commit: 38938220c8b6fde207fb7054dbdd8987bfa5085d Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Tue Apr 26 18:48:22 2016 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Tue Apr 26 18:48:30 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=38938220
sci-biology/emboss: Clean up of files dir Move to readme.gentoo-r1.eclass Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=579728 Package-Manager: portage-2.2.28 Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> sci-biology/emboss/emboss-6.6.0.ebuild | 9 +- sci-biology/emboss/files/22emboss | 4 - .../emboss/files/6.3.1_p4-unbundle-libs.patch | 600 --------------------- sci-biology/emboss/files/README.Gentoo | 28 - .../emboss/files/emboss-5.0.0-as-needed.patch | 24 - .../emboss/files/emboss-6.3.1_p4-r1_plcol.patch | 112 ---- sci-biology/emboss/files/emboss-README.Gentoo-1 | 34 -- sci-biology/emboss/files/emboss-README.Gentoo-2 | 34 -- 8 files changed, 7 insertions(+), 838 deletions(-) diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild index a853743..5c4c77d 100644 --- a/sci-biology/emboss/emboss-6.6.0.ebuild +++ b/sci-biology/emboss/emboss-6.6.0.ebuild @@ -1,11 +1,12 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2016 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ EAPI=5 AUTOTOOLS_AUTORECONF=1 -inherit autotools-utils emboss-r1 eutils readme.gentoo + +inherit autotools-utils emboss-r1 eutils readme.gentoo-r1 DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"; @@ -59,3 +60,7 @@ src_install() { mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ die "Failed to move CODON directory." } + +pkg_postinst() { + readme.gentoo_print_elog +} diff --git a/sci-biology/emboss/files/22emboss b/sci-biology/emboss/files/22emboss deleted file mode 100644 index 177643c..0000000 --- a/sci-biology/emboss/files/22emboss +++ /dev/null @@ -1,4 +0,0 @@ -# plplot libs dir -PLPLOT_LIB="/usr/share/EMBOSS/" -# ACD files location -EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" diff --git a/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch b/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch deleted file mode 100644 index 5e46374..0000000 --- a/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch +++ /dev/null @@ -1,600 +0,0 @@ -diff --git a/Makefile.am b/Makefile.am -index 4fe2ed1..7f3a95f 100644 ---- a/Makefile.am -+++ b/Makefile.am -@@ -5,12 +5,21 @@ ACLOCAL_AMFLAGS = -I m4 - - AUTOMAKE_OPTIONS = gnits - --SUBDIRS = plplot ajax nucleus emboss test doc jemboss -+if !ESYSTEMLIBS -+EXTRA_DIRS = plplot -+endif -+ -+if GJEMBOSS -+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) - - # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\" - - # files with nonstandard names in this directory --EXTRA_DIST = COMPAT LICENSE KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh -+EXTRA_DIST = COMPAT KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh - - # tar to pick up the other directories - # then remove any CVS subdirectories -diff --git a/README.fixes b/README.fixes -new file mode 100644 -index 0000000..3c56d79 ---- /dev/null -+++ b/README.fixes -@@ -0,0 +1,9 @@ -+The files in this directory are bugfix replacements for files in -+the EMBOSS-6.3.1 distribution. Just drop the replacement files in -+the location shown and redo the 'make install.' -+ -+Fix 1. EMBOSS-6.3.1/configure -+ EMBOSS-6.3.1/m4/mysql.m4 -+ -+21 Jul 2010: Addresses a problem whereby, in some circumstances, inclusion of -+ hpdf support prevented inclusion of MySQL support. -diff --git a/ajax/Makefile.am b/ajax/Makefile.am -index 4a44f6f..cf27ff8 100644 ---- a/ajax/Makefile.am -+++ b/ajax/Makefile.am -@@ -1,6 +1,6 @@ - ## Process this file with automake to produce Makefile.in - if !ESYSTEMLIBS --EXTRA_DIRS = expat zlib -+EXTRA_DIRS = pcre expat zlib - endif - --SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd -+SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd -diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am -index 02bcaa7..368ddfe 100644 ---- a/ajax/acd/Makefile.am -+++ b/ajax/acd/Makefile.am -@@ -13,10 +13,13 @@ CYGWIN_LDACD = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \ - endif - - if !ESYSTEMLIBS --EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ -+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre -+else -+EXTRA_INCLUDES = $(PLPLOT_CFLAGS) - endif - --INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ -+INCLUDES = \ - $(EXTRA_INCLUDES) \ - -I$(top_srcdir)/ajax/core \ - -I$(top_srcdir)/ajax/graphics \ -@@ -38,3 +41,4 @@ LINKFLAGS = $(VERS_INF) - endif - - libacd_la_LDFLAGS = $(LINKFLAGS) -+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la -diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am -index da57727..857ca5f 100644 ---- a/ajax/ajaxdb/Makefile.am -+++ b/ajax/ajaxdb/Makefile.am -@@ -13,11 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \ - endif - - if !ESYSTEMLIBS --EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ -+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre - endif - - --INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ -+INCLUDES = \ - $(EXTRA_INCLUDES) \ - -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl - -@@ -37,3 +38,4 @@ LINKFLAGS = $(VERS_INF) - endif - - libajaxdb_la_LDFLAGS = $(LINKFLAGS) -+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la -diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am -index af27cb0..8fa4a3a 100644 ---- a/ajax/core/Makefile.am -+++ b/ajax/core/Makefile.am -@@ -12,13 +12,18 @@ CYGWIN_LDAJAX = -L../../plplot -L../expat -L../pcre -L../zlib \ - endif - - if !ESYSTEMLIBS --EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ -+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre -+else -+EXTRA_LIBS = -lexpat -lpcre - endif - -+EXTRA_DIST = ajax-pcre-config.h.in -+DISTCLEAN = ajax-pcre-config.h - - INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \ - -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \ ---I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES) -+$(EXTRA_INCLUDES) $(POSTGRESQL_CFLAGS) $(MYSQL_CFLAGS) - - AJAXSRC = ajalign.c ajarr.c ajassert.c \ - ajbase.c ajcall.c ajcod.c \ -@@ -44,7 +49,7 @@ ajindex.h ajjava.h ajlist.h \ - ajmath.h ajmatrices.h ajmem.h ajmess.h \ - ajnam.h ajnexus.h ajobo.h \ - ajpat.h ajpdb.h ajpdbio.h ajphylo.h \ --ajrange.h ajreg.h ajreport.h ajresource.h \ -+ajrange.h ajreg.h ajax-pcre-config.h ajreport.h ajresource.h \ - ajseq.h ajseqabi.h ajseqbam.h ajseqdata.h ajseqread.h ajseqtype.h ajseqwrite.h \ - ajsort.h ajsql.h ajstr.h ajsys.h \ - ajtable.h ajtax.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h -@@ -61,3 +66,4 @@ LINKFLAGS = $(VERS_INF) - endif - - libajax_la_LDFLAGS = $(LINKFLAGS) -+libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLAGS) -diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-config.h.in -new file mode 100644 -index 0000000..b09e4e6 ---- /dev/null -+++ b/ajax/core/ajax-pcre-config.h.in -@@ -0,0 +1 @@ -+@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE -diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h -index 06793be..659f462 100644 ---- a/ajax/core/ajreg.h -+++ b/ajax/core/ajreg.h -@@ -16,9 +16,14 @@ extern "C" - #define ajreg_h - - #include "ajax.h" -+#include "ajax-pcre-config.h" -+#ifndef AJAX_USE_SYSTEM_PCRE - #include "pcre_config.h" - #include "pcre_internal.h" - #include "pcreposix.h" -+#else -+#include <pcre.h> -+#endif - - #define AJREG_OVECSIZE 30 - -@@ -41,7 +46,11 @@ extern "C" - ******************************************************************************/ - - typedef struct AjSRegexp { -+#ifndef AJAX_USE_SYSTEM_PCRE - real_pcre *pcre; -+#else -+ pcre *pcre; -+#endif - pcre_extra *extra; - int *ovector; - const char* orig; -diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am -index ca33a84..87e51bd 100644 ---- a/ajax/ensembl/Makefile.am -+++ b/ajax/ensembl/Makefile.am -@@ -10,12 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplo - endif - - if !ESYSTEMLIBS --EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \ -+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre - endif - - --INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \ ---I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core -+INCLUDES = $(EXTRA_INCLUDES) \ -+-I$(top_srcdir)/ajax/core - - ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \ - ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \ -@@ -56,3 +57,4 @@ LINKFLAGS = $(VERS_INF) - endif - - libensembl_la_LDFLAGS = $(LINKFLAGS) -+libensembl_la_LIBADD = ../core/libajax.la -diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am -index ab45afc..f61c605 100644 ---- a/ajax/graphics/Makefile.am -+++ b/ajax/graphics/Makefile.am -@@ -10,11 +10,15 @@ CYGWIN_LDAJAXG = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplot - endif - - if !ESYSTEMLIBS --EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \ -+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre -+else -+EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM -+EXTRA_LIBS = $(PLPLOT_LIBS) - endif - - --INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ -+INCLUDES = \ - $(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core - - AJAXGSRC = ajgraph.c ajhist.c -@@ -32,3 +36,4 @@ LINKFLAGS = $(VERS_INF) - endif - - libajaxg_la_LDFLAGS = $(LINKFLAGS) -+libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS) -diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c -index 25e75e4..60f2743 100644 ---- a/ajax/graphics/ajgraph.c -+++ b/ajax/graphics/ajgraph.c -@@ -34,10 +34,8 @@ - #include <float.h> - #define AZ 28 - -- - #include "plplotP.h" - -- - static void GraphArray(ajuint numofpoints, - float *x, float *y); - static void GraphArrayGaps(ajuint numofpoints, -@@ -1049,13 +1047,26 @@ static void GraphDefCharSize(float size) - ** @@ - ******************************************************************************/ - -+#define _GNU_SOURCE -+#include <stdio.h> -+ - static void GraphSetName(const AjPGraph thys, - const AjPStr txt, const char *ext) - { - if(!thys->ready) - { -+#ifdef USE_PLXSFNAM_SHIM -+ char *fullname; -+#endif - ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); -+#ifdef USE_PLXSFNAM_SHIM -+ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext); -+ ajDebug("=g= plsfnam ('%S') instead\n", fullname); -+ plsfnam(fullname); -+ free(fullname); -+#else - plxsfnam(ajStrGetPtr(txt), ext); -+#endif - ajStrAssignS(&graphBasename, txt); - ajStrAssignC(&graphExtension, ext); - if(ajStrGetCharFirst(graphExtension) == '.') -diff --git a/configure.in b/configure.in -index ddb4f81..3f4fe5e 100644 ---- a/configure.in -+++ b/configure.in -@@ -235,15 +235,6 @@ AC_PROG_INSTALL - AC_PROG_LN_S - AC_PROG_MAKE_SET - --dnl Intel MacOSX 10.6 puts X11 in a non-standard place --if test "${with_x}" != "no" ; then --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" --fi --fi --fi - - # Checks for header files. - #as# AC_PATH_X -@@ -292,9 +283,6 @@ AC_CHECK_FUNCS(memmove) - #as# select socket sqrt strchr strcspn strdup strerror strpbrk \ - #as# strrchr strspn strstr strtol]) - --if test "${with_x}" != "no" ; then --LF_EMBOSS_PATH_XLIB --fi - - dnl Library checks - AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket") -@@ -316,14 +304,16 @@ CHECK_PNGDRIVER - CHECK_AUTH - CHECK_AMD64 - -+AM_CONDITIONAL(GJEMBOSS, test "$JAVA_OK" = "yes") -+ - AX_LIB_MYSQL - AX_LIB_POSTGRESQL - - CFLAGS="$CFLAGS $MYSQL_CFLAGS" - LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS" - --CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS" --LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS" -+CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS" -+LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS" - - - dnl Check for 'ant' for packaging Jemboss and export result -@@ -443,13 +433,36 @@ fi - - dnl Test if --enable-systemlibs given - have_systemlibs=no -+DEFINE_USE_SYSTEM_PCRE="#undef" - AC_ARG_ENABLE(systemlibs, - AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])) -+AC_MSG_CHECKING(for systemlib usage) - if test "${enable_systemlibs}" = "yes" ; then - have_systemlibs=yes -+ DEFINE_USE_SYSTEM_PCRE="#define" -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+ PKG_CHECK_MODULES([ZLIB], [zlib]) -+else -+ dnl X11 is only used by plplot -+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place -+ if test "${with_x}" != "no" ; then -+ 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" -+ fi -+ fi -+ fi -+ if test "${with_x}" != "no" ; then -+ LF_EMBOSS_PATH_XLIB -+ fi -+ AC_MSG_NOTICE(USING bundled LIBS) - fi - AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes") - AC_SUBST(ESYSTEMLIBS) -+AC_SUBST(DEFINE_USE_SYSTEM_PCRE) -+AC_SUBST(PLPLOT_CFLAGS) -+AC_SUBST(PLPLOT_LIBS) - - - -@@ -457,7 +470,6 @@ AC_SUBST(ESYSTEMLIBS) - - dnl Test if purify exists and if --enable-purify given if so - dnl set "-g" -- - AC_MSG_CHECKING(for purify) - dnl if(purify -version) < /dev/null > /dev/null 2>&1; then - AC_ARG_ENABLE(purify, -@@ -683,6 +695,7 @@ CHECK_THREADS - - - AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile -+ajax/core/ajax-pcre-config.h - ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile - ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile - ajax/acd/Makefile -diff --git a/emboss/Makefile.am b/emboss/Makefile.am -index 0820517..a0257b2 100644 ---- a/emboss/Makefile.am -+++ b/emboss/Makefile.am -@@ -79,14 +79,17 @@ wordcount wordfinder wordmatch wossname \ - yank - - if !ESYSTEMLIBS --EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ -+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre -+else -+EXTRA_INCLUDES = $(PLPLOT_CFLAGS) - endif - --INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \ -+INCLUDES = -I$(top_srcdir)/nucleus \ - $(EXTRA_INCLUDES) \ - -I$(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$(top_srcdir)/plplot -+ -I$(top_srcdir)/ajax/acd - - - aaindexextract_SOURCES = aaindexextract.c -@@ -319,7 +322,7 @@ testplot_SOURCES = testplot.c - treetypedisplay_SOURCES = treetypedisplay.c - - if !ESYSTEMLIBS --EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la -+EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../plplot/libeplplot.la ../ajax/pcre/libepcre.la - endif - - -@@ -327,7 +330,6 @@ 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) \ -- ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \ - $(XLIB) - - pkgdata_DATA = emboss.default.template -diff --git a/m4/mysql.m4 b/m4/mysql.m4 -index fe413af..ebea25c 100644 ---- a/m4/mysql.m4 -+++ b/m4/mysql.m4 -@@ -1,4 +1,6 @@ --##### http://autoconf-archive.cryp.to/ax_lib_mysql.html -+# =========================================================================== -+# http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html -+# =========================================================================== - # - # SYNOPSIS - # -@@ -6,19 +8,18 @@ - # - # DESCRIPTION - # --# This macro provides tests of availability of MySQL client library --# of particular version or newer. -+# 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. -+# 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) -+# 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 -@@ -33,27 +34,23 @@ - # - # HAVE_MYSQL - # --# LAST MODIFICATION -+# LICENSE - # --# 2006-07-16 --# 2007-01-09 MS: mysql_config --cflags may set gcc -fomit-frame-pointers, --# which prevents gdb from displaying stack traces. --# Changed mysql_config --cflags to mysql_config --include -+# Copyright (c) 2008 Mateusz Loskot <[email protected]> - # --# COPYLEFT --# --# Copyright (c) 2006 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. -+# 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@:>@], -+ 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" -@@ -66,19 +63,20 @@ AC_DEFUN([AX_LIB_MYSQL], - ], - [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 (libpq) -+ dnl Check MySQL libraries - dnl - - if test "$want_mysql" = "yes"; then - -- if test -z "$MYSQL_CONFIG" -o test; then -- AC_PATH_PROG([MYSQL_CONFIG], [mysql_config], [no]) -+ if test -z "$MYSQL_CONFIG" ; then -+ AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no]) - fi - - if test "$MYSQL_CONFIG" != "no"; then -@@ -90,35 +88,8 @@ dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`" - - MYSQL_VERSION=`$MYSQL_CONFIG --version` - --dnl It isn't enough to just test for mysql_config as Fedora --dnl provides it in the mysql RPM even though mysql-devel may --dnl not be installed -- -- EMBCFLAGS=$CFLAGS -- EMBLDFLAGS=$LDFLAGS -- CFLAGS=$MYSQL_CFLAGS -- LDFLAGS=$MYSQL_LDFLAGS -- -- AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h> -- #include "mysql.h"]], -- [[mysql_info(NULL)]])], -- [havemysql=yes], -- [havemysql=no]) -- -- CFLAGS=$EMBCFLAGS -- LDFLAGS=$EMBLDFLAGS -- -- if test "$havemysql" = yes; then -- AC_DEFINE([HAVE_MYSQL], [1], -- [Define to 1 if MySQL libraries are available]) -- found_mysql="yes" -- AC_MSG_RESULT([yes]) -- else -- MYSQL_CFLAGS="" -- MYSQL_LDFLAGS="" -- found_mysql="no" -- AC_MSG_RESULT([no]) -- fi -+ found_mysql="yes" -+ AC_MSG_RESULT([yes]) - else - found_mysql="no" - AC_MSG_RESULT([no]) -@@ -170,6 +141,11 @@ dnl not be installed - fi - fi - -+ if test "$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/nucleus/Makefile.am b/nucleus/Makefile.am -index c244786..ff301b9 100644 ---- a/nucleus/Makefile.am -+++ b/nucleus/Makefile.am -@@ -19,13 +19,16 @@ CYGWIN_LIBS = -L../plplot -L../ajax/pcre -L../ajax/expat -L../ajax/zlib \ - -lezlib -leplplot - else - if !ESYSTEMLIBS --EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ -+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre -+else -+EXTRA_INCLUDES = $(PLPLOT_CFLAGS) - endif - endif - - --INCLUDES = -I$(top_srcdir)/plplot $(X_CFLAGS) -I$(srcdir)/ \ -- -I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \ -+INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \ -+ -I$(top_srcdir)/ajax \ - $(EXTRA_INCLUDES) \ - -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ - -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ -@@ -55,3 +58,4 @@ LINKFLAGS = $(VERS_INF) - endif - - libnucleus_la_LDFLAGS = $(LINKFLAGS) -+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la diff --git a/sci-biology/emboss/files/README.Gentoo b/sci-biology/emboss/files/README.Gentoo deleted file mode 100644 index ce37576..0000000 --- a/sci-biology/emboss/files/README.Gentoo +++ /dev/null @@ -1,28 +0,0 @@ -Using EMBOSS on Gentoo systems - -Codon data files location - -The codon data files that are distributed with EMBOSS are installed in the -"/usr/share/EMBOSS/data/CODONS.orig" directory instead of the usual -"/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 /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 -"/usr/share/EMBOSS/data/embossre.equ.orig" rather than the usual -"/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 /usr/share/EMBOSS/data - ln -s embossre.equ.orig embossre.equ diff --git a/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch b/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch deleted file mode 100644 index 9915f95..0000000 --- a/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -Naur EMBOSS-5.0.0.old/ajax/Makefile.in EMBOSS-5.0.0/ajax/Makefile.in ---- EMBOSS-5.0.0.old/ajax/Makefile.in 2007-07-12 05:53:32.000000000 -0500 -+++ EMBOSS-5.0.0/ajax/Makefile.in 2008-01-25 16:43:51.000000000 -0500 -@@ -244,7 +244,7 @@ - top_srcdir = @top_srcdir@ - @ISCYGWIN_FALSE@lib_LTLIBRARIES = libajax.la libajaxg.la - @ISCYGWIN_TRUE@lib_LTLIBRARIES = libajax.la --@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = -+@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = -lm -L../plplot/.libs -leplplot - @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_FALSE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -leplplot -lm - @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_TRUE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -lajax -leplplot -lm - @ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -L../plplot -leplplot -diff -Naur EMBOSS-5.0.0.old/plplot/Makefile.in EMBOSS-5.0.0/plplot/Makefile.in ---- EMBOSS-5.0.0.old/plplot/Makefile.in 2007-07-12 05:53:36.000000000 -0500 -+++ EMBOSS-5.0.0/plplot/Makefile.in 2008-01-25 16:42:51.000000000 -0500 -@@ -229,7 +229,7 @@ - lib_LTLIBRARIES = libeplplot.la - @AMPNG_FALSE@@ISAIXIA64_TRUE@@ISSHARED_TRUE@AM_CFLAGS = -Wl,-G -lX11 - @AMPNG_TRUE@@ISAIXIA64_TRUE@@ISSHARED_TRUE@AM_CFLAGS = -Wl,-G -lgd -lpng -lz -lX11 -lm --@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = -+@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = PATCH_PLPLOT - @ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -lX11 -lgd -lpng -lz - INCLUDES = $(X_CFLAGS) -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\" - PLPLOTSRC = pdfutils.c plargs.c plbox.c plcont.c plcore.c \ diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch deleted file mode 100644 index 0f5e592..0000000 --- a/sci-biology/emboss/files/emboss-6.3.1_p4-r1_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-README.Gentoo-1 b/sci-biology/emboss/files/emboss-README.Gentoo-1 deleted file mode 100644 index 81e7198..0000000 --- a/sci-biology/emboss/files/emboss-README.Gentoo-1 +++ /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 -``/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual -``/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 /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 ``/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual -``/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 /usr/share/EMBOSS/data - # ln -s embossre.equ.orig embossre.equ 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
