|
 |
177c4d5 |
diff -up EMBOSS-6.4.0/ajax/acd/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/acd/Makefile.am
|
|
|
177c4d5 |
--- EMBOSS-6.4.0/ajax/acd/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200
|
|
|
177c4d5 |
+++ EMBOSS-6.4.0/ajax/acd/Makefile.am 2011-11-23 17:03:07.033953627 +0100
|
|
|
177c4d5 |
@@ -13,11 +13,11 @@ CYGWIN_LDACD = -L../../plplot -L../pcre
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
if !ESYSTEMLIBS
|
|
|
177c4d5 |
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
|
|
|
177c4d5 |
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
|
|
|
177c4d5 |
--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
|
|
|
177c4d5 |
+-I$(top_srcdir)/plplot \
|
|
|
177c4d5 |
$(EXTRA_INCLUDES) \
|
|
|
177c4d5 |
-I$(top_srcdir)/ajax/graphics \
|
|
|
177c4d5 |
-I$(top_srcdir)/ajax/ensembl \
|
|
|
177c4d5 |
diff -up EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am
|
|
|
177c4d5 |
--- EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200
|
|
|
177c4d5 |
+++ EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am 2011-11-23 17:03:07.033953627 +0100
|
|
|
177c4d5 |
@@ -13,13 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pc
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
if !ESYSTEMLIBS
|
|
|
177c4d5 |
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
|
|
|
177c4d5 |
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
|
|
|
177c4d5 |
-I$(top_srcdir)/plplot \
|
|
|
177c4d5 |
--I$(top_srcdir)/ajax/pcre \
|
|
|
177c4d5 |
$(EXTRA_INCLUDES) \
|
|
|
177c4d5 |
$(AXIS2C_CPPFLAGS) \
|
|
|
177c4d5 |
-I$(top_srcdir)/ajax/ensembl
|
|
|
177c4d5 |
diff -up EMBOSS-6.4.0/ajax/core/ajreg.h.system-pcre EMBOSS-6.4.0/ajax/core/ajreg.h
|
|
|
177c4d5 |
--- EMBOSS-6.4.0/ajax/core/ajreg.h.system-pcre 2010-04-14 09:44:20.000000000 +0200
|
|
|
177c4d5 |
+++ EMBOSS-6.4.0/ajax/core/ajreg.h 2011-11-23 17:03:07.034953633 +0100
|
|
|
177c4d5 |
@@ -16,9 +16,8 @@ extern "C"
|
|
|
177c4d5 |
#define ajreg_h
|
|
|
177c4d5 |
|
|
|
177c4d5 |
#include "ajax.h"
|
|
|
177c4d5 |
-#include "pcre_config.h"
|
|
|
177c4d5 |
-#include "pcre_internal.h"
|
|
|
177c4d5 |
-#include "pcreposix.h"
|
|
|
177c4d5 |
+#include <pcre.h>
|
|
|
177c4d5 |
+#include <pcreposix.h>
|
|
|
177c4d5 |
|
|
|
177c4d5 |
#define AJREG_OVECSIZE 30
|
|
|
177c4d5 |
|
|
|
177c4d5 |
@@ -41,7 +40,7 @@ extern "C"
|
|
|
177c4d5 |
******************************************************************************/
|
|
|
177c4d5 |
|
|
|
177c4d5 |
typedef struct AjSRegexp {
|
|
|
177c4d5 |
- real_pcre *pcre;
|
|
|
177c4d5 |
+ struct real_pcre *pcre;
|
|
|
177c4d5 |
pcre_extra *extra;
|
|
|
177c4d5 |
int *ovector;
|
|
|
177c4d5 |
const char* orig;
|
|
|
177c4d5 |
diff -up EMBOSS-6.4.0/ajax/core/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/core/Makefile.am
|
|
|
177c4d5 |
--- EMBOSS-6.4.0/ajax/core/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200
|
|
|
177c4d5 |
+++ EMBOSS-6.4.0/ajax/core/Makefile.am 2011-11-23 17:03:07.035953639 +0100
|
|
|
177c4d5 |
@@ -12,14 +12,14 @@ CYGWIN_LDAJAX = -L../../plplot -L../expa
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
if !ESYSTEMLIBS
|
|
|
177c4d5 |
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
|
|
|
177c4d5 |
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
AM_CPPFLAGS = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \
|
|
|
177c4d5 |
-DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \
|
|
|
177c4d5 |
$(MYSQL_CPPFLAGS) $(POSTGRESQL_CPPFLAGS) \
|
|
|
177c4d5 |
--I. -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES)
|
|
|
177c4d5 |
+-I. -I$(top_srcdir)/plplot $(EXTRA_INCLUDES)
|
|
|
177c4d5 |
|
|
|
177c4d5 |
AJAXSRC = ajalign.c ajarr.c \
|
|
|
177c4d5 |
ajassem.c ajassemread.c ajassemwrite.c \
|
|
|
177c4d5 |
diff -up EMBOSS-6.4.0/ajax/ensembl/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/ensembl/Makefile.am
|
|
|
177c4d5 |
--- EMBOSS-6.4.0/ajax/ensembl/Makefile.am.system-pcre 2011-07-07 00:01:27.000000000 +0200
|
|
|
177c4d5 |
+++ EMBOSS-6.4.0/ajax/ensembl/Makefile.am 2011-11-23 17:03:07.035953639 +0100
|
|
|
177c4d5 |
@@ -10,14 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../e
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
if !ESYSTEMLIBS
|
|
|
177c4d5 |
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
|
|
|
177c4d5 |
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/pcre
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
|
|
|
177c4d5 |
-I$(top_srcdir)/plplot \
|
|
|
177c4d5 |
-$(EXTRA_INCLUDES) \
|
|
|
177c4d5 |
--I$(top_srcdir)/ajax/pcre
|
|
|
177c4d5 |
+$(EXTRA_INCLUDES)
|
|
|
177c4d5 |
|
|
|
177c4d5 |
ENSEMBLSRC = \
|
|
|
177c4d5 |
ensalign.c \
|
|
|
177c4d5 |
diff -up EMBOSS-6.4.0/ajax/graphics/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/graphics/Makefile.am
|
|
|
177c4d5 |
--- EMBOSS-6.4.0/ajax/graphics/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200
|
|
|
177c4d5 |
+++ EMBOSS-6.4.0/ajax/graphics/Makefile.am 2011-11-23 17:03:07.036953645 +0100
|
|
|
177c4d5 |
@@ -10,13 +10,12 @@ CYGWIN_LDAJAXG = -L../../plplot -L../exp
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
if !ESYSTEMLIBS
|
|
|
177c4d5 |
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
|
|
|
177c4d5 |
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/pcre
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
|
|
|
177c4d5 |
-I$(top_srcdir)/plplot \
|
|
|
177c4d5 |
--I$(top_srcdir)/ajax/pcre \
|
|
|
177c4d5 |
$(EXTRA_INCLUDES)
|
|
|
177c4d5 |
|
|
|
177c4d5 |
AJAXGSRC = ajgraph.c ajhist.c
|
|
|
177c4d5 |
diff -up EMBOSS-6.4.0/ajax/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/Makefile.am
|
|
|
177c4d5 |
--- EMBOSS-6.4.0/ajax/Makefile.am.system-pcre 2010-06-16 12:26:45.000000000 +0200
|
|
|
177c4d5 |
+++ EMBOSS-6.4.0/ajax/Makefile.am 2011-11-23 17:03:07.037953651 +0100
|
|
|
177c4d5 |
@@ -1,6 +1,6 @@
|
|
|
177c4d5 |
## Process this file with automake to produce Makefile.in
|
|
|
177c4d5 |
if !ESYSTEMLIBS
|
|
|
177c4d5 |
-EXTRA_DIRS = expat zlib
|
|
|
177c4d5 |
+EXTRA_DIRS = expat zlib pcre
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
-SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
|
|
|
177c4d5 |
+SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
|
|
|
177c4d5 |
diff -up EMBOSS-6.4.0/configure.in.system-pcre EMBOSS-6.4.0/configure.in
|
|
|
177c4d5 |
--- EMBOSS-6.4.0/configure.in.system-pcre 2011-06-23 20:47:57.000000000 +0200
|
|
|
177c4d5 |
+++ EMBOSS-6.4.0/configure.in 2011-11-23 17:05:22.496688169 +0100
|
|
|
177c4d5 |
@@ -459,31 +459,6 @@ esac
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
-dnl PCRE library definitions - see the MAJOR and MINOR values
|
|
|
177c4d5 |
-dnl to see which version's configure.in these lines come from
|
|
|
177c4d5 |
-
|
|
|
177c4d5 |
-dnl Provide the current PCRE version information. Do not use numbers
|
|
|
177c4d5 |
-dnl with leading zeros for the minor version, as they end up in a C
|
|
|
177c4d5 |
-dnl macro, and may be treated as octal constants. Stick to single
|
|
|
177c4d5 |
-dnl digits for minor numbers less than 10. There are unlikely to be
|
|
|
177c4d5 |
-dnl that many releases anyway.
|
|
|
177c4d5 |
-
|
|
|
177c4d5 |
-PCRE_MAJOR=7
|
|
|
177c4d5 |
-PCRE_MINOR=9
|
|
|
177c4d5 |
-PCRE_DATE=11-Apr-2009
|
|
|
177c4d5 |
-PCRE_VERSION=${PCRE_MAJOR}.${PCRE_MINOR}
|
|
|
177c4d5 |
-
|
|
|
177c4d5 |
-dnl Default values for miscellaneous macros
|
|
|
177c4d5 |
-
|
|
|
177c4d5 |
-POSIX_MALLOC_THRESHOLD=-DPOSIX_MALLOC_THRESHOLD=10
|
|
|
177c4d5 |
-
|
|
|
177c4d5 |
-dnl Provide versioning information for libtool shared libraries that
|
|
|
177c4d5 |
-dnl are built by default on Unix systems.
|
|
|
177c4d5 |
-
|
|
|
177c4d5 |
-PCRE_LIB_VERSION=0:1:0
|
|
|
177c4d5 |
-PCRE_POSIXLIB_VERSION=0:0:0
|
|
|
177c4d5 |
-
|
|
|
177c4d5 |
-
|
|
|
177c4d5 |
dnl Define where the EMBOSS package is located
|
|
|
177c4d5 |
AC_SUBST([AJAX_FIXED_ROOT])
|
|
|
177c4d5 |
AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
|
|
|
177c4d5 |
@@ -667,6 +642,7 @@ AC_ARG_ENABLE([systemlibs],
|
|
|
177c4d5 |
[AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])])
|
|
|
177c4d5 |
if test "${enable_systemlibs}" = "yes" ; then
|
|
|
177c4d5 |
have_systemlibs=yes
|
|
|
177c4d5 |
+ AC_CHECK_LIB(pcre, pcre_compile)
|
|
|
177c4d5 |
fi
|
|
|
177c4d5 |
AM_CONDITIONAL([ESYSTEMLIBS], [test "$have_systemlibs" = "yes"])
|
|
|
177c4d5 |
AC_SUBST([ESYSTEMLIBS])
|
|
|
177c4d5 |
@@ -832,7 +808,6 @@ AC_CONFIG_FILES([Makefile
|
|
|
177c4d5 |
ajax/ensembl/Makefile
|
|
|
177c4d5 |
ajax/expat/Makefile
|
|
|
177c4d5 |
ajax/graphics/Makefile
|
|
|
177c4d5 |
- ajax/pcre/Makefile
|
|
|
177c4d5 |
ajax/zlib/Makefile
|
|
|
177c4d5 |
doc/Makefile
|
|
|
177c4d5 |
doc/manuals/Makefile
|
|
|
177c4d5 |
diff -up EMBOSS-6.4.0/emboss/Makefile.am.system-pcre EMBOSS-6.4.0/emboss/Makefile.am
|
|
|
177c4d5 |
--- EMBOSS-6.4.0/emboss/Makefile.am.system-pcre 2011-07-08 18:46:55.000000000 +0200
|
|
|
177c4d5 |
+++ EMBOSS-6.4.0/emboss/Makefile.am 2011-11-23 17:03:07.038953657 +0100
|
|
|
177c4d5 |
@@ -102,12 +102,11 @@ wossdata wossinput wossname wossoperatio
|
|
|
177c4d5 |
yank
|
|
|
177c4d5 |
|
|
|
177c4d5 |
if !ESYSTEMLIBS
|
|
|
177c4d5 |
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
|
|
|
177c4d5 |
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \
|
|
|
177c4d5 |
-I$(top_srcdir)/nucleus \
|
|
|
177c4d5 |
- -I$(top_srcdir)/ajax/pcre \
|
|
|
177c4d5 |
$(EXTRA_INCLUDES) \
|
|
|
177c4d5 |
$(AXIS2C_CPPFLAGS) \
|
|
|
177c4d5 |
-I$(top_srcdir)/ajax/graphics \
|
|
|
177c4d5 |
@@ -399,14 +398,14 @@ testplot_SOURCES = testplot.c
|
|
|
177c4d5 |
treetypedisplay_SOURCES = treetypedisplay.c
|
|
|
177c4d5 |
|
|
|
177c4d5 |
if !ESYSTEMLIBS
|
|
|
177c4d5 |
-EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la
|
|
|
177c4d5 |
+EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../ajax/pcre/libepcre.la
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \
|
|
|
177c4d5 |
../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \
|
|
|
177c4d5 |
../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \
|
|
|
177c4d5 |
$(EXTRA_LDS) \
|
|
|
177c4d5 |
- ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \
|
|
|
177c4d5 |
+ ../plplot/libeplplot.la \
|
|
|
177c4d5 |
$(XLIB)
|
|
|
177c4d5 |
|
|
|
177c4d5 |
pkgdata_DATA = $(EXTRA_DIST)
|
|
|
177c4d5 |
diff -up EMBOSS-6.4.0/nucleus/Makefile.am.system-pcre EMBOSS-6.4.0/nucleus/Makefile.am
|
|
|
177c4d5 |
--- EMBOSS-6.4.0/nucleus/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200
|
|
|
177c4d5 |
+++ EMBOSS-6.4.0/nucleus/Makefile.am 2011-11-23 17:03:07.039953663 +0100
|
|
|
177c4d5 |
@@ -19,14 +19,14 @@ CYGWIN_LIBS = -L../plplot -L../ajax/pcre
|
|
|
177c4d5 |
-lezlib -leplplot
|
|
|
177c4d5 |
else
|
|
|
177c4d5 |
if !ESYSTEMLIBS
|
|
|
177c4d5 |
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
|
|
|
177c4d5 |
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
endif
|
|
|
177c4d5 |
|
|
|
177c4d5 |
|
|
|
177c4d5 |
AM_CPPFLAGS = -I$(top_srcdir)/ajax/core -I$(top_srcdir)/plplot \
|
|
|
177c4d5 |
$(X_CFLAGS) -I$(srcdir)/ \
|
|
|
177c4d5 |
- -I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \
|
|
|
177c4d5 |
+ -I$(top_srcdir)/ajax \
|
|
|
177c4d5 |
$(EXTRA_INCLUDES) \
|
|
|
177c4d5 |
-I$(top_srcdir)/ajax/graphics \
|
|
|
177c4d5 |
-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
|