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EMBOSS
EMBOSS-6.6.0-system-pcre.patch
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File EMBOSS-6.6.0-system-pcre.patch of Package EMBOSS
Index: EMBOSS-6.6.0/ajax/acd/Makefile.am =================================================================== --- EMBOSS-6.6.0.orig/ajax/acd/Makefile.am +++ EMBOSS-6.6.0/ajax/acd/Makefile.am @@ -7,10 +7,10 @@ libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVW libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics -libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre if !ESYSTEMLIBS libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre endif libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS) Index: EMBOSS-6.6.0/configure.in =================================================================== --- EMBOSS-6.6.0.orig/configure.in +++ EMBOSS-6.6.0/configure.in @@ -630,31 +630,6 @@ AS_CASE([${host_os}], -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\\\"" @@ -848,7 +823,7 @@ AC_ARG_ENABLE([systemlibs], [AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])]) AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - +AM_COND_IF([ESYSTEMLIBS], AC_CHECK_LIB(pcre, pcre_compile)) @@ -1000,7 +975,6 @@ AC_CONFIG_FILES([Makefile ajax/ensembl/Makefile ajax/expat/Makefile ajax/graphics/Makefile - ajax/pcre/Makefile ajax/zlib/Makefile doc/Makefile doc/manuals/Makefile Index: EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am =================================================================== --- EMBOSS-6.6.0.orig/ajax/ajaxdb/Makefile.am +++ EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am @@ -5,10 +5,10 @@ lib_LTLIBRARIES = libajaxdb.la libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl -libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre if !ESYSTEMLIBS libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre endif libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS) Index: EMBOSS-6.6.0/ajax/Makefile.am =================================================================== --- EMBOSS-6.6.0.orig/ajax/Makefile.am +++ EMBOSS-6.6.0/ajax/Makefile.am @@ -1,7 +1,8 @@ ## Process this file with automake to produce Makefile.in -SUBDIRS = pcre +SUBDIRS = if !ESYSTEMLIBS -SUBDIRS += expat zlib +SUBDIRS += pcre expat zlib + endif SUBDIRS += core graphics ensembl ajaxdb acd Index: EMBOSS-6.6.0/ajax/core/ajreg.h =================================================================== --- EMBOSS-6.6.0.orig/ajax/core/ajreg.h +++ EMBOSS-6.6.0/ajax/core/ajreg.h @@ -39,9 +39,8 @@ #include "ajdefine.h" #include "ajstr.h" -#include "pcre_config.h" -#include "pcre_internal.h" -#include "pcreposix.h" +#include <pcre.h> +#include <pcreposix.h> AJ_BEGIN_DECLS @@ -84,7 +83,7 @@ AJ_BEGIN_DECLS typedef struct AjSRegexp { - real_pcre *pcre; + struct real_pcre *pcre; pcre_extra *extra; int *ovector; const char* orig; Index: EMBOSS-6.6.0/ajax/core/Makefile.am =================================================================== --- EMBOSS-6.6.0.orig/ajax/core/Makefile.am +++ EMBOSS-6.6.0/ajax/core/Makefile.am @@ -4,10 +4,11 @@ lib_LTLIBRARIES = libajax.la libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre +libajax_la_CPPFLAGS = if !ESYSTEMLIBS libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre endif libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS) Index: EMBOSS-6.6.0/ajax/ensembl/Makefile.am =================================================================== --- EMBOSS-6.6.0.orig/ajax/ensembl/Makefile.am +++ EMBOSS-6.6.0/ajax/ensembl/Makefile.am @@ -4,10 +4,11 @@ lib_LTLIBRARIES = libensembl.la libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre +libensembl_la_CPPFLAGS = if !ESYSTEMLIBS libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre endif libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS) Index: EMBOSS-6.6.0/ajax/graphics/Makefile.am =================================================================== --- EMBOSS-6.6.0.orig/ajax/graphics/Makefile.am +++ EMBOSS-6.6.0/ajax/graphics/Makefile.am @@ -4,9 +4,10 @@ lib_LTLIBRARIES = libajaxg.la libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre +libajaxg_la_CPPFLAGS = if !ESYSTEMLIBS libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat +libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre endif libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS) Index: EMBOSS-6.6.0/nucleus/Makefile.am =================================================================== --- EMBOSS-6.6.0.orig/nucleus/Makefile.am +++ EMBOSS-6.6.0/nucleus/Makefile.am @@ -11,10 +11,10 @@ endif endif libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot -libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre if !ESYSTEMLIBS libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre endif libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl Index: EMBOSS-6.6.0/emboss/Makefile.am =================================================================== --- EMBOSS-6.6.0.orig/emboss/Makefile.am +++ EMBOSS-6.6.0/emboss/Makefile.am @@ -30,10 +30,10 @@ AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics -AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre if !ESYSTEMLIBS AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre endif AM_CPPFLAGS += -I$(top_srcdir)/nucleus AM_CPPFLAGS += -I$(top_srcdir)/plplot @@ -49,8 +49,8 @@ LDADD += ../ajax/core/libajax.la if !ESYSTEMLIBS LDADD += ../ajax/zlib/libezlib.la LDADD += ../ajax/expat/libeexpat.la -endif LDADD += ../ajax/pcre/libepcre.la +endif LDADD += ../plplot/libeplplot.la LDADD += $(XLIB)
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