diff options
Diffstat (limited to 'sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch')
| -rw-r--r-- | sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch | 346 |
1 files changed, 0 insertions, 346 deletions
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch b/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch deleted file mode 100644 index b548de5a39a5..000000000000 --- a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch +++ /dev/null @@ -1,346 +0,0 @@ -Fix and modernise build system -* Remove all *FLAGS setting, just append to the user-supplied ones -* Add --enable-doc and --enable-examples configure flags -* Install documentation and examples in correct directories -* Discover libxml2 and libxslt dependencies using PKG_CHECK_MODULES -* Install python and perl modules correctly - ---- a/configure.ac -+++ b/configure.ac -@@ -76,61 +76,10 @@ - AM_CONDITIONAL(WANT_STRLCPY, test ["$have_strlcpy" = no]) - - # Check for compiler-specific settings --LARGE_FILE_SUPPORT=`getconf LFS_CFLAGS` --if test "${GCC}" = "yes"; then -- ac_cc_opt="-O3" -- ac_cc_debug_opt="-O0" -- ac_cc_warn="-Wall -Wno-unused" -- ac_cc_debug="-ggdb" -- # Check for OS X llvm (clang) compiler -- if `gcc --version |grep llvm >/dev/null`; then -- ac_cc_debug="-g" -- fi -- CFLAGS="-std="gnu89" $ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" --else -- ac_cc_opt="-O" -- ac_cc_debug_opt="" -- ac_cc_warn="" -- ac_cc_debug="-g" -- CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT" --fi -- --# Set up default libxml2 settings --# check for installed copy of libxml2 --build_libxml2="yes" --if test -n "$XML2_CONFIG"; then -- # Require at least version 2.6 -- required_libxml2_version="2006000" -- LIBXML2_VERSION="`$XML2_CONFIG --version | \ -- awk 'BEGIN { FS = "."; } { printf "%d", ($1 * 1000 + $2) * 1000 + $3;}'`" -- if test -n "$LIBXML2_VERSION" && \ -- test "$LIBXML2_VERSION" -ge "$required_libxml2_version"; then -- build_libxml2="no" -- LIBXML2_LIBS="`$XML2_CONFIG --libs`" -- LIBXML2_CFLAGS="`$XML2_CONFIG --cflags`" -- fi --fi --if test -z "$LIBXML2_LIBS"; then -- AC_MSG_WARN([libxml2 library not found]) -- LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la" -- LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" --fi -- --# Set up default libxslt settings --# check for installed copy of libxslt --build_libxslt="yes" --if test -n "$XSLT_CONFIG"; then -- build_libxslt="no" -- LIBXSLT_LIBS="`$XSLT_CONFIG --libs` -lexslt" -- LIBXSLT_CFLAGS="`$XSLT_CONFIG --cflags`" --fi --if test -z "$LIBXSLT_LIBS"; then -- AC_MSG_WARN([libxslt library not found]) -- LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la" -- LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la" -- LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt" -- LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" --fi -+AC_PROG_MKDIR_P -+AC_SYS_LARGEFILE -+CFLAGS="-std=gnu89 -Wall -Wno-unused ${CFLAGS}" -+CPPFLAGS="-DUNIX -D__USE_FIXED_PROTOTYPES__ ${CPPFLAGS}" - - # who is installing - USER=`whoami` -@@ -279,6 +227,16 @@ - AM_CONDITIONAL(PARALLEL, test ["$parallel" != no]) - AM_CONDITIONAL(PARALLEL_IS_LAM, test -n ["$lammpi"]) - -+dnl Documentation -+AC_ARG_ENABLE([doc], -+ AS_HELP_STRING([--enable-doc], [Enable installation of documentation])) -+AM_CONDITIONAL([ENABLE_DOC], [test "x$enable_doc" = "xyes"]) -+ -+dnl Examples -+AC_ARG_ENABLE([examples], -+ AS_HELP_STRING([--enable-examples], [Enable installation of examples])) -+AM_CONDITIONAL([ENABLE_EXAMPLES], [test "x$enable_examples" = "xyes"]) -+ - AC_ARG_ENABLE( - webservice, - [ --enable-webservice=deploy_dir Deploy the MEME service on an existing Opal 2.5+ installation], -@@ -309,24 +267,35 @@ - AM_CONDITIONAL(WEBEITHER, test ["x$OPAL_DEPLOY" != "x" -o "x$OPAL_URL" != "xno"]) - - # enable building of included libxml2 --AC_ARG_ENABLE( -- build_libxml2, -- [ --enable-build-libxml2 Build included version of libxml2. Default is to use pre-existing locally installed copy.], -- build_libxml2=$enableval; \ -- LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"; \ -- LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" , ) --AM_CONDITIONAL(BUILD_LIBXML2, test ["$build_libxml2" = yes]) -+AC_ARG_ENABLE([build-libxml2], -+ AS_HELP_STRING([--enable-build-libxml2], [Build included version of libxml2. Default is to use pre-existing locally installed copy.])) -+AS_IF([test "x$enable_build_libxml2" = "xyes"], [ -+ dnl Enable building of bundled libs -+ LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" -+ LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la" -+ ],[ -+ dnl Use system libraries -+ PKG_CHECK_MODULES([LIBXML2], [libxml-2.0 >= 2.6]) -+]) -+AM_CONDITIONAL([BUILD_LIBXML2], [test "x$enable_build_libxml2" = "xyes"]) -+ - - # enable building of included libxslt --AC_ARG_ENABLE( -- build_libxslt, -- [ --enable-build-libxslt Build included version of libxslt. Default is to use pre-existing locally installed copy.], -- build_libxslt=$enableval; \ -- LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"; \ -- LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"; \ -- LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"; \ -- LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" , ) --AM_CONDITIONAL(BUILD_LIBXSLT, test ["$build_libxslt" = yes]) -+AC_ARG_ENABLE([build-libxslt], -+ AS_HELP_STRING([--enable-build-libxslt], [Build included version of libxslt. Default is to use pre-existing locally installed copy.])) -+AS_IF([test "x$enable_build_libxslt" = "xyes"], [ -+ dnl Enable building of bundled libs -+ LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" -+ LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la" -+ -+ LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt" -+ LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la" -+ ],[ -+ dnl Use system libraries -+ PKG_CHECK_MODULES([LIBXSLT], [libxslt]) -+ PKG_CHECK_MODULES([LIBEXSLT], [libexslt]) -+]) -+AM_CONDITIONAL([BUILD_LIBXSLT], [test "x$enable_build_libxslt" = "xyes"]) - - # set website url - AC_ARG_WITH( -@@ -427,13 +396,13 @@ - [AC_PATH_PROG(PERL, perl)]) - AC_DEFINE_UNQUOTED(PERL, "$PERL", [Path to Perl] ) - -+AC_ARG_WITH([perl-dir], -+ AS_HELP_STRING([--with-perl-dir], [Perl modules directory]), [perlmoddir="$with_perl_dir"], [perlmoddir="lib/perl"]) -+AC_SUBST([perlmoddir]) -+ -+ - # set path to Python --AC_ARG_WITH( -- python, -- [ --with-python=NAME Set path to Python. Default is to take from user's PATH.], -- [PYTHON=$withval], -- [AC_PATH_PROG(PYTHON, python)]) --AC_DEFINE_UNQUOTED(PYTHON, "$PYTHON", [Path to Python] ) -+AM_PATH_PYTHON - - # set path to convert utility - AC_ARG_WITH( -@@ -586,13 +555,15 @@ - Configuration parameters - ======================== - -- Install path: ${prefix} -+ Install path (prefix): ${prefix} - Install UID: ${MEME_USER} - Version: ${VERSION} -- C compiler: ${CC} -- C compiler flags: ${CFLAGS} -- Linker: ${LD} -- Special Libs: ${LIBS} -+ C compiler (CC): ${CC} -+ C compiler flags (CFLAGS): ${CFLAGS} -+ C preproc flags (CPPFLAGS): ${CPPFLAGS} -+ Linker (LD): ${LD} -+ Linker flags (LDFLAGS): ${LDFLAGS} -+ Special Libs (LIBS): ${LIBS} - MPICC ${MPICC} - MPIRUN ${MPIRUN} - MPI_CMD ${MPI_CMD} ---- a/doc/css/Makefile.am -+++ b/doc/css/Makefile.am -@@ -5,7 +5,7 @@ - - EXTRA_DIST = $(NORMAL_FILES) - --if ! WEBSITE --doccssdir = $(prefix)/doc/css -+if ENABLE_DOC -+doccssdir = $(htmldir)/css - doccss_DATA = $(NORMAL_FILES) - endif ---- a/doc/examples/compute_prior_dist_example_output_files/Makefile.am -+++ b/doc/examples/compute_prior_dist_example_output_files/Makefile.am -@@ -7,8 +7,8 @@ - EXAMPLES = \ - prior.dist.txt - --if ! WEBSITE --exdir = $(prefix)/doc/examples/compute_prior_dist_example_output_files -+if ENABLE_EXAMPLES -+exdir = $(docdir)/examples/compute_prior_dist_example_output_files - ex_DATA = $(EXAMPLES) - endif - ---- a/doc/examples/Makefile.am -+++ b/doc/examples/Makefile.am -@@ -22,8 +22,8 @@ - # load the EXAMPLE_OUTPUT_FILES variable - include examples.mk - --if ! WEBSITE --exdir = $(prefix)/doc/examples -+if ENABLE_EXAMPLES -+exdir = $(docdir)/examples - nobase_dist_ex_DATA = $(EXAMPLES) $(EXAMPLE_OUTPUT_FILES) - endif - ---- a/doc/examples/sample_opal_scripts/Makefile.am -+++ b/doc/examples/sample_opal_scripts/Makefile.am -@@ -15,8 +15,8 @@ - MemeClient.pl \ - MemeClient.py - --if ! WEBSITE --exdir = $(prefix)/doc/examples/sample_opal_scripts -+if ENABLE_EXAMPLES -+exdir = $(docdir)/examples/sample_opal_scripts - ex_DATA = $(EXAMPLES) - endif - ---- a/doc/images/Makefile.am -+++ b/doc/images/Makefile.am -@@ -30,8 +30,8 @@ - - MEME_IMAGES = $(PROGRAM_ICONS) $(OTHER_IMAGES) - --if ! WEBSITE --memeimgdir = $(prefix)/doc/images -+if ENABLE_DOC -+memeimgdir = $(htmldir)/images - memeimg_DATA = $(MEME_IMAGES) - endif - ---- a/doc/js/Makefile.am -+++ b/doc/js/Makefile.am -@@ -41,8 +41,8 @@ - - BUILT_SOURCES = $(BUILT_FILES) - --if ! WEBSITE --docjsdir = $(prefix)/doc/js -+if ENABLE_DOC -+docjsdir = $(htmldir)/js - docjs_DATA = $(NORMAL_FILES) $(BUILT_FILES) $(SYMLINK_FILES) - endif - ---- a/doc/Makefile.am -+++ b/doc/Makefile.am -@@ -129,8 +129,8 @@ - update-sequence-db.html \ - ismb94.pdf - --if ! WEBSITE --memedocdir = $(prefix)/doc -+if ENABLE_DOC -+memedocdir = $(htmldir) - memedoc_DATA = $(NORMAL_FILES) - endif - ---- a/Makefile.am -+++ b/Makefile.am -@@ -52,7 +52,7 @@ - endif - - dbdir: -- mkdir -p $(MEME_DB) -+ $(MKDIR_P) $(DESTDIR)/$(MEME_DB) - - all-local: - if WEBSITE -@@ -64,8 +64,8 @@ - endif - - install-data-local: -- mkdir -p $(MEME_LOGS) -- chmod a+w $(MEME_LOGS) -+ $(MKDIR_P) $(DESTDIR)/$(MEME_LOGS) -+ chmod a+w $(DESTDIR)/$(MEME_LOGS) - - distdir = $(PACKAGE)_$(VERSION) - ---- a/scripts/Makefile.am -+++ b/scripts/Makefile.am -@@ -22,8 +22,8 @@ - -e 's%@WHICHJAVA@%$(JAVA)%' \ - -e 's%@WHICHCONVERT@%$(CONVERT)%' \ - -e 's%@WHICHGHOSTSCRIPT@%$(GHOSTSCRIPT)%' \ -- -e 's%@PERLLIBDIR@%$(libdir)/perl%' \ -- -e 's%@PYTHONLIBDIR@%$(libdir)/python%' \ -+ -e 's%@PERLLIBDIR@%$(perlmoddir)%' \ -+ -e 's%@PYTHONLIBDIR@%$(pythondir)%' \ - -e 's%@JAVALIBDIR@%$(libdir)/java%' \ - -e 's%@LAM_BIN@%$(LAMBIN)%' \ - -e 's%@APPCONFIGDIR@%$(sysconfdir)%' \ -@@ -62,7 +62,7 @@ - DiffXML.pm \ - HypergeometricDynProg.pm - --perlmoddir=$(libdir)/perl -+perlmoddir = $(exec_prefix)/@perlmoddir@ - perlmod_SCRIPTS = \ - $(BUILT_PERL_MOD) \ - $(NORMAL_PERL_MOD) -@@ -76,8 +76,7 @@ - hypergeometric.py \ - sequence.py - --pythonlibdir=$(libdir)/python --pythonlib_SCRIPTS = \ -+python_PYTHON = \ - $(BUILT_PYTHON_LIB) \ - $(NORMAL_PYTHON_LIB) - ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -19,7 +19,13 @@ - ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION) - ARCHIVE_DATE = $(shell cat ../ARCHIVE_DATE) - --SUBDIRS = filters libxml2 libxslt libexslt . parallel -+SUBDIRS = filters . parallel -+if BUILD_LIBXML2 -+SUBDIRS += libxml2 -+endif -+if BUILD_LIBXSLT -+SUBDIRS += libxslt libexslt -+endif - - BUILT_SOURCES = dir.h projrel.h - |