diff -up EMBOSS-6.4.0/ajax/acd/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/acd/Makefile.am
--- EMBOSS-6.4.0/ajax/acd/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200
+++ EMBOSS-6.4.0/ajax/acd/Makefile.am 2011-11-23 17:03:07.033953627 +0100
@@ -13,11 +13,11 @@ CYGWIN_LDACD = -L../../plplot -L../pcre
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$(top_srcdir)/ajax/pcre
endif
AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+-I$(top_srcdir)/plplot \
$(EXTRA_INCLUDES) \
-I$(top_srcdir)/ajax/graphics \
-I$(top_srcdir)/ajax/ensembl \
diff -up EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am
--- EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200
+++ EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am 2011-11-23 17:03:07.033953627 +0100
@@ -13,13 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pc
endif
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
endif
AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
-I$(top_srcdir)/plplot \
--I$(top_srcdir)/ajax/pcre \
$(EXTRA_INCLUDES) \
$(AXIS2C_CPPFLAGS) \
-I$(top_srcdir)/ajax/ensembl
diff -up EMBOSS-6.4.0/ajax/core/ajreg.h.system-pcre EMBOSS-6.4.0/ajax/core/ajreg.h
--- EMBOSS-6.4.0/ajax/core/ajreg.h.system-pcre 2010-04-14 09:44:20.000000000 +0200
+++ EMBOSS-6.4.0/ajax/core/ajreg.h 2011-11-23 17:03:07.034953633 +0100
@@ -16,9 +16,8 @@ extern "C"
#define ajreg_h
#include "ajax.h"
-#include "pcre_config.h"
-#include "pcre_internal.h"
-#include "pcreposix.h"
+#include <pcre.h>
+#include <pcreposix.h>
#define AJREG_OVECSIZE 30
@@ -41,7 +40,7 @@ extern "C"
******************************************************************************/
typedef struct AjSRegexp {
- real_pcre *pcre;
+ struct real_pcre *pcre;
pcre_extra *extra;
int *ovector;
const char* orig;
diff -up EMBOSS-6.4.0/ajax/core/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/core/Makefile.am
--- EMBOSS-6.4.0/ajax/core/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200
+++ EMBOSS-6.4.0/ajax/core/Makefile.am 2011-11-23 17:03:07.035953639 +0100
@@ -12,14 +12,14 @@ CYGWIN_LDAJAX = -L../../plplot -L../expa
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$(top_srcdir)/ajax/pcre
endif
AM_CPPFLAGS = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \
-DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \
$(MYSQL_CPPFLAGS) $(POSTGRESQL_CPPFLAGS) \
--I. -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES)
+-I. -I$(top_srcdir)/plplot $(EXTRA_INCLUDES)
AJAXSRC = ajalign.c ajarr.c \
ajassem.c ajassemread.c ajassemwrite.c \
diff -up EMBOSS-6.4.0/ajax/ensembl/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/ensembl/Makefile.am
--- EMBOSS-6.4.0/ajax/ensembl/Makefile.am.system-pcre 2011-07-07 00:01:27.000000000 +0200
+++ EMBOSS-6.4.0/ajax/ensembl/Makefile.am 2011-11-23 17:03:07.035953639 +0100
@@ -10,14 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../e
endif
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/pcre
endif
AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
-I$(top_srcdir)/plplot \
-$(EXTRA_INCLUDES) \
--I$(top_srcdir)/ajax/pcre
+$(EXTRA_INCLUDES)
ENSEMBLSRC = \
ensalign.c \
diff -up EMBOSS-6.4.0/ajax/graphics/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/graphics/Makefile.am
--- EMBOSS-6.4.0/ajax/graphics/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200
+++ EMBOSS-6.4.0/ajax/graphics/Makefile.am 2011-11-23 17:03:07.036953645 +0100
@@ -10,13 +10,12 @@ CYGWIN_LDAJAXG = -L../../plplot -L../exp
endif
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/pcre
endif
AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
-I$(top_srcdir)/plplot \
--I$(top_srcdir)/ajax/pcre \
$(EXTRA_INCLUDES)
AJAXGSRC = ajgraph.c ajhist.c
diff -up EMBOSS-6.4.0/ajax/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/Makefile.am
--- EMBOSS-6.4.0/ajax/Makefile.am.system-pcre 2010-06-16 12:26:45.000000000 +0200
+++ EMBOSS-6.4.0/ajax/Makefile.am 2011-11-23 17:03:07.037953651 +0100
@@ -1,6 +1,6 @@
## Process this file with automake to produce Makefile.in
if !ESYSTEMLIBS
-EXTRA_DIRS = expat zlib
+EXTRA_DIRS = expat zlib pcre
endif
-SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
+SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
diff -up EMBOSS-6.4.0/configure.in.system-pcre EMBOSS-6.4.0/configure.in
--- EMBOSS-6.4.0/configure.in.system-pcre 2011-06-23 20:47:57.000000000 +0200
+++ EMBOSS-6.4.0/configure.in 2011-11-23 17:05:22.496688169 +0100
@@ -459,31 +459,6 @@ esac
-dnl PCRE library definitions - see the MAJOR and MINOR values
-dnl to see which version's configure.in these lines come from
-
-dnl Provide the current PCRE version information. Do not use numbers
-dnl with leading zeros for the minor version, as they end up in a C
-dnl macro, and may be treated as octal constants. Stick to single
-dnl digits for minor numbers less than 10. There are unlikely to be
-dnl that many releases anyway.
-
-PCRE_MAJOR=7
-PCRE_MINOR=9
-PCRE_DATE=11-Apr-2009
-PCRE_VERSION=${PCRE_MAJOR}.${PCRE_MINOR}
-
-dnl Default values for miscellaneous macros
-
-POSIX_MALLOC_THRESHOLD=-DPOSIX_MALLOC_THRESHOLD=10
-
-dnl Provide versioning information for libtool shared libraries that
-dnl are built by default on Unix systems.
-
-PCRE_LIB_VERSION=0:1:0
-PCRE_POSIXLIB_VERSION=0:0:0
-
-
dnl Define where the EMBOSS package is located
AC_SUBST([AJAX_FIXED_ROOT])
AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
@@ -667,6 +642,7 @@ AC_ARG_ENABLE([systemlibs],
[AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])])
if test "${enable_systemlibs}" = "yes" ; then
have_systemlibs=yes
+ AC_CHECK_LIB(pcre, pcre_compile)
fi
AM_CONDITIONAL([ESYSTEMLIBS], [test "$have_systemlibs" = "yes"])
AC_SUBST([ESYSTEMLIBS])
@@ -832,7 +808,6 @@ AC_CONFIG_FILES([Makefile
ajax/ensembl/Makefile
ajax/expat/Makefile
ajax/graphics/Makefile
- ajax/pcre/Makefile
ajax/zlib/Makefile
doc/Makefile
doc/manuals/Makefile
diff -up EMBOSS-6.4.0/emboss/Makefile.am.system-pcre EMBOSS-6.4.0/emboss/Makefile.am
--- EMBOSS-6.4.0/emboss/Makefile.am.system-pcre 2011-07-08 18:46:55.000000000 +0200
+++ EMBOSS-6.4.0/emboss/Makefile.am 2011-11-23 17:03:07.038953657 +0100
@@ -102,12 +102,11 @@ wossdata wossinput wossname wossoperatio
yank
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
endif
AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
-I$(top_srcdir)/nucleus \
- -I$(top_srcdir)/ajax/pcre \
$(EXTRA_INCLUDES) \
$(AXIS2C_CPPFLAGS) \
-I$(top_srcdir)/ajax/graphics \
@@ -399,14 +398,14 @@ 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 ../ajax/pcre/libepcre.la
endif
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 \
+ ../plplot/libeplplot.la \
$(XLIB)
pkgdata_DATA = $(EXTRA_DIST)
diff -up EMBOSS-6.4.0/nucleus/Makefile.am.system-pcre EMBOSS-6.4.0/nucleus/Makefile.am
--- EMBOSS-6.4.0/nucleus/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200
+++ EMBOSS-6.4.0/nucleus/Makefile.am 2011-11-23 17:03:07.039953663 +0100
@@ -19,14 +19,14 @@ CYGWIN_LIBS = -L../plplot -L../ajax/pcre
-lezlib -leplplot
else
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
endif
endif
AM_CPPFLAGS = -I$(top_srcdir)/ajax/core -I$(top_srcdir)/plplot \
$(X_CFLAGS) -I$(srcdir)/ \
- -I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \
+ -I$(top_srcdir)/ajax \
$(EXTRA_INCLUDES) \
-I$(top_srcdir)/ajax/graphics \
-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \