| 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 <mateusz@loskot.net> |
| # |
| -# COPYLEFT |
| -# |
| -# Copyright (c) 2006 Mateusz Loskot <mateusz@loskot.net> |
| -# |
| -# 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 |