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Fedora:: spot
EPEL:: spot
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Commit: 28e4118c5a9e50533858a4d107ff34dd0dc5b35f
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diff -up EMBOSS-6.3.1/ajax/acd/Makefile.am.system-pcre EMBOSS-6.3.1/ajax/acd/Makefile.am
--- EMBOSS-6.3.1/ajax/acd/Makefile.am.system-pcre	2010-06-16 07:36:00.000000000 -0400
+++ EMBOSS-6.3.1/ajax/acd/Makefile.am	2010-08-02 15:53:45.289153815 -0400
@@ -13,10 +13,10 @@ 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
 
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+INCLUDES = -I$(top_srcdir)/plplot \
 $(EXTRA_INCLUDES) \
 -I$(top_srcdir)/ajax/core \
 -I$(top_srcdir)/ajax/graphics \
diff -up EMBOSS-6.3.1/ajax/acd/Makefile.in.system-pcre EMBOSS-6.3.1/ajax/acd/Makefile.in
--- EMBOSS-6.3.1/ajax/acd/Makefile.in.system-pcre	2010-07-19 07:55:40.000000000 -0400
+++ EMBOSS-6.3.1/ajax/acd/Makefile.in	2010-08-02 15:54:22.726269678 -0400
@@ -130,8 +130,6 @@ ESYSTEMLIBS = @ESYSTEMLIBS@
 EXEEXT = @EXEEXT@
 FGREP = @FGREP@
 GREP = @GREP@
-HAVE_MEMMOVE = @HAVE_MEMMOVE@
-HAVE_STRERROR = @HAVE_STRERROR@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -258,8 +256,8 @@ AM_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFL
 @ISCYGWIN_TRUE@-L../graphics -L../ensembl -L../ajaxdb -lajaxdb -lensembl -lajaxg -lajax \
 @ISCYGWIN_TRUE@-leplplot -leexpat -lepcre -lezlib
 
-@ESYSTEMLIBS_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+@ESYSTEMLIBS_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
+INCLUDES = -I$(top_srcdir)/plplot \
 $(EXTRA_INCLUDES) \
 -I$(top_srcdir)/ajax/core \
 -I$(top_srcdir)/ajax/graphics \
@@ -286,9 +284,9 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefi
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu ajax/acd/Makefile'; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits ajax/acd/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu ajax/acd/Makefile
+	  $(AUTOMAKE) --gnits ajax/acd/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
diff -up EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am.system-pcre EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am
--- EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am.system-pcre	2010-06-16 07:36:00.000000000 -0400
+++ EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am	2010-08-02 15:54:56.056144703 -0400
@@ -13,11 +13,11 @@ 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
 
 
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+INCLUDES = -I$(top_srcdir)/plplot \
 $(EXTRA_INCLUDES) \
 -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl
 
diff -up EMBOSS-6.3.1/ajax/ajaxdb/Makefile.in.system-pcre EMBOSS-6.3.1/ajax/ajaxdb/Makefile.in
--- EMBOSS-6.3.1/ajax/ajaxdb/Makefile.in.system-pcre	2010-07-19 07:55:40.000000000 -0400
+++ EMBOSS-6.3.1/ajax/ajaxdb/Makefile.in	2010-08-02 15:55:40.350270055 -0400
@@ -130,8 +130,6 @@ ESYSTEMLIBS = @ESYSTEMLIBS@
 EXEEXT = @EXEEXT@
 FGREP = @FGREP@
 GREP = @GREP@
-HAVE_MEMMOVE = @HAVE_MEMMOVE@
-HAVE_STRERROR = @HAVE_STRERROR@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -257,8 +255,8 @@ AM_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFL
 @ISCYGWIN_TRUE@CYGWIN_LDAJAXDB = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \
 @ISCYGWIN_TRUE@-L../ensembl -lensembl lajax -leplplot -leexpat -lepcre -lezlib
 
-@ESYSTEMLIBS_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+@ESYSTEMLIBS_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
+INCLUDES = -I$(top_srcdir)/plplot \
 $(EXTRA_INCLUDES) \
 -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl
 
@@ -284,9 +282,9 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefi
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu ajax/ajaxdb/Makefile'; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits ajax/ajaxdb/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu ajax/ajaxdb/Makefile
+	  $(AUTOMAKE) --gnits ajax/ajaxdb/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
diff -up EMBOSS-6.3.1/ajax/core/ajreg.h.system-pcre EMBOSS-6.3.1/ajax/core/ajreg.h
--- EMBOSS-6.3.1/ajax/core/ajreg.h.system-pcre	2010-04-14 03:44:20.000000000 -0400
+++ EMBOSS-6.3.1/ajax/core/ajreg.h	2010-08-02 15:51:12.877269709 -0400
@@ -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-6.3.1/ajax/core/Makefile.am.system-pcre EMBOSS-6.3.1/ajax/core/Makefile.am
--- EMBOSS-6.3.1/ajax/core/Makefile.am.system-pcre	2010-06-16 07:36:00.000000000 -0400
+++ EMBOSS-6.3.1/ajax/core/Makefile.am	2010-08-02 15:56:46.987145446 -0400
@@ -12,13 +12,13 @@ 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
 
 
 INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \
 -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \
--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES)
+-I$(top_srcdir)/plplot $(EXTRA_INCLUDES)
 
 AJAXSRC = ajalign.c ajarr.c ajassert.c \
 ajbase.c ajcall.c ajcod.c \
diff -up EMBOSS-6.3.1/ajax/core/Makefile.in.system-pcre EMBOSS-6.3.1/ajax/core/Makefile.in
--- EMBOSS-6.3.1/ajax/core/Makefile.in.system-pcre	2010-07-19 07:55:40.000000000 -0400
+++ EMBOSS-6.3.1/ajax/core/Makefile.in	2010-08-02 15:57:14.969269966 -0400
@@ -139,8 +139,6 @@ ESYSTEMLIBS = @ESYSTEMLIBS@
 EXEEXT = @EXEEXT@
 FGREP = @FGREP@
 GREP = @GREP@
-HAVE_MEMMOVE = @HAVE_MEMMOVE@
-HAVE_STRERROR = @HAVE_STRERROR@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -266,10 +264,10 @@ AM_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFL
 @ISCYGWIN_TRUE@CYGWIN_LDAJAX = -L../../plplot -L../expat -L../pcre -L../zlib \
 @ISCYGWIN_TRUE@-leplplot -leexpat -lepcre -lezlib
 
-@ESYSTEMLIBS_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+@ESYSTEMLIBS_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
 INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \
 -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \
--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES)
+-I$(top_srcdir)/plplot $(EXTRA_INCLUDES)
 
 AJAXSRC = ajalign.c ajarr.c ajassert.c \
 ajbase.c ajcall.c ajcod.c \
@@ -318,9 +316,9 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefi
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu ajax/core/Makefile'; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits ajax/core/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu ajax/core/Makefile
+	  $(AUTOMAKE) --gnits ajax/core/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
diff -up EMBOSS-6.3.1/ajax/ensembl/Makefile.am.system-pcre EMBOSS-6.3.1/ajax/ensembl/Makefile.am
--- EMBOSS-6.3.1/ajax/ensembl/Makefile.am.system-pcre	2010-06-16 07:36:00.000000000 -0400
+++ EMBOSS-6.3.1/ajax/ensembl/Makefile.am	2010-08-02 15:57:44.938305995 -0400
@@ -10,12 +10,12 @@ 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
 
 
 INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \
--I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core
+-I$(top_srcdir)/ajax/core
 
 ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \
 ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \
diff -up EMBOSS-6.3.1/ajax/ensembl/Makefile.in.system-pcre EMBOSS-6.3.1/ajax/ensembl/Makefile.in
--- EMBOSS-6.3.1/ajax/ensembl/Makefile.in.system-pcre	2010-07-19 07:55:40.000000000 -0400
+++ EMBOSS-6.3.1/ajax/ensembl/Makefile.in	2010-08-02 15:58:24.860163822 -0400
@@ -143,8 +143,6 @@ ESYSTEMLIBS = @ESYSTEMLIBS@
 EXEEXT = @EXEEXT@
 FGREP = @FGREP@
 GREP = @GREP@
-HAVE_MEMMOVE = @HAVE_MEMMOVE@
-HAVE_STRERROR = @HAVE_STRERROR@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -266,9 +264,9 @@ lib_LTLIBRARIES = libensembl.la
 AM_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS)
 @ISCYGWIN_TRUE@CYGWIN_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import
 @ISCYGWIN_TRUE@CYGWIN_LDENSEMBL = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplot -leexpat -lepcre
-@ESYSTEMLIBS_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
+@ESYSTEMLIBS_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/pcre
 INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \
--I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core
+-I$(top_srcdir)/ajax/core
 
 ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \
 ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \
@@ -316,9 +314,9 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefi
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu ajax/ensembl/Makefile'; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits ajax/ensembl/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu ajax/ensembl/Makefile
+	  $(AUTOMAKE) --gnits ajax/ensembl/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
diff -up EMBOSS-6.3.1/ajax/graphics/Makefile.am.system-pcre EMBOSS-6.3.1/ajax/graphics/Makefile.am
--- EMBOSS-6.3.1/ajax/graphics/Makefile.am.system-pcre	2010-06-16 07:36:00.000000000 -0400
+++ EMBOSS-6.3.1/ajax/graphics/Makefile.am	2010-08-02 15:59:19.049155233 -0400
@@ -10,11 +10,11 @@ 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
 
 
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+INCLUDES = -I$(top_srcdir)/plplot \
 $(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core
 
 AJAXGSRC = ajgraph.c ajhist.c
diff -up EMBOSS-6.3.1/ajax/graphics/Makefile.in.system-pcre EMBOSS-6.3.1/ajax/graphics/Makefile.in
--- EMBOSS-6.3.1/ajax/graphics/Makefile.in.system-pcre	2010-07-19 07:55:40.000000000 -0400
+++ EMBOSS-6.3.1/ajax/graphics/Makefile.in	2010-08-02 15:59:40.355144835 -0400
@@ -130,8 +130,6 @@ ESYSTEMLIBS = @ESYSTEMLIBS@
 EXEEXT = @EXEEXT@
 FGREP = @FGREP@
 GREP = @GREP@
-HAVE_MEMMOVE = @HAVE_MEMMOVE@
-HAVE_STRERROR = @HAVE_STRERROR@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -253,8 +251,8 @@ lib_LTLIBRARIES = libajaxg.la
 AM_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS)
 @ISCYGWIN_TRUE@CYGWIN_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import
 @ISCYGWIN_TRUE@CYGWIN_LDAJAXG = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplot -leexpat -lepcre
-@ESYSTEMLIBS_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+@ESYSTEMLIBS_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/pcre
+INCLUDES = -I$(top_srcdir)/plplot \
 $(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core
 
 AJAXGSRC = ajgraph.c ajhist.c
@@ -277,9 +275,9 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefi
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu ajax/graphics/Makefile'; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits ajax/graphics/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu ajax/graphics/Makefile
+	  $(AUTOMAKE) --gnits ajax/graphics/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
diff -up EMBOSS-6.3.1/ajax/Makefile.am.system-pcre EMBOSS-6.3.1/ajax/Makefile.am
--- EMBOSS-6.3.1/ajax/Makefile.am.system-pcre	2010-06-16 06:26:45.000000000 -0400
+++ EMBOSS-6.3.1/ajax/Makefile.am	2010-08-02 16:00:21.489296489 -0400
@@ -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-6.3.1/ajax/Makefile.in.system-pcre EMBOSS-6.3.1/ajax/Makefile.in
--- EMBOSS-6.3.1/ajax/Makefile.in.system-pcre	2010-07-19 07:55:40.000000000 -0400
+++ EMBOSS-6.3.1/ajax/Makefile.in	2010-08-02 16:00:52.531270101 -0400
@@ -121,8 +121,6 @@ ESYSTEMLIBS = @ESYSTEMLIBS@
 EXEEXT = @EXEEXT@
 FGREP = @FGREP@
 GREP = @GREP@
-HAVE_MEMMOVE = @HAVE_MEMMOVE@
-HAVE_STRERROR = @HAVE_STRERROR@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -240,8 +238,8 @@ target_alias = @target_alias@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-@ESYSTEMLIBS_FALSE@EXTRA_DIRS = expat zlib
-SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
+@ESYSTEMLIBS_FALSE@EXTRA_DIRS = expat zlib pcre
+SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
 all: all-recursive
 
 .SUFFIXES:
@@ -254,9 +252,9 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefi
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu ajax/Makefile'; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits ajax/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu ajax/Makefile
+	  $(AUTOMAKE) --gnits ajax/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
diff -up EMBOSS-6.3.1/configure.in.system-pcre EMBOSS-6.3.1/configure.in
--- EMBOSS-6.3.1/configure.in.system-pcre	2010-07-19 07:45:34.000000000 -0400
+++ EMBOSS-6.3.1/configure.in	2010-08-02 16:23:19.710145317 -0400
@@ -196,30 +196,6 @@ fi
 dnl endian test for indexing system
 AC_C_BIGENDIAN(CPPFLAGS="$CPPFLAGS -DBENDIAN",CPPFLAGS="$CPPFLAGS -DLENDIAN")
 
-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)
@@ -447,6 +423,7 @@ 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)
@@ -683,7 +660,7 @@ CHECK_THREADS
 
 
 AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile
-ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile
+ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile
 ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile
 ajax/acd/Makefile
 emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile
diff -up EMBOSS-6.3.1/configure.system-pcre EMBOSS-6.3.1/configure
--- EMBOSS-6.3.1/configure.system-pcre	2010-08-02 16:26:26.125269290 -0400
+++ EMBOSS-6.3.1/configure	2010-08-02 16:23:38.092267468 -0400
@@ -11891,20 +11891,6 @@ $as_echo "#define AC_APPLE_UNIVERSAL_BUI
 
 
 
-PCRE_MAJOR=7
-PCRE_MINOR=9
-PCRE_DATE=11-Apr-2009
-PCRE_VERSION=${PCRE_MAJOR}.${PCRE_MINOR}
-
-
-POSIX_MALLOC_THRESHOLD=-DPOSIX_MALLOC_THRESHOLD=10
-
-
-PCRE_LIB_VERSION=0:1:0
-PCRE_POSIXLIB_VERSION=0:0:0
-
-
-
 AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
 
 EMBOSS_TOP=`pwd`
@@ -14915,6 +14901,51 @@ fi
 
 if test "${enable_systemlibs}" = "yes" ; then
     have_systemlibs=yes
+    { $as_echo "$as_me:${as_lineno-$LINENO}: checking for pcre_compile in -lpcre" >&5
+$as_echo_n "checking for pcre_compile in -lpcre... " >&6; }
+if test "${ac_cv_lib_pcre_pcre_compile+set}" = set; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lpcre  $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char pcre_compile ();
+int
+main ()
+{
+return pcre_compile ();
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+  ac_cv_lib_pcre_pcre_compile=yes
+else
+  ac_cv_lib_pcre_pcre_compile=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+    conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_pcre_pcre_compile" >&5
+$as_echo "$ac_cv_lib_pcre_pcre_compile" >&6; }
+if test "x$ac_cv_lib_pcre_pcre_compile" = x""yes; then :
+  cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBPCRE 1
+_ACEOF
+
+  LIBS="-lpcre $LIBS"
+
+fi
+
 fi
  if test "$have_systemlibs" = "yes"; then
   ESYSTEMLIBS_TRUE=
@@ -15268,7 +15299,7 @@ fi
 
 
 
-ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile ajax/acd/Makefile emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/testdb/Makefile emboss/data/Makefile emboss/data/AAINDEX/Makefile emboss/data/CODONS/Makefile emboss/data/REBASE/Makefile emboss/data/JASPAR_CORE/Makefile emboss/data/JASPAR_FAM/Makefile emboss/data/JASPAR_PHYLOFACTS/Makefile emboss/data/JASPAR_CNE/Makefile emboss/data/JASPAR_POLII/Makefile emboss/data/JASPAR_SPLICE/Makefile emboss/data/JASPAR_PBM/Makefile emboss/data/JASPAR_PBM_HLH/Makefile emboss/data/JASPAR_PBM_HOMEO/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile doc/Makefile doc/manuals/Makefile doc/tutorials/Makefile doc/programs/Makefile doc/programs/html/Makefile doc/programs/text/Makefile jemboss/Makefile jemboss/images/Makefile jemboss/lib/Makefile jemboss/lib/axis/Makefile jemboss/resources/Makefile jemboss/utils/Makefile Makefile"
+ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile ajax/acd/Makefile emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/testdb/Makefile emboss/data/Makefile emboss/data/AAINDEX/Makefile emboss/data/CODONS/Makefile emboss/data/REBASE/Makefile emboss/data/JASPAR_CORE/Makefile emboss/data/JASPAR_FAM/Makefile emboss/data/JASPAR_PHYLOFACTS/Makefile emboss/data/JASPAR_CNE/Makefile emboss/data/JASPAR_POLII/Makefile emboss/data/JASPAR_SPLICE/Makefile emboss/data/JASPAR_PBM/Makefile emboss/data/JASPAR_PBM_HLH/Makefile emboss/data/JASPAR_PBM_HOMEO/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile doc/Makefile doc/manuals/Makefile doc/tutorials/Makefile doc/programs/Makefile doc/programs/html/Makefile doc/programs/text/Makefile jemboss/Makefile jemboss/images/Makefile jemboss/lib/Makefile jemboss/lib/axis/Makefile jemboss/resources/Makefile jemboss/utils/Makefile Makefile"
 
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
@@ -16326,7 +16357,6 @@ do
     "plplot/lib/Makefile") CONFIG_FILES="$CONFIG_FILES plplot/lib/Makefile" ;;
     "nucleus/Makefile") CONFIG_FILES="$CONFIG_FILES nucleus/Makefile" ;;
     "ajax/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/Makefile" ;;
-    "ajax/pcre/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/pcre/Makefile" ;;
     "ajax/expat/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/expat/Makefile" ;;
     "ajax/zlib/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/zlib/Makefile" ;;
     "ajax/core/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/core/Makefile" ;;
diff -up EMBOSS-6.3.1/emboss/Makefile.am.system-pcre EMBOSS-6.3.1/emboss/Makefile.am
--- EMBOSS-6.3.1/emboss/Makefile.am.system-pcre	2010-06-16 06:26:45.000000000 -0400
+++ EMBOSS-6.3.1/emboss/Makefile.am	2010-08-02 16:11:45.469145034 -0400
@@ -79,10 +79,10 @@ wordcount wordfinder wordmatch wossname 
 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
 
-INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \
+INCLUDES = -I$(top_srcdir)/nucleus \
 	$(EXTRA_INCLUDES) \
 	-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
 	-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
@@ -319,7 +319,7 @@ 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
 
 
@@ -327,7 +327,7 @@ LDADD = ../nucleus/libnucleus.la ../ajax
 	../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 = emboss.default.template
diff -up EMBOSS-6.3.1/emboss/Makefile.in.system-pcre EMBOSS-6.3.1/emboss/Makefile.in
--- EMBOSS-6.3.1/emboss/Makefile.in.system-pcre	2010-07-19 07:55:41.000000000 -0400
+++ EMBOSS-6.3.1/emboss/Makefile.in	2010-08-02 16:20:31.985155163 -0400
@@ -136,7 +136,7 @@ am__DEPENDENCIES_1 =
 aaindexextract_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_abiview_OBJECTS = abiview.$(OBJEXT)
 abiview_OBJECTS = $(am_abiview_OBJECTS)
@@ -144,7 +144,7 @@ abiview_LDADD = $(LDADD)
 abiview_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_acdc_OBJECTS = acdc.$(OBJEXT)
 acdc_OBJECTS = $(am_acdc_OBJECTS)
@@ -152,7 +152,7 @@ acdc_LDADD = $(LDADD)
 acdc_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_acdgalaxy_OBJECTS = acdgalaxy.$(OBJEXT)
 acdgalaxy_OBJECTS = $(am_acdgalaxy_OBJECTS)
@@ -160,7 +160,7 @@ acdgalaxy_LDADD = $(LDADD)
 acdgalaxy_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_acdlog_OBJECTS = acdlog.$(OBJEXT)
 acdlog_OBJECTS = $(am_acdlog_OBJECTS)
@@ -168,7 +168,7 @@ acdlog_LDADD = $(LDADD)
 acdlog_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_acdpretty_OBJECTS = acdpretty.$(OBJEXT)
 acdpretty_OBJECTS = $(am_acdpretty_OBJECTS)
@@ -176,7 +176,7 @@ acdpretty_LDADD = $(LDADD)
 acdpretty_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_acdrelations_OBJECTS = acdrelations.$(OBJEXT)
 acdrelations_OBJECTS = $(am_acdrelations_OBJECTS)
@@ -184,7 +184,7 @@ acdrelations_LDADD = $(LDADD)
 acdrelations_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_acdtable_OBJECTS = acdtable.$(OBJEXT)
 acdtable_OBJECTS = $(am_acdtable_OBJECTS)
@@ -192,7 +192,7 @@ acdtable_LDADD = $(LDADD)
 acdtable_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_acdtrace_OBJECTS = acdtrace.$(OBJEXT)
 acdtrace_OBJECTS = $(am_acdtrace_OBJECTS)
@@ -200,7 +200,7 @@ acdtrace_LDADD = $(LDADD)
 acdtrace_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_acdvalid_OBJECTS = acdvalid.$(OBJEXT)
 acdvalid_OBJECTS = $(am_acdvalid_OBJECTS)
@@ -208,7 +208,7 @@ acdvalid_LDADD = $(LDADD)
 acdvalid_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_acdxsd_OBJECTS = acdxsd.$(OBJEXT)
 acdxsd_OBJECTS = $(am_acdxsd_OBJECTS)
@@ -216,7 +216,7 @@ acdxsd_LDADD = $(LDADD)
 acdxsd_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_ajtest_OBJECTS = ajtest.$(OBJEXT)
 ajtest_OBJECTS = $(am_ajtest_OBJECTS)
@@ -224,7 +224,7 @@ ajtest_LDADD = $(LDADD)
 ajtest_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_aligncopy_OBJECTS = aligncopy.$(OBJEXT)
 aligncopy_OBJECTS = $(am_aligncopy_OBJECTS)
@@ -232,7 +232,7 @@ aligncopy_LDADD = $(LDADD)
 aligncopy_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_aligncopypair_OBJECTS = aligncopypair.$(OBJEXT)
 aligncopypair_OBJECTS = $(am_aligncopypair_OBJECTS)
@@ -240,7 +240,7 @@ aligncopypair_LDADD = $(LDADD)
 aligncopypair_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_antigenic_OBJECTS = antigenic.$(OBJEXT)
 antigenic_OBJECTS = $(am_antigenic_OBJECTS)
@@ -248,7 +248,7 @@ antigenic_LDADD = $(LDADD)
 antigenic_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_backtranambig_OBJECTS = backtranambig.$(OBJEXT)
 backtranambig_OBJECTS = $(am_backtranambig_OBJECTS)
@@ -256,7 +256,7 @@ backtranambig_LDADD = $(LDADD)
 backtranambig_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_backtranseq_OBJECTS = backtranseq.$(OBJEXT)
 backtranseq_OBJECTS = $(am_backtranseq_OBJECTS)
@@ -264,7 +264,7 @@ backtranseq_LDADD = $(LDADD)
 backtranseq_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_banana_OBJECTS = banana.$(OBJEXT)
 banana_OBJECTS = $(am_banana_OBJECTS)
@@ -272,7 +272,7 @@ banana_LDADD = $(LDADD)
 banana_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_biosed_OBJECTS = biosed.$(OBJEXT)
 biosed_OBJECTS = $(am_biosed_OBJECTS)
@@ -280,7 +280,7 @@ biosed_LDADD = $(LDADD)
 biosed_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_btwisted_OBJECTS = btwisted.$(OBJEXT)
 btwisted_OBJECTS = $(am_btwisted_OBJECTS)
@@ -288,7 +288,7 @@ btwisted_LDADD = $(LDADD)
 btwisted_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_cai_OBJECTS = cai.$(OBJEXT)
 cai_OBJECTS = $(am_cai_OBJECTS)
@@ -296,7 +296,7 @@ cai_LDADD = $(LDADD)
 cai_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_chaos_OBJECTS = chaos.$(OBJEXT)
 chaos_OBJECTS = $(am_chaos_OBJECTS)
@@ -304,7 +304,7 @@ chaos_LDADD = $(LDADD)
 chaos_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_charge_OBJECTS = charge.$(OBJEXT)
 charge_OBJECTS = $(am_charge_OBJECTS)
@@ -312,7 +312,7 @@ charge_LDADD = $(LDADD)
 charge_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_checktrans_OBJECTS = checktrans.$(OBJEXT)
 checktrans_OBJECTS = $(am_checktrans_OBJECTS)
@@ -320,7 +320,7 @@ checktrans_LDADD = $(LDADD)
 checktrans_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_chips_OBJECTS = chips.$(OBJEXT)
 chips_OBJECTS = $(am_chips_OBJECTS)
@@ -328,7 +328,7 @@ chips_LDADD = $(LDADD)
 chips_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_cirdna_OBJECTS = cirdna.$(OBJEXT)
 cirdna_OBJECTS = $(am_cirdna_OBJECTS)
@@ -336,7 +336,7 @@ cirdna_LDADD = $(LDADD)
 cirdna_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_codcmp_OBJECTS = codcmp.$(OBJEXT)
 codcmp_OBJECTS = $(am_codcmp_OBJECTS)
@@ -344,7 +344,7 @@ codcmp_LDADD = $(LDADD)
 codcmp_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 codcopy_SOURCES = codcopy.c
 codcopy_OBJECTS = codcopy.$(OBJEXT)
@@ -352,7 +352,7 @@ codcopy_LDADD = $(LDADD)
 codcopy_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_coderet_OBJECTS = coderet.$(OBJEXT)
 coderet_OBJECTS = $(am_coderet_OBJECTS)
@@ -360,7 +360,7 @@ coderet_LDADD = $(LDADD)
 coderet_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_complex_OBJECTS = complex.$(OBJEXT)
 complex_OBJECTS = $(am_complex_OBJECTS)
@@ -368,7 +368,7 @@ complex_LDADD = $(LDADD)
 complex_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_compseq_OBJECTS = compseq.$(OBJEXT)
 compseq_OBJECTS = $(am_compseq_OBJECTS)
@@ -376,7 +376,7 @@ compseq_LDADD = $(LDADD)
 compseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_cons_OBJECTS = cons.$(OBJEXT)
 cons_OBJECTS = $(am_cons_OBJECTS)
@@ -384,7 +384,7 @@ cons_LDADD = $(LDADD)
 cons_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_consambig_OBJECTS = consambig.$(OBJEXT)
 consambig_OBJECTS = $(am_consambig_OBJECTS)
@@ -392,7 +392,7 @@ consambig_LDADD = $(LDADD)
 consambig_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_corbatest_OBJECTS = corbatest.$(OBJEXT)
 corbatest_OBJECTS = $(am_corbatest_OBJECTS)
@@ -400,7 +400,7 @@ corbatest_LDADD = $(LDADD)
 corbatest_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_cpgplot_OBJECTS = cpgplot.$(OBJEXT)
 cpgplot_OBJECTS = $(am_cpgplot_OBJECTS)
@@ -408,7 +408,7 @@ cpgplot_LDADD = $(LDADD)
 cpgplot_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_cpgreport_OBJECTS = cpgreport.$(OBJEXT)
 cpgreport_OBJECTS = $(am_cpgreport_OBJECTS)
@@ -416,7 +416,7 @@ cpgreport_LDADD = $(LDADD)
 cpgreport_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_cusp_OBJECTS = cusp.$(OBJEXT)
 cusp_OBJECTS = $(am_cusp_OBJECTS)
@@ -424,7 +424,7 @@ cusp_LDADD = $(LDADD)
 cusp_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_cutgextract_OBJECTS = cutgextract.$(OBJEXT)
 cutgextract_OBJECTS = $(am_cutgextract_OBJECTS)
@@ -432,7 +432,7 @@ cutgextract_LDADD = $(LDADD)
 cutgextract_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_cutseq_OBJECTS = cutseq.$(OBJEXT)
 cutseq_OBJECTS = $(am_cutseq_OBJECTS)
@@ -440,7 +440,7 @@ cutseq_LDADD = $(LDADD)
 cutseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_dan_OBJECTS = dan.$(OBJEXT)
 dan_OBJECTS = $(am_dan_OBJECTS)
@@ -448,7 +448,7 @@ dan_LDADD = $(LDADD)
 dan_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_dbiblast_OBJECTS = dbiblast.$(OBJEXT)
 dbiblast_OBJECTS = $(am_dbiblast_OBJECTS)
@@ -456,7 +456,7 @@ dbiblast_LDADD = $(LDADD)
 dbiblast_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_dbifasta_OBJECTS = dbifasta.$(OBJEXT)
 dbifasta_OBJECTS = $(am_dbifasta_OBJECTS)
@@ -464,7 +464,7 @@ dbifasta_LDADD = $(LDADD)
 dbifasta_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_dbiflat_OBJECTS = dbiflat.$(OBJEXT)
 dbiflat_OBJECTS = $(am_dbiflat_OBJECTS)
@@ -472,7 +472,7 @@ dbiflat_LDADD = $(LDADD)
 dbiflat_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_dbigcg_OBJECTS = dbigcg.$(OBJEXT)
 dbigcg_OBJECTS = $(am_dbigcg_OBJECTS)
@@ -480,7 +480,7 @@ dbigcg_LDADD = $(LDADD)
 dbigcg_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_dbxfasta_OBJECTS = dbxfasta.$(OBJEXT)
 dbxfasta_OBJECTS = $(am_dbxfasta_OBJECTS)
@@ -488,7 +488,7 @@ dbxfasta_LDADD = $(LDADD)
 dbxfasta_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_dbxflat_OBJECTS = dbxflat.$(OBJEXT)
 dbxflat_OBJECTS = $(am_dbxflat_OBJECTS)
@@ -496,7 +496,7 @@ dbxflat_LDADD = $(LDADD)
 dbxflat_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_dbxgcg_OBJECTS = dbxgcg.$(OBJEXT)
 dbxgcg_OBJECTS = $(am_dbxgcg_OBJECTS)
@@ -504,7 +504,7 @@ dbxgcg_LDADD = $(LDADD)
 dbxgcg_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_degapseq_OBJECTS = degapseq.$(OBJEXT)
 degapseq_OBJECTS = $(am_degapseq_OBJECTS)
@@ -512,7 +512,7 @@ degapseq_LDADD = $(LDADD)
 degapseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_density_OBJECTS = density.$(OBJEXT)
 density_OBJECTS = $(am_density_OBJECTS)
@@ -520,7 +520,7 @@ density_LDADD = $(LDADD)
 density_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_descseq_OBJECTS = descseq.$(OBJEXT)
 descseq_OBJECTS = $(am_descseq_OBJECTS)
@@ -528,7 +528,7 @@ descseq_LDADD = $(LDADD)
 descseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_diffseq_OBJECTS = diffseq.$(OBJEXT)
 diffseq_OBJECTS = $(am_diffseq_OBJECTS)
@@ -536,7 +536,7 @@ diffseq_LDADD = $(LDADD)
 diffseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_digest_OBJECTS = digest.$(OBJEXT)
 digest_OBJECTS = $(am_digest_OBJECTS)
@@ -544,7 +544,7 @@ digest_LDADD = $(LDADD)
 digest_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_distmat_OBJECTS = distmat.$(OBJEXT)
 distmat_OBJECTS = $(am_distmat_OBJECTS)
@@ -552,7 +552,7 @@ distmat_LDADD = $(LDADD)
 distmat_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 domtesta_SOURCES = domtesta.c
 domtesta_OBJECTS = domtesta.$(OBJEXT)
@@ -560,7 +560,7 @@ domtesta_LDADD = $(LDADD)
 domtesta_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 domtestb_SOURCES = domtestb.c
 domtestb_OBJECTS = domtestb.$(OBJEXT)
@@ -568,7 +568,7 @@ domtestb_LDADD = $(LDADD)
 domtestb_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 domtestc_SOURCES = domtestc.c
 domtestc_OBJECTS = domtestc.$(OBJEXT)
@@ -576,7 +576,7 @@ domtestc_LDADD = $(LDADD)
 domtestc_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 domtestd_SOURCES = domtestd.c
 domtestd_OBJECTS = domtestd.$(OBJEXT)
@@ -584,7 +584,7 @@ domtestd_LDADD = $(LDADD)
 domtestd_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_dotmatcher_OBJECTS = dotmatcher.$(OBJEXT)
 dotmatcher_OBJECTS = $(am_dotmatcher_OBJECTS)
@@ -592,7 +592,7 @@ dotmatcher_LDADD = $(LDADD)
 dotmatcher_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_dotpath_OBJECTS = dotpath.$(OBJEXT)
 dotpath_OBJECTS = $(am_dotpath_OBJECTS)
@@ -600,7 +600,7 @@ dotpath_LDADD = $(LDADD)
 dotpath_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_dottup_OBJECTS = dottup.$(OBJEXT)
 dottup_OBJECTS = $(am_dottup_OBJECTS)
@@ -608,7 +608,7 @@ dottup_LDADD = $(LDADD)
 dottup_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_dreg_OBJECTS = dreg.$(OBJEXT)
 dreg_OBJECTS = $(am_dreg_OBJECTS)
@@ -616,7 +616,7 @@ dreg_LDADD = $(LDADD)
 dreg_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_edamclean_OBJECTS = edamclean.$(OBJEXT)
 edamclean_OBJECTS = $(am_edamclean_OBJECTS)
@@ -624,7 +624,7 @@ edamclean_LDADD = $(LDADD)
 edamclean_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_edialign_OBJECTS = edialign.$(OBJEXT)
 edialign_OBJECTS = $(am_edialign_OBJECTS)
@@ -632,7 +632,7 @@ edialign_LDADD = $(LDADD)
 edialign_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_einverted_OBJECTS = einverted.$(OBJEXT)
 einverted_OBJECTS = $(am_einverted_OBJECTS)
@@ -640,7 +640,7 @@ einverted_LDADD = $(LDADD)
 einverted_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_embossdata_OBJECTS = embossdata.$(OBJEXT)
 embossdata_OBJECTS = $(am_embossdata_OBJECTS)
@@ -648,7 +648,7 @@ embossdata_LDADD = $(LDADD)
 embossdata_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_embossversion_OBJECTS = embossversion.$(OBJEXT)
 embossversion_OBJECTS = $(am_embossversion_OBJECTS)
@@ -656,7 +656,7 @@ embossversion_LDADD = $(LDADD)
 embossversion_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_emma_OBJECTS = emma.$(OBJEXT)
 emma_OBJECTS = $(am_emma_OBJECTS)
@@ -664,7 +664,7 @@ emma_LDADD = $(LDADD)
 emma_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_emowse_OBJECTS = emowse.$(OBJEXT)
 emowse_OBJECTS = $(am_emowse_OBJECTS)
@@ -672,7 +672,7 @@ emowse_LDADD = $(LDADD)
 emowse_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_ensembltest_OBJECTS = ensembltest.$(OBJEXT)
 ensembltest_OBJECTS = $(am_ensembltest_OBJECTS)
@@ -680,7 +680,7 @@ ensembltest_LDADD = $(LDADD)
 ensembltest_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_entrails_OBJECTS = entrails.$(OBJEXT)
 entrails_OBJECTS = $(am_entrails_OBJECTS)
@@ -688,7 +688,7 @@ entrails_LDADD = $(LDADD)
 entrails_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_entrailsbook_OBJECTS = entrailsbook.$(OBJEXT)
 entrailsbook_OBJECTS = $(am_entrailsbook_OBJECTS)
@@ -696,7 +696,7 @@ entrailsbook_LDADD = $(LDADD)
 entrailsbook_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_entrailshtml_OBJECTS = entrailshtml.$(OBJEXT)
 entrailshtml_OBJECTS = $(am_entrailshtml_OBJECTS)
@@ -704,7 +704,7 @@ entrailshtml_LDADD = $(LDADD)
 entrailshtml_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_entrailswiki_OBJECTS = entrailswiki.$(OBJEXT)
 entrailswiki_OBJECTS = $(am_entrailswiki_OBJECTS)
@@ -712,7 +712,7 @@ entrailswiki_LDADD = $(LDADD)
 entrailswiki_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_entret_OBJECTS = entret.$(OBJEXT)
 entret_OBJECTS = $(am_entret_OBJECTS)
@@ -720,7 +720,7 @@ entret_LDADD = $(LDADD)
 entret_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_epestfind_OBJECTS = epestfind.$(OBJEXT)
 epestfind_OBJECTS = $(am_epestfind_OBJECTS)
@@ -728,7 +728,7 @@ epestfind_LDADD = $(LDADD)
 epestfind_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_eprimer3_OBJECTS = eprimer3.$(OBJEXT)
 eprimer3_OBJECTS = $(am_eprimer3_OBJECTS)
@@ -736,7 +736,7 @@ eprimer3_LDADD = $(LDADD)
 eprimer3_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_equicktandem_OBJECTS = equicktandem.$(OBJEXT)
 equicktandem_OBJECTS = $(am_equicktandem_OBJECTS)
@@ -744,7 +744,7 @@ equicktandem_LDADD = $(LDADD)
 equicktandem_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_est2genome_OBJECTS = est2genome.$(OBJEXT)
 est2genome_OBJECTS = $(am_est2genome_OBJECTS)
@@ -752,7 +752,7 @@ est2genome_LDADD = $(LDADD)
 est2genome_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_etandem_OBJECTS = etandem.$(OBJEXT)
 etandem_OBJECTS = $(am_etandem_OBJECTS)
@@ -760,7 +760,7 @@ etandem_LDADD = $(LDADD)
 etandem_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_extractalign_OBJECTS = extractalign.$(OBJEXT)
 extractalign_OBJECTS = $(am_extractalign_OBJECTS)
@@ -768,7 +768,7 @@ extractalign_LDADD = $(LDADD)
 extractalign_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_extractfeat_OBJECTS = extractfeat.$(OBJEXT)
 extractfeat_OBJECTS = $(am_extractfeat_OBJECTS)
@@ -776,7 +776,7 @@ extractfeat_LDADD = $(LDADD)
 extractfeat_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_extractseq_OBJECTS = extractseq.$(OBJEXT)
 extractseq_OBJECTS = $(am_extractseq_OBJECTS)
@@ -784,7 +784,7 @@ extractseq_LDADD = $(LDADD)
 extractseq_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_featcopy_OBJECTS = featcopy.$(OBJEXT)
 featcopy_OBJECTS = $(am_featcopy_OBJECTS)
@@ -792,7 +792,7 @@ featcopy_LDADD = $(LDADD)
 featcopy_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_featreport_OBJECTS = featreport.$(OBJEXT)
 featreport_OBJECTS = $(am_featreport_OBJECTS)
@@ -800,7 +800,7 @@ featreport_LDADD = $(LDADD)
 featreport_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_findkm_OBJECTS = findkm.$(OBJEXT)
 findkm_OBJECTS = $(am_findkm_OBJECTS)
@@ -808,7 +808,7 @@ findkm_LDADD = $(LDADD)
 findkm_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_freak_OBJECTS = freak.$(OBJEXT)
 freak_OBJECTS = $(am_freak_OBJECTS)
@@ -816,7 +816,7 @@ freak_LDADD = $(LDADD)
 freak_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_fuzznuc_OBJECTS = fuzznuc.$(OBJEXT)
 fuzznuc_OBJECTS = $(am_fuzznuc_OBJECTS)
@@ -824,7 +824,7 @@ fuzznuc_LDADD = $(LDADD)
 fuzznuc_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_fuzzpro_OBJECTS = fuzzpro.$(OBJEXT)
 fuzzpro_OBJECTS = $(am_fuzzpro_OBJECTS)
@@ -832,7 +832,7 @@ fuzzpro_LDADD = $(LDADD)
 fuzzpro_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_fuzztran_OBJECTS = fuzztran.$(OBJEXT)
 fuzztran_OBJECTS = $(am_fuzztran_OBJECTS)
@@ -840,7 +840,7 @@ fuzztran_LDADD = $(LDADD)
 fuzztran_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_garnier_OBJECTS = garnier.$(OBJEXT)
 garnier_OBJECTS = $(am_garnier_OBJECTS)
@@ -848,7 +848,7 @@ garnier_LDADD = $(LDADD)
 garnier_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_geecee_OBJECTS = geecee.$(OBJEXT)
 geecee_OBJECTS = $(am_geecee_OBJECTS)
@@ -856,7 +856,7 @@ geecee_LDADD = $(LDADD)
 geecee_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_getorf_OBJECTS = getorf.$(OBJEXT)
 getorf_OBJECTS = $(am_getorf_OBJECTS)
@@ -864,7 +864,7 @@ getorf_LDADD = $(LDADD)
 getorf_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_helixturnhelix_OBJECTS = helixturnhelix.$(OBJEXT)
 helixturnhelix_OBJECTS = $(am_helixturnhelix_OBJECTS)
@@ -872,7 +872,7 @@ helixturnhelix_LDADD = $(LDADD)
 helixturnhelix_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_histogramtest_OBJECTS = histogramtest.$(OBJEXT)
 histogramtest_OBJECTS = $(am_histogramtest_OBJECTS)
@@ -880,7 +880,7 @@ histogramtest_LDADD = $(LDADD)
 histogramtest_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_hmoment_OBJECTS = hmoment.$(OBJEXT)
 hmoment_OBJECTS = $(am_hmoment_OBJECTS)
@@ -888,7 +888,7 @@ hmoment_LDADD = $(LDADD)
 hmoment_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_iep_OBJECTS = iep.$(OBJEXT)
 iep_OBJECTS = $(am_iep_OBJECTS)
@@ -896,7 +896,7 @@ iep_LDADD = $(LDADD)
 iep_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_infoalign_OBJECTS = infoalign.$(OBJEXT)
 infoalign_OBJECTS = $(am_infoalign_OBJECTS)
@@ -904,7 +904,7 @@ infoalign_LDADD = $(LDADD)
 infoalign_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_infobase_OBJECTS = infobase.$(OBJEXT)
 infobase_OBJECTS = $(am_infobase_OBJECTS)
@@ -912,7 +912,7 @@ infobase_LDADD = $(LDADD)
 infobase_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_inforesidue_OBJECTS = inforesidue.$(OBJEXT)
 inforesidue_OBJECTS = $(am_inforesidue_OBJECTS)
@@ -920,7 +920,7 @@ inforesidue_LDADD = $(LDADD)
 inforesidue_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_infoseq_OBJECTS = infoseq.$(OBJEXT)
 infoseq_OBJECTS = $(am_infoseq_OBJECTS)
@@ -928,7 +928,7 @@ infoseq_LDADD = $(LDADD)
 infoseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_intconv_OBJECTS = intconv.$(OBJEXT)
 intconv_OBJECTS = $(am_intconv_OBJECTS)
@@ -936,7 +936,7 @@ intconv_LDADD = $(LDADD)
 intconv_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_isochore_OBJECTS = isochore.$(OBJEXT)
 isochore_OBJECTS = $(am_isochore_OBJECTS)
@@ -944,7 +944,7 @@ isochore_LDADD = $(LDADD)
 isochore_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_jaspextract_OBJECTS = jaspextract.$(OBJEXT)
 jaspextract_OBJECTS = $(am_jaspextract_OBJECTS)
@@ -952,7 +952,7 @@ jaspextract_LDADD = $(LDADD)
 jaspextract_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_jaspscan_OBJECTS = jaspscan.$(OBJEXT)
 jaspscan_OBJECTS = $(am_jaspscan_OBJECTS)
@@ -960,7 +960,7 @@ jaspscan_LDADD = $(LDADD)
 jaspscan_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_jembossctl_OBJECTS = jembossctl.$(OBJEXT)
 jembossctl_OBJECTS = $(am_jembossctl_OBJECTS)
@@ -968,7 +968,7 @@ jembossctl_LDADD = $(LDADD)
 jembossctl_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_lindna_OBJECTS = lindna.$(OBJEXT)
 lindna_OBJECTS = $(am_lindna_OBJECTS)
@@ -976,7 +976,7 @@ lindna_LDADD = $(LDADD)
 lindna_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_listor_OBJECTS = listor.$(OBJEXT)
 listor_OBJECTS = $(am_listor_OBJECTS)
@@ -984,7 +984,7 @@ listor_LDADD = $(LDADD)
 listor_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 makenucseq_SOURCES = makenucseq.c
 makenucseq_OBJECTS = makenucseq.$(OBJEXT)
@@ -992,7 +992,7 @@ makenucseq_LDADD = $(LDADD)
 makenucseq_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 makeprotseq_SOURCES = makeprotseq.c
 makeprotseq_OBJECTS = makeprotseq.$(OBJEXT)
@@ -1000,7 +1000,7 @@ makeprotseq_LDADD = $(LDADD)
 makeprotseq_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_marscan_OBJECTS = marscan.$(OBJEXT)
 marscan_OBJECTS = $(am_marscan_OBJECTS)
@@ -1008,7 +1008,7 @@ marscan_LDADD = $(LDADD)
 marscan_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_martattributes_OBJECTS = martattributes.$(OBJEXT)
 martattributes_OBJECTS = $(am_martattributes_OBJECTS)
@@ -1016,7 +1016,7 @@ martattributes_LDADD = $(LDADD)
 martattributes_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_martdatasets_OBJECTS = martdatasets.$(OBJEXT)
 martdatasets_OBJECTS = $(am_martdatasets_OBJECTS)
@@ -1024,7 +1024,7 @@ martdatasets_LDADD = $(LDADD)
 martdatasets_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_martfilters_OBJECTS = martfilters.$(OBJEXT)
 martfilters_OBJECTS = $(am_martfilters_OBJECTS)
@@ -1032,7 +1032,7 @@ martfilters_LDADD = $(LDADD)
 martfilters_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_martquery_OBJECTS = martquery.$(OBJEXT)
 martquery_OBJECTS = $(am_martquery_OBJECTS)
@@ -1040,7 +1040,7 @@ martquery_LDADD = $(LDADD)
 martquery_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_martregistry_OBJECTS = martregistry.$(OBJEXT)
 martregistry_OBJECTS = $(am_martregistry_OBJECTS)
@@ -1048,7 +1048,7 @@ martregistry_LDADD = $(LDADD)
 martregistry_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_martseqs_OBJECTS = martseqs.$(OBJEXT)
 martseqs_OBJECTS = $(am_martseqs_OBJECTS)
@@ -1056,7 +1056,7 @@ martseqs_LDADD = $(LDADD)
 martseqs_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_maskambignuc_OBJECTS = maskambignuc.$(OBJEXT)
 maskambignuc_OBJECTS = $(am_maskambignuc_OBJECTS)
@@ -1064,7 +1064,7 @@ maskambignuc_LDADD = $(LDADD)
 maskambignuc_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_maskambigprot_OBJECTS = maskambigprot.$(OBJEXT)
 maskambigprot_OBJECTS = $(am_maskambigprot_OBJECTS)
@@ -1072,7 +1072,7 @@ maskambigprot_LDADD = $(LDADD)
 maskambigprot_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_maskfeat_OBJECTS = maskfeat.$(OBJEXT)
 maskfeat_OBJECTS = $(am_maskfeat_OBJECTS)
@@ -1080,7 +1080,7 @@ maskfeat_LDADD = $(LDADD)
 maskfeat_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_maskseq_OBJECTS = maskseq.$(OBJEXT)
 maskseq_OBJECTS = $(am_maskseq_OBJECTS)
@@ -1088,7 +1088,7 @@ maskseq_LDADD = $(LDADD)
 maskseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_matcher_OBJECTS = matcher.$(OBJEXT)
 matcher_OBJECTS = $(am_matcher_OBJECTS)
@@ -1096,7 +1096,7 @@ matcher_LDADD = $(LDADD)
 matcher_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_megamerger_OBJECTS = megamerger.$(OBJEXT)
 megamerger_OBJECTS = $(am_megamerger_OBJECTS)
@@ -1104,7 +1104,7 @@ megamerger_LDADD = $(LDADD)
 megamerger_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_merger_OBJECTS = merger.$(OBJEXT)
 merger_OBJECTS = $(am_merger_OBJECTS)
@@ -1112,7 +1112,7 @@ merger_LDADD = $(LDADD)
 merger_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_msbar_OBJECTS = msbar.$(OBJEXT)
 msbar_OBJECTS = $(am_msbar_OBJECTS)
@@ -1120,7 +1120,7 @@ msbar_LDADD = $(LDADD)
 msbar_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_mwcontam_OBJECTS = mwcontam.$(OBJEXT)
 mwcontam_OBJECTS = $(am_mwcontam_OBJECTS)
@@ -1128,7 +1128,7 @@ mwcontam_LDADD = $(LDADD)
 mwcontam_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_mwfilter_OBJECTS = mwfilter.$(OBJEXT)
 mwfilter_OBJECTS = $(am_mwfilter_OBJECTS)
@@ -1136,7 +1136,7 @@ mwfilter_LDADD = $(LDADD)
 mwfilter_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_needle_OBJECTS = needle.$(OBJEXT)
 needle_OBJECTS = $(am_needle_OBJECTS)
@@ -1144,7 +1144,7 @@ needle_LDADD = $(LDADD)
 needle_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_needleall_OBJECTS = needleall.$(OBJEXT)
 needleall_OBJECTS = $(am_needleall_OBJECTS)
@@ -1152,7 +1152,7 @@ needleall_LDADD = $(LDADD)
 needleall_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_newcoils_OBJECTS = newcoils.$(OBJEXT)
 newcoils_OBJECTS = $(am_newcoils_OBJECTS)
@@ -1160,7 +1160,7 @@ newcoils_LDADD = $(LDADD)
 newcoils_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_newcpgreport_OBJECTS = newcpgreport.$(OBJEXT)
 newcpgreport_OBJECTS = $(am_newcpgreport_OBJECTS)
@@ -1168,7 +1168,7 @@ newcpgreport_LDADD = $(LDADD)
 newcpgreport_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_newcpgseek_OBJECTS = newcpgseek.$(OBJEXT)
 newcpgseek_OBJECTS = $(am_newcpgseek_OBJECTS)
@@ -1176,7 +1176,7 @@ newcpgseek_LDADD = $(LDADD)
 newcpgseek_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_newseq_OBJECTS = newseq.$(OBJEXT)
 newseq_OBJECTS = $(am_newseq_OBJECTS)
@@ -1184,7 +1184,7 @@ newseq_LDADD = $(LDADD)
 newseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_nohtml_OBJECTS = nohtml.$(OBJEXT)
 nohtml_OBJECTS = $(am_nohtml_OBJECTS)
@@ -1192,7 +1192,7 @@ nohtml_LDADD = $(LDADD)
 nohtml_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_noreturn_OBJECTS = noreturn.$(OBJEXT)
 noreturn_OBJECTS = $(am_noreturn_OBJECTS)
@@ -1200,7 +1200,7 @@ noreturn_LDADD = $(LDADD)
 noreturn_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_nospace_OBJECTS = nospace.$(OBJEXT)
 nospace_OBJECTS = $(am_nospace_OBJECTS)
@@ -1208,7 +1208,7 @@ nospace_LDADD = $(LDADD)
 nospace_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_notab_OBJECTS = notab.$(OBJEXT)
 notab_OBJECTS = $(am_notab_OBJECTS)
@@ -1216,7 +1216,7 @@ notab_LDADD = $(LDADD)
 notab_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_notseq_OBJECTS = notseq.$(OBJEXT)
 notseq_OBJECTS = $(am_notseq_OBJECTS)
@@ -1224,7 +1224,7 @@ notseq_LDADD = $(LDADD)
 notseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_nthseq_OBJECTS = nthseq.$(OBJEXT)
 nthseq_OBJECTS = $(am_nthseq_OBJECTS)
@@ -1232,7 +1232,7 @@ nthseq_LDADD = $(LDADD)
 nthseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_nthseqset_OBJECTS = nthseqset.$(OBJEXT)
 nthseqset_OBJECTS = $(am_nthseqset_OBJECTS)
@@ -1240,7 +1240,7 @@ nthseqset_LDADD = $(LDADD)
 nthseqset_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_octanol_OBJECTS = octanol.$(OBJEXT)
 octanol_OBJECTS = $(am_octanol_OBJECTS)
@@ -1248,7 +1248,7 @@ octanol_LDADD = $(LDADD)
 octanol_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_oddcomp_OBJECTS = oddcomp.$(OBJEXT)
 oddcomp_OBJECTS = $(am_oddcomp_OBJECTS)
@@ -1256,7 +1256,7 @@ oddcomp_LDADD = $(LDADD)
 oddcomp_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_origsplitter_OBJECTS = origsplitter.$(OBJEXT)
 origsplitter_OBJECTS = $(am_origsplitter_OBJECTS)
@@ -1264,7 +1264,7 @@ origsplitter_LDADD = $(LDADD)
 origsplitter_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_origunion_OBJECTS = origunion.$(OBJEXT)
 origunion_OBJECTS = $(am_origunion_OBJECTS)
@@ -1272,7 +1272,7 @@ origunion_LDADD = $(LDADD)
 origunion_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_palindrome_OBJECTS = palindrome.$(OBJEXT)
 palindrome_OBJECTS = $(am_palindrome_OBJECTS)
@@ -1280,7 +1280,7 @@ palindrome_LDADD = $(LDADD)
 palindrome_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_pasteseq_OBJECTS = pasteseq.$(OBJEXT)
 pasteseq_OBJECTS = $(am_pasteseq_OBJECTS)
@@ -1288,7 +1288,7 @@ pasteseq_LDADD = $(LDADD)
 pasteseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_patmatdb_OBJECTS = patmatdb.$(OBJEXT)
 patmatdb_OBJECTS = $(am_patmatdb_OBJECTS)
@@ -1296,7 +1296,7 @@ patmatdb_LDADD = $(LDADD)
 patmatdb_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_patmatmotifs_OBJECTS = patmatmotifs.$(OBJEXT)
 patmatmotifs_OBJECTS = $(am_patmatmotifs_OBJECTS)
@@ -1304,7 +1304,7 @@ patmatmotifs_LDADD = $(LDADD)
 patmatmotifs_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_patmattest_OBJECTS = patmattest.$(OBJEXT)
 patmattest_OBJECTS = $(am_patmattest_OBJECTS)
@@ -1312,7 +1312,7 @@ patmattest_LDADD = $(LDADD)
 patmattest_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_pepcoil_OBJECTS = pepcoil.$(OBJEXT)
 pepcoil_OBJECTS = $(am_pepcoil_OBJECTS)
@@ -1320,7 +1320,7 @@ pepcoil_LDADD = $(LDADD)
 pepcoil_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_pepinfo_OBJECTS = pepinfo.$(OBJEXT)
 pepinfo_OBJECTS = $(am_pepinfo_OBJECTS)
@@ -1328,7 +1328,7 @@ pepinfo_LDADD = $(LDADD)
 pepinfo_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_pepnet_OBJECTS = pepnet.$(OBJEXT)
 pepnet_OBJECTS = $(am_pepnet_OBJECTS)
@@ -1336,7 +1336,7 @@ pepnet_LDADD = $(LDADD)
 pepnet_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_pepstats_OBJECTS = pepstats.$(OBJEXT)
 pepstats_OBJECTS = $(am_pepstats_OBJECTS)
@@ -1344,7 +1344,7 @@ pepstats_LDADD = $(LDADD)
 pepstats_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_pepwheel_OBJECTS = pepwheel.$(OBJEXT)
 pepwheel_OBJECTS = $(am_pepwheel_OBJECTS)
@@ -1352,7 +1352,7 @@ pepwheel_LDADD = $(LDADD)
 pepwheel_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_pepwindow_OBJECTS = pepwindow.$(OBJEXT)
 pepwindow_OBJECTS = $(am_pepwindow_OBJECTS)
@@ -1360,7 +1360,7 @@ pepwindow_LDADD = $(LDADD)
 pepwindow_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_pepwindowall_OBJECTS = pepwindowall.$(OBJEXT)
 pepwindowall_OBJECTS = $(am_pepwindowall_OBJECTS)
@@ -1368,7 +1368,7 @@ pepwindowall_LDADD = $(LDADD)
 pepwindowall_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_plotcon_OBJECTS = plotcon.$(OBJEXT)
 plotcon_OBJECTS = $(am_plotcon_OBJECTS)
@@ -1376,7 +1376,7 @@ plotcon_LDADD = $(LDADD)
 plotcon_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_plotorf_OBJECTS = plotorf.$(OBJEXT)
 plotorf_OBJECTS = $(am_plotorf_OBJECTS)
@@ -1384,7 +1384,7 @@ plotorf_LDADD = $(LDADD)
 plotorf_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_polydot_OBJECTS = polydot.$(OBJEXT)
 polydot_OBJECTS = $(am_polydot_OBJECTS)
@@ -1392,7 +1392,7 @@ polydot_LDADD = $(LDADD)
 polydot_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_preg_OBJECTS = preg.$(OBJEXT)
 preg_OBJECTS = $(am_preg_OBJECTS)
@@ -1400,7 +1400,7 @@ preg_LDADD = $(LDADD)
 preg_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_prettyplot_OBJECTS = prettyplot.$(OBJEXT)
 prettyplot_OBJECTS = $(am_prettyplot_OBJECTS)
@@ -1408,7 +1408,7 @@ prettyplot_LDADD = $(LDADD)
 prettyplot_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_prettyseq_OBJECTS = prettyseq.$(OBJEXT)
 prettyseq_OBJECTS = $(am_prettyseq_OBJECTS)
@@ -1416,7 +1416,7 @@ prettyseq_LDADD = $(LDADD)
 prettyseq_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_prima_OBJECTS = prima.$(OBJEXT)
 prima_OBJECTS = $(am_prima_OBJECTS)
@@ -1424,7 +1424,7 @@ prima_LDADD = $(LDADD)
 prima_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_primers_OBJECTS = primers.$(OBJEXT)
 primers_OBJECTS = $(am_primers_OBJECTS)
@@ -1432,7 +1432,7 @@ primers_LDADD = $(LDADD)
 primers_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_primersearch_OBJECTS = primersearch.$(OBJEXT)
 primersearch_OBJECTS = $(am_primersearch_OBJECTS)
@@ -1440,7 +1440,7 @@ primersearch_LDADD = $(LDADD)
 primersearch_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_printsextract_OBJECTS = printsextract.$(OBJEXT)
 printsextract_OBJECTS = $(am_printsextract_OBJECTS)
@@ -1448,7 +1448,7 @@ printsextract_LDADD = $(LDADD)
 printsextract_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_profit_OBJECTS = profit.$(OBJEXT)
 profit_OBJECTS = $(am_profit_OBJECTS)
@@ -1456,7 +1456,7 @@ profit_LDADD = $(LDADD)
 profit_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_prophecy_OBJECTS = prophecy.$(OBJEXT)
 prophecy_OBJECTS = $(am_prophecy_OBJECTS)
@@ -1464,7 +1464,7 @@ prophecy_LDADD = $(LDADD)
 prophecy_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_prophet_OBJECTS = prophet.$(OBJEXT)
 prophet_OBJECTS = $(am_prophet_OBJECTS)
@@ -1472,7 +1472,7 @@ prophet_LDADD = $(LDADD)
 prophet_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_prosextract_OBJECTS = prosextract.$(OBJEXT)
 prosextract_OBJECTS = $(am_prosextract_OBJECTS)
@@ -1480,7 +1480,7 @@ prosextract_LDADD = $(LDADD)
 prosextract_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_pscan_OBJECTS = pscan.$(OBJEXT)
 pscan_OBJECTS = $(am_pscan_OBJECTS)
@@ -1488,7 +1488,7 @@ pscan_LDADD = $(LDADD)
 pscan_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_psiphi_OBJECTS = psiphi.$(OBJEXT)
 psiphi_OBJECTS = $(am_psiphi_OBJECTS)
@@ -1496,7 +1496,7 @@ psiphi_LDADD = $(LDADD)
 psiphi_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_rebaseextract_OBJECTS = rebaseextract.$(OBJEXT)
 rebaseextract_OBJECTS = $(am_rebaseextract_OBJECTS)
@@ -1504,7 +1504,7 @@ rebaseextract_LDADD = $(LDADD)
 rebaseextract_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_recoder_OBJECTS = recoder.$(OBJEXT)
 recoder_OBJECTS = $(am_recoder_OBJECTS)
@@ -1512,7 +1512,7 @@ recoder_LDADD = $(LDADD)
 recoder_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_redata_OBJECTS = redata.$(OBJEXT)
 redata_OBJECTS = $(am_redata_OBJECTS)
@@ -1520,7 +1520,7 @@ redata_LDADD = $(LDADD)
 redata_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_remap_OBJECTS = remap.$(OBJEXT)
 remap_OBJECTS = $(am_remap_OBJECTS)
@@ -1528,7 +1528,7 @@ remap_LDADD = $(LDADD)
 remap_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_restover_OBJECTS = restover.$(OBJEXT)
 restover_OBJECTS = $(am_restover_OBJECTS)
@@ -1536,7 +1536,7 @@ restover_LDADD = $(LDADD)
 restover_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_restrict_OBJECTS = restrict.$(OBJEXT)
 restrict_OBJECTS = $(am_restrict_OBJECTS)
@@ -1544,7 +1544,7 @@ restrict_LDADD = $(LDADD)
 restrict_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_revseq_OBJECTS = revseq.$(OBJEXT)
 revseq_OBJECTS = $(am_revseq_OBJECTS)
@@ -1552,7 +1552,7 @@ revseq_LDADD = $(LDADD)
 revseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_seealso_OBJECTS = seealso.$(OBJEXT)
 seealso_OBJECTS = $(am_seealso_OBJECTS)
@@ -1560,7 +1560,7 @@ seealso_LDADD = $(LDADD)
 seealso_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_seqinfo_OBJECTS = seqinfo.$(OBJEXT)
 seqinfo_OBJECTS = $(am_seqinfo_OBJECTS)
@@ -1568,7 +1568,7 @@ seqinfo_LDADD = $(LDADD)
 seqinfo_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_seqmatchall_OBJECTS = seqmatchall.$(OBJEXT)
 seqmatchall_OBJECTS = $(am_seqmatchall_OBJECTS)
@@ -1576,7 +1576,7 @@ seqmatchall_LDADD = $(LDADD)
 seqmatchall_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_seqret_OBJECTS = seqret.$(OBJEXT)
 seqret_OBJECTS = $(am_seqret_OBJECTS)
@@ -1584,7 +1584,7 @@ seqret_LDADD = $(LDADD)
 seqret_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_seqretall_OBJECTS = seqretall.$(OBJEXT)
 seqretall_OBJECTS = $(am_seqretall_OBJECTS)
@@ -1592,7 +1592,7 @@ seqretall_LDADD = $(LDADD)
 seqretall_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_seqretallfeat_OBJECTS = seqretallfeat.$(OBJEXT)
 seqretallfeat_OBJECTS = $(am_seqretallfeat_OBJECTS)
@@ -1600,7 +1600,7 @@ seqretallfeat_LDADD = $(LDADD)
 seqretallfeat_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_seqretset_OBJECTS = seqretset.$(OBJEXT)
 seqretset_OBJECTS = $(am_seqretset_OBJECTS)
@@ -1608,7 +1608,7 @@ seqretset_LDADD = $(LDADD)
 seqretset_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_seqretsetall_OBJECTS = seqretsetall.$(OBJEXT)
 seqretsetall_OBJECTS = $(am_seqretsetall_OBJECTS)
@@ -1616,7 +1616,7 @@ seqretsetall_LDADD = $(LDADD)
 seqretsetall_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_seqretsingle_OBJECTS = seqretsingle.$(OBJEXT)
 seqretsingle_OBJECTS = $(am_seqretsingle_OBJECTS)
@@ -1624,7 +1624,7 @@ seqretsingle_LDADD = $(LDADD)
 seqretsingle_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_seqretsplit_OBJECTS = seqretsplit.$(OBJEXT)
 seqretsplit_OBJECTS = $(am_seqretsplit_OBJECTS)
@@ -1632,7 +1632,7 @@ seqretsplit_LDADD = $(LDADD)
 seqretsplit_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_seqrettype_OBJECTS = seqrettype.$(OBJEXT)
 seqrettype_OBJECTS = $(am_seqrettype_OBJECTS)
@@ -1640,7 +1640,7 @@ seqrettype_LDADD = $(LDADD)
 seqrettype_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_showalign_OBJECTS = showalign.$(OBJEXT)
 showalign_OBJECTS = $(am_showalign_OBJECTS)
@@ -1648,7 +1648,7 @@ showalign_LDADD = $(LDADD)
 showalign_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_showdb_OBJECTS = showdb.$(OBJEXT)
 showdb_OBJECTS = $(am_showdb_OBJECTS)
@@ -1656,7 +1656,7 @@ showdb_LDADD = $(LDADD)
 showdb_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_showfeat_OBJECTS = showfeat.$(OBJEXT)
 showfeat_OBJECTS = $(am_showfeat_OBJECTS)
@@ -1664,7 +1664,7 @@ showfeat_LDADD = $(LDADD)
 showfeat_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_showorf_OBJECTS = showorf.$(OBJEXT)
 showorf_OBJECTS = $(am_showorf_OBJECTS)
@@ -1672,7 +1672,7 @@ showorf_LDADD = $(LDADD)
 showorf_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_showpep_OBJECTS = showpep.$(OBJEXT)
 showpep_OBJECTS = $(am_showpep_OBJECTS)
@@ -1680,7 +1680,7 @@ showpep_LDADD = $(LDADD)
 showpep_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_showseq_OBJECTS = showseq.$(OBJEXT)
 showseq_OBJECTS = $(am_showseq_OBJECTS)
@@ -1688,7 +1688,7 @@ showseq_LDADD = $(LDADD)
 showseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_shuffleseq_OBJECTS = shuffleseq.$(OBJEXT)
 shuffleseq_OBJECTS = $(am_shuffleseq_OBJECTS)
@@ -1696,7 +1696,7 @@ shuffleseq_LDADD = $(LDADD)
 shuffleseq_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_sigcleave_OBJECTS = sigcleave.$(OBJEXT)
 sigcleave_OBJECTS = $(am_sigcleave_OBJECTS)
@@ -1704,7 +1704,7 @@ sigcleave_LDADD = $(LDADD)
 sigcleave_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_silent_OBJECTS = silent.$(OBJEXT)
 silent_OBJECTS = $(am_silent_OBJECTS)
@@ -1712,7 +1712,7 @@ silent_LDADD = $(LDADD)
 silent_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_sirna_OBJECTS = sirna.$(OBJEXT)
 sirna_OBJECTS = $(am_sirna_OBJECTS)
@@ -1720,7 +1720,7 @@ sirna_LDADD = $(LDADD)
 sirna_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_sixpack_OBJECTS = sixpack.$(OBJEXT)
 sixpack_OBJECTS = $(am_sixpack_OBJECTS)
@@ -1728,7 +1728,7 @@ sixpack_LDADD = $(LDADD)
 sixpack_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_sizeseq_OBJECTS = sizeseq.$(OBJEXT)
 sizeseq_OBJECTS = $(am_sizeseq_OBJECTS)
@@ -1736,7 +1736,7 @@ sizeseq_LDADD = $(LDADD)
 sizeseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_skipredundant_OBJECTS = skipredundant.$(OBJEXT)
 skipredundant_OBJECTS = $(am_skipredundant_OBJECTS)
@@ -1744,7 +1744,7 @@ skipredundant_LDADD = $(LDADD)
 skipredundant_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_skipseq_OBJECTS = skipseq.$(OBJEXT)
 skipseq_OBJECTS = $(am_skipseq_OBJECTS)
@@ -1752,7 +1752,7 @@ skipseq_LDADD = $(LDADD)
 skipseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 splitsource_SOURCES = splitsource.c
 splitsource_OBJECTS = splitsource.$(OBJEXT)
@@ -1760,7 +1760,7 @@ splitsource_LDADD = $(LDADD)
 splitsource_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_splitter_OBJECTS = splitter.$(OBJEXT)
 splitter_OBJECTS = $(am_splitter_OBJECTS)
@@ -1768,7 +1768,7 @@ splitter_LDADD = $(LDADD)
 splitter_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_sqltest_OBJECTS = sqltest.$(OBJEXT)
 sqltest_OBJECTS = $(am_sqltest_OBJECTS)
@@ -1776,7 +1776,7 @@ sqltest_LDADD = $(LDADD)
 sqltest_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_stretcher_OBJECTS = stretcher.$(OBJEXT)
 stretcher_OBJECTS = $(am_stretcher_OBJECTS)
@@ -1784,7 +1784,7 @@ stretcher_LDADD = $(LDADD)
 stretcher_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_stssearch_OBJECTS = stssearch.$(OBJEXT)
 stssearch_OBJECTS = $(am_stssearch_OBJECTS)
@@ -1792,7 +1792,7 @@ stssearch_LDADD = $(LDADD)
 stssearch_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_supermatcher_OBJECTS = supermatcher.$(OBJEXT)
 supermatcher_OBJECTS = $(am_supermatcher_OBJECTS)
@@ -1800,7 +1800,7 @@ supermatcher_LDADD = $(LDADD)
 supermatcher_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_syco_OBJECTS = syco.$(OBJEXT)
 syco_OBJECTS = $(am_syco_OBJECTS)
@@ -1808,7 +1808,7 @@ syco_LDADD = $(LDADD)
 syco_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_tcode_OBJECTS = tcode.$(OBJEXT)
 tcode_OBJECTS = $(am_tcode_OBJECTS)
@@ -1816,7 +1816,7 @@ tcode_LDADD = $(LDADD)
 tcode_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_testplot_OBJECTS = testplot.$(OBJEXT)
 testplot_OBJECTS = $(am_testplot_OBJECTS)
@@ -1824,7 +1824,7 @@ testplot_LDADD = $(LDADD)
 testplot_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_textsearch_OBJECTS = textsearch.$(OBJEXT)
 textsearch_OBJECTS = $(am_textsearch_OBJECTS)
@@ -1832,7 +1832,7 @@ textsearch_LDADD = $(LDADD)
 textsearch_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_tfextract_OBJECTS = tfextract.$(OBJEXT)
 tfextract_OBJECTS = $(am_tfextract_OBJECTS)
@@ -1840,7 +1840,7 @@ tfextract_LDADD = $(LDADD)
 tfextract_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_tfm_OBJECTS = tfm.$(OBJEXT)
 tfm_OBJECTS = $(am_tfm_OBJECTS)
@@ -1848,7 +1848,7 @@ tfm_LDADD = $(LDADD)
 tfm_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_tfscan_OBJECTS = tfscan.$(OBJEXT)
 tfscan_OBJECTS = $(am_tfscan_OBJECTS)
@@ -1856,7 +1856,7 @@ tfscan_LDADD = $(LDADD)
 tfscan_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_tmap_OBJECTS = tmap.$(OBJEXT)
 tmap_OBJECTS = $(am_tmap_OBJECTS)
@@ -1864,7 +1864,7 @@ tmap_LDADD = $(LDADD)
 tmap_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_tranalign_OBJECTS = tranalign.$(OBJEXT)
 tranalign_OBJECTS = $(am_tranalign_OBJECTS)
@@ -1872,7 +1872,7 @@ tranalign_LDADD = $(LDADD)
 tranalign_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_transeq_OBJECTS = transeq.$(OBJEXT)
 transeq_OBJECTS = $(am_transeq_OBJECTS)
@@ -1880,7 +1880,7 @@ transeq_LDADD = $(LDADD)
 transeq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_treetypedisplay_OBJECTS = treetypedisplay.$(OBJEXT)
 treetypedisplay_OBJECTS = $(am_treetypedisplay_OBJECTS)
@@ -1888,7 +1888,7 @@ treetypedisplay_LDADD = $(LDADD)
 treetypedisplay_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_trimest_OBJECTS = trimest.$(OBJEXT)
 trimest_OBJECTS = $(am_trimest_OBJECTS)
@@ -1896,7 +1896,7 @@ trimest_LDADD = $(LDADD)
 trimest_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_trimseq_OBJECTS = trimseq.$(OBJEXT)
 trimseq_OBJECTS = $(am_trimseq_OBJECTS)
@@ -1904,7 +1904,7 @@ trimseq_LDADD = $(LDADD)
 trimseq_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_trimspace_OBJECTS = trimspace.$(OBJEXT)
 trimspace_OBJECTS = $(am_trimspace_OBJECTS)
@@ -1912,7 +1912,7 @@ trimspace_LDADD = $(LDADD)
 trimspace_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_twofeat_OBJECTS = twofeat.$(OBJEXT)
 twofeat_OBJECTS = $(am_twofeat_OBJECTS)
@@ -1920,7 +1920,7 @@ twofeat_LDADD = $(LDADD)
 twofeat_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_union_OBJECTS = union.$(OBJEXT)
 union_OBJECTS = $(am_union_OBJECTS)
@@ -1928,7 +1928,7 @@ union_LDADD = $(LDADD)
 union_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_vectorstrip_OBJECTS = vectorstrip.$(OBJEXT)
 vectorstrip_OBJECTS = $(am_vectorstrip_OBJECTS)
@@ -1936,7 +1936,7 @@ vectorstrip_LDADD = $(LDADD)
 vectorstrip_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_water_OBJECTS = water.$(OBJEXT)
 water_OBJECTS = $(am_water_OBJECTS)
@@ -1944,7 +1944,7 @@ water_LDADD = $(LDADD)
 water_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_whichdb_OBJECTS = whichdb.$(OBJEXT)
 whichdb_OBJECTS = $(am_whichdb_OBJECTS)
@@ -1952,7 +1952,7 @@ whichdb_LDADD = $(LDADD)
 whichdb_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_wobble_OBJECTS = wobble.$(OBJEXT)
 wobble_OBJECTS = $(am_wobble_OBJECTS)
@@ -1960,7 +1960,7 @@ wobble_LDADD = $(LDADD)
 wobble_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_wordcount_OBJECTS = wordcount.$(OBJEXT)
 wordcount_OBJECTS = $(am_wordcount_OBJECTS)
@@ -1968,7 +1968,7 @@ wordcount_LDADD = $(LDADD)
 wordcount_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_wordfinder_OBJECTS = wordfinder.$(OBJEXT)
 wordfinder_OBJECTS = $(am_wordfinder_OBJECTS)
@@ -1976,7 +1976,7 @@ wordfinder_LDADD = $(LDADD)
 wordfinder_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_wordmatch_OBJECTS = wordmatch.$(OBJEXT)
 wordmatch_OBJECTS = $(am_wordmatch_OBJECTS)
@@ -1984,7 +1984,7 @@ wordmatch_LDADD = $(LDADD)
 wordmatch_DEPENDENCIES = ../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 \
+	../ajax/core/libajax.la $(EXTRA_LDS) \
 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)
 am_wossname_OBJECTS = wossname.$(OBJEXT)
 wossname_OBJECTS = $(am_wossname_OBJECTS)
@@ -1992,7 +1992,7 @@ wossname_LDADD = $(LDADD)
 wossname_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 am_yank_OBJECTS = yank.$(OBJEXT)
 yank_OBJECTS = $(am_yank_OBJECTS)
@@ -2000,7 +2000,7 @@ yank_LDADD = $(LDADD)
 yank_DEPENDENCIES = ../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 \
+	$(EXTRA_LDS) ../plplot/libeplplot.la \
 	$(am__DEPENDENCIES_1)
 DEFAULT_INCLUDES = -I.@am__isrc@
 depcomp = $(SHELL) $(top_srcdir)/depcomp
@@ -2284,8 +2284,6 @@ ESYSTEMLIBS = @ESYSTEMLIBS@
 EXEEXT = @EXEEXT@
 FGREP = @FGREP@
 GREP = @GREP@
-HAVE_MEMMOVE = @HAVE_MEMMOVE@
-HAVE_STRERROR = @HAVE_STRERROR@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -2412,8 +2410,8 @@ EXTRA_DIST = emboss.default.template
 @ISAIXIA64_TRUE@@ISSHARED_TRUE@ -lacd -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre -lezlib
 
 AM_CFLAGS = $(AIX_CFLAGS) $(WARN_CFLAGS) $(DEVWARN_CFLAGS)
-@ESYSTEMLIBS_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
-INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \
+@ESYSTEMLIBS_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
+INCLUDES = -I$(top_srcdir)/nucleus \
 	$(EXTRA_INCLUDES) \
 	-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
 	-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
@@ -2645,12 +2643,12 @@ seqrettype_SOURCES = seqrettype.c
 sqltest_SOURCES = sqltest.c
 testplot_SOURCES = testplot.c
 treetypedisplay_SOURCES = treetypedisplay.c
-@ESYSTEMLIBS_FALSE@EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la
+@ESYSTEMLIBS_FALSE@EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../ajax/pcre/libepcre.la
 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 = emboss.default.template
@@ -2667,9 +2665,9 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefi
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/Makefile'; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu emboss/Makefile
+	  $(AUTOMAKE) --gnits emboss/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
@@ -2732,6 +2730,22 @@ clean-binPROGRAMS:
 	echo " rm -f" $$list; \
 	rm -f $$list
 
+installcheck-binPROGRAMS: $(bin_PROGRAMS)
+	bad=0; pid=$$$$; list="$(bin_PROGRAMS)"; for p in $$list; do \
+	  case ' $(AM_INSTALLCHECK_STD_OPTIONS_EXEMPT) ' in \
+	   *" $$p "* | *" $(srcdir)/$$p "*) continue;; \
+	  esac; \
+	  f=`echo "$$p" | \
+	     sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
+	  for opt in --help --version; do \
+	    if "$(DESTDIR)$(bindir)/$$f" $$opt >c$${pid}_.out \
+	         2>c$${pid}_.err </dev/null \
+		 && test -n "`cat c$${pid}_.out`" \
+		 && test -z "`cat c$${pid}_.err`"; then :; \
+	    else echo "$$f does not support $$opt" 1>&2; bad=1; fi; \
+	  done; \
+	done; rm -f c$${pid}_.???; exit $$bad
+
 clean-checkPROGRAMS:
 	@list='$(check_PROGRAMS)'; test -n "$$list" || exit 0; \
 	echo " rm -f" $$list; \
@@ -4007,7 +4021,7 @@ install-ps: install-ps-recursive
 
 install-ps-am:
 
-installcheck-am:
+installcheck-am: installcheck-binPROGRAMS
 
 maintainer-clean: maintainer-clean-recursive
 	-rm -rf ./$(DEPDIR)
@@ -4042,12 +4056,12 @@ uninstall-am: uninstall-binPROGRAMS unin
 	install-exec install-exec-am install-html install-html-am \
 	install-info install-info-am install-man install-pdf \
 	install-pdf-am install-pkgdataDATA install-ps install-ps-am \
-	install-strip installcheck installcheck-am installdirs \
-	installdirs-am maintainer-clean maintainer-clean-generic \
-	mostlyclean mostlyclean-compile mostlyclean-generic \
-	mostlyclean-libtool pdf pdf-am ps ps-am tags tags-recursive \
-	uninstall uninstall-am uninstall-binPROGRAMS \
-	uninstall-pkgdataDATA
+	install-strip installcheck installcheck-am \
+	installcheck-binPROGRAMS installdirs installdirs-am \
+	maintainer-clean maintainer-clean-generic mostlyclean \
+	mostlyclean-compile mostlyclean-generic mostlyclean-libtool \
+	pdf pdf-am ps ps-am tags tags-recursive uninstall uninstall-am \
+	uninstall-binPROGRAMS uninstall-pkgdataDATA
 
 
 #if PURIFY
diff -up EMBOSS-6.3.1/nucleus/Makefile.am.system-pcre EMBOSS-6.3.1/nucleus/Makefile.am
--- EMBOSS-6.3.1/nucleus/Makefile.am.system-pcre	2010-06-16 07:36:00.000000000 -0400
+++ EMBOSS-6.3.1/nucleus/Makefile.am	2010-08-02 16:21:49.942306124 -0400
@@ -19,13 +19,13 @@ 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
 
 
 INCLUDES = -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/core -I$(top_srcdir)/ajax/graphics \
 	-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
diff -up EMBOSS-6.3.1/nucleus/Makefile.in.system-pcre EMBOSS-6.3.1/nucleus/Makefile.in
--- EMBOSS-6.3.1/nucleus/Makefile.in.system-pcre	2010-07-19 07:55:42.000000000 -0400
+++ EMBOSS-6.3.1/nucleus/Makefile.in	2010-08-02 16:22:34.280145171 -0400
@@ -134,8 +134,6 @@ ESYSTEMLIBS = @ESYSTEMLIBS@
 EXEEXT = @EXEEXT@
 FGREP = @FGREP@
 GREP = @GREP@
-HAVE_MEMMOVE = @HAVE_MEMMOVE@
-HAVE_STRERROR = @HAVE_STRERROR@
 INSTALL = @INSTALL@
 INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -264,9 +262,9 @@ AM_CFLAGS = $(AIX_CFLAGS) $(WARN_CFLAGS)
 @ISCYGWIN_TRUE@-L../ajax/acd -lacd -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre \
 @ISCYGWIN_TRUE@-lezlib -leplplot
 
-@ESYSTEMLIBS_FALSE@@ISCYGWIN_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+@ESYSTEMLIBS_FALSE@@ISCYGWIN_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre
 INCLUDES = -I$(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/core -I$(top_srcdir)/ajax/graphics \
 	-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
@@ -303,9 +301,9 @@ $(srcdir)/Makefile.in:  $(srcdir)/Makefi
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu nucleus/Makefile'; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits nucleus/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
-	  $(AUTOMAKE) --gnu nucleus/Makefile
+	  $(AUTOMAKE) --gnits nucleus/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
rpms / EMBOSS

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