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a406291 |
diff -up EMBOSS-6.1.0/ajax/ajreg.h.pcre EMBOSS-6.1.0/ajax/ajreg.h
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a406291 |
--- EMBOSS-6.1.0/ajax/ajreg.h.pcre 2007-02-09 19:30:59.000000000 +0100
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a406291 |
+++ EMBOSS-6.1.0/ajax/ajreg.h 2009-09-27 03:17:19.000000000 +0200
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a406291 |
@@ -16,8 +16,8 @@ extern "C"
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a406291 |
#define ajreg_h
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a406291 |
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a406291 |
#include "ajax.h"
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a406291 |
-#include "pcre_internal.h"
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a406291 |
-#include "pcreposix.h"
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a406291 |
+#include <pcre.h>
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a406291 |
+#include <pcreposix.h>
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a406291 |
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a406291 |
#define AJREG_OVECSIZE 30
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a406291 |
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a406291 |
@@ -37,7 +37,7 @@ extern "C"
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a406291 |
******************************************************************************/
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a406291 |
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a406291 |
typedef struct AjSRegexp {
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a406291 |
- real_pcre *pcre;
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a406291 |
+ struct real_pcre *pcre;
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a406291 |
pcre_extra *extra;
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a406291 |
int *ovector;
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a406291 |
const char* orig;
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a406291 |
diff -up EMBOSS-6.1.0/ajax/Makefile.in.pcre EMBOSS-6.1.0/ajax/Makefile.in
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a406291 |
--- EMBOSS-6.1.0/ajax/Makefile.in.pcre 2009-07-15 01:15:58.000000000 +0200
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a406291 |
+++ EMBOSS-6.1.0/ajax/Makefile.in 2009-09-27 03:17:19.000000000 +0200
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a406291 |
@@ -81,7 +81,7 @@ am__libajax_la_SOURCES_DIST = ajacd.c aj
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a406291 |
ajphylo.c ajrange.c ajreg.c ajreport.c ajseq.c ajseqabi.c \
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a406291 |
ajseqdb.c ajseqread.c ajseqtype.c ajseqwrite.c ajsort.c \
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a406291 |
ajstr.c ajsys.c ajtable.c ajtime.c ajtranslate.c ajtree.c \
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a406291 |
- ajutil.c ajvector.c pcre.c pcre_study.c pcreposix.c ajgraph.c \
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a406291 |
+ ajutil.c ajvector.c \
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a406291 |
ajhist.c
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am__objects_1 = ajacd.lo ajalign.lo ajarr.lo ajassert.lo ajbase.lo \
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a406291 |
ajcall.lo ajcod.lo ajdan.lo ajdmx.lo ajdom.lo ajdomain.lo \
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a406291 |
@@ -92,7 +92,7 @@ am__objects_1 = ajacd.lo ajalign.lo ajar
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a406291 |
ajreport.lo ajseq.lo ajseqabi.lo ajseqdb.lo ajseqread.lo \
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a406291 |
ajseqtype.lo ajseqwrite.lo ajsort.lo ajstr.lo ajsys.lo \
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a406291 |
ajtable.lo ajtime.lo ajtranslate.lo ajtree.lo ajutil.lo \
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a406291 |
- ajvector.lo pcre.lo pcre_study.lo pcreposix.lo
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a406291 |
+ ajvector.lo
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a406291 |
am__objects_2 = ajgraph.lo ajhist.lo
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@ISCYGWIN_FALSE@am_libajax_la_OBJECTS = $(am__objects_1)
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a406291 |
@ISCYGWIN_TRUE@am_libajax_la_OBJECTS = $(am__objects_1) \
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a406291 |
@@ -159,7 +159,6 @@ EXEEXT = @EXEEXT@
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a406291 |
FGREP = @FGREP@
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a406291 |
GREP = @GREP@
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a406291 |
HAVE_MEMMOVE = @HAVE_MEMMOVE@
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a406291 |
-HAVE_STRERROR = @HAVE_STRERROR@
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a406291 |
INSTALL = @INSTALL@
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a406291 |
INSTALL_DATA = @INSTALL_DATA@
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a406291 |
INSTALL_PROGRAM = @INSTALL_PROGRAM@
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a406291 |
@@ -172,7 +171,7 @@ LD = @LD@
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a406291 |
LDFLAGS = @LDFLAGS@
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a406291 |
LIBOBJS = @LIBOBJS@
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a406291 |
#LDFLAGS = -no-undefined
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a406291 |
-LIBS =
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a406291 |
+LIBS = @LIBS@
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a406291 |
LIBTOOL = @LIBTOOL@
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a406291 |
LIPO = @LIPO@
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a406291 |
LN_S = @LN_S@
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a406291 |
@@ -193,13 +192,6 @@ PACKAGE_STRING = @PACKAGE_STRING@
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a406291 |
PACKAGE_TARNAME = @PACKAGE_TARNAME@
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a406291 |
PACKAGE_VERSION = @PACKAGE_VERSION@
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a406291 |
PATH_SEPARATOR = @PATH_SEPARATOR@
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a406291 |
-PCRE_DATE = @PCRE_DATE@
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a406291 |
-PCRE_LIB_VERSION = @PCRE_LIB_VERSION@
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a406291 |
-PCRE_MAJOR = @PCRE_MAJOR@
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a406291 |
-PCRE_MINOR = @PCRE_MINOR@
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a406291 |
-PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@
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a406291 |
-PCRE_VERSION = @PCRE_VERSION@
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a406291 |
-POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@
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a406291 |
RANLIB = @RANLIB@
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a406291 |
SED = @SED@
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a406291 |
SET_MAKE = @SET_MAKE@
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a406291 |
@@ -272,8 +264,6 @@ top_srcdir = @top_srcdir@
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a406291 |
@ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_FALSE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -leplplot -lm
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a406291 |
@ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_TRUE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -lajax -leplplot -lm
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a406291 |
@ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -L../plplot -leplplot
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a406291 |
-PCRELIBVERSION = @PCRE_LIB_VERSION@
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a406291 |
-PCREPOSIXLIBVERSION = @PCRE_POSIXLIB_VERSION@
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a406291 |
INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) -DPREFIX=\"$(prefix)\" -I$(top_srcdir)/plplot $(POSIX_MALLOC_THRESHOLD)
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a406291 |
AJAXSRC = ajacd.c ajalign.c ajarr.c ajassert.c \
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a406291 |
ajbase.c ajcall.c ajcod.c \
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a406291 |
@@ -288,8 +278,7 @@ ajrange.c ajreg.c ajreport.c \
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a406291 |
ajseq.c ajseqabi.c ajseqdb.c ajseqread.c ajseqtype.c ajseqwrite.c \
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a406291 |
ajsort.c ajstr.c ajsys.c \
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a406291 |
ajtable.c ajtime.c ajtranslate.c ajtree.c \
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a406291 |
-ajutil.c ajvector.c \
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a406291 |
-pcre.c pcre_study.c pcreposix.c
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a406291 |
+ajutil.c ajvector.c
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a406291 |
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a406291 |
AJAXGSRC = ajgraph.c ajhist.c
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a406291 |
include_HEADERS = ajax.h ajarch.h ajdefine.h \
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a406291 |
@@ -303,9 +292,7 @@ ajpat.h ajpdb.h ajpdbio.h ajphylo.h \
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a406291 |
ajrange.h ajreg.h ajreport.h \
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a406291 |
ajseq.h ajseqabi.h ajseqdata.h ajseqdb.h ajseqread.h ajseqtype.h ajseqwrite.h \
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a406291 |
ajsort.h ajstr.h ajsys.h \
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a406291 |
-ajtable.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h \
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a406291 |
-pcre.h pcre_chartables.c pcre_config.h pcre_get.c pcre_printint.c \
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a406291 |
-pcre_internal.h pcreposix.h
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a406291 |
+ajtable.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h
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a406291 |
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a406291 |
@ISCYGWIN_FALSE@libajax_la_SOURCES = $(AJAXSRC)
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a406291 |
@ISCYGWIN_TRUE@libajax_la_SOURCES = $(AJAXSRC) $(AJAXGSRC)
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a406291 |
@@ -440,9 +427,6 @@ distclean-compile:
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a406291 |
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajtree.Plo@am__quote@
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a406291 |
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajutil.Plo@am__quote@
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a406291 |
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajvector.Plo@am__quote@
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a406291 |
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pcre.Plo@am__quote@
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a406291 |
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pcre_study.Plo@am__quote@
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a406291 |
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pcreposix.Plo@am__quote@
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a406291 |
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a406291 |
.c.o:
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a406291 |
@am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
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a406291 |
diff -up EMBOSS-6.1.0/configure.pcre EMBOSS-6.1.0/configure
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a406291 |
--- EMBOSS-6.1.0/configure.pcre 2009-07-15 01:15:56.000000000 +0200
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a406291 |
+++ EMBOSS-6.1.0/configure 2009-09-27 03:21:32.000000000 +0200
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a406291 |
@@ -16724,6 +16724,73 @@ _ACEOF
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a406291 |
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a406291 |
fi
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a406291 |
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a406291 |
+{ echo "$as_me:$LINENO: checking for pcre_compile in -lpcre" >&5
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a406291 |
+echo $ECHO_N "checking for pcre_compile in -lpcre... $ECHO_C" >&6; }
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a406291 |
+if test "${ac_cv_lib_pcre_pcre_compile+set}" = set; then
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a406291 |
+ echo $ECHO_N "(cached) $ECHO_C" >&6
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a406291 |
+else
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a406291 |
+ ac_check_lib_save_LIBS=$LIBS
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a406291 |
+LIBS="-lpcre $LIBS"
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a406291 |
+cat >conftest.$ac_ext <<_ACEOF
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a406291 |
+/* confdefs.h. */
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a406291 |
+_ACEOF
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a406291 |
+cat confdefs.h >>conftest.$ac_ext
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a406291 |
+cat >>conftest.$ac_ext <<_ACEOF
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a406291 |
+/* end confdefs.h. */
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a406291 |
+
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a406291 |
+/* Override any GCC internal prototype to avoid an error.
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a406291 |
+ Use char because int might match the return type of a GCC
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a406291 |
+ builtin and then its argument prototype would still apply. */
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a406291 |
+#ifdef __cplusplus
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a406291 |
+extern "C"
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a406291 |
+#endif
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a406291 |
+char pcre_compile ();
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a406291 |
+int
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a406291 |
+main ()
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a406291 |
+{
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a406291 |
+return pcre_compile ();
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a406291 |
+ ;
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a406291 |
+ return 0;
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a406291 |
+}
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a406291 |
+_ACEOF
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a406291 |
+rm -f conftest.$ac_objext conftest$ac_exeext
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a406291 |
+if { (ac_try="$ac_link"
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a406291 |
+case "(($ac_try" in
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a406291 |
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
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a406291 |
+ *) ac_try_echo=$ac_try;;
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a406291 |
+esac
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a406291 |
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
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a406291 |
+ (eval "$ac_link") 2>conftest.er1
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a406291 |
+ ac_status=$?
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a406291 |
+ grep -v '^ *+' conftest.er1 >conftest.err
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a406291 |
+ rm -f conftest.er1
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a406291 |
+ cat conftest.err >&5
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a406291 |
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
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a406291 |
+ (exit $ac_status); } && {
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a406291 |
+ test -z "$ac_c_werror_flag" ||
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a406291 |
+ test ! -s conftest.err
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a406291 |
+ } && test -s conftest$ac_exeext &&
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a406291 |
+ $as_test_x conftest$ac_exeext; then
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a406291 |
+ ac_cv_lib_pcre_pcre_compile=yes
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a406291 |
+else
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a406291 |
+ echo "$as_me: failed program was:" >&5
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a406291 |
+sed 's/^/| /' conftest.$ac_ext >&5
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a406291 |
+
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a406291 |
+ ac_cv_lib_pcre_pcre_compile=no
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a406291 |
+fi
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a406291 |
+
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a406291 |
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
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a406291 |
+ conftest$ac_exeext conftest.$ac_ext
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a406291 |
+LIBS=$ac_check_lib_save_LIBS
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a406291 |
+fi
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a406291 |
+{ echo "$as_me:$LINENO: result: $ac_cv_lib_pcre_pcre_compile" >&5
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a406291 |
+echo "${ECHO_T}$ac_cv_lib_pcre_pcre_compile" >&6; }
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a406291 |
+if test "x$ac_cv_lib_pcre_pcre_compile" = x""yes; then
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a406291 |
+ LIBS="-lpcre $LIBS"
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a406291 |
+else
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a406291 |
+ LIBS="$LIBS"
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a406291 |
+fi
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a406291 |
+
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a406291 |
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a406291 |
if test "`uname`" = "FreeBSD" && ${with_pngdriver} != "no"; then
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a406291 |
{ $as_echo "$as_me:$LINENO: checking for main in -liconv" >&5
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