From 6ac824edcb5c78492e08d260413ff65e351ae5db Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Wed, 9 Mar 2011 13:09:22 +0000 Subject: Bump to latest upstream patches (Portage version: 2.2.0_alpha26/cvs/Linux x86_64) --- sci-biology/emboss/files/6.3.1-unbundle-libs.patch | 600 --------------------- .../emboss/files/6.3.1_p4-unbundle-libs.patch | 600 +++++++++++++++++++++ 2 files changed, 600 insertions(+), 600 deletions(-) delete mode 100644 sci-biology/emboss/files/6.3.1-unbundle-libs.patch create mode 100644 sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch (limited to 'sci-biology/emboss/files') diff --git a/sci-biology/emboss/files/6.3.1-unbundle-libs.patch b/sci-biology/emboss/files/6.3.1-unbundle-libs.patch deleted file mode 100644 index 5e463744a739..000000000000 --- a/sci-biology/emboss/files/6.3.1-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) $(MYSQL_LDFLAGS) -diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-config.h.in -new file mode 100644 -index 0000000..b09e4e6 ---- /dev/null -+++ b/ajax/core/ajax-pcre-config.h.in -@@ -0,0 +1 @@ -+@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE -diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h -index 06793be..659f462 100644 ---- a/ajax/core/ajreg.h -+++ b/ajax/core/ajreg.h -@@ -16,9 +16,14 @@ extern "C" - #define ajreg_h - - #include "ajax.h" -+#include "ajax-pcre-config.h" -+#ifndef AJAX_USE_SYSTEM_PCRE - #include "pcre_config.h" - #include "pcre_internal.h" - #include "pcreposix.h" -+#else -+#include -+#endif - - #define AJREG_OVECSIZE 30 - -@@ -41,7 +46,11 @@ extern "C" - ******************************************************************************/ - - typedef struct AjSRegexp { -+#ifndef AJAX_USE_SYSTEM_PCRE - real_pcre *pcre; -+#else -+ pcre *pcre; -+#endif - pcre_extra *extra; - int *ovector; - const char* orig; -diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am -index ca33a84..87e51bd 100644 ---- a/ajax/ensembl/Makefile.am -+++ b/ajax/ensembl/Makefile.am -@@ -10,12 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplo - endif - - if !ESYSTEMLIBS --EXTRA_INCLUDES = -I$(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 $(EXTRA_LIBS) -diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c -index 25e75e4..60f2743 100644 ---- a/ajax/graphics/ajgraph.c -+++ b/ajax/graphics/ajgraph.c -@@ -34,10 +34,8 @@ - #include - #define AZ 28 - -- - #include "plplotP.h" - -- - static void GraphArray(ajuint numofpoints, - float *x, float *y); - static void GraphArrayGaps(ajuint numofpoints, -@@ -1049,13 +1047,26 @@ static void GraphDefCharSize(float size) - ** @@ - ******************************************************************************/ - -+#define _GNU_SOURCE -+#include -+ - static void GraphSetName(const AjPGraph thys, - const AjPStr txt, const char *ext) - { - if(!thys->ready) - { -+#ifdef USE_PLXSFNAM_SHIM -+ char *fullname; -+#endif - ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); -+#ifdef USE_PLXSFNAM_SHIM -+ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext); -+ ajDebug("=g= plsfnam ('%S') instead\n", fullname); -+ plsfnam(fullname); -+ free(fullname); -+#else - plxsfnam(ajStrGetPtr(txt), ext); -+#endif - ajStrAssignS(&graphBasename, txt); - ajStrAssignC(&graphExtension, ext); - if(ajStrGetCharFirst(graphExtension) == '.') -diff --git a/configure.in b/configure.in -index ddb4f81..3f4fe5e 100644 ---- a/configure.in -+++ b/configure.in -@@ -235,15 +235,6 @@ AC_PROG_INSTALL - AC_PROG_LN_S - AC_PROG_MAKE_SET - --dnl Intel MacOSX 10.6 puts X11 in a non-standard place --if test "${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 - # --# COPYLEFT --# --# Copyright (c) 2006 Mateusz Loskot --# --# 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 -- #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/6.3.1_p4-unbundle-libs.patch b/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch new file mode 100644 index 000000000000..5e463744a739 --- /dev/null +++ b/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch @@ -0,0 +1,600 @@ +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) $(MYSQL_LDFLAGS) +diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-config.h.in +new file mode 100644 +index 0000000..b09e4e6 +--- /dev/null ++++ b/ajax/core/ajax-pcre-config.h.in +@@ -0,0 +1 @@ ++@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE +diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h +index 06793be..659f462 100644 +--- a/ajax/core/ajreg.h ++++ b/ajax/core/ajreg.h +@@ -16,9 +16,14 @@ extern "C" + #define ajreg_h + + #include "ajax.h" ++#include "ajax-pcre-config.h" ++#ifndef AJAX_USE_SYSTEM_PCRE + #include "pcre_config.h" + #include "pcre_internal.h" + #include "pcreposix.h" ++#else ++#include ++#endif + + #define AJREG_OVECSIZE 30 + +@@ -41,7 +46,11 @@ extern "C" + ******************************************************************************/ + + typedef struct AjSRegexp { ++#ifndef AJAX_USE_SYSTEM_PCRE + real_pcre *pcre; ++#else ++ pcre *pcre; ++#endif + pcre_extra *extra; + int *ovector; + const char* orig; +diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am +index ca33a84..87e51bd 100644 +--- a/ajax/ensembl/Makefile.am ++++ b/ajax/ensembl/Makefile.am +@@ -10,12 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplo + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(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 $(EXTRA_LIBS) +diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c +index 25e75e4..60f2743 100644 +--- a/ajax/graphics/ajgraph.c ++++ b/ajax/graphics/ajgraph.c +@@ -34,10 +34,8 @@ + #include + #define AZ 28 + +- + #include "plplotP.h" + +- + static void GraphArray(ajuint numofpoints, + float *x, float *y); + static void GraphArrayGaps(ajuint numofpoints, +@@ -1049,13 +1047,26 @@ static void GraphDefCharSize(float size) + ** @@ + ******************************************************************************/ + ++#define _GNU_SOURCE ++#include ++ + static void GraphSetName(const AjPGraph thys, + const AjPStr txt, const char *ext) + { + if(!thys->ready) + { ++#ifdef USE_PLXSFNAM_SHIM ++ char *fullname; ++#endif + ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); ++#ifdef USE_PLXSFNAM_SHIM ++ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext); ++ ajDebug("=g= plsfnam ('%S') instead\n", fullname); ++ plsfnam(fullname); ++ free(fullname); ++#else + plxsfnam(ajStrGetPtr(txt), ext); ++#endif + ajStrAssignS(&graphBasename, txt); + ajStrAssignC(&graphExtension, ext); + if(ajStrGetCharFirst(graphExtension) == '.') +diff --git a/configure.in b/configure.in +index ddb4f81..3f4fe5e 100644 +--- a/configure.in ++++ b/configure.in +@@ -235,15 +235,6 @@ AC_PROG_INSTALL + AC_PROG_LN_S + AC_PROG_MAKE_SET + +-dnl Intel MacOSX 10.6 puts X11 in a non-standard place +-if test "${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 + # +-# COPYLEFT +-# +-# Copyright (c) 2006 Mateusz Loskot +-# +-# 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 +- #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 -- cgit v1.2.3-65-gdbad