @@ -249,10 +258,6 @@ config.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -267,199 +272,141 @@ config.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +tree/../alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +tree/../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +tree/../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +tree/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +tree/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/include/stdlib.h: -tree/../alignment/Alignment.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/sys/select.h: -tree/../alignment/Sequence.h: +/usr/include/bits/select.h: -tree/../alignment/../general/userparams.h: +/usr/include/bits/sigset.h: -tree/../alignment/../general/UserParameters.h: +/usr/include/sys/sysmacros.h: -tree/../alignment/../general/utils.h: +/usr/include/alloca.h: -tree/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -469,8 +416,6 @@ tree/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -485,7 +430,7 @@ tree/../alignment/../general/SquareMat.h: tree/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -505,7 +450,7 @@ tree/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: tree/../alignment/../general/utils.h: @@ -526,3 +471,11 @@ tree/../alignment/../general/VectorOutOfRange.h: tree/../alignment/../general/SequenceNotFoundException.h: tree/AlignmentSteps.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: diff --git a/binaries/src/clustalw/src/.deps/TreeInterface.Po b/binaries/src/clustalw/src/.deps/TreeInterface.Po index 114c91d..3edbd3c 100644 --- a/binaries/src/clustalw/src/.deps/TreeInterface.Po +++ b/binaries/src/clustalw/src/.deps/TreeInterface.Po @@ -1,185 +1,170 @@ -TreeInterface.o TreeInterface.o: tree/TreeInterface.cpp config.h \ - tree/TreeInterface.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - tree/AlignmentSteps.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - tree/../alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - tree/../alignment/Sequence.h tree/../alignment/../general/userparams.h \ - tree/../alignment/../general/UserParameters.h \ - tree/../alignment/../general/utils.h \ - tree/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - tree/../alignment/../general/clustalw.h \ - tree/../alignment/../general/general.h \ - tree/../alignment/../general/Array2D.h \ - tree/../alignment/../general/SquareMat.h \ - tree/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - tree/../alignment/../general/utils.h \ - tree/../alignment/../substitutionMatrix/globalmatrix.h \ - tree/../alignment/../substitutionMatrix/SubMatrix.h \ - tree/../alignment/../substitutionMatrix/../general/clustalw.h \ - tree/../alignment/../substitutionMatrix/../general/userparams.h \ - tree/../alignment/../substitutionMatrix/../general/utils.h \ - tree/../alignment/../substitutionMatrix/../general/Array2D.h \ - tree/../alignment/../general/VectorOutOfRange.h \ - tree/../alignment/../general/SequenceNotFoundException.h \ - tree/../general/clustalw.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc \ - tree/UnRootedClusterTree.h tree/ClusterTree.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc \ - tree/NJTree.h tree/ClusterTreeAlgorithm.h tree/../general/userparams.h \ - tree/ClusterTreeOutput.h tree/../general/OutputFile.h tree/Tree.h \ - tree/../multipleAlign/MSA.h tree/../multipleAlign/ProfileBase.h \ - tree/../multipleAlign/../alignment/Alignment.h \ - tree/../multipleAlign/../tree/AlignmentSteps.h \ - tree/../multipleAlign/ProfileAlignAlgorithm.h \ - tree/../general/debuglogObject.h tree/../general/DebugLog.h \ - tree/UPGMA/RootedGuideTree.h tree/UPGMA/Node.h tree/UPGMA/upgmadata.h \ - tree/UPGMA/../../alignment/Alignment.h tree/UPGMA/RootedClusterTree.h \ - tree/UPGMA/../ClusterTree.h tree/UPGMA/RootedGuideTree.h \ - tree/UPGMA/../AlignmentSteps.h +TreeInterface.o: tree/TreeInterface.cpp config.h 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -319,151 +312,107 @@ tree/TreeInterface.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/include/stdint.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: +tree/AlignmentSteps.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -tree/AlignmentSteps.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +tree/../alignment/Alignment.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: -/usr/include/wctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +tree/../alignment/Sequence.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +tree/../alignment/../general/userparams.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +tree/../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +tree/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +tree/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/select.h: -tree/../alignment/Alignment.h: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/libio.h: -tree/../alignment/Sequence.h: +/usr/include/_G_config.h: -tree/../alignment/../general/userparams.h: +/usr/include/bits/stdio_lim.h: -tree/../alignment/../general/UserParameters.h: +/usr/include/bits/sys_errlist.h: -tree/../alignment/../general/utils.h: +/usr/include/bits/stdio.h: -tree/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -473,8 +422,6 @@ tree/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -489,7 +436,7 @@ tree/../alignment/../general/SquareMat.h: tree/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -509,7 +456,7 @@ tree/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: tree/../alignment/../general/utils.h: @@ -531,19 +478,25 @@ tree/../alignment/../general/SequenceNotFoundException.h: tree/../general/clustalw.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: tree/UnRootedClusterTree.h: tree/ClusterTree.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: tree/NJTree.h: @@ -575,6 +528,8 @@ tree/UPGMA/RootedGuideTree.h: tree/UPGMA/Node.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/limits: + tree/UPGMA/upgmadata.h: tree/UPGMA/../../alignment/Alignment.h: diff --git a/binaries/src/clustalw/src/.deps/UPGMAAlgorithm.Po b/binaries/src/clustalw/src/.deps/UPGMAAlgorithm.Po index 643625d..4e309f6 100644 --- a/binaries/src/clustalw/src/.deps/UPGMAAlgorithm.Po +++ b/binaries/src/clustalw/src/.deps/UPGMAAlgorithm.Po @@ -1,162 +1,154 @@ -UPGMAAlgorithm.o UPGMAAlgorithm.o: tree/UPGMA/UPGMAAlgorithm.cpp config.h \ - tree/UPGMA/UPGMAAlgorithm.h tree/UPGMA/Node.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - tree/UPGMA/../../general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - tree/UPGMA/../../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - tree/UPGMA/../AlignmentSteps.h tree/UPGMA/RootedGuideTree.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc \ - tree/UPGMA/../../alignment/Alignment.h \ - tree/UPGMA/../../alignment/Sequence.h \ - tree/UPGMA/../../alignment/../general/userparams.h \ - tree/UPGMA/../../alignment/../general/UserParameters.h \ - tree/UPGMA/../../alignment/../general/utils.h \ - tree/UPGMA/../../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - tree/UPGMA/../../alignment/../general/clustalw.h \ - tree/UPGMA/../../alignment/../general/general.h \ - tree/UPGMA/../../alignment/../general/utils.h \ - tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h \ - tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h \ - tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h \ - tree/UPGMA/../../alignment/../substitutionMatrix/../general/userparams.h \ - tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h \ - tree/UPGMA/../../alignment/../substitutionMatrix/../general/Array2D.h \ - tree/UPGMA/../../alignment/../general/VectorOutOfRange.h \ - tree/UPGMA/../../alignment/../general/SequenceNotFoundException.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/list \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_list.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/list.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc \ - tree/UPGMA/../../general/SymMatrix.h \ - tree/UPGMA/../../general/debuglogObject.h \ - tree/UPGMA/../../general/DebugLog.h +UPGMAAlgorithm.o: tree/UPGMA/UPGMAAlgorithm.cpp config.h \ + tree/UPGMA/UPGMAAlgorithm.h tree/UPGMA/Node.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/limits \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + 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tree/UPGMA/../../alignment/Alignment.h \ + tree/UPGMA/../../alignment/Sequence.h \ + tree/UPGMA/../../alignment/../general/userparams.h \ + tree/UPGMA/../../alignment/../general/UserParameters.h \ + tree/UPGMA/../../alignment/../general/utils.h \ + tree/UPGMA/../../alignment/../general/Utility.h /usr/include/string.h \ + /usr/include/errno.h /usr/include/bits/errno.h \ + /usr/include/linux/errno.h /usr/include/asm/errno.h \ + /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ + tree/UPGMA/../../alignment/../general/clustalw.h \ + tree/UPGMA/../../alignment/../general/general.h \ + tree/UPGMA/../../alignment/../general/utils.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/userparams.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h \ + tree/UPGMA/../../alignment/../substitutionMatrix/../general/Array2D.h \ + tree/UPGMA/../../alignment/../general/VectorOutOfRange.h \ + tree/UPGMA/../../alignment/../general/SequenceNotFoundException.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_list.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/list.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ctime \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc \ + tree/UPGMA/../../general/SymMatrix.h \ + tree/UPGMA/../../general/debuglogObject.h \ + tree/UPGMA/../../general/DebugLog.h config.h: @@ -164,13 +156,13 @@ tree/UPGMA/UPGMAAlgorithm.h: tree/UPGMA/Node.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/limits: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -180,131 +172,135 @@ tree/UPGMA/Node.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: 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-/usr/include/bits/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: -/usr/include/bits/typesizes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/include/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/include/sys/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/include/bits/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/include/bits/sigset.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/include/bits/time.h: +/usr/include/wchar.h: -/usr/include/sys/sysmacros.h: +/usr/include/stdio.h: -/usr/include/bits/pthreadtypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: -/usr/include/alloca.h: +/usr/include/bits/wchar.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/include/xlocale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/libio.h: +/usr/include/locale.h: -/usr/include/_G_config.h: +/usr/include/bits/locale.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/include/gconv.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/include/bits/types.h: -/usr/include/bits/sys_errlist.h: +/usr/include/bits/typesizes.h: -/usr/include/bits/stdio.h: +/usr/include/endian.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/endian.h: -/usr/include/locale.h: +/usr/include/bits/byteswap.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -318,79 +314,9 @@ tree/UPGMA/Node.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: tree/UPGMA/upgmadata.h: @@ -400,65 +326,53 @@ tree/UPGMA/../../general/general.h: tree/UPGMA/../../general/Array2D.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: /usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: tree/UPGMA/../../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: tree/UPGMA/../../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -478,19 +392,55 @@ tree/UPGMA/../../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/sys/types.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/alloca.h: tree/UPGMA/../AlignmentSteps.h: tree/UPGMA/RootedGuideTree.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/include/libio.h: + +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: tree/UPGMA/../../alignment/Alignment.h: @@ -504,6 +454,8 @@ tree/UPGMA/../../alignment/../general/utils.h: tree/UPGMA/../../alignment/../general/Utility.h: +/usr/include/string.h: + /usr/include/errno.h: /usr/include/bits/errno.h: @@ -512,8 +464,6 @@ tree/UPGMA/../../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -540,15 +490,25 @@ tree/UPGMA/../../alignment/../general/VectorOutOfRange.h: tree/UPGMA/../../alignment/../general/SequenceNotFoundException.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/list: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/list: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_list.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/list.tcc: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_list.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/list.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ctime: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: tree/UPGMA/../../general/SymMatrix.h: diff --git a/binaries/src/clustalw/src/.deps/UnRootedClusterTree.Po b/binaries/src/clustalw/src/.deps/UnRootedClusterTree.Po index 575130d..b664d41 100644 --- a/binaries/src/clustalw/src/.deps/UnRootedClusterTree.Po +++ b/binaries/src/clustalw/src/.deps/UnRootedClusterTree.Po @@ -1,159 +1,147 @@ -UnRootedClusterTree.o UnRootedClusterTree.o: \ - tree/UnRootedClusterTree.cpp config.h tree/UnRootedClusterTree.h \ - tree/ClusterTree.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/bits/types.h \ - /usr/include/bits/typesizes.h /usr/include/libio.h \ - /usr/include/_G_config.h /usr/include/wchar.h /usr/include/bits/wchar.h \ - /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/sched.h /usr/include/time.h /usr/include/bits/sched.h \ - /usr/include/bits/time.h /usr/include/signal.h \ - /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ - /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ - /usr/include/sys/select.h /usr/include/bits/select.h \ - /usr/include/sys/sysmacros.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - tree/../alignment/Alignment.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - tree/../alignment/Sequence.h tree/../alignment/../general/userparams.h \ - tree/../alignment/../general/UserParameters.h \ - tree/../alignment/../general/utils.h \ - tree/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - tree/../alignment/../general/clustalw.h \ - tree/../alignment/../general/general.h \ - tree/../alignment/../general/Array2D.h \ - tree/../alignment/../general/SquareMat.h \ - tree/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - tree/../alignment/../general/utils.h \ - tree/../alignment/../substitutionMatrix/globalmatrix.h \ - tree/../alignment/../substitutionMatrix/SubMatrix.h \ - tree/../alignment/../substitutionMatrix/../general/clustalw.h \ - tree/../alignment/../substitutionMatrix/../general/userparams.h \ - tree/../alignment/../substitutionMatrix/../general/utils.h \ - tree/../alignment/../substitutionMatrix/../general/Array2D.h \ - tree/../alignment/../general/VectorOutOfRange.h \ - tree/../alignment/../general/SequenceNotFoundException.h tree/NJTree.h \ - tree/ClusterTreeAlgorithm.h tree/../general/clustalw.h \ - tree/../general/userparams.h tree/ClusterTreeOutput.h \ - tree/../general/OutputFile.h tree/../general/utils.h \ - tree/RandomGenerator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc +UnRootedClusterTree.o: tree/UnRootedClusterTree.cpp config.h \ + tree/UnRootedClusterTree.h tree/ClusterTree.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + tree/../alignment/Alignment.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + tree/../alignment/Sequence.h tree/../alignment/../general/userparams.h \ + tree/../alignment/../general/UserParameters.h \ + tree/../alignment/../general/utils.h \ + tree/../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + tree/../alignment/../general/clustalw.h \ + tree/../alignment/../general/general.h \ + tree/../alignment/../general/Array2D.h \ + tree/../alignment/../general/SquareMat.h \ + tree/../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + tree/../alignment/../general/utils.h \ + tree/../alignment/../substitutionMatrix/globalmatrix.h \ + tree/../alignment/../substitutionMatrix/SubMatrix.h \ + tree/../alignment/../substitutionMatrix/../general/clustalw.h \ + tree/../alignment/../substitutionMatrix/../general/userparams.h \ + tree/../alignment/../substitutionMatrix/../general/utils.h \ + tree/../alignment/../substitutionMatrix/../general/Array2D.h \ + tree/../alignment/../general/VectorOutOfRange.h \ + tree/../alignment/../general/SequenceNotFoundException.h tree/NJTree.h \ + tree/ClusterTreeAlgorithm.h tree/../general/clustalw.h \ + tree/../general/userparams.h tree/ClusterTreeOutput.h \ + tree/../general/OutputFile.h tree/../general/utils.h \ + tree/RandomGenerator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc config.h: @@ -161,19 +149,19 @@ tree/UnRootedClusterTree.h: tree/ClusterTree.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -183,72 +171,92 @@ tree/ClusterTree.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: + +/usr/include/bits/wchar.h: /usr/include/xlocale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/include/bits/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/include/bits/typesizes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/libio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/_G_config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/include/gconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/sys_errlist.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/bits/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/iconv.h: +/usr/include/locale.h: -/usr/include/libintl.h: +/usr/include/bits/locale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/include/bits/types.h: -/usr/include/pthread.h: +/usr/include/bits/typesizes.h: /usr/include/endian.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: + /usr/include/sched.h: /usr/include/time.h: @@ -257,10 +265,6 @@ tree/ClusterTree.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -275,193 +279,143 @@ tree/ClusterTree.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +tree/../alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +tree/../alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +tree/../alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/include/stdlib.h: -tree/../alignment/Alignment.h: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/sys/select.h: -tree/../alignment/Sequence.h: +/usr/include/bits/select.h: -tree/../alignment/../general/userparams.h: +/usr/include/bits/sigset.h: -tree/../alignment/../general/UserParameters.h: +/usr/include/sys/sysmacros.h: -tree/../alignment/../general/utils.h: +/usr/include/alloca.h: -tree/../alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -471,8 +425,6 @@ tree/../alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -487,7 +439,7 @@ tree/../alignment/../general/SquareMat.h: tree/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -507,7 +459,7 @@ tree/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: tree/../alignment/../general/utils.h: @@ -543,6 +495,6 @@ tree/../general/utils.h: tree/RandomGenerator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: diff --git a/binaries/src/clustalw/src/.deps/UserParameters.Po b/binaries/src/clustalw/src/.deps/UserParameters.Po index 5fd5967..1c925ec 100644 --- a/binaries/src/clustalw/src/.deps/UserParameters.Po +++ b/binaries/src/clustalw/src/.deps/UserParameters.Po @@ -1,136 +1,127 @@ -UserParameters.o UserParameters.o: general/UserParameters.cpp config.h \ - /usr/include/stdio.h /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ - /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/limits \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/climits \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \ + /usr/include/limits.h /usr/include/bits/posix1_lim.h \ + /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ + /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + general/UserParameters.h general/utils.h general/Utility.h \ + /usr/include/string.h /usr/include/errno.h /usr/include/bits/errno.h \ + /usr/include/linux/errno.h /usr/include/asm/errno.h \ + /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ + general/clustalw.h general/general.h general/Array2D.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + general/SquareMat.h general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + clustalw_version.h config.h: @@ -146,7 +137,7 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: /usr/include/bits/types.h: @@ -158,11 +149,7 @@ config.h: /usr/include/wchar.h: -/usr/include/bits/wchar.h: - -/usr/include/gconv.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: /usr/include/bits/stdio_lim.h: @@ -170,109 +157,113 @@ config.h: /usr/include/bits/stdio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/xlocale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/include/stdlib.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/include/bits/waitflags.h: +/usr/include/bits/wchar.h: -/usr/include/bits/waitstatus.h: +/usr/include/xlocale.h: -/usr/include/endian.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/include/bits/endian.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/include/sys/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/include/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/include/sys/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/include/bits/select.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/include/bits/sigset.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/bits/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/sys/sysmacros.h: +/usr/include/locale.h: -/usr/include/bits/pthreadtypes.h: +/usr/include/bits/locale.h: -/usr/include/alloca.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/include/endian.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/endian.h: -/usr/include/locale.h: +/usr/include/bits/byteswap.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: /usr/include/pthread.h: /usr/include/sched.h: +/usr/include/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -286,133 +277,105 @@ config.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: +/usr/include/sys/select.h: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/include/wctype.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/limits: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/climits: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/include/limits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/include/bits/posix1_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +/usr/include/bits/local_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/linux/limits.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/bits/posix2_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/bits/xopen_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: general/UserParameters.h: @@ -420,6 +383,8 @@ general/utils.h: general/Utility.h: +/usr/include/string.h: + /usr/include/errno.h: /usr/include/bits/errno.h: @@ -428,8 +393,6 @@ general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -440,19 +403,23 @@ general/general.h: general/Array2D.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: general/SquareMat.h: general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -472,8 +439,8 @@ general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: clustalw_version.h: diff --git a/binaries/src/clustalw/src/.deps/Utility.Po b/binaries/src/clustalw/src/.deps/Utility.Po index 407855c..c0ddf9f 100644 --- a/binaries/src/clustalw/src/.deps/Utility.Po +++ b/binaries/src/clustalw/src/.deps/Utility.Po @@ -1,144 +1,130 @@ -Utility.o Utility.o: general/Utility.cpp config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - 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/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - general/Utility.h /usr/include/errno.h /usr/include/bits/errno.h \ - /usr/include/linux/errno.h /usr/include/asm/errno.h \ - /usr/include/asm-x86_64/errno.h /usr/include/asm-generic/errno.h \ - /usr/include/asm-generic/errno-base.h general/clustalw.h \ - general/general.h general/Array2D.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /usr/include/math.h /usr/include/bits/huge_val.h \ - /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ - /usr/include/bits/inf.h /usr/include/bits/nan.h \ - /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ - /usr/include/bits/mathinline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - general/userparams.h general/UserParameters.h general/utils.h +Utility.o: general/Utility.cpp config.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \ + /usr/include/locale.h /usr/include/bits/locale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/algorithm \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algo.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/algorithmfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_heap.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + general/Utility.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h general/clustalw.h \ + general/general.h general/Array2D.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \ + general/SquareMat.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + general/userparams.h general/UserParameters.h general/utils.h config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -148,78 +134,98 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/include/string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: + +/usr/include/bits/wchar.h: /usr/include/xlocale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h: -/usr/include/bits/types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h: -/usr/include/bits/typesizes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/libio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/_G_config.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/include/gconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/stdio_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h: -/usr/include/bits/sys_errlist.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/bits/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/iconv.h: +/usr/include/locale.h: -/usr/include/libintl.h: +/usr/include/bits/locale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/include/bits/types.h: -/usr/include/pthread.h: +/usr/include/bits/typesizes.h: /usr/include/endian.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: + /usr/include/sched.h: /usr/include/time.h: @@ -228,10 +234,6 @@ config.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -246,163 +248,111 @@ config.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: - -/usr/include/stdint.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/include/stdlib.h: - -/usr/include/bits/waitflags.h: - -/usr/include/bits/waitstatus.h: - -/usr/include/sys/types.h: - -/usr/include/sys/select.h: - -/usr/include/bits/select.h: - -/usr/include/sys/sysmacros.h: - -/usr/include/alloca.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h: +/usr/include/wctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/algorithm: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algo.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf: +/usr/include/bits/waitflags.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype: +/usr/include/bits/sigset.h: -/usr/include/wctype.h: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h: +/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/algorithmfwd.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_heap.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc: +general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +/usr/include/libio.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +/usr/include/_G_config.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/include/bits/stdio_lim.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/include/bits/sys_errlist.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/stdio.h: -general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -412,8 +362,6 @@ general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -424,23 +372,21 @@ general/general.h: general/Array2D.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -460,9 +406,9 @@ general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept: general/userparams.h: diff --git a/binaries/src/clustalw/src/.deps/VectorOutOfRange.Po b/binaries/src/clustalw/src/.deps/VectorOutOfRange.Po index 5adcbc5..ebdb0be 100644 --- a/binaries/src/clustalw/src/.deps/VectorOutOfRange.Po +++ b/binaries/src/clustalw/src/.deps/VectorOutOfRange.Po @@ -1,131 +1,102 @@ -VectorOutOfRange.o VectorOutOfRange.o: general/VectorOutOfRange.cpp \ - config.h general/VectorOutOfRange.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \ - /usr/include/limits.h /usr/include/bits/posix1_lim.h \ - /usr/include/bits/local_lim.h /usr/include/linux/limits.h \ - /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \ - /usr/include/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream +VectorOutOfRange.o: general/VectorOutOfRange.cpp config.h \ + general/VectorOutOfRange.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \ + /usr/include/bits/wordsize.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \ + /usr/include/features.h /usr/include/sys/cdefs.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \ + 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -135,129 +106,119 @@ general/VectorOutOfRange.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef: 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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream: diff --git a/binaries/src/clustalw/src/.deps/main.Po b/binaries/src/clustalw/src/.deps/main.Po index a8505ee..389f63d 100644 --- a/binaries/src/clustalw/src/.deps/main.Po +++ b/binaries/src/clustalw/src/.deps/main.Po @@ -1,182 +1,170 @@ -main.o main.o: main.cpp config.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - 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\ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + alignment/Sequence.h alignment/../general/userparams.h \ + alignment/../general/UserParameters.h alignment/../general/utils.h \ + alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h alignment/../general/clustalw.h \ + alignment/../general/general.h alignment/../general/Array2D.h \ + alignment/../general/SquareMat.h alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /usr/include/math.h /usr/include/bits/huge_val.h \ + /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \ + /usr/include/bits/inf.h /usr/include/bits/nan.h \ + /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \ + /usr/include/bits/mathinline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \ + alignment/../general/utils.h \ + alignment/../substitutionMatrix/globalmatrix.h \ + alignment/../substitutionMatrix/SubMatrix.h \ + alignment/../substitutionMatrix/../general/clustalw.h \ + alignment/../substitutionMatrix/../general/userparams.h \ + alignment/../substitutionMatrix/../general/utils.h \ + alignment/../substitutionMatrix/../general/Array2D.h \ + alignment/../general/VectorOutOfRange.h \ + alignment/../general/SequenceNotFoundException.h 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/usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h: /usr/include/features.h: @@ -186,78 +174,98 @@ config.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: 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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/iconv.h: +/usr/include/locale.h: -/usr/include/libintl.h: +/usr/include/bits/locale.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h: +/usr/include/bits/types.h: -/usr/include/pthread.h: +/usr/include/bits/typesizes.h: /usr/include/endian.h: /usr/include/bits/endian.h: +/usr/include/bits/byteswap.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h: + +/usr/include/pthread.h: + /usr/include/sched.h: /usr/include/time.h: @@ -266,10 +274,6 @@ config.h: /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -284,187 +288,123 @@ config.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/include/ctype.h: 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+alignment/../general/UserParameters.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale: +alignment/../general/utils.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc: +alignment/../general/Utility.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream: +/usr/include/stdlib.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc: +/usr/include/bits/waitflags.h: -alignment/Alignment.h: +/usr/include/bits/waitstatus.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector: +/usr/include/sys/types.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h: +/usr/include/sys/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h: +/usr/include/bits/select.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc: +/usr/include/bits/sigset.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: +/usr/include/sys/sysmacros.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/include/alloca.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept: +/usr/include/libio.h: -alignment/Sequence.h: +/usr/include/_G_config.h: -alignment/../general/userparams.h: +/usr/include/bits/stdio_lim.h: -alignment/../general/UserParameters.h: +/usr/include/bits/sys_errlist.h: -alignment/../general/utils.h: +/usr/include/bits/stdio.h: -alignment/../general/Utility.h: +/usr/include/string.h: /usr/include/errno.h: @@ -474,8 +414,6 @@ alignment/../general/Utility.h: /usr/include/asm/errno.h: -/usr/include/asm-x86_64/errno.h: - /usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -490,7 +428,7 @@ alignment/../general/SquareMat.h: alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -510,7 +448,7 @@ alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: alignment/../general/utils.h: @@ -542,6 +480,14 @@ general/Utility.h: fileInput/FileReader.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h: + fileInput/../alignment/Alignment.h: fileInput/../alignment/Sequence.h: @@ -554,11 +500,17 @@ fileInput/FileParser.h: fileInput/InFileStream.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: fileInput/ClustalFileParser.h: @@ -590,11 +542,11 @@ interface/../alignment/Alignment.h: interface/../alignment/AlignmentOutput.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cassert: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cassert: /usr/include/assert.h: @@ -623,3 +575,5 @@ general/DebugLog.h: general/ClustalWResources.h: general/Stats.h: + +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ctime: diff --git a/binaries/src/clustalw/src/Alignment.o b/binaries/src/clustalw/src/Alignment.o new file mode 100644 index 0000000..d7b58f6 Binary files /dev/null and b/binaries/src/clustalw/src/Alignment.o differ diff --git a/binaries/src/clustalw/src/AlignmentOutput.o b/binaries/src/clustalw/src/AlignmentOutput.o new file mode 100644 index 0000000..82fa465 Binary files /dev/null and b/binaries/src/clustalw/src/AlignmentOutput.o differ diff --git a/binaries/src/clustalw/src/AlignmentSteps.o b/binaries/src/clustalw/src/AlignmentSteps.o new file mode 100644 index 0000000..4b0f1e2 Binary files /dev/null and b/binaries/src/clustalw/src/AlignmentSteps.o differ diff --git a/binaries/src/clustalw/src/Clustal.cpp b/binaries/src/clustalw/src/Clustal.cpp index 646b34a..453bcc0 100644 --- a/binaries/src/clustalw/src/Clustal.cpp +++ b/binaries/src/clustalw/src/Clustal.cpp @@ -1043,8 +1043,11 @@ int Clustal::profile2Input(string profile2Name) userParameters->setSeqName(profile2Name); userParameters->setProfile2Name(profile2Name); + FileReader readProfileFile; + cout << "before profileInput\n"; code = readProfileFile.profileInput(&alignmentObj); + cout << "after profileInput\n"; if(!userParameters->getInteractive()) { @@ -1058,7 +1061,9 @@ int Clustal::profile2Input(string profile2Name) else cerr << "ERROR: Unhandled error code (" << code << ") returned from profileInput.\n"; // AW: should we really exit here? What if called from clustalx? - exit(2); + // DD: fixed + if(!userParameters->getGui()) + exit(2); } } return code; diff --git a/binaries/src/clustalw/src/Clustal.o b/binaries/src/clustalw/src/Clustal.o new file mode 100644 index 0000000..e0533a6 Binary files /dev/null and b/binaries/src/clustalw/src/Clustal.o differ diff --git a/binaries/src/clustalw/src/ClustalFileParser.o b/binaries/src/clustalw/src/ClustalFileParser.o new file mode 100644 index 0000000..3342bdb Binary files /dev/null and b/binaries/src/clustalw/src/ClustalFileParser.o differ diff --git a/binaries/src/clustalw/src/ClustalWResources.o b/binaries/src/clustalw/src/ClustalWResources.o new file mode 100644 index 0000000..0f6b146 Binary files /dev/null and b/binaries/src/clustalw/src/ClustalWResources.o differ diff --git a/binaries/src/clustalw/src/ClusterTree.o b/binaries/src/clustalw/src/ClusterTree.o new file mode 100644 index 0000000..31f3d73 Binary files /dev/null and b/binaries/src/clustalw/src/ClusterTree.o differ diff --git a/binaries/src/clustalw/src/ClusterTreeOutput.o b/binaries/src/clustalw/src/ClusterTreeOutput.o new file mode 100644 index 0000000..9e2ecbc Binary files /dev/null and b/binaries/src/clustalw/src/ClusterTreeOutput.o differ diff --git a/binaries/src/clustalw/src/CommandLineParser.o b/binaries/src/clustalw/src/CommandLineParser.o new file mode 100644 index 0000000..4618847 Binary files /dev/null and b/binaries/src/clustalw/src/CommandLineParser.o differ diff --git a/binaries/src/clustalw/src/DebugLog.o b/binaries/src/clustalw/src/DebugLog.o new file mode 100644 index 0000000..9bfd54f Binary files /dev/null and b/binaries/src/clustalw/src/DebugLog.o differ diff --git a/binaries/src/clustalw/src/EMBLFileParser.o b/binaries/src/clustalw/src/EMBLFileParser.o new file mode 100644 index 0000000..ebb664a Binary files /dev/null and b/binaries/src/clustalw/src/EMBLFileParser.o differ diff --git a/binaries/src/clustalw/src/FastPairwiseAlign.o b/binaries/src/clustalw/src/FastPairwiseAlign.o new file mode 100644 index 0000000..93fd677 Binary files /dev/null and b/binaries/src/clustalw/src/FastPairwiseAlign.o differ diff --git a/binaries/src/clustalw/src/FileParser.o b/binaries/src/clustalw/src/FileParser.o new file mode 100644 index 0000000..bfe134f Binary files /dev/null and b/binaries/src/clustalw/src/FileParser.o differ diff --git a/binaries/src/clustalw/src/FileReader.o b/binaries/src/clustalw/src/FileReader.o new file mode 100644 index 0000000..82b73aa Binary files /dev/null and b/binaries/src/clustalw/src/FileReader.o differ diff --git a/binaries/src/clustalw/src/FullPairwiseAlign.o b/binaries/src/clustalw/src/FullPairwiseAlign.o new file mode 100644 index 0000000..c1a10c0 Binary files /dev/null and b/binaries/src/clustalw/src/FullPairwiseAlign.o differ diff --git a/binaries/src/clustalw/src/GDEFileParser.o b/binaries/src/clustalw/src/GDEFileParser.o new file mode 100644 index 0000000..d82a348 Binary files /dev/null and b/binaries/src/clustalw/src/GDEFileParser.o differ diff --git a/binaries/src/clustalw/src/Help.cpp b/binaries/src/clustalw/src/Help.cpp index a2e354d..8b1c390 100644 --- a/binaries/src/clustalw/src/Help.cpp +++ b/binaries/src/clustalw/src/Help.cpp @@ -319,7 +319,7 @@ Help::Help() s.marker = "5"; s.title = "Help for output format options."; - s.content = "Six output formats are offered. You can choose any (or all 6 if you wish). \n" + s.content = "Several output formats are offered. You can choose any (or all 6 if you wish). \n" "\n" "CLUSTAL format output is a self explanatory alignment format. It shows the\n" "sequences aligned in blocks. It can be read in again at a later date to\n" @@ -330,6 +330,9 @@ Help::Help() "alignments (e.g. PRETTY, PROFILEMAKE, PLOTALIGN). It is the same as the GCG\n" ".msf format files (multiple sequence file); new in version 7 of GCG.\n" "\n" +"Fasta output cis widely used because of it's simplicity. Each sequence name is\n" +"preceeded by a '>'-sign. The sequence itself is printed out in the following lines\n" +"\n" "PHYLIP format output can be used for input to the PHYLIP package of Joe \n" "Felsenstein. This is an extremely widely used package for doing every \n" "imaginable form of phylogenetic analysis (MUCH more than the the modest intro-\n" @@ -645,7 +648,7 @@ Help::Help() "-TYPE= :PROTEIN or DNA sequences\n" "-NEGATIVE :protein alignment with negative values in matrix\n" "-OUTFILE= :sequence alignment file name\n" -"-OUTPUT= :GCG, GDE, PHYLIP, PIR or NEXUS\n" +"-OUTPUT= :CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTA\n" "-OUTORDER= :INPUT or ALIGNED\n" "-CASE :LOWER or UPPER (for GDE output only)\n" "-SEQNOS= :OFF or ON (for Clustal output only)\n" diff --git a/binaries/src/clustalw/src/Help.o b/binaries/src/clustalw/src/Help.o new file mode 100644 index 0000000..1495b5b Binary files /dev/null and b/binaries/src/clustalw/src/Help.o differ diff --git a/binaries/src/clustalw/src/InFileStream.o b/binaries/src/clustalw/src/InFileStream.o new file mode 100644 index 0000000..6663b0d Binary files /dev/null and b/binaries/src/clustalw/src/InFileStream.o differ diff --git a/binaries/src/clustalw/src/InteractiveMenu.o b/binaries/src/clustalw/src/InteractiveMenu.o new file mode 100644 index 0000000..9d7c963 Binary files /dev/null and b/binaries/src/clustalw/src/InteractiveMenu.o differ diff --git a/binaries/src/clustalw/src/InvalidCombination.o b/binaries/src/clustalw/src/InvalidCombination.o new file mode 100644 index 0000000..30c3e00 Binary files /dev/null and b/binaries/src/clustalw/src/InvalidCombination.o differ diff --git a/binaries/src/clustalw/src/Iteration.o b/binaries/src/clustalw/src/Iteration.o new file mode 100644 index 0000000..ec737ae Binary files /dev/null and b/binaries/src/clustalw/src/Iteration.o differ diff --git a/binaries/src/clustalw/src/LowScoreSegProfile.o b/binaries/src/clustalw/src/LowScoreSegProfile.o new file mode 100644 index 0000000..491edee Binary files /dev/null and b/binaries/src/clustalw/src/LowScoreSegProfile.o differ diff --git a/binaries/src/clustalw/src/MSA.o b/binaries/src/clustalw/src/MSA.o new file mode 100644 index 0000000..2c4aaab Binary files /dev/null and b/binaries/src/clustalw/src/MSA.o differ diff --git a/binaries/src/clustalw/src/MSFFileParser.o b/binaries/src/clustalw/src/MSFFileParser.o new file mode 100644 index 0000000..30b9690 Binary files /dev/null and b/binaries/src/clustalw/src/MSFFileParser.o differ diff --git a/binaries/src/clustalw/src/Makefile b/binaries/src/clustalw/src/Makefile index c8dab48..d1b763d 100644 --- a/binaries/src/clustalw/src/Makefile +++ b/binaries/src/clustalw/src/Makefile @@ -1,8 +1,9 @@ -# Makefile.in generated by automake 1.10.2 from Makefile.am. +# Makefile.in generated by automake 1.11.1 from Makefile.am. # src/Makefile. Generated from Makefile.in by configure. # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, -# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +# 2003, 2004, 2005, 2006, 2007, 2008, 2009 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. @@ -21,8 +22,9 @@ pkgdatadir = $(datadir)/clustalw -pkglibdir = $(libdir)/clustalw pkgincludedir = $(includedir)/clustalw +pkglibdir = $(libdir)/clustalw +pkglibexecdir = $(libexecdir)/clustalw am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd install_sh_DATA = $(install_sh) -c -m 644 install_sh_PROGRAM = $(install_sh) -c @@ -49,8 +51,8 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ mkinstalldirs = $(install_sh) -d CONFIG_HEADER = config.h CONFIG_CLEAN_FILES = clustalw_version.h +CONFIG_CLEAN_VPATH_FILES = am__installdirs = "$(DESTDIR)$(bindir)" -binPROGRAMS_INSTALL = $(INSTALL_PROGRAM) PROGRAMS = $(bin_PROGRAMS) am_clustalw2_OBJECTS = FullPairwiseAlign.$(OBJEXT) \ FastPairwiseAlign.$(OBJEXT) MSFFileParser.$(OBJEXT) \ @@ -82,6 +84,7 @@ clustalw2_LDADD = $(LDADD) DEFAULT_INCLUDES = -I. depcomp = $(SHELL) $(top_srcdir)/depcomp am__depfiles_maybe = depfiles +am__mv = mv -f CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) CXXLD = $(CXX) @@ -102,21 +105,49 @@ RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \ ps-recursive uninstall-recursive RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \ distclean-recursive maintainer-clean-recursive +AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \ + $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \ + distdir ETAGS = etags CTAGS = ctags DIST_SUBDIRS = $(SUBDIRS) DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) -ACLOCAL = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run aclocal-1.10 -AMTAR = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run tar -AUTOCONF = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoconf -AUTOHEADER = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoheader -AUTOMAKE = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run automake-1.10 +am__relativize = \ + dir0=`pwd`; \ + sed_first='s,^\([^/]*\)/.*$$,\1,'; \ + sed_rest='s,^[^/]*/*,,'; \ + sed_last='s,^.*/\([^/]*\)$$,\1,'; \ + sed_butlast='s,/*[^/]*$$,,'; \ + while test -n "$$dir1"; do \ + first=`echo "$$dir1" | sed -e "$$sed_first"`; \ + if test "$$first" != "."; then \ + if test "$$first" = ".."; then \ + dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \ + dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \ + else \ + first2=`echo "$$dir2" | sed -e "$$sed_first"`; \ + if test "$$first2" = "$$first"; then \ + dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \ + else \ + dir2="../$$dir2"; \ + fi; \ + dir0="$$dir0"/"$$first"; \ + fi; \ + fi; \ + dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \ + done; \ + reldir="$$dir2" +ACLOCAL = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run aclocal-1.11 +AMTAR = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run tar +AUTOCONF = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoconf +AUTOHEADER = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoheader +AUTOMAKE = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run automake-1.11 AWK = gawk CC = gcc CCDEPMODE = depmode=gcc3 CFLAGS = -g -O2 CLUSTALW_NAME = ClustalW -CLUSTALW_VERSION = 2.0.12 +CLUSTALW_VERSION = 2.1 CPPFLAGS = CXX = g++ CXXCPP = g++ -E @@ -140,25 +171,26 @@ LDFLAGS = LIBOBJS = LIBS = LTLIBOBJS = -MAKEINFO = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run makeinfo +MAKEINFO = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run makeinfo MKDIR_P = /bin/mkdir -p OBJEXT = o PACKAGE = clustalw PACKAGE_BUGREPORT = clustalw@ucd.ie PACKAGE_NAME = clustalw -PACKAGE_STRING = clustalw 2.0.12 +PACKAGE_STRING = clustalw 2.1 PACKAGE_TARNAME = clustalw -PACKAGE_VERSION = 2.0.12 +PACKAGE_URL = +PACKAGE_VERSION = 2.1 PATH_SEPARATOR = : RANLIB = ranlib SET_MAKE = SHELL = /bin/sh STRIP = -VERSION = 2.0.12 -abs_builddir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/src -abs_srcdir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/src -abs_top_builddir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw -abs_top_srcdir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw +VERSION = 2.1 +abs_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/src +abs_srcdir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/src +abs_top_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw +abs_top_srcdir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw ac_ct_CC = gcc ac_ct_CXX = g++ am__include = include @@ -186,7 +218,7 @@ host_vendor = unknown htmldir = ${docdir} includedir = ${prefix}/include infodir = ${datarootdir}/info -install_sh = $(SHELL) /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/install-sh +install_sh = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/install-sh libdir = ${exec_prefix}/lib libexecdir = ${exec_prefix}/libexec localedir = ${datarootdir}/locale @@ -349,9 +381,9 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps) exit 1;; \ esac; \ done; \ - echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \ - cd $(top_srcdir) && \ - $(AUTOMAKE) --foreign src/Makefile + echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \ + $(am__cd) $(top_srcdir) && \ + $(AUTOMAKE) --foreign src/Makefile .PRECIOUS: Makefile Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status @case '$?' in \ @@ -369,6 +401,7 @@ $(top_srcdir)/configure: $(am__configure_deps) cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh $(ACLOCAL_M4): $(am__aclocal_m4_deps) cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh +$(am__aclocal_m4_deps): config.h: stamp-h1 @if test ! -f $@; then \ @@ -380,7 +413,7 @@ stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status @rm -f stamp-h1 cd $(top_builddir) && $(SHELL) ./config.status src/config.h $(srcdir)/config.h.in: $(am__configure_deps) - cd $(top_srcdir) && $(AUTOHEADER) + ($(am__cd) $(top_srcdir) && $(AUTOHEADER)) rm -f stamp-h1 touch $@ @@ -391,23 +424,37 @@ clustalw_version.h: $(top_builddir)/config.status $(srcdir)/clustalw_version.h.i install-binPROGRAMS: $(bin_PROGRAMS) @$(NORMAL_INSTALL) test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)" - @list='$(bin_PROGRAMS)'; for p in $$list; do \ - p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \ - if test -f $$p \ - ; then \ - f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \ - echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) '$$p' '$(DESTDIR)$(bindir)/$$f'"; \ - $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \ - else :; fi; \ - done + @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \ + for p in $$list; do echo "$$p $$p"; done | \ + sed 's/$(EXEEXT)$$//' | \ + while read p p1; do if test -f $$p; \ + then echo "$$p"; echo "$$p"; else :; fi; \ + done | \ + sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \ + -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \ + sed 'N;N;N;s,\n, ,g' | \ + $(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \ + { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \ + if ($$2 == $$4) files[d] = files[d] " " $$1; \ + else { print "f", $$3 "/" $$4, $$1; } } \ + END { for (d in files) print "f", d, files[d] }' | \ + while read type dir files; do \ + if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \ + test -z "$$files" || { \ + echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \ + $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \ + } \ + ; done uninstall-binPROGRAMS: @$(NORMAL_UNINSTALL) - @list='$(bin_PROGRAMS)'; for p in $$list; do \ - f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \ - echo " rm -f '$(DESTDIR)$(bindir)/$$f'"; \ - rm -f "$(DESTDIR)$(bindir)/$$f"; \ - done + @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \ + files=`for p in $$list; do echo "$$p"; done | \ + sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \ + -e 's/$$/$(EXEEXT)/' `; \ + test -n "$$list" || exit 0; \ + echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \ + cd "$(DESTDIR)$(bindir)" && rm -f $$files clean-binPROGRAMS: -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS) @@ -475,728 +522,728 @@ include ./$(DEPDIR)/main.Po .cpp.o: $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< - mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po + $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po # source='$<' object='$@' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXXCOMPILE) -c -o $@ $< .cpp.obj: $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'` - mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po + $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po # source='$<' object='$@' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'` FullPairwiseAlign.o: ./pairwise/FullPairwiseAlign.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FullPairwiseAlign.o -MD -MP -MF $(DEPDIR)/FullPairwiseAlign.Tpo -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo '$(srcdir)/'`./pairwise/FullPairwiseAlign.cpp - mv -f $(DEPDIR)/FullPairwiseAlign.Tpo $(DEPDIR)/FullPairwiseAlign.Po + $(am__mv) $(DEPDIR)/FullPairwiseAlign.Tpo $(DEPDIR)/FullPairwiseAlign.Po # source='./pairwise/FullPairwiseAlign.cpp' object='FullPairwiseAlign.o' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo '$(srcdir)/'`./pairwise/FullPairwiseAlign.cpp FullPairwiseAlign.obj: ./pairwise/FullPairwiseAlign.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FullPairwiseAlign.obj -MD -MP -MF $(DEPDIR)/FullPairwiseAlign.Tpo -c -o FullPairwiseAlign.obj `if test -f './pairwise/FullPairwiseAlign.cpp'; then $(CYGPATH_W) './pairwise/FullPairwiseAlign.cpp'; else $(CYGPATH_W) '$(srcdir)/./pairwise/FullPairwiseAlign.cpp'; fi` - mv -f $(DEPDIR)/FullPairwiseAlign.Tpo $(DEPDIR)/FullPairwiseAlign.Po + $(am__mv) $(DEPDIR)/FullPairwiseAlign.Tpo $(DEPDIR)/FullPairwiseAlign.Po # source='./pairwise/FullPairwiseAlign.cpp' object='FullPairwiseAlign.obj' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FullPairwiseAlign.obj `if test -f './pairwise/FullPairwiseAlign.cpp'; then $(CYGPATH_W) './pairwise/FullPairwiseAlign.cpp'; else $(CYGPATH_W) '$(srcdir)/./pairwise/FullPairwiseAlign.cpp'; fi` FastPairwiseAlign.o: ./pairwise/FastPairwiseAlign.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FastPairwiseAlign.o -MD -MP -MF $(DEPDIR)/FastPairwiseAlign.Tpo -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo '$(srcdir)/'`./pairwise/FastPairwiseAlign.cpp - mv -f $(DEPDIR)/FastPairwiseAlign.Tpo $(DEPDIR)/FastPairwiseAlign.Po + $(am__mv) $(DEPDIR)/FastPairwiseAlign.Tpo $(DEPDIR)/FastPairwiseAlign.Po # source='./pairwise/FastPairwiseAlign.cpp' object='FastPairwiseAlign.o' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo '$(srcdir)/'`./pairwise/FastPairwiseAlign.cpp FastPairwiseAlign.obj: ./pairwise/FastPairwiseAlign.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FastPairwiseAlign.obj -MD -MP -MF $(DEPDIR)/FastPairwiseAlign.Tpo -c -o FastPairwiseAlign.obj `if test -f './pairwise/FastPairwiseAlign.cpp'; then $(CYGPATH_W) './pairwise/FastPairwiseAlign.cpp'; else $(CYGPATH_W) '$(srcdir)/./pairwise/FastPairwiseAlign.cpp'; fi` - mv -f $(DEPDIR)/FastPairwiseAlign.Tpo $(DEPDIR)/FastPairwiseAlign.Po + $(am__mv) $(DEPDIR)/FastPairwiseAlign.Tpo $(DEPDIR)/FastPairwiseAlign.Po # source='./pairwise/FastPairwiseAlign.cpp' object='FastPairwiseAlign.obj' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FastPairwiseAlign.obj `if test -f './pairwise/FastPairwiseAlign.cpp'; then $(CYGPATH_W) './pairwise/FastPairwiseAlign.cpp'; else $(CYGPATH_W) '$(srcdir)/./pairwise/FastPairwiseAlign.cpp'; fi` MSFFileParser.o: ./fileInput/MSFFileParser.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT MSFFileParser.o -MD -MP -MF $(DEPDIR)/MSFFileParser.Tpo -c -o MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo '$(srcdir)/'`./fileInput/MSFFileParser.cpp - mv -f $(DEPDIR)/MSFFileParser.Tpo $(DEPDIR)/MSFFileParser.Po + $(am__mv) $(DEPDIR)/MSFFileParser.Tpo $(DEPDIR)/MSFFileParser.Po # source='./fileInput/MSFFileParser.cpp' object='MSFFileParser.o' libtool=no \ # 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$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FileReader.obj -MD -MP -MF $(DEPDIR)/FileReader.Tpo -c -o FileReader.obj `if test -f './fileInput/FileReader.cpp'; then $(CYGPATH_W) './fileInput/FileReader.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/FileReader.cpp'; fi` - mv -f $(DEPDIR)/FileReader.Tpo $(DEPDIR)/FileReader.Po + $(am__mv) $(DEPDIR)/FileReader.Tpo $(DEPDIR)/FileReader.Po # source='./fileInput/FileReader.cpp' object='FileReader.obj' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FileReader.obj `if test -f './fileInput/FileReader.cpp'; then $(CYGPATH_W) './fileInput/FileReader.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/FileReader.cpp'; fi` PIRFileParser.o: ./fileInput/PIRFileParser.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PIRFileParser.o -MD -MP -MF $(DEPDIR)/PIRFileParser.Tpo -c -o PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo '$(srcdir)/'`./fileInput/PIRFileParser.cpp - mv -f $(DEPDIR)/PIRFileParser.Tpo $(DEPDIR)/PIRFileParser.Po + $(am__mv) $(DEPDIR)/PIRFileParser.Tpo $(DEPDIR)/PIRFileParser.Po # source='./fileInput/PIRFileParser.cpp' object='PIRFileParser.o' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo '$(srcdir)/'`./fileInput/PIRFileParser.cpp PIRFileParser.obj: ./fileInput/PIRFileParser.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PIRFileParser.obj -MD -MP -MF $(DEPDIR)/PIRFileParser.Tpo -c -o PIRFileParser.obj `if test -f './fileInput/PIRFileParser.cpp'; then $(CYGPATH_W) './fileInput/PIRFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/PIRFileParser.cpp'; fi` - mv -f $(DEPDIR)/PIRFileParser.Tpo $(DEPDIR)/PIRFileParser.Po + $(am__mv) $(DEPDIR)/PIRFileParser.Tpo $(DEPDIR)/PIRFileParser.Po # source='./fileInput/PIRFileParser.cpp' object='PIRFileParser.obj' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PIRFileParser.obj `if test -f './fileInput/PIRFileParser.cpp'; then $(CYGPATH_W) './fileInput/PIRFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/PIRFileParser.cpp'; fi` RSFFileParser.o: ./fileInput/RSFFileParser.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT RSFFileParser.o -MD -MP -MF $(DEPDIR)/RSFFileParser.Tpo -c -o RSFFileParser.o `test -f './fileInput/RSFFileParser.cpp' || echo '$(srcdir)/'`./fileInput/RSFFileParser.cpp - mv -f $(DEPDIR)/RSFFileParser.Tpo $(DEPDIR)/RSFFileParser.Po + $(am__mv) 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libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o RSFFileParser.obj `if test -f './fileInput/RSFFileParser.cpp'; then $(CYGPATH_W) './fileInput/RSFFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/RSFFileParser.cpp'; fi` GDEFileParser.o: ./fileInput/GDEFileParser.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT GDEFileParser.o -MD -MP -MF $(DEPDIR)/GDEFileParser.Tpo -c -o GDEFileParser.o `test -f './fileInput/GDEFileParser.cpp' || echo '$(srcdir)/'`./fileInput/GDEFileParser.cpp - mv -f $(DEPDIR)/GDEFileParser.Tpo $(DEPDIR)/GDEFileParser.Po + $(am__mv) $(DEPDIR)/GDEFileParser.Tpo $(DEPDIR)/GDEFileParser.Po # source='./fileInput/GDEFileParser.cpp' object='GDEFileParser.o' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) 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else $(CYGPATH_W) '$(srcdir)/./general/SymMatrix.cpp'; fi` Stats.o: ./general/Stats.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Stats.o -MD -MP -MF $(DEPDIR)/Stats.Tpo -c -o Stats.o `test -f './general/Stats.cpp' || echo '$(srcdir)/'`./general/Stats.cpp - mv -f $(DEPDIR)/Stats.Tpo $(DEPDIR)/Stats.Po + $(am__mv) $(DEPDIR)/Stats.Tpo $(DEPDIR)/Stats.Po # source='./general/Stats.cpp' object='Stats.o' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Stats.o `test -f './general/Stats.cpp' || echo '$(srcdir)/'`./general/Stats.cpp Stats.obj: ./general/Stats.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Stats.obj -MD -MP -MF $(DEPDIR)/Stats.Tpo -c -o Stats.obj `if test -f './general/Stats.cpp'; then $(CYGPATH_W) './general/Stats.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/Stats.cpp'; fi` - mv -f $(DEPDIR)/Stats.Tpo $(DEPDIR)/Stats.Po + $(am__mv) $(DEPDIR)/Stats.Tpo $(DEPDIR)/Stats.Po # source='./general/Stats.cpp' object='Stats.obj' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Stats.obj `if test -f './general/Stats.cpp'; then $(CYGPATH_W) './general/Stats.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/Stats.cpp'; fi` Help.o: ./Help.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Help.o -MD -MP -MF $(DEPDIR)/Help.Tpo -c -o Help.o `test -f './Help.cpp' || echo '$(srcdir)/'`./Help.cpp - mv -f $(DEPDIR)/Help.Tpo $(DEPDIR)/Help.Po + $(am__mv) $(DEPDIR)/Help.Tpo $(DEPDIR)/Help.Po # source='./Help.cpp' object='Help.o' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Help.o `test -f './Help.cpp' || echo '$(srcdir)/'`./Help.cpp Help.obj: ./Help.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Help.obj -MD -MP -MF $(DEPDIR)/Help.Tpo -c -o Help.obj `if test -f './Help.cpp'; then $(CYGPATH_W) './Help.cpp'; else $(CYGPATH_W) '$(srcdir)/./Help.cpp'; fi` - mv -f $(DEPDIR)/Help.Tpo $(DEPDIR)/Help.Po + $(am__mv) $(DEPDIR)/Help.Tpo $(DEPDIR)/Help.Po # source='./Help.cpp' object='Help.obj' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Help.obj `if test -f './Help.cpp'; then $(CYGPATH_W) './Help.cpp'; else $(CYGPATH_W) '$(srcdir)/./Help.cpp'; fi` Alignment.o: ./alignment/Alignment.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Alignment.o -MD -MP -MF $(DEPDIR)/Alignment.Tpo -c -o 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$(DEPDIR)/Alignment.Po # source='./alignment/Alignment.cpp' object='Alignment.obj' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Alignment.obj `if test -f './alignment/Alignment.cpp'; then $(CYGPATH_W) './alignment/Alignment.cpp'; else $(CYGPATH_W) '$(srcdir)/./alignment/Alignment.cpp'; fi` AlignmentOutput.o: ./alignment/AlignmentOutput.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT AlignmentOutput.o -MD -MP -MF $(DEPDIR)/AlignmentOutput.Tpo -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo '$(srcdir)/'`./alignment/AlignmentOutput.cpp - mv -f $(DEPDIR)/AlignmentOutput.Tpo $(DEPDIR)/AlignmentOutput.Po + $(am__mv) $(DEPDIR)/AlignmentOutput.Tpo $(DEPDIR)/AlignmentOutput.Po # source='./alignment/AlignmentOutput.cpp' object='AlignmentOutput.o' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo '$(srcdir)/'`./alignment/AlignmentOutput.cpp AlignmentOutput.obj: ./alignment/AlignmentOutput.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT AlignmentOutput.obj -MD -MP -MF $(DEPDIR)/AlignmentOutput.Tpo -c -o AlignmentOutput.obj `if test -f './alignment/AlignmentOutput.cpp'; then $(CYGPATH_W) './alignment/AlignmentOutput.cpp'; else $(CYGPATH_W) '$(srcdir)/./alignment/AlignmentOutput.cpp'; fi` - mv -f $(DEPDIR)/AlignmentOutput.Tpo $(DEPDIR)/AlignmentOutput.Po + $(am__mv) $(DEPDIR)/AlignmentOutput.Tpo $(DEPDIR)/AlignmentOutput.Po # source='./alignment/AlignmentOutput.cpp' object='AlignmentOutput.obj' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o AlignmentOutput.obj `if test -f './alignment/AlignmentOutput.cpp'; then $(CYGPATH_W) './alignment/AlignmentOutput.cpp'; else $(CYGPATH_W) '$(srcdir)/./alignment/AlignmentOutput.cpp'; fi` ObjectiveScore.o: ./alignment/ObjectiveScore.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ObjectiveScore.o -MD -MP -MF $(DEPDIR)/ObjectiveScore.Tpo -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo '$(srcdir)/'`./alignment/ObjectiveScore.cpp - mv -f $(DEPDIR)/ObjectiveScore.Tpo $(DEPDIR)/ObjectiveScore.Po + $(am__mv) $(DEPDIR)/ObjectiveScore.Tpo $(DEPDIR)/ObjectiveScore.Po # source='./alignment/ObjectiveScore.cpp' object='ObjectiveScore.o' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo 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fi` Sequence.o: ./alignment/Sequence.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Sequence.o -MD -MP -MF $(DEPDIR)/Sequence.Tpo -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo '$(srcdir)/'`./alignment/Sequence.cpp - mv -f $(DEPDIR)/Sequence.Tpo $(DEPDIR)/Sequence.Po + $(am__mv) $(DEPDIR)/Sequence.Tpo $(DEPDIR)/Sequence.Po # source='./alignment/Sequence.cpp' object='Sequence.o' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo '$(srcdir)/'`./alignment/Sequence.cpp Sequence.obj: ./alignment/Sequence.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Sequence.obj -MD -MP -MF $(DEPDIR)/Sequence.Tpo -c -o Sequence.obj `if test -f './alignment/Sequence.cpp'; then $(CYGPATH_W) 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$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT main.o -MD -MP -MF $(DEPDIR)/main.Tpo -c -o main.o `test -f './main.cpp' || echo '$(srcdir)/'`./main.cpp - mv -f $(DEPDIR)/main.Tpo $(DEPDIR)/main.Po + $(am__mv) $(DEPDIR)/main.Tpo $(DEPDIR)/main.Po # source='./main.cpp' object='main.o' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o main.o `test -f './main.cpp' || echo '$(srcdir)/'`./main.cpp main.obj: ./main.cpp $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT main.obj -MD -MP -MF $(DEPDIR)/main.Tpo -c -o main.obj `if test -f './main.cpp'; then $(CYGPATH_W) './main.cpp'; else $(CYGPATH_W) '$(srcdir)/./main.cpp'; fi` - mv -f $(DEPDIR)/main.Tpo $(DEPDIR)/main.Po + $(am__mv) $(DEPDIR)/main.Tpo $(DEPDIR)/main.Po # source='./main.cpp' object='main.obj' libtool=no \ # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o main.obj `if test -f './main.cpp'; then $(CYGPATH_W) './main.cpp'; else $(CYGPATH_W) '$(srcdir)/./main.cpp'; fi` @@ -1208,7 +1255,7 @@ main.obj: ./main.cpp # (which will cause the Makefiles to be regenerated when you run `make'); # (2) otherwise, pass the desired values on the `make' command line. $(RECURSIVE_TARGETS): - @failcom='exit 1'; \ + @fail= failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -1225,7 +1272,7 @@ $(RECURSIVE_TARGETS): else \ local_target="$$target"; \ fi; \ - (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ + ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ || eval $$failcom; \ done; \ if test "$$dot_seen" = "no"; then \ @@ -1233,7 +1280,7 @@ $(RECURSIVE_TARGETS): fi; test -z "$$fail" $(RECURSIVE_CLEAN_TARGETS): - @failcom='exit 1'; \ + @fail= failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -1259,16 +1306,16 @@ $(RECURSIVE_CLEAN_TARGETS): else \ local_target="$$target"; \ fi; \ - (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ + ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ || eval $$failcom; \ done && test -z "$$fail" tags-recursive: list='$(SUBDIRS)'; for subdir in $$list; do \ - test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \ + test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \ done ctags-recursive: list='$(SUBDIRS)'; for subdir in $$list; do \ - test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \ + test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \ done ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES) @@ -1283,7 +1330,7 @@ tags: TAGS TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ $(TAGS_FILES) $(LISP) - tags=; \ + set x; \ here=`pwd`; \ if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \ include_option=--etags-include; \ @@ -1295,7 +1342,7 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ list='$(SUBDIRS)'; for subdir in $$list; do \ if test "$$subdir" = .; then :; else \ test ! -f $$subdir/TAGS || \ - tags="$$tags $$include_option=$$here/$$subdir/TAGS"; \ + set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \ fi; \ done; \ list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \ @@ -1304,29 +1351,34 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ done | \ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ END { if (nonempty) { for (i in files) print i; }; }'`; \ - if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \ + shift; \ + if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \ test -n "$$unique" || unique=$$empty_fix; \ - $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ - $$tags $$unique; \ + if test $$# -gt 0; then \ + $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ + "$$@" $$unique; \ + else \ + $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ + $$unique; \ + fi; \ fi ctags: CTAGS CTAGS: ctags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ $(TAGS_FILES) $(LISP) - tags=; \ list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \ unique=`for i in $$list; do \ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ done | \ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ END { if (nonempty) { for (i in files) print i; }; }'`; \ - test -z "$(CTAGS_ARGS)$$tags$$unique" \ + test -z "$(CTAGS_ARGS)$$unique" \ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \ - $$tags $$unique + $$unique GTAGS: here=`$(am__cd) $(top_builddir) && pwd` \ - && cd $(top_srcdir) \ - && gtags -i $(GTAGS_ARGS) $$here + && $(am__cd) $(top_srcdir) \ + && gtags -i $(GTAGS_ARGS) "$$here" distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags @@ -1347,29 +1399,44 @@ distdir: $(DISTFILES) if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \ if test -d $$d/$$file; then \ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \ + if test -d "$(distdir)/$$file"; then \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ + fi; \ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \ - cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \ + cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ fi; \ - cp -pR $$d/$$file $(distdir)$$dir || exit 1; \ + cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \ else \ - test -f $(distdir)/$$file \ - || cp -p $$d/$$file $(distdir)/$$file \ + test -f "$(distdir)/$$file" \ + || cp -p $$d/$$file "$(distdir)/$$file" \ || exit 1; \ fi; \ done - list='$(DIST_SUBDIRS)'; for subdir in $$list; do \ + @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \ if test "$$subdir" = .; then :; else \ test -d "$(distdir)/$$subdir" \ || $(MKDIR_P) "$(distdir)/$$subdir" \ || exit 1; \ - distdir=`$(am__cd) $(distdir) && pwd`; \ - top_distdir=`$(am__cd) $(top_distdir) && pwd`; \ - (cd $$subdir && \ + fi; \ + done + @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \ + if test "$$subdir" = .; then :; else \ + dir1=$$subdir; dir2="$(distdir)/$$subdir"; \ + $(am__relativize); \ + new_distdir=$$reldir; \ + dir1=$$subdir; dir2="$(top_distdir)"; \ + $(am__relativize); \ + new_top_distdir=$$reldir; \ + echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \ + echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \ + ($(am__cd) $$subdir && \ $(MAKE) $(AM_MAKEFLAGS) \ - top_distdir="$$top_distdir" \ - distdir="$$distdir/$$subdir" \ + top_distdir="$$new_top_distdir" \ + distdir="$$new_distdir" \ am__remove_distdir=: \ am__skip_length_check=: \ + am__skip_mode_fix=: \ distdir) \ || exit 1; \ fi; \ @@ -1402,6 +1469,7 @@ clean-generic: distclean-generic: -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES) + -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES) maintainer-clean-generic: @echo "This command is intended for maintainers to use" @@ -1422,6 +1490,8 @@ dvi-am: html: html-recursive +html-am: + info: info-recursive info-am: @@ -1430,18 +1500,28 @@ install-data-am: install-dvi: install-dvi-recursive +install-dvi-am: + install-exec-am: install-binPROGRAMS install-html: install-html-recursive +install-html-am: + install-info: install-info-recursive +install-info-am: + install-man: install-pdf: install-pdf-recursive +install-pdf-am: + install-ps: install-ps-recursive +install-ps-am: + installcheck-am: maintainer-clean: maintainer-clean-recursive @@ -1463,8 +1543,8 @@ ps-am: uninstall-am: uninstall-binPROGRAMS -.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) install-am \ - install-strip +.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \ + ctags-recursive install-am install-strip tags-recursive .PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \ all all-am check check-am clean clean-binPROGRAMS \ @@ -1481,6 +1561,7 @@ uninstall-am: uninstall-binPROGRAMS mostlyclean-generic pdf pdf-am ps ps-am tags tags-recursive \ uninstall uninstall-am uninstall-binPROGRAMS + # 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/clustalw/src/Makefile.in b/binaries/src/clustalw/src/Makefile.in index 679917c..acb6d88 100644 --- a/binaries/src/clustalw/src/Makefile.in +++ b/binaries/src/clustalw/src/Makefile.in @@ -1,8 +1,9 @@ -# Makefile.in generated by automake 1.10.2 from Makefile.am. +# Makefile.in generated by automake 1.11.1 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. +# 2003, 2004, 2005, 2006, 2007, 2008, 2009 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. @@ -21,8 +22,9 @@ VPATH = @srcdir@ pkgdatadir = $(datadir)/@PACKAGE@ -pkglibdir = $(libdir)/@PACKAGE@ pkgincludedir = $(includedir)/@PACKAGE@ +pkglibdir = $(libdir)/@PACKAGE@ +pkglibexecdir = $(libexecdir)/@PACKAGE@ am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd install_sh_DATA = $(install_sh) -c -m 644 install_sh_PROGRAM = $(install_sh) -c @@ -49,8 +51,8 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ mkinstalldirs = $(install_sh) -d CONFIG_HEADER = config.h CONFIG_CLEAN_FILES = clustalw_version.h +CONFIG_CLEAN_VPATH_FILES = am__installdirs = "$(DESTDIR)$(bindir)" -binPROGRAMS_INSTALL = $(INSTALL_PROGRAM) PROGRAMS = $(bin_PROGRAMS) am_clustalw2_OBJECTS = FullPairwiseAlign.$(OBJEXT) \ FastPairwiseAlign.$(OBJEXT) MSFFileParser.$(OBJEXT) \ @@ -82,6 +84,7 @@ clustalw2_LDADD = $(LDADD) DEFAULT_INCLUDES = -I.@am__isrc@ depcomp = $(SHELL) $(top_srcdir)/depcomp am__depfiles_maybe = depfiles +am__mv = mv -f CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) CXXLD = $(CXX) @@ -102,10 +105,38 @@ RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \ ps-recursive uninstall-recursive RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \ distclean-recursive maintainer-clean-recursive +AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \ + $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \ + distdir ETAGS = etags CTAGS = ctags DIST_SUBDIRS = $(SUBDIRS) DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) +am__relativize = \ + dir0=`pwd`; \ + sed_first='s,^\([^/]*\)/.*$$,\1,'; \ + sed_rest='s,^[^/]*/*,,'; \ + sed_last='s,^.*/\([^/]*\)$$,\1,'; \ + sed_butlast='s,/*[^/]*$$,,'; \ + while test -n "$$dir1"; do \ + first=`echo "$$dir1" | sed -e "$$sed_first"`; \ + if test "$$first" != "."; then \ + if test "$$first" = ".."; then \ + dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \ + dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \ + else \ + first2=`echo "$$dir2" | sed -e "$$sed_first"`; \ + if test "$$first2" = "$$first"; then \ + dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \ + else \ + dir2="../$$dir2"; \ + fi; \ + dir0="$$dir0"/"$$first"; \ + fi; \ + fi; \ + dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \ + done; \ + reldir="$$dir2" ACLOCAL = @ACLOCAL@ AMTAR = @AMTAR@ AUTOCONF = @AUTOCONF@ @@ -148,6 +179,7 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ +PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ RANLIB = @RANLIB@ @@ -349,9 +381,9 @@ $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps) exit 1;; \ esac; \ done; \ - echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \ - cd $(top_srcdir) && \ - $(AUTOMAKE) --foreign src/Makefile + echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \ + $(am__cd) $(top_srcdir) && \ + $(AUTOMAKE) --foreign src/Makefile .PRECIOUS: Makefile Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status @case '$?' in \ @@ -369,6 +401,7 @@ $(top_srcdir)/configure: $(am__configure_deps) cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh $(ACLOCAL_M4): $(am__aclocal_m4_deps) cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh +$(am__aclocal_m4_deps): config.h: stamp-h1 @if test ! -f $@; then \ @@ -380,7 +413,7 @@ stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status @rm -f stamp-h1 cd $(top_builddir) && $(SHELL) ./config.status src/config.h $(srcdir)/config.h.in: $(am__configure_deps) - cd $(top_srcdir) && $(AUTOHEADER) + ($(am__cd) $(top_srcdir) && $(AUTOHEADER)) rm -f stamp-h1 touch $@ @@ -391,23 +424,37 @@ clustalw_version.h: $(top_builddir)/config.status $(srcdir)/clustalw_version.h.i install-binPROGRAMS: $(bin_PROGRAMS) @$(NORMAL_INSTALL) test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)" - @list='$(bin_PROGRAMS)'; for p in $$list; do \ - p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \ - if test -f $$p \ - ; then \ - f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \ - echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) '$$p' '$(DESTDIR)$(bindir)/$$f'"; \ - $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \ - else :; fi; \ - done + @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \ + for p in $$list; do echo "$$p $$p"; done | \ + sed 's/$(EXEEXT)$$//' | \ + while read p p1; do if test -f $$p; \ + then echo "$$p"; echo "$$p"; else :; fi; \ + done | \ + sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \ + -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \ + sed 'N;N;N;s,\n, ,g' | \ + $(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \ + { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \ + if ($$2 == $$4) files[d] = files[d] " " $$1; \ + else { print "f", $$3 "/" $$4, $$1; } } \ + END { for (d in files) print "f", d, files[d] }' | \ + while read type dir files; do \ + if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \ + test -z "$$files" || { \ + echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \ + $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \ + } \ + ; done uninstall-binPROGRAMS: @$(NORMAL_UNINSTALL) - @list='$(bin_PROGRAMS)'; for p in $$list; do \ - f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \ - echo " rm -f '$(DESTDIR)$(bindir)/$$f'"; \ - rm -f "$(DESTDIR)$(bindir)/$$f"; \ - done + @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \ + files=`for p in $$list; do echo "$$p"; done | \ + sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \ + -e 's/$$/$(EXEEXT)/' `; \ + test -n "$$list" || exit 0; \ + echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \ + cd "$(DESTDIR)$(bindir)" && rm -f $$files clean-binPROGRAMS: -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS) @@ -475,728 +522,728 @@ distclean-compile: .cpp.o: @am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< -@am__fastdepCXX_TRUE@ mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po +@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po @AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@ @AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@ @am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $< .cpp.obj: @am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'` -@am__fastdepCXX_TRUE@ mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po +@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo 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+@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/main.Tpo $(DEPDIR)/main.Po @AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='./main.cpp' object='main.obj' libtool=no @AMDEPBACKSLASH@ @AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@ @am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o main.obj `if test -f './main.cpp'; then $(CYGPATH_W) './main.cpp'; else $(CYGPATH_W) '$(srcdir)/./main.cpp'; fi` @@ -1208,7 +1255,7 @@ main.obj: ./main.cpp # (which will cause the Makefiles to be regenerated when you run `make'); # (2) otherwise, pass the desired values on the `make' command line. $(RECURSIVE_TARGETS): - @failcom='exit 1'; \ + @fail= failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -1225,7 +1272,7 @@ $(RECURSIVE_TARGETS): else \ local_target="$$target"; \ fi; \ - (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ + ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ || eval $$failcom; \ done; \ if test "$$dot_seen" = "no"; then \ @@ -1233,7 +1280,7 @@ $(RECURSIVE_TARGETS): fi; test -z "$$fail" $(RECURSIVE_CLEAN_TARGETS): - @failcom='exit 1'; \ + @fail= failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -1259,16 +1306,16 @@ $(RECURSIVE_CLEAN_TARGETS): else \ local_target="$$target"; \ fi; \ - (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ + ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \ || eval $$failcom; \ done && test -z "$$fail" tags-recursive: list='$(SUBDIRS)'; for subdir in $$list; do \ - test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \ + test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \ done ctags-recursive: list='$(SUBDIRS)'; for subdir in $$list; do \ - test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \ + test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \ done ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES) @@ -1283,7 +1330,7 @@ tags: TAGS TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ $(TAGS_FILES) $(LISP) - tags=; \ + set x; \ here=`pwd`; \ if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \ include_option=--etags-include; \ @@ -1295,7 +1342,7 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ list='$(SUBDIRS)'; for subdir in $$list; do \ if test "$$subdir" = .; then :; else \ test ! -f $$subdir/TAGS || \ - tags="$$tags $$include_option=$$here/$$subdir/TAGS"; \ + set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \ fi; \ done; \ list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \ @@ -1304,29 +1351,34 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ done | \ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ END { if (nonempty) { for (i in files) print i; }; }'`; \ - if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \ + shift; \ + if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \ test -n "$$unique" || unique=$$empty_fix; \ - $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ - $$tags $$unique; \ + if test $$# -gt 0; then \ + $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ + "$$@" $$unique; \ + else \ + $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \ + $$unique; \ + fi; \ fi ctags: CTAGS CTAGS: ctags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \ $(TAGS_FILES) $(LISP) - tags=; \ list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \ unique=`for i in $$list; do \ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ done | \ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ END { if (nonempty) { for (i in files) print i; }; }'`; \ - test -z "$(CTAGS_ARGS)$$tags$$unique" \ + test -z "$(CTAGS_ARGS)$$unique" \ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \ - $$tags $$unique + $$unique GTAGS: here=`$(am__cd) $(top_builddir) && pwd` \ - && cd $(top_srcdir) \ - && gtags -i $(GTAGS_ARGS) $$here + && $(am__cd) $(top_srcdir) \ + && gtags -i $(GTAGS_ARGS) "$$here" distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags @@ -1347,29 +1399,44 @@ distdir: $(DISTFILES) if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \ if test -d $$d/$$file; then \ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \ + if test -d "$(distdir)/$$file"; then \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ + fi; \ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \ - cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \ + cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \ + find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \ fi; \ - cp -pR $$d/$$file $(distdir)$$dir || exit 1; \ + cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \ else \ - test -f $(distdir)/$$file \ - || cp -p $$d/$$file $(distdir)/$$file \ + test -f "$(distdir)/$$file" \ + || cp -p $$d/$$file "$(distdir)/$$file" \ || exit 1; \ fi; \ done - list='$(DIST_SUBDIRS)'; for subdir in $$list; do \ + @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \ if test "$$subdir" = .; then :; else \ test -d "$(distdir)/$$subdir" \ || $(MKDIR_P) "$(distdir)/$$subdir" \ || exit 1; \ - distdir=`$(am__cd) $(distdir) && pwd`; \ - top_distdir=`$(am__cd) $(top_distdir) && pwd`; \ - (cd $$subdir && \ + fi; \ + done + @list='$(DIST_SUBDIRS)'; for subdir in $$list; do \ + if test "$$subdir" = .; then :; else \ + dir1=$$subdir; dir2="$(distdir)/$$subdir"; \ + $(am__relativize); \ + new_distdir=$$reldir; \ + dir1=$$subdir; dir2="$(top_distdir)"; \ + $(am__relativize); \ + new_top_distdir=$$reldir; \ + echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \ + echo " am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \ + ($(am__cd) $$subdir && \ $(MAKE) $(AM_MAKEFLAGS) \ - top_distdir="$$top_distdir" \ - distdir="$$distdir/$$subdir" \ + top_distdir="$$new_top_distdir" \ + distdir="$$new_distdir" \ am__remove_distdir=: \ am__skip_length_check=: \ + am__skip_mode_fix=: \ distdir) \ || exit 1; \ fi; \ @@ -1402,6 +1469,7 @@ clean-generic: distclean-generic: -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES) + -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES) maintainer-clean-generic: @echo "This command is intended for maintainers to use" @@ -1422,6 +1490,8 @@ dvi-am: html: html-recursive +html-am: + info: info-recursive info-am: @@ -1430,18 +1500,28 @@ install-data-am: install-dvi: install-dvi-recursive +install-dvi-am: + install-exec-am: install-binPROGRAMS install-html: install-html-recursive +install-html-am: + install-info: install-info-recursive +install-info-am: + install-man: install-pdf: install-pdf-recursive +install-pdf-am: + install-ps: install-ps-recursive +install-ps-am: + installcheck-am: maintainer-clean: maintainer-clean-recursive @@ -1463,8 +1543,8 @@ ps-am: uninstall-am: uninstall-binPROGRAMS -.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) install-am \ - install-strip +.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \ + ctags-recursive install-am install-strip tags-recursive .PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \ all all-am check check-am clean clean-binPROGRAMS \ @@ -1481,6 +1561,7 @@ uninstall-am: uninstall-binPROGRAMS mostlyclean-generic pdf pdf-am ps ps-am tags tags-recursive \ uninstall uninstall-am uninstall-binPROGRAMS + # 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/clustalw/src/MyersMillerProfileAlign.o b/binaries/src/clustalw/src/MyersMillerProfileAlign.o new file mode 100644 index 0000000..b01e857 Binary files /dev/null and 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b/binaries/src/clustalw/src/UserParameters.o new file mode 100644 index 0000000..25e7ee2 Binary files /dev/null and b/binaries/src/clustalw/src/UserParameters.o differ diff --git a/binaries/src/clustalw/src/Utility.o b/binaries/src/clustalw/src/Utility.o new file mode 100644 index 0000000..04e3519 Binary files /dev/null and b/binaries/src/clustalw/src/Utility.o differ diff --git a/binaries/src/clustalw/src/VectorOutOfRange.o b/binaries/src/clustalw/src/VectorOutOfRange.o new file mode 100644 index 0000000..97bdbaf Binary files /dev/null and b/binaries/src/clustalw/src/VectorOutOfRange.o differ diff --git a/binaries/src/clustalw/src/alignment/Alignment.cpp b/binaries/src/clustalw/src/alignment/Alignment.cpp index 1b54c20..8101a90 100644 --- a/binaries/src/clustalw/src/alignment/Alignment.cpp +++ b/binaries/src/clustalw/src/alignment/Alignment.cpp @@ -806,6 +806,7 @@ void Alignment::calculateMaxLengths() /* * This function checks to see if all names are different. It returns true if they * are all different, and false if there are 2 the same. + * currently quadratic - would be nice to speed up */ bool Alignment::checkAllNamesDifferent(string *offendingSeq) { diff --git a/binaries/src/clustalw/src/alignment/AlignmentOutput.cpp b/binaries/src/clustalw/src/alignment/AlignmentOutput.cpp index a0b9de3..2e658ce 100644 --- a/binaries/src/clustalw/src/alignment/AlignmentOutput.cpp +++ b/binaries/src/clustalw/src/alignment/AlignmentOutput.cpp @@ -1067,6 +1067,9 @@ void AlignmentOutput::nexusOut(Alignment* alignPtr, outputRegion partToOutput) (*nexusOutFile) << "dimensions ntax=" << alignPtr->getNumSeqs() << " nchar=" << length << ";\n"; //- nige (*nexusOutFile) << "format missing=?\n"; + + // removed - bugzilla bug 204 + /* (*nexusOutFile) << "symbols=\""; for(i = 0; i <= userParameters->getMaxAA(); i++) @@ -1074,6 +1077,8 @@ void AlignmentOutput::nexusOut(Alignment* alignPtr, outputRegion partToOutput) (*nexusOutFile) << userParameters->getAminoAcidCode(i); } (*nexusOutFile) << "\"\n"; + */ + (*nexusOutFile) << "interleave datatype="; bool _dnaFlag = userParameters->getDNAFlag(); string _type = _dnaFlag ? "DNA " : "PROTEIN "; diff --git a/binaries/src/clustalw/src/clustalw2 b/binaries/src/clustalw/src/clustalw2 index 3aa22fa..23a9d5a 100644 Binary files a/binaries/src/clustalw/src/clustalw2 and b/binaries/src/clustalw/src/clustalw2 differ diff --git a/binaries/src/clustalw/src/clustalw_version.h b/binaries/src/clustalw/src/clustalw_version.h index 7120cde..e83b371 100644 --- a/binaries/src/clustalw/src/clustalw_version.h +++ b/binaries/src/clustalw/src/clustalw_version.h @@ -3,7 +3,7 @@ #define CLUSTALW_NAME "ClustalW" -#define CLUSTALW_VERSION "2.0.12" +#define CLUSTALW_VERSION "2.1" #endif diff --git a/binaries/src/clustalw/src/config.h b/binaries/src/clustalw/src/config.h index 06e44ee..2640290 100644 --- a/binaries/src/clustalw/src/config.h +++ b/binaries/src/clustalw/src/config.h @@ -63,19 +63,22 @@ #define PACKAGE_NAME "clustalw" /* Define to the full name and version of this package. */ -#define PACKAGE_STRING "clustalw 2.0.12" +#define PACKAGE_STRING "clustalw 2.1" /* Define to the one symbol short name of this package. */ #define PACKAGE_TARNAME "clustalw" +/* Define to the home page for this package. */ +#define PACKAGE_URL "" + /* Define to the version of this package. */ -#define PACKAGE_VERSION "2.0.12" +#define PACKAGE_VERSION "2.1" /* Define to 1 if you have the ANSI C header files. */ #define STDC_HEADERS 1 /* Version number of package */ -#define VERSION "2.0.12" +#define VERSION "2.1" /* Define to empty if `const' does not conform to ANSI C. */ /* #undef const */ diff --git a/binaries/src/clustalw/src/config.h.in b/binaries/src/clustalw/src/config.h.in index 39a1210..662ce6e 100644 --- a/binaries/src/clustalw/src/config.h.in +++ b/binaries/src/clustalw/src/config.h.in @@ -67,6 +67,9 @@ /* Define to the one symbol short name of this package. */ #undef PACKAGE_TARNAME +/* Define to the home page for this package. */ +#undef PACKAGE_URL + /* Define to the version of this package. */ #undef PACKAGE_VERSION diff --git a/binaries/src/clustalw/src/fileInput/ClustalFileParser.cpp b/binaries/src/clustalw/src/fileInput/ClustalFileParser.cpp index d63b6b6..ea312c0 100644 --- a/binaries/src/clustalw/src/fileInput/ClustalFileParser.cpp +++ b/binaries/src/clustalw/src/fileInput/ClustalFileParser.cpp @@ -52,7 +52,7 @@ ClustalFileParser::~ClustalFileParser() } - Sequence ClustalFileParser::getSeq(int seqNum, string *offendingSeq) +Sequence ClustalFileParser::getSeq(int seqNum, string *offendingSeq) { char line[MAXLINE + 1]; line[0] = EOS; @@ -148,6 +148,9 @@ ClustalFileParser::~ClustalFileParser() } freeFileResources(_fileIn); + // getSecStructure(vector& gapPenaltyMask, + // vector& secStructMask, string& secStructName, int &structPenalties, int length) + if ((int)characterSeq.length() > userParameters->getMaxAllowedSeqLength()) { parseExitCode=SEQUENCETOOBIG; @@ -237,6 +240,12 @@ int ClustalFileParser::countSeqs() void ClustalFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, string& secStructName, int &structPenalties, int length) { + bool guigetss = false; + if(userParameters->getProfileNum() == 1 && userParameters->getStructPenalties1()) + guigetss = true; + if(userParameters->getProfileNum() == 2 && userParameters->getStructPenalties2()) + guigetss = true; + char title[MAXLINE + 1]; title[0] = '\0'; char line[MAXLINE + 1]; @@ -318,7 +327,7 @@ void ClustalFileParser::getSecStructure(vector& gapPenaltyMask, utilityObject->rTrim(sname); utilityObject->blankToUnderscore(sname); - if (userParameters->getInteractive()) + if (userParameters->getInteractive() && !userParameters->getGui()) { strcpy(title, "Found secondary structure in alignment file: "); strcat(title, sname); @@ -329,7 +338,7 @@ void ClustalFileParser::getSecStructure(vector& gapPenaltyMask, { (*lin2) = 'y'; } - if ((*lin2 != 'n') && (*lin2 != 'N')) + if (guigetss || ((*lin2 != 'n') && (*lin2 != 'N'))) { structPenalties = SECST; struct_index = ix; @@ -374,7 +383,7 @@ void ClustalFileParser::getSecStructure(vector& gapPenaltyMask, utilityObject->rTrim(sname); utilityObject->blankToUnderscore(sname); - if (userParameters->getInteractive()) + if (userParameters->getInteractive() && !userParameters->getGui()) { strcpy(title, "Found gap penalty mask in alignment file: "); strcat(title, sname); @@ -385,7 +394,7 @@ void ClustalFileParser::getSecStructure(vector& gapPenaltyMask, { (*lin2) = 'y'; } - if ((*lin2 != 'n') && (*lin2 != 'N')) + if (guigetss || ((*lin2 != 'n') && (*lin2 != 'N'))) { structPenalties = GMASK; struct_index = ix; @@ -563,7 +572,7 @@ void ClustalFileParser::getSecStructure(vector& gapPenaltyMask, } if (!_fileIn->getline(line, MAXLINE + 1)) { - freeFileResources(_fileIn); + freeFileResources(_fileIn); return ; } } diff --git a/binaries/src/clustalw/src/fileInput/EMBLFileParser.cpp b/binaries/src/clustalw/src/fileInput/EMBLFileParser.cpp index 357524f..f33cc92 100644 --- a/binaries/src/clustalw/src/fileInput/EMBLFileParser.cpp +++ b/binaries/src/clustalw/src/fileInput/EMBLFileParser.cpp @@ -240,6 +240,12 @@ int EMBLFileParser::countSeqs() */ void EMBLFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, string& secStructName, int &structPenalties, int length) { + bool guigetss = false; + if(userParameters->getProfileNum() == 1 && userParameters->getStructPenalties1()) + guigetss = true; + if(userParameters->getProfileNum() == 2 && userParameters->getStructPenalties2()) + guigetss = true; + char _title[MAXLINE + 1]; char _line[MAXLINE + 1]; char _lin2[MAXLINE + 1]; @@ -298,7 +304,7 @@ void EMBLFileParser::getSecStructure(vector& gapPenaltyMask, vector& sscanf(_line + 2, "%s", _feature); if (strcmp(_feature, "HELIX") == 0 || strcmp(_feature, "STRAND") == 0) { - if (userParameters->getInteractive()) + if (userParameters->getInteractive() && !userParameters->getGui()) { strcpy(_title, "Found secondary structure in alignment file: "); @@ -310,7 +316,7 @@ void EMBLFileParser::getSecStructure(vector& gapPenaltyMask, vector& { (*_lin2) = 'y'; } - if ((*_lin2 != 'n') && (*_lin2 != 'N')) + if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N'))) { structPenalties = SECST; for (i = 0; i < length; i++) @@ -348,7 +354,7 @@ void EMBLFileParser::getSecStructure(vector& gapPenaltyMask, vector& { (*_lin2) = 'y'; } - if ((*_lin2 != 'n') && (*_lin2 != 'N')) + if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N'))) { structPenalties = GMASK; for (i = 0; i < length; i++) diff --git a/binaries/src/clustalw/src/fileInput/FileReader.cpp b/binaries/src/clustalw/src/fileInput/FileReader.cpp index 957f1aa..57b628d 100644 --- a/binaries/src/clustalw/src/fileInput/FileReader.cpp +++ b/binaries/src/clustalw/src/fileInput/FileReader.cpp @@ -193,7 +193,6 @@ bool FileReader::noEmptySequence(vector seqVector, string *offendingSe } userParameters->setSeqName(line); - // NOTE I made a change here because the profile2Name was not stored! if(userParameters->getProfileNum() == 2 && userParameters->getProfile2Name().empty()) @@ -223,7 +222,7 @@ bool FileReader::noEmptySequence(vector seqVector, string *offendingSe if (noEmptySequence(seqRangeVector, offendingSeq) == false) { return EMPTYSEQUENCE; // Error there are same names. } - + for (int i=0; i < (int)seqRangeVector.size(); i++) { // Andreas Wilm (UCD): fixed wrong default output order // which is important when no alignment (convert!) is done @@ -362,6 +361,7 @@ int FileReader::profileInput(Alignment *alignPtr) } else { + // first seq to be read = profile1_nseqs + 1 int profile1NumOfSeqs = alignPtr->getNumSeqs(); code = readSeqs(alignPtr, profile1NumOfSeqs + 1, &offendingSeq); diff --git a/binaries/src/clustalw/src/fileInput/GDEFileParser.cpp b/binaries/src/clustalw/src/fileInput/GDEFileParser.cpp index 9df9a4a..e430d61 100644 --- a/binaries/src/clustalw/src/fileInput/GDEFileParser.cpp +++ b/binaries/src/clustalw/src/fileInput/GDEFileParser.cpp @@ -218,6 +218,12 @@ int GDEFileParser::countSeqs() void GDEFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, string& secStructName, int &structPenalties, int length) { + bool guigetss = false; + if(userParameters->getProfileNum() == 1 && userParameters->getStructPenalties1()) + guigetss = true; + if(userParameters->getProfileNum() == 2 && userParameters->getStructPenalties2()) + guigetss = true; + char _title[MAXLINE + 1]; char _line[MAXLINE + 1]; char _lin2[MAXLINE + 1]; @@ -289,7 +295,7 @@ void GDEFileParser::getSecStructure(vector& gapPenaltyMask, vector& utilityObject->blankToUnderscore(_sname); secStructName = string(_sname); - if (userParameters->getInteractive()) + if (userParameters->getInteractive() && !userParameters->getGui()) { strcpy(_title, "Found secondary structure in alignment file: "); strcat(_title, _sname); @@ -300,7 +306,7 @@ void GDEFileParser::getSecStructure(vector& gapPenaltyMask, vector& { (*_lin2) = 'y'; } - if ((*_lin2 != 'n') && (*_lin2 != 'N')) + if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N'))) { structPenalties = SECST; for (i = 0; i < length; i++) @@ -371,7 +377,7 @@ void GDEFileParser::getSecStructure(vector& gapPenaltyMask, vector& utilityObject->blankToUnderscore(_sname); secStructName = string(_sname); - if (userParameters->getInteractive()) + if (userParameters->getInteractive() && !userParameters->getGui()) { strcpy(_title, "Found gap penalty mask in alignment file: "); strcat(_title, _sname); @@ -382,7 +388,7 @@ void GDEFileParser::getSecStructure(vector& gapPenaltyMask, vector& { (*_lin2) = 'y'; } - if ((*_lin2 != 'n') && (*_lin2 != 'N')) + if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N'))) { structPenalties = GMASK; for (i = 0; i < length; i++) diff --git a/binaries/src/clustalw/src/fileInput/MSFFileParser.cpp b/binaries/src/clustalw/src/fileInput/MSFFileParser.cpp index 3135ee7..7336826 100644 --- a/binaries/src/clustalw/src/fileInput/MSFFileParser.cpp +++ b/binaries/src/clustalw/src/fileInput/MSFFileParser.cpp @@ -216,7 +216,7 @@ int MSFFileParser::countSeqs() while (_fileIn->getline(_line, MAXLINE + 1)) { - if (utilityObject->blankLine(_line)) + if (utilityObject->blankLineNumericLabel(_line)) { _fileIn->close(); return _numSeqs; diff --git a/binaries/src/clustalw/src/fileInput/RSFFileParser.cpp b/binaries/src/clustalw/src/fileInput/RSFFileParser.cpp index 9662f50..b76f8af 100644 --- a/binaries/src/clustalw/src/fileInput/RSFFileParser.cpp +++ b/binaries/src/clustalw/src/fileInput/RSFFileParser.cpp @@ -240,6 +240,12 @@ int RSFFileParser::countSeqs() void RSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, string& secStructName, int &structPenalties, int length) { + bool guigetss = false; + if(userParameters->getProfileNum() == 1 && userParameters->getStructPenalties1()) + guigetss = true; + if(userParameters->getProfileNum() == 2 && userParameters->getStructPenalties2()) + guigetss = true; + char _title[MAXLINE + 1]; char _line[MAXLINE + 1]; char _lin2[MAXLINE + 1]; @@ -307,7 +313,7 @@ void RSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& { if (keyword(_line, "feature")) { - if (userParameters->getInteractive()) + if (userParameters->getInteractive() && !userParameters->getGui()) { strcpy(_title, "Found secondary structure in alignment file: "); strcat(_title, _sname); @@ -318,7 +324,7 @@ void RSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& { (*_lin2) = 'y'; } - if ((*_lin2 != 'n') && (*_lin2 != 'N')) + if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N'))) { structPenalties = SECST; secStructMask.assign(length, '.'); diff --git a/binaries/src/clustalw/src/general/UserParameters.cpp b/binaries/src/clustalw/src/general/UserParameters.cpp index 3630e3d..c217894 100644 --- a/binaries/src/clustalw/src/general/UserParameters.cpp +++ b/binaries/src/clustalw/src/general/UserParameters.cpp @@ -41,6 +41,7 @@ UserParameters::UserParameters(bool log) //revisionLevel = CLU_SHORT_VERSION_STRING; revisionLevel = CLUSTALW_VERSION; interactive = false; + gui = false; seqName = ""; DNAGapOpen = 15.0; @@ -579,6 +580,11 @@ void UserParameters::setInteractive(bool value) interactive = value; } +void UserParameters::setGui(bool value) +{ + gui = value; +} + void UserParameters::setGapOpen(float value) { gapOpen = value; diff --git a/binaries/src/clustalw/src/general/UserParameters.h b/binaries/src/clustalw/src/general/UserParameters.h index 1e8d2a8..cf49142 100644 --- a/binaries/src/clustalw/src/general/UserParameters.h +++ b/binaries/src/clustalw/src/general/UserParameters.h @@ -46,6 +46,8 @@ class UserParameters void setRevisionLevel(string value); bool getInteractive(){return interactive;}; void setInteractive(bool value); + bool getGui(){return gui;}; + void setGui(bool value); float getGapOpen(){return gapOpen;}; void setGapOpen(float value); float getGapExtend(){return gapExtend;}; @@ -335,6 +337,7 @@ class UserParameters string revisionLevel; bool interactive; + bool gui; float gapOpen; float gapExtend; float PWGapOpen; diff --git a/binaries/src/clustalw/src/general/Utility.cpp b/binaries/src/clustalw/src/general/Utility.cpp index 619d62a..974a53c 100644 --- a/binaries/src/clustalw/src/general/Utility.cpp +++ b/binaries/src/clustalw/src/general/Utility.cpp @@ -281,6 +281,41 @@ bool Utility::blankLine(char *line) /** * + * @param line + * @return + */ +// Utility::blankLine thinks that a line like +// 2125209 .......... .......... .......... .......... .......... +// is blank, causing problems for countSeqs when sequence labels are numeric +// this function will return false if there's a number and a bunch of dots (not ideal, i know) +bool Utility::blankLineNumericLabel(char *line) +{ + int i; + int dots = 0; + bool isnumeric = false; + + for (i = 0; line[i] != '\n' && line[i] != EOS; i++) + { + if (isdigit(line[i]) || isspace(line[i]) || (line[i] == '*') || + (line[i] == ':') || (line[i] == '.')) + ; + else + { + return false; + } + if(line[i] == '.') + dots++; + if(isdigit(line[i])) + isnumeric = true; + } + if(isnumeric && dots > 10) + return false; + else + return true; +} + +/** + * * @param str * @param path */ diff --git a/binaries/src/clustalw/src/general/Utility.h b/binaries/src/clustalw/src/general/Utility.h index b3371e6..79da8d4 100644 --- a/binaries/src/clustalw/src/general/Utility.h +++ b/binaries/src/clustalw/src/general/Utility.h @@ -36,6 +36,7 @@ class Utility bool lineType(char *line, const char *code); bool blankLine(char *line); + bool blankLineNumericLabel(char *line); void getPath(string str, string *path); diff --git a/binaries/src/clustalw/src/interface/CommandLineParser.cpp b/binaries/src/clustalw/src/interface/CommandLineParser.cpp index 3d58c58..b970c70 100644 --- a/binaries/src/clustalw/src/interface/CommandLineParser.cpp +++ b/binaries/src/clustalw/src/interface/CommandLineParser.cpp @@ -116,7 +116,7 @@ CommandLineParser::CommandLineParser(StringArray* args, bool xmenus) seqNoArg = new StringArray(3); seqNoRangeArg = new StringArray(3); scoreArg = new StringArray(3); - outputArg = new StringArray(7); + outputArg = new StringArray(8); outputTreeArg = new StringArray(5); outputSecStrArg = new StringArray(5); cmdLineType = new StringArray(6); @@ -167,7 +167,8 @@ CommandLineParser::CommandLineParser(StringArray* args, bool xmenus) (*outputArg)[3] = "phylip"; (*outputArg)[4] = "nexus"; (*outputArg)[5] = "fasta"; - (*outputArg)[6] = ""; + (*outputArg)[6] = "clustal"; + (*outputArg)[7] = ""; (*outputTreeArg)[0] = "nj"; (*outputTreeArg)[1] = "phylip"; @@ -1479,8 +1480,8 @@ void CommandLineParser::setOptionalParam() #endif if((*paramArg)[setOutput].length() > 0) { - temp = findMatch((*paramArg)[setOutput], outputArg, 6); - if (temp >= 0 && temp <= 5) + temp = findMatch((*paramArg)[setOutput], outputArg, 7); + if (temp >= 0 && temp <= 6) { userParameters->setOutputClustal(false); userParameters->setOutputGCG(false); @@ -1507,9 +1508,12 @@ void CommandLineParser::setOptionalParam() case 4: // NEXUS userParameters->setOutputNexus(true); break; - case 5: // NEXUS + case 5: // FASTA userParameters->setOutputFasta(true); break; + case 6: // CLUSTAL + userParameters->setOutputClustal(true); + break; default: // FIXME AW: 1.83 behaves the same, but shouldnt // we exit here? diff --git a/binaries/src/clustalw/src/main.o b/binaries/src/clustalw/src/main.o new file mode 100644 index 0000000..b84f04d Binary files /dev/null and b/binaries/src/clustalw/src/main.o differ diff --git a/binaries/src/clustalw/src/tree/ClusterTree.cpp b/binaries/src/clustalw/src/tree/ClusterTree.cpp index bbd03ce..828e471 100644 --- a/binaries/src/clustalw/src/tree/ClusterTree.cpp +++ b/binaries/src/clustalw/src/tree/ClusterTree.cpp @@ -73,17 +73,23 @@ void ClusterTree::distanceMatrixOutput(ofstream* outFile, clustalw::DistMatrix* void ClusterTree::overspillMessage(int overspill,int totalDists) { - std::stringstream ssOverSpill; - ssOverSpill << overspill << " of the distances out of a total of " << totalDists - << "\n were out of range for the distance correction." << "\n" - << "\n SUGGESTIONS: 1) remove the most distant sequences" - << "\n or 2) use the PHYLIP package" - << "\n or 3) turn off the correction." - << "\n Note: Use option 3 with caution! With this degree" - << "\n of divergence you will have great difficulty" - << "\n getting robust and reliable trees." << "\n\n"; + std::ostringstream ssOverSpill; + std::ostringstream ssTotalDists; string message; - ssOverSpill >> message; + + ssOverSpill << overspill; + message += ssOverSpill.str(); + message += " of the distances out of a total of "; + ssTotalDists << totalDists; + message += ssTotalDists.str(); + message += "\n were out of range for the distance correction.\n" + "\n SUGGESTIONS: 1) remove the most distant sequences" + "\n or 2) use the PHYLIP package" + "\n or 3) turn off the correction." + "\n Note: Use option 3 with caution! With this degree" + "\n of divergence you will have great difficulty" + "\n getting robust and reliable trees.\n\n"; + clustalw::utilityObject->warning(message.c_str()); } diff --git a/binaries/src/clustalw/src/tree/Tree.cpp b/binaries/src/clustalw/src/tree/Tree.cpp index 48ffa4b..9ceeb1e 100644 --- a/binaries/src/clustalw/src/tree/Tree.cpp +++ b/binaries/src/clustalw/src/tree/Tree.cpp @@ -421,7 +421,7 @@ int Tree::calcSimilarities(clustalw::Alignment* alignPtr, clustalw::DistMatrix* } } } - if (nerrs > 0) + if (nerrs > 0 && !userParameters->getGui()) { string errMess = "The following sequences are too divergent to be aligned:\n"; diff --git a/binaries/windows/clustalw2.exe b/binaries/windows/clustalw2.exe old mode 100644 new mode 100755