commit: cfb0869296a4156fe8c7c65c6031debaae954463 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Wed Feb 4 08:11:55 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Wed Feb 4 08:13:00 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cfb08692
sci-biology/emboss: Drop old Package-Manager: portage-2.2.15 Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> --- sci-biology/emboss/ChangeLog | 3 + sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild | 94 ------ sci-biology/emboss/files/ax_lib_mysql.m4 | 147 ---------- .../emboss/files/emboss-6.3.1_p4-r2_Makefile.patch | 47 --- .../emboss-6.3.1_p4-r2_compilations-paths.patch | 315 --------------------- .../emboss/files/emboss-6.3.1_p4-r2_libtool.patch | 18 -- .../emboss/files/emboss-6.3.1_p4-r2_plcol.patch | 112 -------- ...mboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch | 13 - sci-biology/emboss/files/emboss-README.Gentoo-2 | 34 --- 9 files changed, 3 insertions(+), 780 deletions(-) diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog index a8d74bc..a6558c1 100644 --- a/sci-biology/emboss/ChangeLog +++ b/sci-biology/emboss/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.61 2011/03/09 16:29:05 jlec Exp $ + 04 Feb 2015; Justin Lecher <[email protected]> -emboss-6.3.1_p4-r2.ebuild: + Drop old + 04 Feb 2015; Justin Lecher <[email protected]> metadata.xml: Clean a bit, user readme.gentoo.eclass diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild deleted file mode 100644 index 962d472..0000000 --- a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild +++ /dev/null @@ -1,94 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="4" - -inherit emboss eutils - -EBO_PATCH="4" -EBOV=${PV/_p*} - -DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" -SRC_URI=" - ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz - http://dev.gentoo.org/~jlec/distfiles/${PF}.patch.bz2"; -##[[ -n ${EBO_PATCH} ]] && SRC_URI+=" ftp://${PN}.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz" -[[ -n ${EBO_PATCH} ]] && SRC_URI+=" http://pkgs.fedoraproject.org/lookaside/pkgs/EMBOSS/patch-1-4.gz/7a42594c5eda4adc6457f33e4ab0d8f2/patch-1-${EBO_PATCH}.gz -> ${P}-upstream.patch.gz" - -KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" -IUSE+=" minimal" - -RDEPEND+=" !sys-devel/cons" -PDEPEND+=" - !minimal? ( - sci-biology/aaindex - sci-biology/cutg - sci-biology/prints - sci-biology/prosite - sci-biology/rebase - sci-biology/transfac - sci-libs/plplot - )" - -S="${WORKDIR}"/EMBOSS-${EBOV} - -EBO_EXTRA_ECONF="--includedir=${EPREFIX}/usr/include/emboss" - -DOCS+=" FAQ THANKS" - -src_prepare() { - [[ -n ${EBO_PATCH} ]] && epatch "${WORKDIR}"/${P}-upstream.patch - epatch "${WORKDIR}"/${PF}.patch - epatch "${FILESDIR}/${PF}"_plcol.patch - epatch "${FILESDIR}/${PF}"_compilations-paths.patch - epatch "${FILESDIR}/${PF}"_rename_plwid_to_plwidth.patch - # cp "${FILESDIR}"/ax_lib_mysql.m4 "${S}"/m4/mysql.m4 - emboss_src_prepare - autoreconf -vfi - epatch "${FILESDIR}/${PF}"_libtool.patch -} - -#src_compile() { -# # epatch "${FILESDIR}/${PF}"_Makefile.patch -# sed -i -e "s#GD_LIBS = .*#GD_LIBS =#" Makefile -# sed -i -e "s#^LIBS = .*#LIBS =#" Makefile -# sed -i -e "s#^PLPLOT_LIBS = .*#PLPLOT_LIBS =#" Makefile -# sed -i -e "s#^libnucleus_la_LDFLAGS = .*#libnucleus_la_LDFLAGS = \$(LDFLAGS)#" Makefile -#} - -src_install() { - default - - sed -e "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \ - dodoc README.Gentoo - - # Install env file for setting libplplot and acd files path. - cat <<- EOF > 22emboss - # ACD files location - EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" - EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" - EOF - doenvd 22emboss - - # Clashes #330507, resolved upstream - mv "${ED}"/usr/bin/{digest,pepdigest} || die - - # Remove useless dummy files from the image. - find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files." - - # Move the provided codon files to a different directory. This will avoid - # user confusion and file collisions on case-insensitive file systems (see - # bug #115446). This change is documented in "README.Gentoo". - mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ - die "Failed to move CODON directory." - - # Move the provided restriction enzyme prototypes file to a different name. - # This avoids file collisions with versions of rebase that install their - # own enzyme prototypes file (see bug #118832). - mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ - die "Failed to move enzyme equivalence file." - - # fix /usr/share/doc/emboss-6.3.1_p4-r1/html to point to /usr/share/doc/emboss-6.3.1_p4-r1/programs/html - # instead of /usr/share/EMBOSS/doc/html (which does not exist) -} diff --git a/sci-biology/emboss/files/ax_lib_mysql.m4 b/sci-biology/emboss/files/ax_lib_mysql.m4 deleted file mode 100644 index e27d755..0000000 --- a/sci-biology/emboss/files/ax_lib_mysql.m4 +++ /dev/null @@ -1,147 +0,0 @@ -# =========================================================================== -# http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html -# =========================================================================== -# -# SYNOPSIS -# -# AX_LIB_MYSQL([MINIMUM-VERSION]) -# -# DESCRIPTION -# -# This macro provides tests of availability of MySQL client library of -# particular version or newer. -# -# AX_LIB_MYSQL macro takes only one argument which is optional. If there -# is no required version passed, then macro does not run version test. -# -# The --with-mysql option takes one of three possible values: -# -# no - do not check for MySQL client library -# -# yes - do check for MySQL library in standard locations (mysql_config -# should be in the PATH) -# -# path - complete path to mysql_config utility, use this option if -# mysql_config can't be found in the PATH -# -# This macro calls: -# -# AC_SUBST(MYSQL_CFLAGS) -# AC_SUBST(MYSQL_LDFLAGS) -# AC_SUBST(MYSQL_VERSION) -# -# And sets: -# -# HAVE_MYSQL -# -# LICENSE -# -# Copyright (c) 2008 Mateusz Loskot <[email protected]> -# -# Copying and distribution of this file, with or without modification, are -# permitted in any medium without royalty provided the copyright notice -# and this notice are preserved. This file is offered as-is, without any -# warranty. - -#serial 12 - -AC_DEFUN([AX_LIB_MYSQL], -[ - AC_ARG_WITH([mysql], - AS_HELP_STRING([--with-mysql=@<:@ARG@:>@], - [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config] - ), - [ - if test "$withval" = "no"; then - want_mysql="no" - elif test "$withval" = "yes"; then - want_mysql="yes" - else - want_mysql="yes" - MYSQL_CONFIG="$withval" - fi - ], - [want_mysql="yes"] - ) - AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program]) - - MYSQL_CFLAGS="" - MYSQL_LDFLAGS="" - MYSQL_VERSION="" - - dnl - dnl Check MySQL libraries - dnl - - if test "$want_mysql" = "yes"; then - - if test -z "$MYSQL_CONFIG" ; then - AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no]) - fi - - if test "$MYSQL_CONFIG" != "no"; then - MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`" - MYSQL_LDFLAGS="`$MYSQL_CONFIG --libs`" - - MYSQL_VERSION=`$MYSQL_CONFIG --version` - - found_mysql="yes" - else - found_mysql="no" - fi - fi - - dnl - dnl Check if required version of MySQL is available - dnl - - - mysql_version_req=ifelse([$1], [], [], [$1]) - - if test "$found_mysql" = "yes" -a -n "$mysql_version_req"; then - - AC_MSG_CHECKING([if MySQL version is >= $mysql_version_req]) - - dnl Decompose required version string of MySQL - dnl and calculate its number representation - mysql_version_req_major=`expr $mysql_version_req : '\([[0-9]]*\)'` - mysql_version_req_minor=`expr $mysql_version_req : '[[0-9]]*\.\([[0-9]]*\)'` - mysql_version_req_micro=`expr $mysql_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'` - if test "x$mysql_version_req_micro" = "x"; then - mysql_version_req_micro="0" - fi - - mysql_version_req_number=`expr $mysql_version_req_major \* 1000000 \ - \+ $mysql_version_req_minor \* 1000 \ - \+ $mysql_version_req_micro` - - dnl Decompose version string of installed MySQL - dnl and calculate its number representation - mysql_version_major=`expr $MYSQL_VERSION : '\([[0-9]]*\)'` - mysql_version_minor=`expr $MYSQL_VERSION : '[[0-9]]*\.\([[0-9]]*\)'` - mysql_version_micro=`expr $MYSQL_VERSION : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'` - if test "x$mysql_version_micro" = "x"; then - mysql_version_micro="0" - fi - - mysql_version_number=`expr $mysql_version_major \* 1000000 \ - \+ $mysql_version_minor \* 1000 \ - \+ $mysql_version_micro` - - mysql_version_check=`expr $mysql_version_number \>\= $mysql_version_req_number` - if test "$mysql_version_check" = "1"; then - AC_MSG_RESULT([yes]) - else - AC_MSG_RESULT([no]) - fi - fi - - if test "$found_mysql" = "yes" ; then - AC_DEFINE([HAVE_MYSQL], [1], - [Define to 1 if MySQL libraries are available]) - fi - - AC_SUBST([MYSQL_VERSION]) - AC_SUBST([MYSQL_CFLAGS]) - AC_SUBST([MYSQL_LDFLAGS]) -]) diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch deleted file mode 100644 index 419369e..0000000 --- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_Makefile.patch +++ /dev/null @@ -1,47 +0,0 @@ ---- EMBOSS-6.3.1/nucleus/Makefile 2013-09-11 14:50:25.140219756 +0200 -+++ nucleus/Makefile 2013-09-11 14:52:00.920220006 +0200 -@@ -165,7 +165,7 @@ - ESYSTEMLIBS = - EXEEXT = - FGREP = /bin/grep -F --GD_LIBS = -ljpeg -lfontconfig -lfreetype -lz -lm -lgd -+GD_LIBS = - GREP = /bin/grep - HAVE_MEMMOVE = - HAVE_STRERROR = -@@ -180,7 +180,7 @@ - LD = /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 - LDFLAGS = -Wl,--as-needed - LIBOBJS = --LIBS = -L/usr/lib64/mysql -lmysqlclient -lpthread -lz -lm -lrt -lssl -lcrypto -ldl -lm -lhpdf -lpng16 -L/usr/lib64 -lz -ljpeg -lfontconfig -lfreetype -lz -lm -lgd -+LIBS = - LIBTOOL = $(SHELL) $(top_builddir)/libtool - LIPO = - LN_S = ln -s -@@ -219,7 +219,7 @@ - # zap the crap - PLPLOT_CFLAGS = - PLPLOT_CPPFLAGS = --PLPLOT_LIBS = -lplplotd -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lSM -lICE -lX11 -lXext -lgd -lpng -lz -ljpeg -lfreetype -lSM -lICE -lX11 -lXext -lpthread -lLASi -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfreetype -lfontconfig -lhpdf -lm -lcsirocsa -lnistcd -lqsastime -lfreetype -+PLPLOT_LIBS = - PNG_CFLAGS = -I/usr/include/libpng16 - PNG_LIBS = -lpng16 - POSIX_MALLOC_THRESHOLD = -DPOSIX_MALLOC_THRESHOLD=10 -@@ -336,7 +336,7 @@ - VERS_INF = -version-info 6:3:0 - LINKFLAGS = $(VERS_INF) - #LINKFLAGS = $(VERS_INF) $(CYGWIN_LDFLAGS) $(CYGWIN_LIBS) --libnucleus_la_LDFLAGS = $(LINKFLAGS) -+libnucleus_la_LDFLAGS = $(LDFLAGS) - libnucleus_la_LIBADD = -L../ajax/core -L../ajax/graphics -L../ajax/acd -lajax -lajaxg -lacd - all: all-am - -@@ -407,7 +407,7 @@ - rm -f $${locs}; \ - } - libnucleus.la: $(libnucleus_la_OBJECTS) $(libnucleus_la_DEPENDENCIES) $(EXTRA_libnucleus_la_DEPENDENCIES) -- $(libnucleus_la_LINK) -rpath $(libdir) $(libnucleus_la_OBJECTS) $(libnucleus_la_LIBADD) $(LIBS) -+ $(libnucleus_la_LINK) -rpath $(libdir) $(libnucleus_la_OBJECTS) $(LIBS) - - mostlyclean-compile: - -rm -f *.$(OBJEXT) diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch deleted file mode 100644 index 8f87ef9..0000000 --- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch +++ /dev/null @@ -1,315 +0,0 @@ ---- EMBOSS-6.3.1/configure.in 2013-09-11 03:55:15.510117066 +0200 -+++ configure.in 2013-09-11 03:48:10.410115955 +0200 -@@ -449,7 +447,8 @@ - if test "`uname -a | grep Darwin`"; then - OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` - if test ${OSXX} '>' '10.4'; then -- CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib" -+ CPPFLAGS="$CPPFLAGS -I/usr/X11/include" -+ LDFLAGS="$LDFLAGS -L/usr/X11/lib" - fi - fi - fi -@@ -461,7 +460,7 @@ - AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes") - AC_SUBST(ESYSTEMLIBS) - AC_SUBST(DEFINE_USE_SYSTEM_PCRE) --AC_SUBST(PLPLOT_CFLAGS) -+AC_SUBST(PLPLOT_CPPFLAGS) - AC_SUBST(PLPLOT_LIBS) - - ---- EMBOSS-6.3.1/ajax/graphics/Makefile.am 2013-09-11 03:27:30.110112715 +0200 -+++ ajax/graphics/Makefile.am 2013-09-11 03:58:50.860117628 +0200 -@@ -19,7 +19,7 @@ - - - INCLUDES = \ --$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core -+$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core -I$(top_srcdir)/plplot - - AJAXGSRC = ajgraph.c ajhist.c - ---- EMBOSS-6.3.1/ajax/acd/Makefile.am 2013-09-11 03:27:30.110112715 +0200 -+++ ajax/acd/Makefile.am 2013-09-11 03:59:10.310117679 +0200 -@@ -24,7 +24,8 @@ - -I$(top_srcdir)/ajax/core \ - -I$(top_srcdir)/ajax/graphics \ - -I$(top_srcdir)/ajax/ensembl \ ---I$(top_srcdir)/ajax/ajaxdb -+-I$(top_srcdir)/ajax/ajaxdb \ -+-I$(top_srcdir)/plplot - - ACDSRC = ajacd.c - ---- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 03:27:30.110112715 +0200 -+++ nucleus/Makefile.am 2013-09-11 03:59:28.630117727 +0200 -@@ -32,7 +32,7 @@ - $(EXTRA_INCLUDES) \ - -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ - -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ -- -I$(top_srcdir)/ajax/acd -+ -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot - - NUCLSRC = embaln.c embcom.c embcons.c embdata.c embdbi.c embdmx.c \ - embdomain.c embest.c embexit.c embgroup.c embiep.c embindex.c \ ---- EMBOSS-6.3.1/emboss/Makefile.am 2013-09-11 03:27:30.110112715 +0200 -+++ emboss/Makefile.am 2013-09-11 03:59:46.340117773 +0200 -@@ -89,7 +89,7 @@ - $(EXTRA_INCLUDES) \ - -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ - -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ -- -I$(top_srcdir)/ajax/acd -+ -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot - - - aaindexextract_SOURCES = aaindexextract.c ---- EMBOSS-6.3.1/Makefile.am 2013-09-11 04:19:01.770120791 +0200 -+++ Makefile.am 2013-09-11 04:19:18.460120835 +0200 -@@ -13,8 +13,8 @@ - JEMBOSS_DIR = jemboss - endif - --SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) --DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) -+SUBDIRS = $(EXTRA_DIRS) plplot ajax nucleus emboss test doc $(JEMBOSS_DIR) -+DIST_SUBDIRS = $(EXTRA_DIRS) plplot ajax nucleus emboss test doc $(JEMBOSS_DIR) - - # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\" - ---- EMBOSS-6.3.1/plplot/Makefile.am 2013-09-11 09:34:44.620170277 +0200 -+++ plplot/Makefile.am 2013-09-11 09:35:35.820170411 +0200 -@@ -10,26 +10,27 @@ - if AMPNG - - if AMPDF --TESTPDF_CFLAGS = -Wl,-G -lhpdf -+TESTPDF_LIBS = -Wl,-G -lhpdf - else --TESTPDF_CFLAGS = -Wl,-G -+TESTPDF_LIBS = -Wl,-G - endif - --TESTPNG_CFLAGS = $(TESTPDF_CFLAGS) -lgd -lpng -lz -lX11 -lm -+TESTPNG_LIBS = $(TESTPDF_LIBS) -lgd -lpng -lz -lX11 -lm - else --TESTPNG_CFLAGS = $(TESTPDF_CFLAGS) -lX11 -+TESTPNG_LIBS = $(TESTPDF_LIBS) -lX11 - endif - endif - endif - --AM_CFLAGS = $(TESTPNG_CFLAGS) -+AM_LIBS = $(TESTPNG_LIBS) - - if ISCYGWIN - CYGWIN_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import - CYGWIN_LIBS = -lX11 -lgd -lpng -lz - endif - --INCLUDES = $(X_CFLAGS) -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\" -+INCLUDES = -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\" -+LIBS = $(AM_LIBS) - - PLPLOTSRC = pdfutils.c plargs.c plbox.c plcont.c plcore.c \ - plctrl.c plcvt.c pldtik.c plfill.c plhist.c plline.c plmap.c \ ---- EMBOSS-6.3.1/m4/pngdriver.m4 2013-09-11 10:39:07.680180369 +0200 -+++ m4/pngdriver.m4 2013-09-11 10:44:16.000181174 +0200 -@@ -63,7 +63,8 @@ - if test "`uname`" = "SunOS"; then - AC_CHECK_LIB(iconv, libiconv_close, ICCHECK=1, ICCHECK=0, -L${ALT_HOME}/lib -liconv) - if test $ICCHECK = "1" ; then -- LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib -liconv" -+ LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib" -+ LIBS="${LIBS} -liconv" - fi - LDFLAGS="$LDFLAGS -R$ALT_HOME/lib" - fi ---- EMBOSS-6.3.1/m4/java.m4 2013-09-11 10:39:03.490180358 +0200 -+++ m4/java.m4 2013-09-11 10:46:08.240181467 +0200 -@@ -180,7 +180,7 @@ - - if test "$withval" = "yes" ; then - CFLAGS="$CFLAGS -D_REENTRANT" -- LDFLAGS="$LDFLAGS -lpthread" -+ LDFLAGS="$LDFLAGS" - LIBS="$LIBS -lpthread" - fi - -@@ -192,38 +192,38 @@ - - if test "$withval" = "linux" ; then - CFLAGS="$CFLAGS -D_REENTRANT" -- LDFLAGS="$LDFLAGS -lpthread" -+ LDFLAGS="$LDFLAGS" - LIBS="$LIBS -lpthread" - fi - - if test "$withval" = "solaris" ; then - CFLAGS="$CFLAGS -D_POSIX_C_SOURCE=199506L" -- LDFLAGS="$LDFLAGS -lpthread" -+ LDFLAGS="$LDFLAGS" - LIBS="$LIBS -lpthread" - fi - if test "$withval" = "macos" ; then - CFLAGS="$CFLAGS" -- LDFLAGS="$LDFLAGS -lpthread" -+ LDFLAGS="$LDFLAGS" - LIBS="$LIBS -lpthread" - fi - if test "$withval" = "hpux" ; then - CFLAGS="$CFLAGS -Ae +z -DNATIVE -D_POSIX_C_SOURCE=199506L" -- LDFLAGS="$LDFLAGS -lpthread" -+ LDFLAGS="$LDFLAGS" - LIBS="$LIBS -lpthread" - fi - if test "$withval" = "irix" ; then - CFLAGS="$CFLAGS" -- LDFLAGS="$LDFLAGS -lpthread" -+ LDFLAGS="$LDFLAGS" - LIBS="$LIBS -lpthread" - fi - if test "$withval" = "aix" ; then - CFLAGS="$CFLAGS -D_REENTRANT" -- LDFLAGS="$LDFLAGS -lpthread" -+ LDFLAGS="$LDFLAGS" - LIBS="$LIBS -lpthread" - fi - if test "$withval" = "osf" ; then - CFLAGS="$CFLAGS -D_REENTRANT -D_OSF_SOURCE" -- LDFLAGS="$LDFLAGS -lpthread" -+ LDFLAGS="$LDFLAGS" - LIBS="$LIBS -lpthread" - fi - else ---- EMBOSS-6.3.1/m4/mysql.m4 2013-09-11 11:03:07.160184129 +0200 -+++ m4/mysql.m4 2013-09-11 11:04:39.440184370 +0200 -@@ -85,7 +85,6 @@ - AC_MSG_CHECKING([for MySQL libraries]) - - dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`" -- MYSQL_CFLAGS="`$MYSQL_CONFIG --include`" - MYSQL_LIBS="`$MYSQL_CONFIG --libs`" - - MYSQL_VERSION=`$MYSQL_CONFIG --version` ---- EMBOSS-6.3.1/m4/mysql.m4 2013-09-11 11:38:09.330189621 +0200 -+++ m4/mysql.m4 2013-09-11 11:41:02.170190072 +0200 -@@ -170,6 +170,4 @@ - fi - - AC_SUBST([MYSQL_VERSION]) -- AC_SUBST([MYSQL_CFLAGS]) -- AC_SUBST([MYSQL_LIBS]) - ]) ---- EMBOSS-6.3.1/configure.in 2013-09-11 12:23:17.330196695 +0200 -+++ configure.in 2013-09-11 12:23:21.480196706 +0200 -@@ -8,6 +8,8 @@ - AC_INIT(ajax/core/ajmath.c) - AM_INIT_AUTOMAKE([EMBOSS],[6.3.1]) - -+AC_CONFIG_MACRO_DIR([m4]) -+ - # Make sure CFLAGS is defined to stop LT_INIT adding -g - CFLAGS="$CFLAGS " - ---- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 12:33:14.260198254 +0200 -+++ nucleus/Makefile.am 2013-09-11 12:33:16.650198260 +0200 -@@ -58,4 +58,4 @@ - endif - - libnucleus_la_LDFLAGS = $(LINKFLAGS) --libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la -+libnucleus_la_LIBADD = -L../ajax/core -L../ajax/graphics -L../ajax/acd -lajax -lajaxg -lacd ---- EMBOSS-6.3.1/ajax/ensembl/Makefile.am 2013-09-11 12:41:06.340199487 +0200 -+++ ajax/ensembl/Makefile.am 2013-09-11 12:41:40.460199577 +0200 -@@ -56,5 +56,5 @@ - LINKFLAGS = $(VERS_INF) - endif - --libensembl_la_LDFLAGS = $(LINKFLAGS) --libensembl_la_LIBADD = ../core/libajax.la -+libensembl_la_LDFLAGS = $(LINKFLAGS) -L../core -+libensembl_la_LIBADD = -lajax ---- EMBOSS-6.3.1/ajax/graphics/Makefile.am 2013-09-11 12:42:17.730199674 +0200 -+++ ajax/graphics/Makefile.am 2013-09-11 12:42:47.000199750 +0200 -@@ -35,5 +35,5 @@ - LINKFLAGS = $(VERS_INF) - endif - --libajaxg_la_LDFLAGS = $(LINKFLAGS) --libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS) -+libajaxg_la_LDFLAGS = $(LINKFLAGS) -L../core/ -+libajaxg_la_LIBADD = -lajax $(EXTRA_LIBS) ---- EMBOSS-6.3.1/ajax/acd/Makefile.am 2013-09-11 12:43:11.660199815 +0200 -+++ ajax/acd/Makefile.am 2013-09-11 12:44:01.520199945 +0200 -@@ -41,5 +41,5 @@ - LINKFLAGS = $(VERS_INF) - endif - --libacd_la_LDFLAGS = $(LINKFLAGS) --libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la -+libacd_la_LDFLAGS = $(LINKFLAGS) -L../core -L../graphics -L../ajaxdb -+libacd_la_LIBADD = -lajax -lajaxg -lajaxdb ---- EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am 2013-09-11 12:44:10.980199970 +0200 -+++ ajax/ajaxdb/Makefile.am 2013-09-11 12:44:40.040200046 +0200 -@@ -37,5 +37,5 @@ - LINKFLAGS = $(VERS_INF) - endif - --libajaxdb_la_LDFLAGS = $(LINKFLAGS) --libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la -+libajaxdb_la_LDFLAGS = $(LINKFLAGS) -L../core -L../ensembl -+libajaxdb_la_LIBADD = -lajax -lensembl ---- EMBOSS-6.3.1/configure.in 2013-09-11 13:24:39.720206315 +0200 -+++ configure.in 2013-09-11 13:24:58.610206364 +0200 -@@ -319,10 +319,8 @@ - AX_LIB_MYSQL - AX_LIB_POSTGRESQL - --CFLAGS="$CFLAGS $MYSQL_CFLAGS" - LIBS="${MYSQL_LIBS} ${LIBS}" - --CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS" - LIBS="$POSTGRESQL_LIBS $LIBS" - - ---- EMBOSS-6.3.1/ajax/core/Makefile.am 2013-09-11 13:47:36.790209912 +0200 -+++ ajax/core/Makefile.am 2013-09-11 13:47:40.550209922 +0200 -@@ -65,5 +65,5 @@ - LINKFLAGS = $(VERS_INF) - endif - --libajax_la_LDFLAGS = $(LINKFLAGS) -+libajax_la_LDFLAGS = - libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LIBS) $(MYSQL_LIBS) ---- EMBOSS-6.3.1/nucleus/Makefile.am 2013-09-11 14:03:21.960212381 +0200 -+++ nucleus/Makefile.am 2013-09-11 14:03:58.910212478 +0200 -@@ -22,11 +22,14 @@ - EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ - -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre - else --EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -+EXTRA_INCLUDES = - endif - endif - - -+# zap the crap -+PLPLOT_CFLAGS = -+ - INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \ - -I$(top_srcdir)/ajax \ - $(EXTRA_INCLUDES) \ ---- EMBOSS-6.3.1/emboss/Makefile.am 2013-09-11 14:23:50.570215591 +0200 -+++ emboss/Makefile.am 2013-09-11 14:24:24.950215680 +0200 -@@ -328,9 +328,7 @@ - - LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \ - ../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \ -- ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \ -- $(EXTRA_LDS) \ -- $(XLIB) -+ ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la - - pkgdata_DATA = emboss.default.template - pkgdatadir=$(prefix)/share/$(PACKAGE) diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch deleted file mode 100644 index ad358e1..0000000 --- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_libtool.patch +++ /dev/null @@ -1,18 +0,0 @@ ---- EMBOSS-6.3.1/m4/libtool.m4 2013-09-11 12:03:45.180193633 +0200 -+++ m4/libtool.m4 2013-09-11 12:04:19.280193722 +0200 -@@ -4768,13 +4768,13 @@ - *Sun\ F*) # Sun Fortran 8.3 - tmp_sharedflag='-G' ;; - esac -- _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' -+ _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs ${wl}-soname $wl$soname -Wl,--as-needed -o $lib' - - if test "x$supports_anon_versioning" = xyes; then - _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~ - cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ - echo "local: *; };" >> $output_objdir/$libname.ver~ -- $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib' -+ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -Wl,--as-needed -o $lib' - fi - - case $cc_basename in diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch deleted file mode 100644 index 0f5e592..0000000 --- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_plcol.patch +++ /dev/null @@ -1,112 +0,0 @@ ---- EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2012-07-19 23:29:05.000000000 +0200 -+++ /tmp/ajgraph.c 2012-07-19 23:25:00.000000000 +0200 -@@ -1645,14 +1645,14 @@ - ** @return [void] - ** @@ - ******************************************************************************/ - - static void GraphSetPen(ajint colour) - { -- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]); -- plcol((PLINT)colour); -+ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]); -+ plcol0((PLINT)colour); - - return; - } - - - ---- EMBOSS-6.3.1/plplot/plcore.c 2007-10-24 15:14:43.000000000 +0200 -+++ /tmp/plcore.c 2012-07-19 23:25:00.000000000 +0200 -@@ -1709,13 +1709,13 @@ - if (plsc->zdigmax == 0) - plsc->zdigmax = 3; - - /* Switch to graphics mode and set color and arrow style*/ - - plgra(); -- plcol(1); -+ plcol0(1); - - plstyl(0, &mk, &sp); - plpat(1, &inc, &del); - - plsvect(def_arrow_x, def_arrow_y, 6, 0); - ---- EMBOSS-6.3.1/plplot/plstripc.c 2007-05-08 11:09:37.000000000 +0200 -+++ /tmp/plstripc.c 2012-07-19 23:25:00.000000000 +0200 -@@ -153,17 +153,17 @@ - - plgchr(&sc, &dy); - sc = dy = dy/100; - plwind(-0.01, 1.01, -0.01, 1.01); - for (i=0; i<PEN; i++) { - if (mystripc->npts[i] || first) { -- plcol(mystripc->colline[i]); -+ plcol0(mystripc->colline[i]); - pllsty(mystripc->styline[i]); - pljoin(mystripc->xlpos, mystripc->ylpos - sc, - mystripc->xlpos + 0.1, mystripc->ylpos - sc); -- plcol(mystripc->collab); -+ plcol0(mystripc->collab); - plptex(mystripc->xlpos + 0.11, mystripc->ylpos - sc, - 0., 0., 0, mystripc->legline[i]); - sc += dy; - } - } - plwind(mystripc->xmin, mystripc->xmax, mystripc->ymin, mystripc->ymax); -@@ -184,34 +184,34 @@ - PLFLT x[]={0.,1.,1.,0.}, y[]={0.,0.,1.,1.}; - - /* Set up window */ - - plvpor(0,1,0,1); - plwind(0,1,0,1); -- plcol(0);plpsty(0); -+ plcol0(0);plpsty(0); - plfill(4, &x[0], &y[0]); - plvsta(); - - /* Draw box and same window dimensions */ - mystrip->wxmin=mystrip->xmin; - mystrip->wxmax=mystrip->xmax; - mystrip->wymin=mystrip->ymin; - mystrip->wymax=mystrip->ymax; /* FIXME - can exist some redundancy here */ - - plwind(mystrip->xmin, mystrip->xmax, mystrip->ymin, mystrip->ymax); - - pllsty(1); -- plcol(mystrip->colbox); -+ plcol0(mystrip->colbox); - plbox(mystrip->xspec, 0.0, 0, mystrip->yspec, 0.0, 0); - -- plcol(mystrip->collab); -+ plcol0(mystrip->collab); - pllab(mystrip->labx, mystrip->laby, mystrip->labtop); - - for (i=0; i<PEN; i++) { - if (mystrip->npts[i] > 0) { -- plcol(mystrip->colline[i]);pllsty(mystrip->styline[i]); -+ plcol0(mystrip->colline[i]);pllsty(mystrip->styline[i]); - plline(mystrip->npts[i], mystrip->x[i], mystrip->y[i]); - } - } - - plstrip_legend(mystrip,0); - } -@@ -269,13 +269,13 @@ - if (stripc->xmax - stripc->xmin < stripc->xlen) { - if( yasc == 0) { - - /* If user has changed subwindow, make shure we have the correct one */ - plvsta(); - plwind(stripc->wxmin, stripc->wxmax, stripc->wymin, stripc->wymax); /* FIXME - can exist some redundancy here */ -- plcol(stripc->colline[p]); pllsty(stripc->styline[p]); -+ plcol0(stripc->colline[p]); pllsty(stripc->styline[p]); - if ((stripc->npts[p]-2) < 0) - plP_movwor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]); - else - plP_movwor(stripc->x[p][stripc->npts[p]-2], stripc->y[p][stripc->npts[p]-2]); - plP_drawor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]); - plflush(); diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch deleted file mode 100644 index e66a696..0000000 --- a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- EMBOSS-6.3.1/ajax/graphics/ajgraph.c.ori 2014-07-04 18:25:18.000000000 +0200 -+++ EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2014-07-04 18:25:32.000000000 +0200 -@@ -1329,8 +1329,8 @@ - - void ajGraphicsSetPenwidth(float penwidth) - { -- ajDebug("=g= plwid(%.2f) [width]\n", penwidth); -- plwid((PLINT)penwidth); -+ ajDebug("=g= plwidth(%.2f) [width]\n", penwidth); -+ plwidth((PLINT)penwidth); - - return; - } diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-2 b/sci-biology/emboss/files/emboss-README.Gentoo-2 deleted file mode 100644 index 72fa366..0000000 --- a/sci-biology/emboss/files/emboss-README.Gentoo-2 +++ /dev/null @@ -1,34 +0,0 @@ -Administrating EMBOSS on Gentoo systems -======================================= - - -Codon data files location -------------------------- - -The codon data files that are distributed with EMBOSS are installed in the -``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual -``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between -these codon files and those installed with the CUTG database. The names of -these files sometimes vary only by their case. Having both sets of files in -the same directory is also impossible on systems such as MacOSX, where the -root filesystem is case insensitive. If you do not have the CUTG database -installed and want to use the codon files distributed with EMBOSS, you can -symlink the ``CODONS.orig`` directory to ``CODONS``:: - - # cd EPREFIX/usr/share/EMBOSS/data - # ln -s CODONS.orig CODONS - - -Restriction enzymes equivalence file location ---------------------------------------------- - -The restriction enzymes equivalence file distributed with EMBOSS is installed -as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual -``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file -collision with the equivalence file provided by the Rebase database. If you do -not have the Rebase database installed and want to use the equivalence file -distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to -``embossre.equ``:: - - # cd EPREFIX/usr/share/EMBOSS/data - # ln -s embossre.equ.orig embossre.equ
