From: David Seifert Date: Sat, 19 Nov 2016 15:29:31 +0000 (+0100) Subject: sci-biology/meme: Version bump to 4.11.2_p2 X-Git-Url: http://git.tremily.us/gitweb.cgi?a=commitdiff_plain;h=a474ab0de01ae126ebfd16f834fbe01951da9ad4;p=gentoo.git sci-biology/meme: Version bump to 4.11.2_p2 Gentoo-bug: 599860 * EAPI=6 * Install documentation and examples correctly * Install perl and python modules correctly * Add missing perl runtime dependencies Package-Manager: portage-2.3.2 --- diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest index 3ed08610b06e..4496d777cb23 100644 --- a/sci-biology/meme/Manifest +++ b/sci-biology/meme/Manifest @@ -1 +1,2 @@ +DIST meme_4.11.2.tar.gz 18004930 SHA256 6e3ff843366588ea13fa8060306be9e2c144521912dfb268f03638003bcdd581 SHA512 c97c3815e71e2fb5491548152f00688cdfbf4365f6027657e0ffc68e5d96cdd10a4708e0882ab7a5a61d78d93113c925cf5bb300fbe93fa4b2961becef497894 WHIRLPOOL 6b77d7832342658d5cf546af0b005b59664c811d25a0412df765a15a8c80a75d9618a1f9966c9a2824750eced6605b534d41199382a6f2641e7430540ba19fcf DIST meme_4.8.1.tar.gz 8703632 SHA256 c3ad3ca26bc2a7130c5eceb64e1745275c317a5469e98fc8759a9e56babccb8c SHA512 31833169ffa9bd82387d1872be40b0fc4312f4a05bb7abb84daf372244ce3f2a68c89c96722c0453f7bcd9eb4fc84fd3d66e1278af55d556715b94b0df5f87ba WHIRLPOOL 4b5e8968e6964479081d1fe036ff3aa7a50dc56bafc0031890d2e47dbdc8e0273e62ffe01800d8908b2fa9824a4766254bb0fd94003d9ca14784073d5357793e 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 new file mode 100644 index 000000000000..0f3349c9583e --- /dev/null +++ b/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch @@ -0,0 +1,323 @@ +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 +76,9 @@ + 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_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 = $(NORMAL_FILES) + endif + +--- a/scripts/Makefile.am ++++ b/scripts/Makefile.am +@@ -22,8 +22,8 @@ + -e 's%@WHICHJAVA@%$(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 + diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch new file mode 100644 index 000000000000..30a182f8f43a --- /dev/null +++ b/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch @@ -0,0 +1,383 @@ +--- a/doc/alphabet-format.html ++++ b/doc/alphabet-format.html +@@ -233,7 +233,7 @@ + providing a reference on the meaning of the symbols used. If present, the + symbol name must be the second field.

+

The "name" follows the rules of +- quoted text.

++ quoted text.

+ +
color
+
+--- a/doc/release-notes.html ++++ b/doc/release-notes.html +@@ -14,8 +14,26 @@ +

Motif-based sequence analysis tools

+
+

MEME Suite Release Notes

++
++ MEME version 4.11.2 patch 1 -- June 16, 2016 ++ ++

+

+-

+ MEME version 4.11.2 -- May 5 2016 +

+