|
 |
7b0d192 |
diff -up EMBOSS-6.6.0/ajax/acd/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/acd/Makefile.am
|
|
|
7b0d192 |
--- EMBOSS-6.6.0/ajax/acd/Makefile.am.system-pcre 2013-07-15 17:25:27.000000000 -0400
|
|
|
7b0d192 |
+++ EMBOSS-6.6.0/ajax/acd/Makefile.am 2015-10-30 09:48:28.603257770 -0400
|
|
|
7b0d192 |
@@ -7,10 +7,10 @@ libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVW
|
|
|
7b0d192 |
libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb
|
|
|
7b0d192 |
libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
|
|
|
7b0d192 |
libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
|
|
|
7b0d192 |
-libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
if !ESYSTEMLIBS
|
|
|
7b0d192 |
libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
|
|
|
7b0d192 |
libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
|
|
|
7b0d192 |
+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
endif
|
|
|
7b0d192 |
libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot
|
|
|
7b0d192 |
libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS)
|
|
|
7b0d192 |
diff -up EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am
|
|
|
7b0d192 |
--- EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am.system-pcre 2013-07-15 17:25:28.000000000 -0400
|
|
|
7b0d192 |
+++ EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am 2015-10-30 09:48:28.603257770 -0400
|
|
|
7b0d192 |
@@ -5,10 +5,10 @@ lib_LTLIBRARIES = libajaxdb.la
|
|
|
7b0d192 |
libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
|
|
|
7b0d192 |
|
|
|
7b0d192 |
libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl
|
|
|
7b0d192 |
-libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
if !ESYSTEMLIBS
|
|
|
7b0d192 |
libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
|
|
|
7b0d192 |
libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
|
|
|
7b0d192 |
+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
endif
|
|
|
7b0d192 |
libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot
|
|
|
7b0d192 |
libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS)
|
|
|
7b0d192 |
diff -up EMBOSS-6.6.0/ajax/core/ajreg.h.system-pcre EMBOSS-6.6.0/ajax/core/ajreg.h
|
|
|
7b0d192 |
--- EMBOSS-6.6.0/ajax/core/ajreg.h.system-pcre 2011-10-18 10:23:40.000000000 -0400
|
|
|
7b0d192 |
+++ EMBOSS-6.6.0/ajax/core/ajreg.h 2015-10-30 09:48:28.603257770 -0400
|
|
|
7b0d192 |
@@ -39,9 +39,8 @@
|
|
|
7b0d192 |
#include "ajdefine.h"
|
|
|
7b0d192 |
#include "ajstr.h"
|
|
|
7b0d192 |
|
|
|
7b0d192 |
-#include "pcre_config.h"
|
|
|
7b0d192 |
-#include "pcre_internal.h"
|
|
|
7b0d192 |
-#include "pcreposix.h"
|
|
|
7b0d192 |
+#include <pcre.h>
|
|
|
7b0d192 |
+#include <pcreposix.h>
|
|
|
7b0d192 |
|
|
|
7b0d192 |
AJ_BEGIN_DECLS
|
|
|
7b0d192 |
|
|
|
7b0d192 |
@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS
|
|
|
7b0d192 |
|
|
|
7b0d192 |
typedef struct AjSRegexp
|
|
|
7b0d192 |
{
|
|
|
7b0d192 |
- real_pcre *pcre;
|
|
|
7b0d192 |
+ struct real_pcre *pcre;
|
|
|
7b0d192 |
pcre_extra *extra;
|
|
|
7b0d192 |
int *ovector;
|
|
|
7b0d192 |
const char* orig;
|
|
|
7b0d192 |
diff -up EMBOSS-6.6.0/ajax/core/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/core/Makefile.am
|
|
|
7b0d192 |
--- EMBOSS-6.6.0/ajax/core/Makefile.am.system-pcre 2013-07-15 17:25:28.000000000 -0400
|
|
|
7b0d192 |
+++ EMBOSS-6.6.0/ajax/core/Makefile.am 2015-10-30 09:49:05.159002139 -0400
|
|
|
7b0d192 |
@@ -4,10 +4,11 @@ lib_LTLIBRARIES = libajax.la
|
|
|
7b0d192 |
|
|
|
7b0d192 |
libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
|
|
|
7b0d192 |
|
|
|
7b0d192 |
-libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
+libajax_la_CPPFLAGS =
|
|
|
7b0d192 |
if !ESYSTEMLIBS
|
|
|
7b0d192 |
libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
|
|
|
7b0d192 |
libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
|
|
|
7b0d192 |
+libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
endif
|
|
|
7b0d192 |
libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot
|
|
|
7b0d192 |
libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS)
|
|
|
7b0d192 |
diff -up EMBOSS-6.6.0/ajax/ensembl/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/ensembl/Makefile.am
|
|
|
7b0d192 |
--- EMBOSS-6.6.0/ajax/ensembl/Makefile.am.system-pcre 2013-07-15 17:25:31.000000000 -0400
|
|
|
7b0d192 |
+++ EMBOSS-6.6.0/ajax/ensembl/Makefile.am 2015-10-30 09:49:24.304868253 -0400
|
|
|
7b0d192 |
@@ -4,10 +4,11 @@ lib_LTLIBRARIES = libensembl.la
|
|
|
7b0d192 |
|
|
|
7b0d192 |
libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
|
|
|
7b0d192 |
|
|
|
7b0d192 |
-libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
+libensembl_la_CPPFLAGS =
|
|
|
7b0d192 |
if !ESYSTEMLIBS
|
|
|
7b0d192 |
libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
|
|
|
7b0d192 |
libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
|
|
|
7b0d192 |
+libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
endif
|
|
|
7b0d192 |
libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot
|
|
|
7b0d192 |
libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS)
|
|
|
7b0d192 |
diff -up EMBOSS-6.6.0/ajax/graphics/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/graphics/Makefile.am
|
|
|
7b0d192 |
--- EMBOSS-6.6.0/ajax/graphics/Makefile.am.system-pcre 2013-07-15 17:25:33.000000000 -0400
|
|
|
7b0d192 |
+++ EMBOSS-6.6.0/ajax/graphics/Makefile.am 2015-10-30 09:49:52.210673110 -0400
|
|
|
7b0d192 |
@@ -4,9 +4,10 @@ lib_LTLIBRARIES = libajaxg.la
|
|
|
7b0d192 |
|
|
|
7b0d192 |
libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS)
|
|
|
7b0d192 |
|
|
|
7b0d192 |
-libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
+libajaxg_la_CPPFLAGS =
|
|
|
7b0d192 |
if !ESYSTEMLIBS
|
|
|
7b0d192 |
libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
|
|
|
7b0d192 |
+libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
endif
|
|
|
7b0d192 |
libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot
|
|
|
7b0d192 |
libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS)
|
|
|
7b0d192 |
diff -up EMBOSS-6.6.0/ajax/Makefile.am.system-pcre EMBOSS-6.6.0/ajax/Makefile.am
|
|
|
7b0d192 |
--- EMBOSS-6.6.0/ajax/Makefile.am.system-pcre 2011-08-25 15:45:55.000000000 -0400
|
|
|
7b0d192 |
+++ EMBOSS-6.6.0/ajax/Makefile.am 2015-10-30 09:48:28.604257763 -0400
|
|
|
7b0d192 |
@@ -1,7 +1,7 @@
|
|
|
7b0d192 |
## Process this file with automake to produce Makefile.in
|
|
|
7b0d192 |
|
|
|
7b0d192 |
-SUBDIRS = pcre
|
|
|
7b0d192 |
+SUBDIRS =
|
|
|
7b0d192 |
if !ESYSTEMLIBS
|
|
|
7b0d192 |
-SUBDIRS += expat zlib
|
|
|
7b0d192 |
+SUBDIRS += expat zlib pcre
|
|
|
7b0d192 |
endif
|
|
|
7b0d192 |
SUBDIRS += core graphics ensembl ajaxdb acd
|
|
|
7b0d192 |
diff -up EMBOSS-6.6.0/configure.in.system-pcre EMBOSS-6.6.0/configure.in
|
|
|
7b0d192 |
--- EMBOSS-6.6.0/configure.in.system-pcre 2013-07-15 17:25:27.000000000 -0400
|
|
|
7b0d192 |
+++ EMBOSS-6.6.0/configure.in 2015-10-30 09:48:28.604257763 -0400
|
|
|
7b0d192 |
@@ -630,31 +630,6 @@ AS_CASE([${host_os}],
|
|
|
7b0d192 |
|
|
|
7b0d192 |
|
|
|
7b0d192 |
|
|
|
7b0d192 |
-dnl PCRE library definitions - see the MAJOR and MINOR values
|
|
|
7b0d192 |
-dnl to see which version's configure.in these lines come from
|
|
|
7b0d192 |
-
|
|
|
7b0d192 |
-dnl Provide the current PCRE version information. Do not use numbers
|
|
|
7b0d192 |
-dnl with leading zeros for the minor version, as they end up in a C
|
|
|
7b0d192 |
-dnl macro, and may be treated as octal constants. Stick to single
|
|
|
7b0d192 |
-dnl digits for minor numbers less than 10. There are unlikely to be
|
|
|
7b0d192 |
-dnl that many releases anyway.
|
|
|
7b0d192 |
-
|
|
|
7b0d192 |
-PCRE_MAJOR="7"
|
|
|
7b0d192 |
-PCRE_MINOR="9"
|
|
|
7b0d192 |
-PCRE_DATE="11-Apr-2009"
|
|
|
7b0d192 |
-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
|
|
|
7b0d192 |
-
|
|
|
7b0d192 |
-dnl Default values for miscellaneous macros
|
|
|
7b0d192 |
-
|
|
|
7b0d192 |
-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
|
|
|
7b0d192 |
-
|
|
|
7b0d192 |
-dnl Provide versioning information for libtool shared libraries that
|
|
|
7b0d192 |
-dnl are built by default on Unix systems.
|
|
|
7b0d192 |
-
|
|
|
7b0d192 |
-PCRE_LIB_VERSION="0:1:0"
|
|
|
7b0d192 |
-PCRE_POSIXLIB_VERSION="0:0:0"
|
|
|
7b0d192 |
-
|
|
|
7b0d192 |
-
|
|
|
7b0d192 |
dnl Define where the EMBOSS package is located
|
|
|
7b0d192 |
AC_SUBST([AJAX_FIXED_ROOT])
|
|
|
7b0d192 |
AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
|
|
|
7b0d192 |
@@ -743,19 +718,6 @@ AX_LIB_POSTGRESQL
|
|
|
7b0d192 |
|
|
|
7b0d192 |
|
|
|
7b0d192 |
|
|
|
7b0d192 |
-dnl "Export" these variables for PCRE
|
|
|
7b0d192 |
-
|
|
|
7b0d192 |
-AC_SUBST([HAVE_MEMMOVE])
|
|
|
7b0d192 |
-AC_SUBST([HAVE_STRERROR])
|
|
|
7b0d192 |
-AC_SUBST([PCRE_MAJOR])
|
|
|
7b0d192 |
-AC_SUBST([PCRE_MINOR])
|
|
|
7b0d192 |
-AC_SUBST([PCRE_DATE])
|
|
|
7b0d192 |
-AC_SUBST([PCRE_VERSION])
|
|
|
7b0d192 |
-AC_SUBST([PCRE_LIB_VERSION])
|
|
|
7b0d192 |
-AC_SUBST([PCRE_POSIXLIB_VERSION])
|
|
|
7b0d192 |
-AC_SUBST([POSIX_MALLOC_THRESHOLD])
|
|
|
7b0d192 |
-
|
|
|
7b0d192 |
-
|
|
|
7b0d192 |
|
|
|
7b0d192 |
|
|
|
7b0d192 |
# Enable debugging: --enable-debug, sets CFLAGS
|
|
|
7b0d192 |
@@ -846,7 +808,9 @@ AS_IF([test "x${enable_large}" = "xno"],
|
|
|
7b0d192 |
|
|
|
7b0d192 |
AC_ARG_ENABLE([systemlibs],
|
|
|
7b0d192 |
[AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])])
|
|
|
7b0d192 |
-
|
|
|
7b0d192 |
+if test "x${enable_systemlibs}" = "xyes" ; then
|
|
|
7b0d192 |
+ AC_CHECK_LIB(pcre, pcre_compile)
|
|
|
7b0d192 |
+fi
|
|
|
7b0d192 |
AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
|
|
|
7b0d192 |
|
|
|
7b0d192 |
|
|
|
7b0d192 |
@@ -1000,7 +964,6 @@ AC_CONFIG_FILES([Makefile
|
|
|
7b0d192 |
ajax/ensembl/Makefile
|
|
|
7b0d192 |
ajax/expat/Makefile
|
|
|
7b0d192 |
ajax/graphics/Makefile
|
|
|
7b0d192 |
- ajax/pcre/Makefile
|
|
|
7b0d192 |
ajax/zlib/Makefile
|
|
|
7b0d192 |
doc/Makefile
|
|
|
7b0d192 |
doc/manuals/Makefile
|
|
|
7b0d192 |
diff -up EMBOSS-6.6.0/emboss/Makefile.am.system-pcre EMBOSS-6.6.0/emboss/Makefile.am
|
|
|
7b0d192 |
--- EMBOSS-6.6.0/emboss/Makefile.am.system-pcre 2013-07-15 17:25:46.000000000 -0400
|
|
|
7b0d192 |
+++ EMBOSS-6.6.0/emboss/Makefile.am 2015-10-30 09:48:28.605257756 -0400
|
|
|
7b0d192 |
@@ -30,10 +30,10 @@ AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd
|
|
|
7b0d192 |
AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb
|
|
|
7b0d192 |
AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
|
|
|
7b0d192 |
AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
|
|
|
7b0d192 |
-AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
if !ESYSTEMLIBS
|
|
|
7b0d192 |
AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat
|
|
|
7b0d192 |
AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
|
|
|
7b0d192 |
+AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
endif
|
|
|
7b0d192 |
AM_CPPFLAGS += -I$(top_srcdir)/nucleus
|
|
|
7b0d192 |
AM_CPPFLAGS += -I$(top_srcdir)/plplot
|
|
|
7b0d192 |
@@ -49,8 +49,8 @@ LDADD += ../ajax/core/libajax.la
|
|
|
7b0d192 |
if !ESYSTEMLIBS
|
|
|
7b0d192 |
LDADD += ../ajax/zlib/libezlib.la
|
|
|
7b0d192 |
LDADD += ../ajax/expat/libeexpat.la
|
|
|
7b0d192 |
-endif
|
|
|
7b0d192 |
LDADD += ../ajax/pcre/libepcre.la
|
|
|
7b0d192 |
+endif
|
|
|
7b0d192 |
LDADD += ../plplot/libeplplot.la
|
|
|
7b0d192 |
LDADD += $(XLIB)
|
|
|
7b0d192 |
|
|
|
7b0d192 |
diff -up EMBOSS-6.6.0/nucleus/Makefile.am.system-pcre EMBOSS-6.6.0/nucleus/Makefile.am
|
|
|
7b0d192 |
--- EMBOSS-6.6.0/nucleus/Makefile.am.system-pcre 2013-07-15 17:25:50.000000000 -0400
|
|
|
7b0d192 |
+++ EMBOSS-6.6.0/nucleus/Makefile.am 2015-10-30 09:48:28.605257756 -0400
|
|
|
7b0d192 |
@@ -11,10 +11,10 @@ endif
|
|
|
7b0d192 |
endif
|
|
|
7b0d192 |
|
|
|
7b0d192 |
libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot
|
|
|
7b0d192 |
-libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
if !ESYSTEMLIBS
|
|
|
7b0d192 |
libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat
|
|
|
7b0d192 |
libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
|
|
|
7b0d192 |
+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
|
|
|
7b0d192 |
endif
|
|
|
7b0d192 |
libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
|
|
|
7b0d192 |
libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
|