From 177c4d525e19990273d15a4e3a5a306ffc6f6dcf Mon Sep 17 00:00:00 2001 From: Julian Sikorski Date: Nov 23 2011 22:06:14 +0000 Subject: Updated to 6.4.0 Dropped included new-fix-doc-finding and fix-amd64-check patches Updated system libs patches tabs → spaces to satisfy rpmlint --- diff --git a/.gitignore b/.gitignore index 666ef37..70855a1 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,4 @@ EMBOSS-6.3.1.tar.gz patch-1-4.gz +/EMBOSS-6.4.0.tar.gz +/patch-1-24.gz diff --git a/EMBOSS-6.3.1-fix-amd64-check.patch b/EMBOSS-6.3.1-fix-amd64-check.patch deleted file mode 100644 index e43e4cc..0000000 --- a/EMBOSS-6.3.1-fix-amd64-check.patch +++ /dev/null @@ -1,14 +0,0 @@ -diff -up EMBOSS-6.3.1/m4/amd64.m4.BAD EMBOSS-6.3.1/m4/amd64.m4 ---- EMBOSS-6.3.1/m4/amd64.m4.BAD 2010-11-10 11:13:27.153159001 -0500 -+++ EMBOSS-6.3.1/m4/amd64.m4 2010-11-10 11:14:21.722159000 -0500 -@@ -12,8 +12,8 @@ AC_DEFUN([CHECK_AMD64], - [AC_MSG_CHECKING([if Linux x86_64]) - - --if test "`uname -a | grep Linux`"; then -- if test "`uname -a | grep x86_64`"; then -+if test "`uname -o | grep Linux`"; then -+ if test "`uname -m | grep x86_64`"; then - CFLAGS="${CFLAGS} -D__amd64__" - AC_MSG_RESULT(yes) - else diff --git a/EMBOSS-6.3.1-new-fix-doc-finding.patch b/EMBOSS-6.3.1-new-fix-doc-finding.patch deleted file mode 100644 index ed9d443..0000000 --- a/EMBOSS-6.3.1-new-fix-doc-finding.patch +++ /dev/null @@ -1,109 +0,0 @@ -diff -up EMBOSS-6.3.1/emboss/tfm.c.fix-doc-finding EMBOSS-6.3.1/emboss/tfm.c ---- EMBOSS-6.3.1/emboss/tfm.c.fix-doc-finding 2010-04-13 10:25:56.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/tfm.c 2010-11-10 13:53:05.957159000 -0500 -@@ -143,13 +143,15 @@ static void tfm_FindAppDocRoot(const AjP - AjPStr roottmp = NULL; - AjPStr tmpstr = NULL; - AjPStr embassy = NULL; -- -+ AjPStr doctest = NULL; -+ - AjBool is_windows = ajFalse; - #ifdef WIN32 - is_windows = ajTrue; - #endif - - docrootinst = ajStrNew(); -+ doctest = ajStrNew(); - roottmp = ajStrNew(); - tmpstr = ajStrNew(); - -@@ -163,11 +165,25 @@ static void tfm_FindAppDocRoot(const AjP - /* look at EMBOSS doc files */ - - /* try to open the installed doc directory */ -- if(ajStrGetLen(roottmp)) -- ajStrAssignS(docroot, roottmp); -- else -+ if(ajStrGetLen(roottmp)) -+ { -+ /* -+ ** Check for old-style EMBOSS_DOCROOT and adjust accordingly -+ */ -+ ajFmtPrintS(&doctest,"%S%cprograms%ctext",roottmp,SLASH_CHAR, -+ SLASH_CHAR); -+ ajStrAssignS(&docrootinst,roottmp); -+ ajDirnameFix(&docrootinst); -+ -+ if(!ajDirnameFixExists(&doctest)) -+ { -+ ajDirnameUp(&docrootinst); -+ ajDirnameUp(&docrootinst); -+ } -+ } -+ else - { -- ajStrAssignS(&docrootinst, ajNamValueInstalldir()); -+ ajStrAssignS(&docrootinst, ajNamValueInstalldir()); - ajDirnameFix(&docrootinst); - - if(is_windows) -@@ -184,28 +200,28 @@ static void tfm_FindAppDocRoot(const AjP - else - ajFmtPrintAppS(&docrootinst, "share%sEMBOSS%sdoc%s", - SLASH_STRING,SLASH_STRING,SLASH_STRING); -+ } - -- -- if(html) -- { -- if(ajStrGetLen(embassy)) -+ if(html) -+ { -+ if(ajStrGetLen(embassy)) - ajFmtPrintS(docroot,"%Shtml%sembassy%s%S%s", - docrootinst,SLASH_STRING,SLASH_STRING, - embassy, SLASH_STRING); -- else -- { -- if(is_windows) -- ajFmtPrintS(docroot,"%Sprograms%shtml%s", -- docrootinst,SLASH_STRING,SLASH_STRING); -- else -- ajFmtPrintS(docroot,"%Sprograms%shtml%s", -- docrootinst,SLASH_STRING,SLASH_STRING); -- } -- } - else -+ { -+ if(is_windows) -+ ajFmtPrintS(docroot,"%Sprograms%shtml%s", -+ docrootinst,SLASH_STRING,SLASH_STRING); -+ else -+ ajFmtPrintS(docroot,"%Sprograms%shtml%s", -+ docrootinst,SLASH_STRING,SLASH_STRING); -+ } -+ } -+ else - ajFmtPrintS(docroot,"%Sprograms%stext%s",docrootinst,SLASH_STRING, - SLASH_STRING); -- } -+ - ajDirnameFix(docroot); - ajDebug("installed docroot '%S'\n", *docroot); - -@@ -248,6 +264,7 @@ static void tfm_FindAppDocRoot(const AjP - - ajStrDel(&roottmp); - ajStrDel(&docrootinst); -+ ajStrDel(&doctest); - ajStrDel(&tmpstr); - - return; -@@ -348,4 +365,4 @@ static void tfm_FixImages(AjPStr *line, - ajStrDel(&pre); - - return; --} -+} -\ No newline at end of file diff --git a/EMBOSS-6.3.1-prevent-autotooling.patch b/EMBOSS-6.3.1-prevent-autotooling.patch deleted file mode 100644 index afd3b89..0000000 --- a/EMBOSS-6.3.1-prevent-autotooling.patch +++ /dev/null @@ -1,22568 +0,0 @@ -diff -urP EMBOSS-6.3.1.orig/ajax/acd/Makefile.in EMBOSS-6.3.1/ajax/acd/Makefile.in ---- EMBOSS-6.3.1.orig/ajax/acd/Makefile.in 2010-08-02 17:23:03.929163054 -0400 -+++ EMBOSS-6.3.1/ajax/acd/Makefile.in 2010-08-02 17:23:23.136143079 -0400 -@@ -130,6 +130,8 @@ - EXEEXT = @EXEEXT@ - FGREP = @FGREP@ - GREP = @GREP@ -+HAVE_MEMMOVE = @HAVE_MEMMOVE@ -+HAVE_STRERROR = @HAVE_STRERROR@ - INSTALL = @INSTALL@ - INSTALL_DATA = @INSTALL_DATA@ - INSTALL_PROGRAM = @INSTALL_PROGRAM@ -diff -urP EMBOSS-6.3.1.orig/ajax/ajaxdb/Makefile.in EMBOSS-6.3.1/ajax/ajaxdb/Makefile.in ---- EMBOSS-6.3.1.orig/ajax/ajaxdb/Makefile.in 2010-08-02 17:23:03.930162985 -0400 -+++ EMBOSS-6.3.1/ajax/ajaxdb/Makefile.in 2010-08-02 17:23:23.228143498 -0400 -@@ -43,9 +43,8 @@ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ - $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -- $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -131,6 +130,8 @@ - EXEEXT = @EXEEXT@ - FGREP = @FGREP@ - GREP = @GREP@ -+HAVE_MEMMOVE = @HAVE_MEMMOVE@ -+HAVE_STRERROR = @HAVE_STRERROR@ - INSTALL = @INSTALL@ - INSTALL_DATA = @INSTALL_DATA@ - INSTALL_PROGRAM = @INSTALL_PROGRAM@ -@@ -259,7 +260,7 @@ - @ISCYGWIN_TRUE@-L../ensembl -lensembl lajax -leplplot -leexpat -lepcre -lezlib - - @ESYSTEMLIBS_FALSE@EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib -I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/plplot --INCLUDES = $(PLPLOT_CFLAGS) \ -+INCLUDES = $(PLPLOT_CFLAGS) \ - $(EXTRA_INCLUDES) \ - -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl - -diff -urP EMBOSS-6.3.1.orig/ajax/core/Makefile.in EMBOSS-6.3.1/ajax/core/Makefile.in ---- EMBOSS-6.3.1.orig/ajax/core/Makefile.in 2010-08-02 17:23:03.931143219 -0400 -+++ EMBOSS-6.3.1/ajax/core/Makefile.in 2010-08-02 17:23:23.331143149 -0400 -@@ -43,9 +43,8 @@ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ - $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -- $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -140,6 +139,8 @@ - EXEEXT = @EXEEXT@ - FGREP = @FGREP@ - GREP = @GREP@ -+HAVE_MEMMOVE = @HAVE_MEMMOVE@ -+HAVE_STRERROR = @HAVE_STRERROR@ - INSTALL = @INSTALL@ - INSTALL_DATA = @INSTALL_DATA@ - INSTALL_PROGRAM = @INSTALL_PROGRAM@ -diff -urP EMBOSS-6.3.1.orig/ajax/ensembl/Makefile.in EMBOSS-6.3.1/ajax/ensembl/Makefile.in ---- EMBOSS-6.3.1.orig/ajax/ensembl/Makefile.in 2010-08-02 17:23:03.932150483 -0400 -+++ EMBOSS-6.3.1/ajax/ensembl/Makefile.in 2010-08-02 17:23:23.433143079 -0400 -@@ -43,9 +43,8 @@ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ - $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -- $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -144,6 +143,8 @@ - EXEEXT = @EXEEXT@ - FGREP = @FGREP@ - GREP = @GREP@ -+HAVE_MEMMOVE = @HAVE_MEMMOVE@ -+HAVE_STRERROR = @HAVE_STRERROR@ - INSTALL = @INSTALL@ - INSTALL_DATA = @INSTALL_DATA@ - INSTALL_PROGRAM = @INSTALL_PROGRAM@ -diff -urP EMBOSS-6.3.1.orig/ajax/graphics/Makefile.in EMBOSS-6.3.1/ajax/graphics/Makefile.in ---- EMBOSS-6.3.1.orig/ajax/graphics/Makefile.in 2010-08-02 17:23:03.937163613 -0400 -+++ EMBOSS-6.3.1/ajax/graphics/Makefile.in 2010-08-02 17:23:23.525143079 -0400 -@@ -43,9 +43,8 @@ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ - $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -- $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -131,6 +130,8 @@ - EXEEXT = @EXEEXT@ - FGREP = @FGREP@ - GREP = @GREP@ -+HAVE_MEMMOVE = @HAVE_MEMMOVE@ -+HAVE_STRERROR = @HAVE_STRERROR@ - INSTALL = @INSTALL@ - INSTALL_DATA = @INSTALL_DATA@ - INSTALL_PROGRAM = @INSTALL_PROGRAM@ -diff -urP EMBOSS-6.3.1.orig/ajax/Makefile.in EMBOSS-6.3.1/ajax/Makefile.in ---- EMBOSS-6.3.1.orig/ajax/Makefile.in 2010-08-02 17:23:03.937163613 -0400 -+++ EMBOSS-6.3.1/ajax/Makefile.in 2010-08-02 17:23:23.040142730 -0400 -@@ -40,9 +40,8 @@ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ - $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -- $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -64,7 +63,7 @@ - distdir - ETAGS = etags - CTAGS = ctags --DIST_SUBDIRS = pcre expat zlib core graphics ensembl ajaxdb acd -+DIST_SUBDIRS = expat zlib pcre core graphics ensembl ajaxdb acd - DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) - am__relativize = \ - dir0=`pwd`; \ -@@ -122,6 +121,8 @@ - EXEEXT = @EXEEXT@ - FGREP = @FGREP@ - GREP = @GREP@ -+HAVE_MEMMOVE = @HAVE_MEMMOVE@ -+HAVE_STRERROR = @HAVE_STRERROR@ - INSTALL = @INSTALL@ - INSTALL_DATA = @INSTALL_DATA@ - INSTALL_PROGRAM = @INSTALL_PROGRAM@ -diff -urP EMBOSS-6.3.1.orig/autom4te.cache/output.0 EMBOSS-6.3.1/autom4te.cache/output.0 ---- EMBOSS-6.3.1.orig/autom4te.cache/output.0 1969-12-31 19:00:00.000000000 -0500 -+++ EMBOSS-6.3.1/autom4te.cache/output.0 2010-08-02 17:23:22.875143219 -0400 -@@ -0,0 +1,17831 @@ -+@%:@! /bin/sh -+@%:@ Guess values for system-dependent variables and create Makefiles. -+@%:@ Generated by GNU Autoconf 2.65. -+@%:@ -+@%:@ -+@%:@ Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, -+@%:@ 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, -+@%:@ Inc. -+@%:@ -+@%:@ -+@%:@ This configure script is free software; the Free Software Foundation -+@%:@ gives unlimited permission to copy, distribute and modify it. -+## -------------------- ## -+## M4sh Initialization. ## -+## -------------------- ## -+ -+# Be more Bourne compatible -+DUALCASE=1; export DUALCASE # for MKS sh -+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : -+ emulate sh -+ NULLCMD=: -+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which -+ # is contrary to our usage. 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See mingw*. -+ lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?' -+ lt_cv_file_magic_cmd='$OBJDUMP -f' -+ ;; -+ -+darwin* | rhapsody*) -+ lt_cv_deplibs_check_method=pass_all -+ ;; -+ -+freebsd* | dragonfly*) -+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then -+ case $host_cpu in -+ i*86 ) -+ # Not sure whether the presence of OpenBSD here was a mistake. -+ # Let's accept both of them until this is cleared up. -+ lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library' -+ lt_cv_file_magic_cmd=/usr/bin/file -+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*` -+ ;; -+ esac -+ else -+ lt_cv_deplibs_check_method=pass_all -+ fi -+ ;; -+ -+gnu*) -+ lt_cv_deplibs_check_method=pass_all -+ ;; -+ -+hpux10.20* | hpux11*) -+ lt_cv_file_magic_cmd=/usr/bin/file -+ case $host_cpu in -+ ia64*) -+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64' -+ lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so -+ ;; -+ hppa*64*) -+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]' -+ lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl -+ ;; -+ *) -+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9].[0-9]) shared library' -+ lt_cv_file_magic_test_file=/usr/lib/libc.sl -+ ;; -+ esac -+ ;; -+ -+interix[3-9]*) -+ # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here -+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$' -+ ;; -+ -+irix5* | irix6* | nonstopux*) -+ case $LD in -+ *-32|*"-32 ") libmagic=32-bit;; -+ *-n32|*"-n32 ") libmagic=N32;; -+ *-64|*"-64 ") libmagic=64-bit;; -+ *) libmagic=never-match;; -+ esac -+ lt_cv_deplibs_check_method=pass_all -+ ;; -+ -+# This must be Linux ELF. -+linux* | k*bsd*-gnu) -+ lt_cv_deplibs_check_method=pass_all -+ ;; -+ -+netbsd*) -+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then -+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' -+ else -+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$' -+ fi -+ ;; -+ -+newos6*) -+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)' -+ lt_cv_file_magic_cmd=/usr/bin/file -+ lt_cv_file_magic_test_file=/usr/lib/libnls.so -+ ;; -+ -+*nto* | *qnx*) -+ lt_cv_deplibs_check_method=pass_all -+ ;; -+ -+openbsd*) -+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then -+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$' -+ else -+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' -+ fi -+ ;; -+ -+osf3* | osf4* | osf5*) -+ lt_cv_deplibs_check_method=pass_all -+ ;; -+ -+rdos*) -+ lt_cv_deplibs_check_method=pass_all -+ ;; -+ -+solaris*) -+ lt_cv_deplibs_check_method=pass_all -+ ;; -+ -+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) -+ lt_cv_deplibs_check_method=pass_all -+ ;; -+ -+sysv4 | sysv4.3*) -+ case $host_vendor in -+ motorola) -+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]' -+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` -+ ;; -+ ncr) -+ lt_cv_deplibs_check_method=pass_all -+ ;; -+ sequent) -+ lt_cv_file_magic_cmd='/bin/file' -+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )' -+ ;; -+ sni) -+ lt_cv_file_magic_cmd='/bin/file' -+ lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib" -+ lt_cv_file_magic_test_file=/lib/libc.so -+ ;; -+ siemens) -+ lt_cv_deplibs_check_method=pass_all -+ ;; -+ pc) -+ lt_cv_deplibs_check_method=pass_all -+ ;; -+ esac -+ ;; -+ -+tpf*) -+ lt_cv_deplibs_check_method=pass_all -+ ;; -+esac -+ -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_deplibs_check_method" >&5 -+$as_echo "$lt_cv_deplibs_check_method" >&6; } -+file_magic_cmd=$lt_cv_file_magic_cmd -+deplibs_check_method=$lt_cv_deplibs_check_method -+test -z "$deplibs_check_method" && deplibs_check_method=unknown -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+if test -n "$ac_tool_prefix"; then -+ # Extract the first word of "${ac_tool_prefix}ar", so it can be a program name with args. -+set dummy ${ac_tool_prefix}ar; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_AR+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$AR"; then -+ ac_cv_prog_AR="$AR" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_AR="${ac_tool_prefix}ar" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+AR=$ac_cv_prog_AR -+if test -n "$AR"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AR" >&5 -+$as_echo "$AR" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+fi -+if test -z "$ac_cv_prog_AR"; then -+ ac_ct_AR=$AR -+ # Extract the first word of "ar", so it can be a program name with args. -+set dummy ar; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_ac_ct_AR+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$ac_ct_AR"; then -+ ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_ac_ct_AR="ar" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+ac_ct_AR=$ac_cv_prog_ac_ct_AR -+if test -n "$ac_ct_AR"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_AR" >&5 -+$as_echo "$ac_ct_AR" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ if test "x$ac_ct_AR" = x; then -+ AR="false" -+ else -+ case $cross_compiling:$ac_tool_warned in -+yes:) -+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 -+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} -+ac_tool_warned=yes ;; -+esac -+ AR=$ac_ct_AR -+ fi -+else -+ AR="$ac_cv_prog_AR" -+fi -+ -+test -z "$AR" && AR=ar -+test -z "$AR_FLAGS" && AR_FLAGS=cru -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+if test -n "$ac_tool_prefix"; then -+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. -+set dummy ${ac_tool_prefix}strip; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_STRIP+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$STRIP"; then -+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_STRIP="${ac_tool_prefix}strip" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+STRIP=$ac_cv_prog_STRIP -+if test -n "$STRIP"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5 -+$as_echo "$STRIP" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+fi -+if test -z "$ac_cv_prog_STRIP"; then -+ ac_ct_STRIP=$STRIP -+ # Extract the first word of "strip", so it can be a program name with args. -+set dummy strip; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$ac_ct_STRIP"; then -+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_ac_ct_STRIP="strip" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP -+if test -n "$ac_ct_STRIP"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5 -+$as_echo "$ac_ct_STRIP" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ if test "x$ac_ct_STRIP" = x; then -+ STRIP=":" -+ else -+ case $cross_compiling:$ac_tool_warned in -+yes:) -+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 -+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} -+ac_tool_warned=yes ;; -+esac -+ STRIP=$ac_ct_STRIP -+ fi -+else -+ STRIP="$ac_cv_prog_STRIP" -+fi -+ -+test -z "$STRIP" && STRIP=: -+ -+ -+ -+ -+ -+ -+if test -n "$ac_tool_prefix"; then -+ # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. -+set dummy ${ac_tool_prefix}ranlib; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_RANLIB+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$RANLIB"; then -+ ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+RANLIB=$ac_cv_prog_RANLIB -+if test -n "$RANLIB"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5 -+$as_echo "$RANLIB" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+fi -+if test -z "$ac_cv_prog_RANLIB"; then -+ ac_ct_RANLIB=$RANLIB -+ # Extract the first word of "ranlib", so it can be a program name with args. -+set dummy ranlib; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$ac_ct_RANLIB"; then -+ ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_ac_ct_RANLIB="ranlib" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB -+if test -n "$ac_ct_RANLIB"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5 -+$as_echo "$ac_ct_RANLIB" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ if test "x$ac_ct_RANLIB" = x; then -+ RANLIB=":" -+ else -+ case $cross_compiling:$ac_tool_warned in -+yes:) -+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 -+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} -+ac_tool_warned=yes ;; -+esac -+ RANLIB=$ac_ct_RANLIB -+ fi -+else -+ RANLIB="$ac_cv_prog_RANLIB" -+fi -+ -+test -z "$RANLIB" && RANLIB=: -+ -+ -+ -+ -+ -+ -+# Determine commands to create old-style static archives. -+old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs' -+old_postinstall_cmds='chmod 644 $oldlib' -+old_postuninstall_cmds= -+ -+if test -n "$RANLIB"; then -+ case $host_os in -+ openbsd*) -+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib" -+ ;; -+ *) -+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib" -+ ;; -+ esac -+ old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib" -+fi -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+# If no C compiler was specified, use CC. -+LTCC=${LTCC-"$CC"} -+ -+# If no C compiler flags were specified, use CFLAGS. -+LTCFLAGS=${LTCFLAGS-"$CFLAGS"} -+ -+# Allow CC to be a program name with arguments. -+compiler=$CC -+ -+ -+# Check for command to grab the raw symbol name followed by C symbol from nm. -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking command to parse $NM output from $compiler object" >&5 -+$as_echo_n "checking command to parse $NM output from $compiler object... " >&6; } -+if test "${lt_cv_sys_global_symbol_pipe+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ -+# These are sane defaults that work on at least a few old systems. -+# [They come from Ultrix. What could be older than Ultrix?!! ;)] -+ -+# Character class describing NM global symbol codes. -+symcode='[BCDEGRST]' -+ -+# Regexp to match symbols that can be accessed directly from C. -+sympat='\([_A-Za-z][_A-Za-z0-9]*\)' -+ -+# Define system-specific variables. -+case $host_os in -+aix*) -+ symcode='[BCDT]' -+ ;; -+cygwin* | mingw* | pw32* | cegcc*) -+ symcode='[ABCDGISTW]' -+ ;; -+hpux*) -+ if test "$host_cpu" = ia64; then -+ symcode='[ABCDEGRST]' -+ fi -+ ;; -+irix* | nonstopux*) -+ symcode='[BCDEGRST]' -+ ;; -+osf*) -+ symcode='[BCDEGQRST]' -+ ;; -+solaris*) -+ symcode='[BDRT]' -+ ;; -+sco3.2v5*) -+ symcode='[DT]' -+ ;; -+sysv4.2uw2*) -+ symcode='[DT]' -+ ;; -+sysv5* | sco5v6* | unixware* | OpenUNIX*) -+ symcode='[ABDT]' -+ ;; -+sysv4) -+ symcode='[DFNSTU]' -+ ;; -+esac -+ -+# If we're using GNU nm, then use its standard symbol codes. -+case `$NM -V 2>&1` in -+*GNU* | *'with BFD'*) -+ symcode='[ABCDGIRSTW]' ;; -+esac -+ -+# Transform an extracted symbol line into a proper C declaration. -+# Some systems (esp. on ia64) link data and code symbols differently, -+# so use this general approach. -+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" -+ -+# Transform an extracted symbol line into symbol name and symbol address -+lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (void *) \&\2},/p'" -+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \(lib[^ ]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"lib\2\", (void *) \&\2},/p'" -+ -+# Handle CRLF in mingw tool chain -+opt_cr= -+case $build_os in -+mingw*) -+ opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp -+ ;; -+esac -+ -+# Try without a prefix underscore, then with it. -+for ac_symprfx in "" "_"; do -+ -+ # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. -+ symxfrm="\\1 $ac_symprfx\\2 \\2" -+ -+ # Write the raw and C identifiers. -+ if test "$lt_cv_nm_interface" = "MS dumpbin"; then -+ # Fake it for dumpbin and say T for any non-static function -+ # and D for any global variable. -+ # Also find C++ and __fastcall symbols from MSVC++, -+ # which start with @ or ?. -+ lt_cv_sys_global_symbol_pipe="$AWK '"\ -+" {last_section=section; section=\$ 3};"\ -+" /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ -+" \$ 0!~/External *\|/{next};"\ -+" / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ -+" {if(hide[section]) next};"\ -+" {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ -+" {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ -+" s[1]~/^[@?]/{print s[1], s[1]; next};"\ -+" s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ -+" ' prfx=^$ac_symprfx" -+ else -+ lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" -+ fi -+ -+ # Check to see that the pipe works correctly. -+ pipe_works=no -+ -+ rm -f conftest* -+ cat > conftest.$ac_ext <<_LT_EOF -+#ifdef __cplusplus -+extern "C" { -+#endif -+char nm_test_var; -+void nm_test_func(void); -+void nm_test_func(void){} -+#ifdef __cplusplus -+} -+#endif -+int main(){nm_test_var='a';nm_test_func();return(0);} -+_LT_EOF -+ -+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 -+ (eval $ac_compile) 2>&5 -+ ac_status=$? -+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 -+ test $ac_status = 0; }; then -+ # Now try to grab the symbols. -+ nlist=conftest.nm -+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist\""; } >&5 -+ (eval $NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) 2>&5 -+ ac_status=$? -+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 -+ test $ac_status = 0; } && test -s "$nlist"; then -+ # Try sorting and uniquifying the output. -+ if sort "$nlist" | uniq > "$nlist"T; then -+ mv -f "$nlist"T "$nlist" -+ else -+ rm -f "$nlist"T -+ fi -+ -+ # Make sure that we snagged all the symbols we need. -+ if $GREP ' nm_test_var$' "$nlist" >/dev/null; then -+ if $GREP ' nm_test_func$' "$nlist" >/dev/null; then -+ cat <<_LT_EOF > conftest.$ac_ext -+#ifdef __cplusplus -+extern "C" { -+#endif -+ -+_LT_EOF -+ # Now generate the symbol file. -+ eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' -+ -+ cat <<_LT_EOF >> conftest.$ac_ext -+ -+/* The mapping between symbol names and symbols. */ -+const struct { -+ const char *name; -+ void *address; -+} -+lt__PROGRAM__LTX_preloaded_symbols[] = -+{ -+ { "@PROGRAM@", (void *) 0 }, -+_LT_EOF -+ $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext -+ cat <<\_LT_EOF >> conftest.$ac_ext -+ {0, (void *) 0} -+}; -+ -+/* This works around a problem in FreeBSD linker */ -+#ifdef FREEBSD_WORKAROUND -+static const void *lt_preloaded_setup() { -+ return lt__PROGRAM__LTX_preloaded_symbols; -+} -+#endif -+ -+#ifdef __cplusplus -+} -+#endif -+_LT_EOF -+ # Now try linking the two files. -+ mv conftest.$ac_objext conftstm.$ac_objext -+ lt_save_LIBS="$LIBS" -+ lt_save_CFLAGS="$CFLAGS" -+ LIBS="conftstm.$ac_objext" -+ CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag" -+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5 -+ (eval $ac_link) 2>&5 -+ ac_status=$? -+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 -+ test $ac_status = 0; } && test -s conftest${ac_exeext}; then -+ pipe_works=yes -+ fi -+ LIBS="$lt_save_LIBS" -+ CFLAGS="$lt_save_CFLAGS" -+ else -+ echo "cannot find nm_test_func in $nlist" >&5 -+ fi -+ else -+ echo "cannot find nm_test_var in $nlist" >&5 -+ fi -+ else -+ echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5 -+ fi -+ else -+ echo "$progname: failed program was:" >&5 -+ cat conftest.$ac_ext >&5 -+ fi -+ rm -rf conftest* conftst* -+ -+ # Do not use the global_symbol_pipe unless it works. -+ if test "$pipe_works" = yes; then -+ break -+ else -+ lt_cv_sys_global_symbol_pipe= -+ fi -+done -+ -+fi -+ -+if test -z "$lt_cv_sys_global_symbol_pipe"; then -+ lt_cv_sys_global_symbol_to_cdecl= -+fi -+if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: failed" >&5 -+$as_echo "failed" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: ok" >&5 -+$as_echo "ok" >&6; } -+fi -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+@%:@ Check whether --enable-libtool-lock was given. -+if test "${enable_libtool_lock+set}" = set; then : -+ enableval=$enable_libtool_lock; -+fi -+ -+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes -+ -+# Some flags need to be propagated to the compiler or linker for good -+# libtool support. -+case $host in -+ia64-*-hpux*) -+ # Find out which ABI we are using. -+ echo 'int i;' > conftest.$ac_ext -+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 -+ (eval $ac_compile) 2>&5 -+ ac_status=$? -+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 -+ test $ac_status = 0; }; then -+ case `/usr/bin/file conftest.$ac_objext` in -+ *ELF-32*) -+ HPUX_IA64_MODE="32" -+ ;; -+ *ELF-64*) -+ HPUX_IA64_MODE="64" -+ ;; -+ esac -+ fi -+ rm -rf conftest* -+ ;; -+*-*-irix6*) -+ # Find out which ABI we are using. -+ echo '#line __oline__ "configure"' > conftest.$ac_ext -+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 -+ (eval $ac_compile) 2>&5 -+ ac_status=$? -+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 -+ test $ac_status = 0; }; then -+ if test "$lt_cv_prog_gnu_ld" = yes; then -+ case `/usr/bin/file conftest.$ac_objext` in -+ *32-bit*) -+ LD="${LD-ld} -melf32bsmip" -+ ;; -+ *N32*) -+ LD="${LD-ld} -melf32bmipn32" -+ ;; -+ *64-bit*) -+ LD="${LD-ld} -melf64bmip" -+ ;; -+ esac -+ else -+ case `/usr/bin/file conftest.$ac_objext` in -+ *32-bit*) -+ LD="${LD-ld} -32" -+ ;; -+ *N32*) -+ LD="${LD-ld} -n32" -+ ;; -+ *64-bit*) -+ LD="${LD-ld} -64" -+ ;; -+ esac -+ fi -+ fi -+ rm -rf conftest* -+ ;; -+ -+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \ -+s390*-*linux*|s390*-*tpf*|sparc*-*linux*) -+ # Find out which ABI we are using. -+ echo 'int i;' > conftest.$ac_ext -+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 -+ (eval $ac_compile) 2>&5 -+ ac_status=$? -+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 -+ test $ac_status = 0; }; then -+ case `/usr/bin/file conftest.o` in -+ *32-bit*) -+ case $host in -+ x86_64-*kfreebsd*-gnu) -+ LD="${LD-ld} -m elf_i386_fbsd" -+ ;; -+ x86_64-*linux*) -+ LD="${LD-ld} -m elf_i386" -+ ;; -+ ppc64-*linux*|powerpc64-*linux*) -+ LD="${LD-ld} -m elf32ppclinux" -+ ;; -+ s390x-*linux*) -+ LD="${LD-ld} -m elf_s390" -+ ;; -+ sparc64-*linux*) -+ LD="${LD-ld} -m elf32_sparc" -+ ;; -+ esac -+ ;; -+ *64-bit*) -+ case $host in -+ x86_64-*kfreebsd*-gnu) -+ LD="${LD-ld} -m elf_x86_64_fbsd" -+ ;; -+ x86_64-*linux*) -+ LD="${LD-ld} -m elf_x86_64" -+ ;; -+ ppc*-*linux*|powerpc*-*linux*) -+ LD="${LD-ld} -m elf64ppc" -+ ;; -+ s390*-*linux*|s390*-*tpf*) -+ LD="${LD-ld} -m elf64_s390" -+ ;; -+ sparc*-*linux*) -+ LD="${LD-ld} -m elf64_sparc" -+ ;; -+ esac -+ ;; -+ esac -+ fi -+ rm -rf conftest* -+ ;; -+ -+*-*-sco3.2v5*) -+ # On SCO OpenServer 5, we need -belf to get full-featured binaries. -+ SAVE_CFLAGS="$CFLAGS" -+ CFLAGS="$CFLAGS -belf" -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler needs -belf" >&5 -+$as_echo_n "checking whether the C compiler needs -belf... " >&6; } -+if test "${lt_cv_cc_needs_belf+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_ext=c -+ac_cpp='$CPP $CPPFLAGS' -+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' -+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -+ac_compiler_gnu=$ac_cv_c_compiler_gnu -+ -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+ -+int -+main () -+{ -+ -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ lt_cv_cc_needs_belf=yes -+else -+ lt_cv_cc_needs_belf=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+ ac_ext=c -+ac_cpp='$CPP $CPPFLAGS' -+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' -+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -+ac_compiler_gnu=$ac_cv_c_compiler_gnu -+ -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_cc_needs_belf" >&5 -+$as_echo "$lt_cv_cc_needs_belf" >&6; } -+ if test x"$lt_cv_cc_needs_belf" != x"yes"; then -+ # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf -+ CFLAGS="$SAVE_CFLAGS" -+ fi -+ ;; -+sparc*-*solaris*) -+ # Find out which ABI we are using. -+ echo 'int i;' > conftest.$ac_ext -+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 -+ (eval $ac_compile) 2>&5 -+ ac_status=$? -+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 -+ test $ac_status = 0; }; then -+ case `/usr/bin/file conftest.o` in -+ *64-bit*) -+ case $lt_cv_prog_gnu_ld in -+ yes*) LD="${LD-ld} -m elf64_sparc" ;; -+ *) -+ if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then -+ LD="${LD-ld} -64" -+ fi -+ ;; -+ esac -+ ;; -+ esac -+ fi -+ rm -rf conftest* -+ ;; -+esac -+ -+need_locks="$enable_libtool_lock" -+ -+ -+ case $host_os in -+ rhapsody* | darwin*) -+ if test -n "$ac_tool_prefix"; then -+ # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args. -+set dummy ${ac_tool_prefix}dsymutil; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_DSYMUTIL+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$DSYMUTIL"; then -+ ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+DSYMUTIL=$ac_cv_prog_DSYMUTIL -+if test -n "$DSYMUTIL"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DSYMUTIL" >&5 -+$as_echo "$DSYMUTIL" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+fi -+if test -z "$ac_cv_prog_DSYMUTIL"; then -+ ac_ct_DSYMUTIL=$DSYMUTIL -+ # Extract the first word of "dsymutil", so it can be a program name with args. -+set dummy dsymutil; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_ac_ct_DSYMUTIL+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$ac_ct_DSYMUTIL"; then -+ ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_ac_ct_DSYMUTIL="dsymutil" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL -+if test -n "$ac_ct_DSYMUTIL"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DSYMUTIL" >&5 -+$as_echo "$ac_ct_DSYMUTIL" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ if test "x$ac_ct_DSYMUTIL" = x; then -+ DSYMUTIL=":" -+ else -+ case $cross_compiling:$ac_tool_warned in -+yes:) -+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 -+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} -+ac_tool_warned=yes ;; -+esac -+ DSYMUTIL=$ac_ct_DSYMUTIL -+ fi -+else -+ DSYMUTIL="$ac_cv_prog_DSYMUTIL" -+fi -+ -+ if test -n "$ac_tool_prefix"; then -+ # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args. -+set dummy ${ac_tool_prefix}nmedit; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_NMEDIT+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$NMEDIT"; then -+ ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+NMEDIT=$ac_cv_prog_NMEDIT -+if test -n "$NMEDIT"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $NMEDIT" >&5 -+$as_echo "$NMEDIT" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+fi -+if test -z "$ac_cv_prog_NMEDIT"; then -+ ac_ct_NMEDIT=$NMEDIT -+ # Extract the first word of "nmedit", so it can be a program name with args. -+set dummy nmedit; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_ac_ct_NMEDIT+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$ac_ct_NMEDIT"; then -+ ac_cv_prog_ac_ct_NMEDIT="$ac_ct_NMEDIT" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_ac_ct_NMEDIT="nmedit" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+ac_ct_NMEDIT=$ac_cv_prog_ac_ct_NMEDIT -+if test -n "$ac_ct_NMEDIT"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_NMEDIT" >&5 -+$as_echo "$ac_ct_NMEDIT" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ if test "x$ac_ct_NMEDIT" = x; then -+ NMEDIT=":" -+ else -+ case $cross_compiling:$ac_tool_warned in -+yes:) -+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 -+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} -+ac_tool_warned=yes ;; -+esac -+ NMEDIT=$ac_ct_NMEDIT -+ fi -+else -+ NMEDIT="$ac_cv_prog_NMEDIT" -+fi -+ -+ if test -n "$ac_tool_prefix"; then -+ # Extract the first word of "${ac_tool_prefix}lipo", so it can be a program name with args. -+set dummy ${ac_tool_prefix}lipo; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_LIPO+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$LIPO"; then -+ ac_cv_prog_LIPO="$LIPO" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_LIPO="${ac_tool_prefix}lipo" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+LIPO=$ac_cv_prog_LIPO -+if test -n "$LIPO"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LIPO" >&5 -+$as_echo "$LIPO" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+fi -+if test -z "$ac_cv_prog_LIPO"; then -+ ac_ct_LIPO=$LIPO -+ # Extract the first word of "lipo", so it can be a program name with args. -+set dummy lipo; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_ac_ct_LIPO+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$ac_ct_LIPO"; then -+ ac_cv_prog_ac_ct_LIPO="$ac_ct_LIPO" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_ac_ct_LIPO="lipo" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+ac_ct_LIPO=$ac_cv_prog_ac_ct_LIPO -+if test -n "$ac_ct_LIPO"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_LIPO" >&5 -+$as_echo "$ac_ct_LIPO" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ if test "x$ac_ct_LIPO" = x; then -+ LIPO=":" -+ else -+ case $cross_compiling:$ac_tool_warned in -+yes:) -+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 -+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} -+ac_tool_warned=yes ;; -+esac -+ LIPO=$ac_ct_LIPO -+ fi -+else -+ LIPO="$ac_cv_prog_LIPO" -+fi -+ -+ if test -n "$ac_tool_prefix"; then -+ # Extract the first word of "${ac_tool_prefix}otool", so it can be a program name with args. -+set dummy ${ac_tool_prefix}otool; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_OTOOL+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$OTOOL"; then -+ ac_cv_prog_OTOOL="$OTOOL" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_OTOOL="${ac_tool_prefix}otool" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+OTOOL=$ac_cv_prog_OTOOL -+if test -n "$OTOOL"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL" >&5 -+$as_echo "$OTOOL" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+fi -+if test -z "$ac_cv_prog_OTOOL"; then -+ ac_ct_OTOOL=$OTOOL -+ # Extract the first word of "otool", so it can be a program name with args. -+set dummy otool; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_ac_ct_OTOOL+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$ac_ct_OTOOL"; then -+ ac_cv_prog_ac_ct_OTOOL="$ac_ct_OTOOL" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_ac_ct_OTOOL="otool" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+ac_ct_OTOOL=$ac_cv_prog_ac_ct_OTOOL -+if test -n "$ac_ct_OTOOL"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL" >&5 -+$as_echo "$ac_ct_OTOOL" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ if test "x$ac_ct_OTOOL" = x; then -+ OTOOL=":" -+ else -+ case $cross_compiling:$ac_tool_warned in -+yes:) -+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 -+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} -+ac_tool_warned=yes ;; -+esac -+ OTOOL=$ac_ct_OTOOL -+ fi -+else -+ OTOOL="$ac_cv_prog_OTOOL" -+fi -+ -+ if test -n "$ac_tool_prefix"; then -+ # Extract the first word of "${ac_tool_prefix}otool64", so it can be a program name with args. -+set dummy ${ac_tool_prefix}otool64; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_OTOOL64+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$OTOOL64"; then -+ ac_cv_prog_OTOOL64="$OTOOL64" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_OTOOL64="${ac_tool_prefix}otool64" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+OTOOL64=$ac_cv_prog_OTOOL64 -+if test -n "$OTOOL64"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL64" >&5 -+$as_echo "$OTOOL64" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+fi -+if test -z "$ac_cv_prog_OTOOL64"; then -+ ac_ct_OTOOL64=$OTOOL64 -+ # Extract the first word of "otool64", so it can be a program name with args. -+set dummy otool64; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_ac_ct_OTOOL64+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$ac_ct_OTOOL64"; then -+ ac_cv_prog_ac_ct_OTOOL64="$ac_ct_OTOOL64" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_ac_ct_OTOOL64="otool64" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+fi -+fi -+ac_ct_OTOOL64=$ac_cv_prog_ac_ct_OTOOL64 -+if test -n "$ac_ct_OTOOL64"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL64" >&5 -+$as_echo "$ac_ct_OTOOL64" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ if test "x$ac_ct_OTOOL64" = x; then -+ OTOOL64=":" -+ else -+ case $cross_compiling:$ac_tool_warned in -+yes:) -+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 -+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} -+ac_tool_warned=yes ;; -+esac -+ OTOOL64=$ac_ct_OTOOL64 -+ fi -+else -+ OTOOL64="$ac_cv_prog_OTOOL64" -+fi -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -single_module linker flag" >&5 -+$as_echo_n "checking for -single_module linker flag... " >&6; } -+if test "${lt_cv_apple_cc_single_mod+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ lt_cv_apple_cc_single_mod=no -+ if test -z "${LT_MULTI_MODULE}"; then -+ # By default we will add the -single_module flag. You can override -+ # by either setting the environment variable LT_MULTI_MODULE -+ # non-empty at configure time, or by adding -multi_module to the -+ # link flags. -+ rm -rf libconftest.dylib* -+ echo "int foo(void){return 1;}" > conftest.c -+ echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -+-dynamiclib -Wl,-single_module conftest.c" >&5 -+ $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -+ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err -+ _lt_result=$? -+ if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then -+ lt_cv_apple_cc_single_mod=yes -+ else -+ cat conftest.err >&5 -+ fi -+ rm -rf libconftest.dylib* -+ rm -f conftest.* -+ fi -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_apple_cc_single_mod" >&5 -+$as_echo "$lt_cv_apple_cc_single_mod" >&6; } -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -exported_symbols_list linker flag" >&5 -+$as_echo_n "checking for -exported_symbols_list linker flag... " >&6; } -+if test "${lt_cv_ld_exported_symbols_list+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ lt_cv_ld_exported_symbols_list=no -+ save_LDFLAGS=$LDFLAGS -+ echo "_main" > conftest.sym -+ LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym" -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+ -+int -+main () -+{ -+ -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ lt_cv_ld_exported_symbols_list=yes -+else -+ lt_cv_ld_exported_symbols_list=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+ LDFLAGS="$save_LDFLAGS" -+ -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_exported_symbols_list" >&5 -+$as_echo "$lt_cv_ld_exported_symbols_list" >&6; } -+ case $host_os in -+ rhapsody* | darwin1.[012]) -+ _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;; -+ darwin1.*) -+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; -+ darwin*) # darwin 5.x on -+ # if running on 10.5 or later, the deployment target defaults -+ # to the OS version, if on x86, and 10.4, the deployment -+ # target defaults to 10.4. Don't you love it? -+ case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in -+ 10.0,*86*-darwin8*|10.0,*-darwin[91]*) -+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; -+ 10.[012]*) -+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; -+ 10.*) -+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; -+ esac -+ ;; -+ esac -+ if test "$lt_cv_apple_cc_single_mod" = "yes"; then -+ _lt_dar_single_mod='$single_module' -+ fi -+ if test "$lt_cv_ld_exported_symbols_list" = "yes"; then -+ _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym' -+ else -+ _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}' -+ fi -+ if test "$DSYMUTIL" != ":"; then -+ _lt_dsymutil='~$DSYMUTIL $lib || :' -+ else -+ _lt_dsymutil= -+ fi -+ ;; -+ esac -+ -+ac_ext=c -+ac_cpp='$CPP $CPPFLAGS' -+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' -+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -+ac_compiler_gnu=$ac_cv_c_compiler_gnu -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5 -+$as_echo_n "checking how to run the C preprocessor... 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This will affect the creation of libtool libraries that -+*** depend on shared libraries, but programs linked with such libtool -+*** libraries will work regardless of this problem. Nevertheless, you -+*** may want to report the problem to your system manager and/or to -+*** bug-libtool@gnu.org -+ -+_LT_EOF -+ fi ;; -+ esac -+ fi -+ break -+ fi -+ done -+ IFS="$lt_save_ifs" -+ MAGIC_CMD="$lt_save_MAGIC_CMD" -+ ;; -+esac -+fi -+ -+MAGIC_CMD="$lt_cv_path_MAGIC_CMD" -+if test -n "$MAGIC_CMD"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MAGIC_CMD" >&5 -+$as_echo "$MAGIC_CMD" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+ else -+ MAGIC_CMD=: -+ fi -+fi -+ -+ fi -+ ;; -+esac -+ -+# Use C for the default configuration in the libtool script -+ -+lt_save_CC="$CC" -+ac_ext=c -+ac_cpp='$CPP $CPPFLAGS' -+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' -+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -+ac_compiler_gnu=$ac_cv_c_compiler_gnu -+ -+ -+# Source file extension for C test sources. -+ac_ext=c -+ -+# Object file extension for compiled C test sources. -+objext=o -+objext=$objext -+ -+# Code to be used in simple compile tests -+lt_simple_compile_test_code="int some_variable = 0;" -+ -+# Code to be used in simple link tests -+lt_simple_link_test_code='int main(){return(0);}' -+ -+ -+ -+ -+ -+ -+ -+# If no C compiler was specified, use CC. -+LTCC=${LTCC-"$CC"} -+ -+# If no C compiler flags were specified, use CFLAGS. -+LTCFLAGS=${LTCFLAGS-"$CFLAGS"} -+ -+# Allow CC to be a program name with arguments. -+compiler=$CC -+ -+# Save the default compiler, since it gets overwritten when the other -+# tags are being tested, and _LT_TAGVAR(compiler, []) is a NOP. -+compiler_DEFAULT=$CC -+ -+# save warnings/boilerplate of simple test code -+ac_outfile=conftest.$ac_objext -+echo "$lt_simple_compile_test_code" >conftest.$ac_ext -+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err -+_lt_compiler_boilerplate=`cat conftest.err` -+$RM conftest* -+ -+ac_outfile=conftest.$ac_objext -+echo "$lt_simple_link_test_code" >conftest.$ac_ext -+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err -+_lt_linker_boilerplate=`cat conftest.err` -+$RM -r conftest* -+ -+ -+if test -n "$compiler"; then -+ -+lt_prog_compiler_no_builtin_flag= -+ -+if test "$GCC" = yes; then -+ lt_prog_compiler_no_builtin_flag=' -fno-builtin' -+ -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler supports -fno-rtti -fno-exceptions" >&5 -+$as_echo_n "checking if $compiler supports -fno-rtti -fno-exceptions... " >&6; } -+if test "${lt_cv_prog_compiler_rtti_exceptions+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ lt_cv_prog_compiler_rtti_exceptions=no -+ ac_outfile=conftest.$ac_objext -+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext -+ lt_compiler_flag="-fno-rtti -fno-exceptions" -+ # Insert the option either (1) after the last *FLAGS variable, or -+ # (2) before a word containing "conftest.", or (3) at the end. -+ # Note that $ac_compile itself does not contain backslashes and begins -+ # with a dollar sign (not a hyphen), so the echo should work correctly. -+ # The option is referenced via a variable to avoid confusing sed. -+ lt_compile=`echo "$ac_compile" | $SED \ -+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \ -+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \ -+ -e 's:$: $lt_compiler_flag:'` -+ (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&5) -+ (eval "$lt_compile" 2>conftest.err) -+ ac_status=$? -+ cat conftest.err >&5 -+ echo "$as_me:__oline__: \$? = $ac_status" >&5 -+ if (exit $ac_status) && test -s "$ac_outfile"; then -+ # The compiler can only warn and ignore the option if not recognized -+ # So say no if there are warnings other than the usual output. -+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp -+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2 -+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then -+ lt_cv_prog_compiler_rtti_exceptions=yes -+ fi -+ fi -+ $RM conftest* -+ -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_prog_compiler_rtti_exceptions" >&5 -+$as_echo "$lt_cv_prog_compiler_rtti_exceptions" >&6; } -+ -+if test x"$lt_cv_prog_compiler_rtti_exceptions" = xyes; then -+ lt_prog_compiler_no_builtin_flag="$lt_prog_compiler_no_builtin_flag -fno-rtti -fno-exceptions" -+else -+ : -+fi -+ -+fi -+ -+ -+ -+ -+ -+ -+ lt_prog_compiler_wl= -+lt_prog_compiler_pic= -+lt_prog_compiler_static= -+ -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $compiler option to produce PIC" >&5 -+$as_echo_n "checking for $compiler option to produce PIC... " >&6; } -+ -+ if test "$GCC" = yes; then -+ lt_prog_compiler_wl='-Wl,' -+ lt_prog_compiler_static='-static' -+ -+ case $host_os in -+ aix*) -+ # All AIX code is PIC. -+ if test "$host_cpu" = ia64; then -+ # AIX 5 now supports IA64 processor -+ lt_prog_compiler_static='-Bstatic' -+ fi -+ ;; -+ -+ amigaos*) -+ case $host_cpu in -+ powerpc) -+ # see comment about AmigaOS4 .so support -+ lt_prog_compiler_pic='-fPIC' -+ ;; -+ m68k) -+ # FIXME: we need at least 68020 code to build shared libraries, but -+ # adding the `-m68020' flag to GCC prevents building anything better, -+ # like `-m68040'. -+ lt_prog_compiler_pic='-m68020 -resident32 -malways-restore-a4' -+ ;; -+ esac -+ ;; -+ -+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) -+ # PIC is the default for these OSes. -+ ;; -+ -+ mingw* | cygwin* | pw32* | os2* | cegcc*) -+ # This hack is so that the source file can tell whether it is being -+ # built for inclusion in a dll (and should export symbols for example). -+ # Although the cygwin gcc ignores -fPIC, still need this for old-style -+ # (--disable-auto-import) libraries -+ lt_prog_compiler_pic='-DDLL_EXPORT' -+ ;; -+ -+ darwin* | rhapsody*) -+ # PIC is the default on this platform -+ # Common symbols not allowed in MH_DYLIB files -+ lt_prog_compiler_pic='-fno-common' -+ ;; -+ -+ hpux*) -+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit -+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag -+ # sets the default TLS model and affects inlining. -+ case $host_cpu in -+ hppa*64*) -+ # +Z the default -+ ;; -+ *) -+ lt_prog_compiler_pic='-fPIC' -+ ;; -+ esac -+ ;; -+ -+ interix[3-9]*) -+ # Interix 3.x gcc -fpic/-fPIC options generate broken code. -+ # Instead, we relocate shared libraries at runtime. -+ ;; -+ -+ msdosdjgpp*) -+ # Just because we use GCC doesn't mean we suddenly get shared libraries -+ # on systems that don't support them. -+ lt_prog_compiler_can_build_shared=no -+ enable_shared=no -+ ;; -+ -+ *nto* | *qnx*) -+ # QNX uses GNU C++, but need to define -shared option too, otherwise -+ # it will coredump. -+ lt_prog_compiler_pic='-fPIC -shared' -+ ;; -+ -+ sysv4*MP*) -+ if test -d /usr/nec; then -+ lt_prog_compiler_pic=-Kconform_pic -+ fi -+ ;; -+ -+ *) -+ lt_prog_compiler_pic='-fPIC' -+ ;; -+ esac -+ else -+ # PORTME Check for flag to pass linker flags through the system compiler. -+ case $host_os in -+ aix*) -+ lt_prog_compiler_wl='-Wl,' -+ if test "$host_cpu" = ia64; then -+ # AIX 5 now supports IA64 processor -+ lt_prog_compiler_static='-Bstatic' -+ else -+ lt_prog_compiler_static='-bnso -bI:/lib/syscalls.exp' -+ fi -+ ;; -+ -+ mingw* | cygwin* | pw32* | os2* | cegcc*) -+ # This hack is so that the source file can tell whether it is being -+ # built for inclusion in a dll (and should export symbols for example). -+ lt_prog_compiler_pic='-DDLL_EXPORT' -+ ;; -+ -+ hpux9* | hpux10* | hpux11*) -+ lt_prog_compiler_wl='-Wl,' -+ # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but -+ # not for PA HP-UX. -+ case $host_cpu in -+ hppa*64*|ia64*) -+ # +Z the default -+ ;; -+ *) -+ lt_prog_compiler_pic='+Z' -+ ;; -+ esac -+ # Is there a better lt_prog_compiler_static that works with the bundled CC? -+ lt_prog_compiler_static='${wl}-a ${wl}archive' -+ ;; -+ -+ irix5* | irix6* | nonstopux*) -+ lt_prog_compiler_wl='-Wl,' -+ # PIC (with -KPIC) is the default. -+ lt_prog_compiler_static='-non_shared' -+ ;; -+ -+ linux* | k*bsd*-gnu) -+ case $cc_basename in -+ # old Intel for x86_64 which still supported -KPIC. -+ ecc*) -+ lt_prog_compiler_wl='-Wl,' -+ lt_prog_compiler_pic='-KPIC' -+ lt_prog_compiler_static='-static' -+ ;; -+ # icc used to be incompatible with GCC. -+ # ICC 10 doesn't accept -KPIC any more. -+ icc* | ifort*) -+ lt_prog_compiler_wl='-Wl,' -+ lt_prog_compiler_pic='-fPIC' -+ lt_prog_compiler_static='-static' -+ ;; -+ # Lahey Fortran 8.1. -+ lf95*) -+ lt_prog_compiler_wl='-Wl,' -+ lt_prog_compiler_pic='--shared' -+ lt_prog_compiler_static='--static' -+ ;; -+ pgcc* | pgf77* | pgf90* | pgf95*) -+ # Portland Group compilers (*not* the Pentium gcc compiler, -+ # which looks to be a dead project) -+ lt_prog_compiler_wl='-Wl,' -+ lt_prog_compiler_pic='-fpic' -+ lt_prog_compiler_static='-Bstatic' -+ ;; -+ ccc*) -+ lt_prog_compiler_wl='-Wl,' -+ # All Alpha code is PIC. -+ lt_prog_compiler_static='-non_shared' -+ ;; -+ xl*) -+ # IBM XL C 8.0/Fortran 10.1 on PPC -+ lt_prog_compiler_wl='-Wl,' -+ lt_prog_compiler_pic='-qpic' -+ lt_prog_compiler_static='-qstaticlink' -+ ;; -+ *) -+ case `$CC -V 2>&1 | sed 5q` in -+ *Sun\ C*) -+ # Sun C 5.9 -+ lt_prog_compiler_pic='-KPIC' -+ lt_prog_compiler_static='-Bstatic' -+ lt_prog_compiler_wl='-Wl,' -+ ;; -+ *Sun\ F*) -+ # Sun Fortran 8.3 passes all unrecognized flags to the linker -+ lt_prog_compiler_pic='-KPIC' -+ lt_prog_compiler_static='-Bstatic' -+ lt_prog_compiler_wl='' -+ ;; -+ esac -+ ;; -+ esac -+ ;; -+ -+ newsos6) -+ lt_prog_compiler_pic='-KPIC' -+ lt_prog_compiler_static='-Bstatic' -+ ;; -+ -+ *nto* | *qnx*) -+ # QNX uses GNU C++, but need to define -shared option too, otherwise -+ # it will coredump. -+ lt_prog_compiler_pic='-fPIC -shared' -+ ;; -+ -+ osf3* | osf4* | osf5*) -+ lt_prog_compiler_wl='-Wl,' -+ # All OSF/1 code is PIC. -+ lt_prog_compiler_static='-non_shared' -+ ;; -+ -+ rdos*) -+ lt_prog_compiler_static='-non_shared' -+ ;; -+ -+ solaris*) -+ lt_prog_compiler_pic='-KPIC' -+ lt_prog_compiler_static='-Bstatic' -+ case $cc_basename in -+ f77* | f90* | f95*) -+ lt_prog_compiler_wl='-Qoption ld ';; -+ *) -+ lt_prog_compiler_wl='-Wl,';; -+ esac -+ ;; -+ -+ sunos4*) -+ lt_prog_compiler_wl='-Qoption ld ' -+ lt_prog_compiler_pic='-PIC' -+ lt_prog_compiler_static='-Bstatic' -+ ;; -+ -+ sysv4 | sysv4.2uw2* | sysv4.3*) -+ lt_prog_compiler_wl='-Wl,' -+ lt_prog_compiler_pic='-KPIC' -+ lt_prog_compiler_static='-Bstatic' -+ ;; -+ -+ sysv4*MP*) -+ if test -d /usr/nec ;then -+ lt_prog_compiler_pic='-Kconform_pic' -+ lt_prog_compiler_static='-Bstatic' -+ fi -+ ;; -+ -+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*) -+ lt_prog_compiler_wl='-Wl,' -+ lt_prog_compiler_pic='-KPIC' -+ lt_prog_compiler_static='-Bstatic' -+ ;; -+ -+ unicos*) -+ lt_prog_compiler_wl='-Wl,' -+ lt_prog_compiler_can_build_shared=no -+ ;; -+ -+ uts4*) -+ lt_prog_compiler_pic='-pic' -+ lt_prog_compiler_static='-Bstatic' -+ ;; -+ -+ *) -+ lt_prog_compiler_can_build_shared=no -+ ;; -+ esac -+ fi -+ -+case $host_os in -+ # For platforms which do not support PIC, -DPIC is meaningless: -+ *djgpp*) -+ lt_prog_compiler_pic= -+ ;; -+ *) -+ lt_prog_compiler_pic="$lt_prog_compiler_pic@&t@ -DPIC" -+ ;; -+esac -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_prog_compiler_pic" >&5 -+$as_echo "$lt_prog_compiler_pic" >&6; } -+ -+ -+ -+ -+ -+ -+# -+# Check to make sure the PIC flag actually works. -+# -+if test -n "$lt_prog_compiler_pic"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $compiler PIC flag $lt_prog_compiler_pic works" >&5 -+$as_echo_n "checking if $compiler PIC flag $lt_prog_compiler_pic works... 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If you -+*** really care for shared libraries, you may want to modify your PATH -+*** so that a non-GNU linker is found, and then restart. -+ -+_LT_EOF -+ fi -+ ;; -+ -+ amigaos*) -+ case $host_cpu in -+ powerpc) -+ # see comment about AmigaOS4 .so support -+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' -+ archive_expsym_cmds='' -+ ;; -+ m68k) -+ archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' -+ hardcode_libdir_flag_spec='-L$libdir' -+ hardcode_minus_L=yes -+ ;; -+ esac -+ ;; -+ -+ beos*) -+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then -+ allow_undefined_flag=unsupported -+ # Joseph Beckenbach says some releases of gcc -+ # support --undefined. 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To avoid this, we pick a random, -+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link -+ # time. 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Therefore, libtool -+*** is disabling shared libraries support. We urge you to upgrade GNU -+*** binutils to release 2.9.1 or newer. Another option is to modify -+*** your PATH or compiler configuration so that the native linker is -+*** used, and then restart. -+ -+_LT_EOF -+ elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then -+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' -+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' -+ else -+ ld_shlibs=no -+ fi -+ ;; -+ -+ sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*) -+ case `$LD -v 2>&1` in -+ *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*) -+ ld_shlibs=no -+ cat <<_LT_EOF 1>&2 -+ -+*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not -+*** reliably create shared libraries on SCO systems. Therefore, libtool -+*** is disabling shared libraries support. We urge you to upgrade GNU -+*** binutils to release 2.16.91.0.3 or newer. Another option is to modify -+*** your PATH or compiler configuration so that the native linker is -+*** used, and then restart. -+ -+_LT_EOF -+ ;; -+ *) -+ # For security reasons, it is highly recommended that you always -+ # use absolute paths for naming shared libraries, and exclude the -+ # DT_RUNPATH tag from executables and libraries. But doing so -+ # requires that you compile everything twice, which is a pain. -+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then -+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' -+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' -+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' -+ else -+ ld_shlibs=no -+ fi -+ ;; -+ esac -+ ;; -+ -+ sunos4*) -+ archive_cmds='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags' -+ wlarc= -+ hardcode_direct=yes -+ hardcode_shlibpath_var=no -+ ;; -+ -+ *) -+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then -+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' -+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' -+ else -+ ld_shlibs=no -+ fi -+ ;; -+ esac -+ -+ if test "$ld_shlibs" = no; then -+ runpath_var= -+ hardcode_libdir_flag_spec= -+ export_dynamic_flag_spec= -+ whole_archive_flag_spec= -+ fi -+ else -+ # PORTME fill in a description of your system's linker (not GNU ld) -+ case $host_os in -+ aix3*) -+ allow_undefined_flag=unsupported -+ always_export_symbols=yes -+ archive_expsym_cmds='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname' -+ # Note: this linker hardcodes the directories in LIBPATH if there -+ # are no directories specified by -L. -+ hardcode_minus_L=yes -+ if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then -+ # Neither direct hardcoding nor static linking is supported with a -+ # broken collect2. -+ hardcode_direct=unsupported -+ fi -+ ;; -+ -+ aix[4-9]*) -+ if test "$host_cpu" = ia64; then -+ # On IA64, the linker does run time linking by default, so we don't -+ # have to do anything special. -+ aix_use_runtimelinking=no -+ exp_sym_flag='-Bexport' -+ no_entry_flag="" -+ else -+ # If we're using GNU nm, then we don't want the "-C" option. -+ # -C means demangle to AIX nm, but means don't demangle with GNU nm -+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then -+ export_symbols_cmds='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols' -+ else -+ export_symbols_cmds='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols' -+ fi -+ aix_use_runtimelinking=no -+ -+ # Test if we are trying to use run time linking or normal -+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we -+ # need to do runtime linking. -+ case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*) -+ for ld_flag in $LDFLAGS; do -+ if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then -+ aix_use_runtimelinking=yes -+ break -+ fi -+ done -+ ;; -+ esac -+ -+ exp_sym_flag='-bexport' -+ no_entry_flag='-bnoentry' -+ fi -+ -+ # When large executables or shared objects are built, AIX ld can -+ # have problems creating the table of contents. If linking a library -+ # or program results in "error TOC overflow" add -mminimal-toc to -+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not -+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS. -+ -+ archive_cmds='' -+ hardcode_direct=yes -+ hardcode_direct_absolute=yes -+ hardcode_libdir_separator=':' -+ link_all_deplibs=yes -+ file_list_spec='${wl}-f,' -+ -+ if test "$GCC" = yes; then -+ case $host_os in aix4.[012]|aix4.[012].*) -+ # We only want to do this on AIX 4.2 and lower, the check -+ # below for broken collect2 doesn't work under 4.3+ -+ collect2name=`${CC} -print-prog-name=collect2` -+ if test -f "$collect2name" && -+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null -+ then -+ # We have reworked collect2 -+ : -+ else -+ # We have old collect2 -+ hardcode_direct=unsupported -+ # It fails to find uninstalled libraries when the uninstalled -+ # path is not listed in the libpath. Setting hardcode_minus_L -+ # to unsupported forces relinking -+ hardcode_minus_L=yes -+ hardcode_libdir_flag_spec='-L$libdir' -+ hardcode_libdir_separator= -+ fi -+ ;; -+ esac -+ shared_flag='-shared' -+ if test "$aix_use_runtimelinking" = yes; then -+ shared_flag="$shared_flag "'${wl}-G' -+ fi -+ else -+ # not using gcc -+ if test "$host_cpu" = ia64; then -+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release -+ # chokes on -Wl,-G. The following line is correct: -+ shared_flag='-G' -+ else -+ if test "$aix_use_runtimelinking" = yes; then -+ shared_flag='${wl}-G' -+ else -+ shared_flag='${wl}-bM:SRE' -+ fi -+ fi -+ fi -+ -+ export_dynamic_flag_spec='${wl}-bexpall' -+ # It seems that -bexpall does not export symbols beginning with -+ # underscore (_), so it is better to generate a list of symbols to export. -+ always_export_symbols=yes -+ if test "$aix_use_runtimelinking" = yes; then -+ # Warning - without using the other runtime loading flags (-brtl), -+ # -berok will link without error, but may produce a broken library. -+ allow_undefined_flag='-berok' -+ # Determine the default libpath from the value encoded in an -+ # empty executable. -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+ -+int -+main () -+{ -+ -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ -+lt_aix_libpath_sed=' -+ /Import File Strings/,/^$/ { -+ /^0/ { -+ s/^0 *\(.*\)$/\1/ -+ p -+ } -+ }' -+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` -+# Check for a 64-bit object if we didn't find anything. -+if test -z "$aix_libpath"; then -+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` -+fi -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi -+ -+ hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" -+ archive_expsym_cmds='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" -+ else -+ if test "$host_cpu" = ia64; then -+ hardcode_libdir_flag_spec='${wl}-R $libdir:/usr/lib:/lib' -+ allow_undefined_flag="-z nodefs" -+ archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" -+ else -+ # Determine the default libpath from the value encoded in an -+ # empty executable. -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+ -+int -+main () -+{ -+ -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ -+lt_aix_libpath_sed=' -+ /Import File Strings/,/^$/ { -+ /^0/ { -+ s/^0 *\(.*\)$/\1/ -+ p -+ } -+ }' -+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` -+# Check for a 64-bit object if we didn't find anything. -+if test -z "$aix_libpath"; then -+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` -+fi -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi -+ -+ hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" -+ # Warning - without using the other run time loading flags, -+ # -berok will link without error, but may produce a broken library. -+ no_undefined_flag=' ${wl}-bernotok' -+ allow_undefined_flag=' ${wl}-berok' -+ # Exported symbols can be pulled into shared objects from archives -+ whole_archive_flag_spec='$convenience' -+ archive_cmds_need_lc=yes -+ # This is similar to how AIX traditionally builds its shared libraries. -+ archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' -+ fi -+ fi -+ ;; -+ -+ amigaos*) -+ case $host_cpu in -+ powerpc) -+ # see comment about AmigaOS4 .so support -+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' -+ archive_expsym_cmds='' -+ ;; -+ m68k) -+ archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' -+ hardcode_libdir_flag_spec='-L$libdir' -+ hardcode_minus_L=yes -+ ;; -+ esac -+ ;; -+ -+ bsdi[45]*) -+ export_dynamic_flag_spec=-rdynamic -+ ;; -+ -+ cygwin* | mingw* | pw32* | cegcc*) -+ # When not using gcc, we currently assume that we are using -+ # Microsoft Visual C++. -+ # hardcode_libdir_flag_spec is actually meaningless, as there is -+ # no search path for DLLs. -+ hardcode_libdir_flag_spec=' ' -+ allow_undefined_flag=unsupported -+ # Tell ltmain to make .lib files, not .a files. -+ libext=lib -+ # Tell ltmain to make .dll files, not .so files. -+ shrext_cmds=".dll" -+ # FIXME: Setting linknames here is a bad hack. -+ archive_cmds='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames=' -+ # The linker will automatically build a .lib file if we build a DLL. -+ old_archive_from_new_cmds='true' -+ # FIXME: Should let the user specify the lib program. -+ old_archive_cmds='lib -OUT:$oldlib$oldobjs$old_deplibs' -+ fix_srcfile_path='`cygpath -w "$srcfile"`' -+ enable_shared_with_static_runtimes=yes -+ ;; -+ -+ darwin* | rhapsody*) -+ -+ -+ archive_cmds_need_lc=no -+ hardcode_direct=no -+ hardcode_automatic=yes -+ hardcode_shlibpath_var=unsupported -+ whole_archive_flag_spec='' -+ link_all_deplibs=yes -+ allow_undefined_flag="$_lt_dar_allow_undefined" -+ case $cc_basename in -+ ifort*) _lt_dar_can_shared=yes ;; -+ *) _lt_dar_can_shared=$GCC ;; -+ esac -+ if test "$_lt_dar_can_shared" = "yes"; then -+ output_verbose_link_cmd=echo -+ archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}" -+ module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}" -+ archive_expsym_cmds="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}" -+ module_expsym_cmds="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}" -+ -+ else -+ ld_shlibs=no -+ fi -+ -+ ;; -+ -+ dgux*) -+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' -+ hardcode_libdir_flag_spec='-L$libdir' -+ hardcode_shlibpath_var=no -+ ;; -+ -+ freebsd1*) -+ ld_shlibs=no -+ ;; -+ -+ # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor -+ # support. Future versions do this automatically, but an explicit c++rt0.o -+ # does not break anything, and helps significantly (at the cost of a little -+ # extra space). -+ freebsd2.2*) -+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' -+ hardcode_libdir_flag_spec='-R$libdir' -+ hardcode_direct=yes -+ hardcode_shlibpath_var=no -+ ;; -+ -+ # Unfortunately, older versions of FreeBSD 2 do not have this feature. -+ freebsd2*) -+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' -+ hardcode_direct=yes -+ hardcode_minus_L=yes -+ hardcode_shlibpath_var=no -+ ;; -+ -+ # FreeBSD 3 and greater uses gcc -shared to do shared libraries. -+ freebsd* | dragonfly*) -+ archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' -+ hardcode_libdir_flag_spec='-R$libdir' -+ hardcode_direct=yes -+ hardcode_shlibpath_var=no -+ ;; -+ -+ hpux9*) -+ if test "$GCC" = yes; then -+ archive_cmds='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' -+ else -+ archive_cmds='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' -+ fi -+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' -+ hardcode_libdir_separator=: -+ hardcode_direct=yes -+ -+ # hardcode_minus_L: Not really in the search PATH, -+ # but as the default location of the library. -+ hardcode_minus_L=yes -+ export_dynamic_flag_spec='${wl}-E' -+ ;; -+ -+ hpux10*) -+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then -+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' -+ else -+ archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' -+ fi -+ if test "$with_gnu_ld" = no; then -+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' -+ hardcode_libdir_flag_spec_ld='+b $libdir' -+ hardcode_libdir_separator=: -+ hardcode_direct=yes -+ hardcode_direct_absolute=yes -+ export_dynamic_flag_spec='${wl}-E' -+ # hardcode_minus_L: Not really in the search PATH, -+ # but as the default location of the library. -+ hardcode_minus_L=yes -+ fi -+ ;; -+ -+ hpux11*) -+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then -+ case $host_cpu in -+ hppa*64*) -+ archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' -+ ;; -+ ia64*) -+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' -+ ;; -+ *) -+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' -+ ;; -+ esac -+ else -+ case $host_cpu in -+ hppa*64*) -+ archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' -+ ;; -+ ia64*) -+ archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' -+ ;; -+ *) -+ archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' -+ ;; -+ esac -+ fi -+ if test "$with_gnu_ld" = no; then -+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' -+ hardcode_libdir_separator=: -+ -+ case $host_cpu in -+ hppa*64*|ia64*) -+ hardcode_direct=no -+ hardcode_shlibpath_var=no -+ ;; -+ *) -+ hardcode_direct=yes -+ hardcode_direct_absolute=yes -+ export_dynamic_flag_spec='${wl}-E' -+ -+ # hardcode_minus_L: Not really in the search PATH, -+ # but as the default location of the library. -+ hardcode_minus_L=yes -+ ;; -+ esac -+ fi -+ ;; -+ -+ irix5* | irix6* | nonstopux*) -+ if test "$GCC" = yes; then -+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' -+ # Try to use the -exported_symbol ld option, if it does not -+ # work, assume that -exports_file does not work either and -+ # implicitly export all symbols. -+ save_LDFLAGS="$LDFLAGS" -+ LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null" -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+int foo(void) {} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib' -+ -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+ LDFLAGS="$save_LDFLAGS" -+ else -+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' -+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib' -+ fi -+ archive_cmds_need_lc='no' -+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' -+ hardcode_libdir_separator=: -+ inherit_rpath=yes -+ link_all_deplibs=yes -+ ;; -+ -+ netbsd*) -+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then -+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out -+ else -+ archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF -+ fi -+ hardcode_libdir_flag_spec='-R$libdir' -+ hardcode_direct=yes -+ hardcode_shlibpath_var=no -+ ;; -+ -+ newsos6) -+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' -+ hardcode_direct=yes -+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' -+ hardcode_libdir_separator=: -+ hardcode_shlibpath_var=no -+ ;; -+ -+ *nto* | *qnx*) -+ ;; -+ -+ openbsd*) -+ if test -f /usr/libexec/ld.so; then -+ hardcode_direct=yes -+ hardcode_shlibpath_var=no -+ hardcode_direct_absolute=yes -+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then -+ archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' -+ archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' -+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir' -+ export_dynamic_flag_spec='${wl}-E' -+ else -+ case $host_os in -+ openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*) -+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' -+ hardcode_libdir_flag_spec='-R$libdir' -+ ;; -+ *) -+ archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' -+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir' -+ ;; -+ esac -+ fi -+ else -+ ld_shlibs=no -+ fi -+ ;; -+ -+ os2*) -+ hardcode_libdir_flag_spec='-L$libdir' -+ hardcode_minus_L=yes -+ allow_undefined_flag=unsupported -+ archive_cmds='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' -+ old_archive_from_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' -+ ;; -+ -+ osf3*) -+ if test "$GCC" = yes; then -+ allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' -+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' -+ else -+ allow_undefined_flag=' -expect_unresolved \*' -+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' -+ fi -+ archive_cmds_need_lc='no' -+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' -+ hardcode_libdir_separator=: -+ ;; -+ -+ osf4* | osf5*) # as osf3* with the addition of -msym flag -+ if test "$GCC" = yes; then -+ allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' -+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' -+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' -+ else -+ allow_undefined_flag=' -expect_unresolved \*' -+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' -+ archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~ -+ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp' -+ -+ # Both c and cxx compiler support -rpath directly -+ hardcode_libdir_flag_spec='-rpath $libdir' -+ fi -+ archive_cmds_need_lc='no' -+ hardcode_libdir_separator=: -+ ;; -+ -+ solaris*) -+ no_undefined_flag=' -z defs' -+ if test "$GCC" = yes; then -+ wlarc='${wl}' -+ archive_cmds='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' -+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ -+ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' -+ else -+ case `$CC -V 2>&1` in -+ *"Compilers 5.0"*) -+ wlarc='' -+ archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' -+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ -+ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp' -+ ;; -+ *) -+ wlarc='${wl}' -+ archive_cmds='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags' -+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ -+ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' -+ ;; -+ esac -+ fi -+ hardcode_libdir_flag_spec='-R$libdir' -+ hardcode_shlibpath_var=no -+ case $host_os in -+ solaris2.[0-5] | solaris2.[0-5].*) ;; -+ *) -+ # The compiler driver will combine and reorder linker options, -+ # but understands `-z linker_flag'. GCC discards it without `$wl', -+ # but is careful enough not to reorder. -+ # Supported since Solaris 2.6 (maybe 2.5.1?) -+ if test "$GCC" = yes; then -+ whole_archive_flag_spec='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract' -+ else -+ whole_archive_flag_spec='-z allextract$convenience -z defaultextract' -+ fi -+ ;; -+ esac -+ link_all_deplibs=yes -+ ;; -+ -+ sunos4*) -+ if test "x$host_vendor" = xsequent; then -+ # Use $CC to link under sequent, because it throws in some extra .o -+ # files that make .init and .fini sections work. -+ archive_cmds='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags' -+ else -+ archive_cmds='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags' -+ fi -+ hardcode_libdir_flag_spec='-L$libdir' -+ hardcode_direct=yes -+ hardcode_minus_L=yes -+ hardcode_shlibpath_var=no -+ ;; -+ -+ sysv4) -+ case $host_vendor in -+ sni) -+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' -+ hardcode_direct=yes # is this really true??? -+ ;; -+ siemens) -+ ## LD is ld it makes a PLAMLIB -+ ## CC just makes a GrossModule. -+ archive_cmds='$LD -G -o $lib $libobjs $deplibs $linker_flags' -+ reload_cmds='$CC -r -o $output$reload_objs' -+ hardcode_direct=no -+ ;; -+ motorola) -+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' -+ hardcode_direct=no #Motorola manual says yes, but my tests say they lie -+ ;; -+ esac -+ runpath_var='LD_RUN_PATH' -+ hardcode_shlibpath_var=no -+ ;; -+ -+ sysv4.3*) -+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' -+ hardcode_shlibpath_var=no -+ export_dynamic_flag_spec='-Bexport' -+ ;; -+ -+ sysv4*MP*) -+ if test -d /usr/nec; then -+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' -+ hardcode_shlibpath_var=no -+ runpath_var=LD_RUN_PATH -+ hardcode_runpath_var=yes -+ ld_shlibs=yes -+ fi -+ ;; -+ -+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*) -+ no_undefined_flag='${wl}-z,text' -+ archive_cmds_need_lc=no -+ hardcode_shlibpath_var=no -+ runpath_var='LD_RUN_PATH' -+ -+ if test "$GCC" = yes; then -+ archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' -+ archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' -+ else -+ archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' -+ archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' -+ fi -+ ;; -+ -+ sysv5* | sco3.2v5* | sco5v6*) -+ # Note: We can NOT use -z defs as we might desire, because we do not -+ # link with -lc, and that would cause any symbols used from libc to -+ # always be unresolved, which means just about no library would -+ # ever link correctly. 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The import file would start with -+ # the line `#! .'. This would cause the generated library to -+ # depend on `.', always an invalid library. This was fixed in -+ # development snapshots of GCC prior to 3.0. -+ case $host_os in -+ aix4 | aix4.[01] | aix4.[01].*) -+ if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)' -+ echo ' yes ' -+ echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then -+ : -+ else -+ can_build_shared=no -+ fi -+ ;; -+ esac -+ # AIX (on Power*) has no versioning support, so currently we can not hardcode correct -+ # soname into executable. Probably we can add versioning support to -+ # collect2, so additional links can be useful in future. -+ if test "$aix_use_runtimelinking" = yes; then -+ # If using run time linking (on AIX 4.2 or later) use lib.so -+ # instead of lib.a to let people know that these are not -+ # typical AIX shared libraries. -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' -+ else -+ # We preserve .a as extension for shared libraries through AIX4.2 -+ # and later when we are not doing run time linking. -+ library_names_spec='${libname}${release}.a $libname.a' -+ soname_spec='${libname}${release}${shared_ext}$major' -+ fi -+ shlibpath_var=LIBPATH -+ fi -+ ;; -+ -+amigaos*) -+ case $host_cpu in -+ powerpc) -+ # Since July 2007 AmigaOS4 officially supports .so libraries. -+ # When compiling the executable, add -use-dynld -Lsobjs: to the compileline. -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' -+ ;; -+ m68k) -+ library_names_spec='$libname.ixlibrary $libname.a' -+ # Create ${libname}_ixlibrary.a entries in /sys/libs. -+ finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done' -+ ;; -+ esac -+ ;; -+ -+beos*) -+ library_names_spec='${libname}${shared_ext}' -+ dynamic_linker="$host_os ld.so" -+ shlibpath_var=LIBRARY_PATH -+ ;; -+ -+bsdi[45]*) -+ version_type=linux -+ need_version=no -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' -+ soname_spec='${libname}${release}${shared_ext}$major' -+ finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir' -+ shlibpath_var=LD_LIBRARY_PATH -+ sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib" -+ sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib" -+ # the default ld.so.conf also contains /usr/contrib/lib and -+ # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow -+ # libtool to hard-code these into programs -+ ;; -+ -+cygwin* | mingw* | pw32* | cegcc*) -+ version_type=windows -+ shrext_cmds=".dll" -+ need_version=no -+ need_lib_prefix=no -+ -+ case $GCC,$host_os in -+ yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*) -+ library_names_spec='$libname.dll.a' -+ # DLL is installed to $(libdir)/../bin by postinstall_cmds -+ postinstall_cmds='base_file=`basename \${file}`~ -+ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~ -+ dldir=$destdir/`dirname \$dlpath`~ -+ test -d \$dldir || mkdir -p \$dldir~ -+ $install_prog $dir/$dlname \$dldir/$dlname~ -+ chmod a+x \$dldir/$dlname~ -+ if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then -+ eval '\''$striplib \$dldir/$dlname'\'' || exit \$?; -+ fi' -+ postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~ -+ dlpath=$dir/\$dldll~ -+ $RM \$dlpath' -+ shlibpath_overrides_runpath=yes -+ -+ case $host_os in -+ cygwin*) -+ # Cygwin DLLs use 'cyg' prefix rather than 'lib' -+ soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}' -+ sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib" -+ ;; -+ mingw* | cegcc*) -+ # MinGW DLLs use traditional 'lib' prefix -+ soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}' -+ sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"` -+ if $ECHO "$sys_lib_search_path_spec" | $GREP ';[c-zC-Z]:/' >/dev/null; then -+ # It is most probably a Windows format PATH printed by -+ # mingw gcc, but we are running on Cygwin. Gcc prints its search -+ # path with ; separators, and with drive letters. We can handle the -+ # drive letters (cygwin fileutils understands them), so leave them, -+ # especially as we might pass files found there to a mingw objdump, -+ # which wouldn't understand a cygwinified path. Ahh. -+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'` -+ else -+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"` -+ fi -+ ;; -+ pw32*) -+ # pw32 DLLs use 'pw' prefix rather than 'lib' -+ library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}' -+ ;; -+ esac -+ ;; -+ -+ *) -+ library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib' -+ ;; -+ esac -+ dynamic_linker='Win32 ld.exe' -+ # FIXME: first we should search . and the directory the executable is in -+ shlibpath_var=PATH -+ ;; -+ -+darwin* | rhapsody*) -+ dynamic_linker="$host_os dyld" -+ version_type=darwin -+ need_lib_prefix=no -+ need_version=no -+ library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext' -+ soname_spec='${libname}${release}${major}$shared_ext' -+ shlibpath_overrides_runpath=yes -+ shlibpath_var=DYLD_LIBRARY_PATH -+ shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`' -+ -+ sys_lib_search_path_spec="$sys_lib_search_path_spec /usr/local/lib" -+ sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib' -+ ;; -+ -+dgux*) -+ version_type=linux -+ need_lib_prefix=no -+ need_version=no -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext' -+ soname_spec='${libname}${release}${shared_ext}$major' -+ shlibpath_var=LD_LIBRARY_PATH -+ ;; -+ -+freebsd1*) -+ dynamic_linker=no -+ ;; -+ -+freebsd* | dragonfly*) -+ # DragonFly does not have aout. When/if they implement a new -+ # versioning mechanism, adjust this. -+ if test -x /usr/bin/objformat; then -+ objformat=`/usr/bin/objformat` -+ else -+ case $host_os in -+ freebsd[123]*) objformat=aout ;; -+ *) objformat=elf ;; -+ esac -+ fi -+ version_type=freebsd-$objformat -+ case $version_type in -+ freebsd-elf*) -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' -+ need_version=no -+ need_lib_prefix=no -+ ;; -+ freebsd-*) -+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix' -+ need_version=yes -+ ;; -+ esac -+ shlibpath_var=LD_LIBRARY_PATH -+ case $host_os in -+ freebsd2*) -+ shlibpath_overrides_runpath=yes -+ ;; -+ freebsd3.[01]* | freebsdelf3.[01]*) -+ shlibpath_overrides_runpath=yes -+ hardcode_into_libs=yes -+ ;; -+ freebsd3.[2-9]* | freebsdelf3.[2-9]* | \ -+ freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1) -+ shlibpath_overrides_runpath=no -+ hardcode_into_libs=yes -+ ;; -+ *) # from 4.6 on, and DragonFly -+ shlibpath_overrides_runpath=yes -+ hardcode_into_libs=yes -+ ;; -+ esac -+ ;; -+ -+gnu*) -+ version_type=linux -+ need_lib_prefix=no -+ need_version=no -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}' -+ soname_spec='${libname}${release}${shared_ext}$major' -+ shlibpath_var=LD_LIBRARY_PATH -+ hardcode_into_libs=yes -+ ;; -+ -+hpux9* | hpux10* | hpux11*) -+ # Give a soname corresponding to the major version so that dld.sl refuses to -+ # link against other versions. -+ version_type=sunos -+ need_lib_prefix=no -+ need_version=no -+ case $host_cpu in -+ ia64*) -+ shrext_cmds='.so' -+ hardcode_into_libs=yes -+ dynamic_linker="$host_os dld.so" -+ shlibpath_var=LD_LIBRARY_PATH -+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' -+ soname_spec='${libname}${release}${shared_ext}$major' -+ if test "X$HPUX_IA64_MODE" = X32; then -+ sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib" -+ else -+ sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64" -+ fi -+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec -+ ;; -+ hppa*64*) -+ shrext_cmds='.sl' -+ hardcode_into_libs=yes -+ dynamic_linker="$host_os dld.sl" -+ shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH -+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' -+ soname_spec='${libname}${release}${shared_ext}$major' -+ sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64" -+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec -+ ;; -+ *) -+ shrext_cmds='.sl' -+ dynamic_linker="$host_os dld.sl" -+ shlibpath_var=SHLIB_PATH -+ shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' -+ soname_spec='${libname}${release}${shared_ext}$major' -+ ;; -+ esac -+ # HP-UX runs *really* slowly unless shared libraries are mode 555. -+ postinstall_cmds='chmod 555 $lib' -+ ;; -+ -+interix[3-9]*) -+ version_type=linux -+ need_lib_prefix=no -+ need_version=no -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' -+ soname_spec='${libname}${release}${shared_ext}$major' -+ dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)' -+ shlibpath_var=LD_LIBRARY_PATH -+ shlibpath_overrides_runpath=no -+ hardcode_into_libs=yes -+ ;; -+ -+irix5* | irix6* | nonstopux*) -+ case $host_os in -+ nonstopux*) version_type=nonstopux ;; -+ *) -+ if test "$lt_cv_prog_gnu_ld" = yes; then -+ version_type=linux -+ else -+ version_type=irix -+ fi ;; -+ esac -+ need_lib_prefix=no -+ need_version=no -+ soname_spec='${libname}${release}${shared_ext}$major' -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}' -+ case $host_os in -+ irix5* | nonstopux*) -+ libsuff= shlibsuff= -+ ;; -+ *) -+ case $LD in # libtool.m4 will add one of these switches to LD -+ *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") -+ libsuff= shlibsuff= libmagic=32-bit;; -+ *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ") -+ libsuff=32 shlibsuff=N32 libmagic=N32;; -+ *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ") -+ libsuff=64 shlibsuff=64 libmagic=64-bit;; -+ *) libsuff= shlibsuff= libmagic=never-match;; -+ esac -+ ;; -+ esac -+ shlibpath_var=LD_LIBRARY${shlibsuff}_PATH -+ shlibpath_overrides_runpath=no -+ sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}" -+ sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}" -+ hardcode_into_libs=yes -+ ;; -+ -+# No shared lib support for Linux oldld, aout, or coff. -+linux*oldld* | linux*aout* | linux*coff*) -+ dynamic_linker=no -+ ;; -+ -+# This must be Linux ELF. -+linux* | k*bsd*-gnu) -+ version_type=linux -+ need_lib_prefix=no -+ need_version=no -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' -+ soname_spec='${libname}${release}${shared_ext}$major' -+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir' -+ shlibpath_var=LD_LIBRARY_PATH -+ shlibpath_overrides_runpath=no -+ # Some binutils ld are patched to set DT_RUNPATH -+ save_LDFLAGS=$LDFLAGS -+ save_libdir=$libdir -+ eval "libdir=/foo; wl=\"$lt_prog_compiler_wl\"; \ -+ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec\"" -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+ -+int -+main () -+{ -+ -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then : -+ shlibpath_overrides_runpath=yes -+fi -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+ LDFLAGS=$save_LDFLAGS -+ libdir=$save_libdir -+ -+ # This implies no fast_install, which is unacceptable. -+ # Some rework will be needed to allow for fast_install -+ # before this can be enabled. -+ hardcode_into_libs=yes -+ -+ # Add ABI-specific directories to the system library path. -+ sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /lib /usr/lib" -+ -+ # Append ld.so.conf contents to the search path -+ if test -f /etc/ld.so.conf; then -+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '` -+ sys_lib_dlsearch_path_spec="$sys_lib_dlsearch_path_spec $lt_ld_extra" -+ fi -+ -+ # We used to test for /lib/ld.so.1 and disable shared libraries on -+ # powerpc, because MkLinux only supported shared libraries with the -+ # GNU dynamic linker. Since this was broken with cross compilers, -+ # most powerpc-linux boxes support dynamic linking these days and -+ # people can always --disable-shared, the test was removed, and we -+ # assume the GNU/Linux dynamic linker is in use. -+ dynamic_linker='GNU/Linux ld.so' -+ ;; -+ -+netbsd*) -+ version_type=sunos -+ need_lib_prefix=no -+ need_version=no -+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' -+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' -+ dynamic_linker='NetBSD (a.out) ld.so' -+ else -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' -+ soname_spec='${libname}${release}${shared_ext}$major' -+ dynamic_linker='NetBSD ld.elf_so' -+ fi -+ shlibpath_var=LD_LIBRARY_PATH -+ shlibpath_overrides_runpath=yes -+ hardcode_into_libs=yes -+ ;; -+ -+newsos6) -+ version_type=linux -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' -+ shlibpath_var=LD_LIBRARY_PATH -+ shlibpath_overrides_runpath=yes -+ ;; -+ -+*nto* | *qnx*) -+ version_type=qnx -+ need_lib_prefix=no -+ need_version=no -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' -+ soname_spec='${libname}${release}${shared_ext}$major' -+ shlibpath_var=LD_LIBRARY_PATH -+ shlibpath_overrides_runpath=no -+ hardcode_into_libs=yes -+ dynamic_linker='ldqnx.so' -+ ;; -+ -+openbsd*) -+ version_type=sunos -+ sys_lib_dlsearch_path_spec="/usr/lib" -+ need_lib_prefix=no -+ # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs. -+ case $host_os in -+ openbsd3.3 | openbsd3.3.*) need_version=yes ;; -+ *) need_version=no ;; -+ esac -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' -+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' -+ shlibpath_var=LD_LIBRARY_PATH -+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then -+ case $host_os in -+ openbsd2.[89] | openbsd2.[89].*) -+ shlibpath_overrides_runpath=no -+ ;; -+ *) -+ shlibpath_overrides_runpath=yes -+ ;; -+ esac -+ else -+ shlibpath_overrides_runpath=yes -+ fi -+ ;; -+ -+os2*) -+ libname_spec='$name' -+ shrext_cmds=".dll" -+ need_lib_prefix=no -+ library_names_spec='$libname${shared_ext} $libname.a' -+ dynamic_linker='OS/2 ld.exe' -+ shlibpath_var=LIBPATH -+ ;; -+ -+osf3* | osf4* | osf5*) -+ version_type=osf -+ need_lib_prefix=no -+ need_version=no -+ soname_spec='${libname}${release}${shared_ext}$major' -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' -+ shlibpath_var=LD_LIBRARY_PATH -+ sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib" -+ sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec" -+ ;; -+ -+rdos*) -+ dynamic_linker=no -+ ;; -+ -+solaris*) -+ version_type=linux -+ need_lib_prefix=no -+ need_version=no -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' -+ soname_spec='${libname}${release}${shared_ext}$major' -+ shlibpath_var=LD_LIBRARY_PATH -+ shlibpath_overrides_runpath=yes -+ hardcode_into_libs=yes -+ # ldd complains unless libraries are executable -+ postinstall_cmds='chmod +x $lib' -+ ;; 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-+ -+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) -+ version_type=freebsd-elf -+ need_lib_prefix=no -+ need_version=no -+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' -+ soname_spec='${libname}${release}${shared_ext}$major' -+ shlibpath_var=LD_LIBRARY_PATH -+ shlibpath_overrides_runpath=yes -+ hardcode_into_libs=yes -+ if test "$with_gnu_ld" = yes; then -+ sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib' -+ else -+ sys_lib_search_path_spec='/usr/ccs/lib /usr/lib' -+ case $host_os in -+ sco3.2v5*) -+ sys_lib_search_path_spec="$sys_lib_search_path_spec /lib" -+ ;; -+ esac -+ fi -+ sys_lib_dlsearch_path_spec='/usr/lib' -+ ;; -+ -+tpf*) -+ # TPF is a cross-target only. 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" >&6; } -+if test "${ac_cv_lib_svld_dlopen+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-lsvld $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$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 dlopen (); -+int -+main () -+{ -+return dlopen (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_svld_dlopen=yes -+else -+ ac_cv_lib_svld_dlopen=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_svld_dlopen" >&5 -+$as_echo "$ac_cv_lib_svld_dlopen" >&6; } -+if test "x$ac_cv_lib_svld_dlopen" = x""yes; then : -+ lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld" -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dld_link in -ldld" >&5 -+$as_echo_n "checking for dld_link in -ldld... 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" >&6; } -+if test "${lt_cv_dlopen_self+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test "$cross_compiling" = yes; then : -+ lt_cv_dlopen_self=cross -+else -+ lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2 -+ lt_status=$lt_dlunknown -+ cat > conftest.$ac_ext <<_LT_EOF -+#line __oline__ "configure" -+#include "confdefs.h" -+ -+#if HAVE_DLFCN_H -+#include -+#endif -+ -+#include -+ -+#ifdef RTLD_GLOBAL -+# define LT_DLGLOBAL RTLD_GLOBAL -+#else -+# ifdef DL_GLOBAL -+# define LT_DLGLOBAL DL_GLOBAL -+# else -+# define LT_DLGLOBAL 0 -+# endif -+#endif -+ -+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we -+ find out it does not work in some platform. */ -+#ifndef LT_DLLAZY_OR_NOW -+# ifdef RTLD_LAZY -+# define LT_DLLAZY_OR_NOW RTLD_LAZY -+# else -+# ifdef DL_LAZY -+# define LT_DLLAZY_OR_NOW DL_LAZY -+# else -+# ifdef RTLD_NOW -+# define LT_DLLAZY_OR_NOW RTLD_NOW -+# else -+# ifdef DL_NOW -+# define LT_DLLAZY_OR_NOW DL_NOW -+# else -+# define LT_DLLAZY_OR_NOW 0 -+# endif -+# endif -+# endif -+# endif -+#endif -+ -+void fnord() { int i=42;} -+int main () -+{ -+ void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW); -+ int status = $lt_dlunknown; -+ -+ if (self) -+ { -+ if (dlsym (self,"fnord")) status = $lt_dlno_uscore; -+ else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore; -+ /* dlclose (self); */ -+ } -+ else -+ puts (dlerror ()); -+ -+ return status; -+} -+_LT_EOF -+ if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5 -+ (eval $ac_link) 2>&5 -+ ac_status=$? -+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 -+ test $ac_status = 0; } && test -s conftest${ac_exeext} 2>/dev/null; then -+ (./conftest; exit; ) >&5 2>/dev/null -+ lt_status=$? -+ case x$lt_status in -+ x$lt_dlno_uscore) lt_cv_dlopen_self=yes ;; -+ x$lt_dlneed_uscore) lt_cv_dlopen_self=yes ;; -+ x$lt_dlunknown|x*) lt_cv_dlopen_self=no ;; -+ esac -+ else : -+ # compilation failed -+ lt_cv_dlopen_self=no -+ fi -+fi -+rm -fr conftest* -+ -+ -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_dlopen_self" >&5 -+$as_echo "$lt_cv_dlopen_self" >&6; } -+ -+ if test "x$lt_cv_dlopen_self" = xyes; then -+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\" -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a statically linked program can dlopen itself" >&5 -+$as_echo_n "checking whether a statically linked program can dlopen itself... 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" >&6; } -+ test "$can_build_shared" = "no" && enable_shared=no -+ -+ # On AIX, shared libraries and static libraries use the same namespace, and -+ # are all built from PIC. -+ case $host_os in -+ aix3*) -+ test "$enable_shared" = yes && enable_static=no -+ if test -n "$RANLIB"; then -+ archive_cmds="$archive_cmds~\$RANLIB \$lib" -+ postinstall_cmds='$RANLIB $lib' -+ fi -+ ;; -+ -+ aix[4-9]*) -+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then -+ test "$enable_shared" = yes && enable_static=no -+ fi -+ ;; -+ esac -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $enable_shared" >&5 -+$as_echo "$enable_shared" >&6; } -+ -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to build static libraries" >&5 -+$as_echo_n "checking whether to build static libraries... " >&6; } -+ # Make sure either enable_shared or enable_static is yes. -+ test "$enable_shared" = yes || enable_static=yes -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $enable_static" >&5 -+$as_echo "$enable_static" >&6; } -+ -+ -+ -+ -+fi -+ac_ext=c -+ac_cpp='$CPP $CPPFLAGS' -+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' -+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -+ac_compiler_gnu=$ac_cv_c_compiler_gnu -+ -+CC="$lt_save_CC" -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ ac_config_commands="$ac_config_commands libtool" -+ -+ -+ -+ -+# Only expand once: -+ -+ -+ -+# Checks for programs. -+#as# AC_PROG_CXX -+for ac_prog in gawk mawk nawk awk -+do -+ # Extract the first word of "$ac_prog", so it can be a program name with args. -+set dummy $ac_prog; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... 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But -lsocket is broken on IRIX 5.2 (and is not necessary -+ # on later versions), says Simon Leinen: it contains gethostby* -+ # variants that don't use the name server (or something). -lsocket -+ # must be given before -lnsl if both are needed. We assume that -+ # if connect needs -lnsl, so does gethostbyname. -+ ac_fn_c_check_func "$LINENO" "connect" "ac_cv_func_connect" -+if test "x$ac_cv_func_connect" = x""yes; then : -+ -+fi -+ -+ if test $ac_cv_func_connect = no; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for connect in -lsocket" >&5 -+$as_echo_n "checking for connect in -lsocket... " >&6; } -+if test "${ac_cv_lib_socket_connect+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-lsocket $X_EXTRA_LIBS $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$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 connect (); -+int -+main () -+{ -+return connect (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_socket_connect=yes -+else -+ ac_cv_lib_socket_connect=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_socket_connect" >&5 -+$as_echo "$ac_cv_lib_socket_connect" >&6; } -+if test "x$ac_cv_lib_socket_connect" = x""yes; then : -+ X_EXTRA_LIBS="-lsocket $X_EXTRA_LIBS" -+fi -+ -+ fi -+ -+ # Guillermo Gomez says -lposix is necessary on A/UX. -+ ac_fn_c_check_func "$LINENO" "remove" "ac_cv_func_remove" -+if test "x$ac_cv_func_remove" = x""yes; then : -+ -+fi -+ -+ if test $ac_cv_func_remove = no; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for remove in -lposix" >&5 -+$as_echo_n "checking for remove in -lposix... " >&6; } -+if test "${ac_cv_lib_posix_remove+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-lposix $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$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 remove (); -+int -+main () -+{ -+return remove (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_posix_remove=yes -+else -+ ac_cv_lib_posix_remove=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_posix_remove" >&5 -+$as_echo "$ac_cv_lib_posix_remove" >&6; } -+if test "x$ac_cv_lib_posix_remove" = x""yes; then : -+ X_EXTRA_LIBS="$X_EXTRA_LIBS -lposix" -+fi -+ -+ fi -+ -+ # BSDI BSD/OS 2.1 needs -lipc for XOpenDisplay. -+ ac_fn_c_check_func "$LINENO" "shmat" "ac_cv_func_shmat" -+if test "x$ac_cv_func_shmat" = x""yes; then : -+ -+fi -+ -+ if test $ac_cv_func_shmat = no; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for shmat in -lipc" >&5 -+$as_echo_n "checking for shmat in -lipc... " >&6; } -+if test "${ac_cv_lib_ipc_shmat+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-lipc $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$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 shmat (); -+int -+main () -+{ -+return shmat (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_ipc_shmat=yes -+else -+ ac_cv_lib_ipc_shmat=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_ipc_shmat" >&5 -+$as_echo "$ac_cv_lib_ipc_shmat" >&6; } -+if test "x$ac_cv_lib_ipc_shmat" = x""yes; then : -+ X_EXTRA_LIBS="$X_EXTRA_LIBS -lipc" -+fi -+ -+ fi -+ fi -+ -+ # Check for libraries that X11R6 Xt/Xaw programs need. -+ ac_save_LDFLAGS=$LDFLAGS -+ test -n "$x_libraries" && LDFLAGS="$LDFLAGS -L$x_libraries" -+ # SM needs ICE to (dynamically) link under SunOS 4.x (so we have to -+ # check for ICE first), but we must link in the order -lSM -lICE or -+ # we get undefined symbols. So assume we have SM if we have ICE. -+ # These have to be linked with before -lX11, unlike the other -+ # libraries we check for below, so use a different variable. -+ # John Interrante, Karl Berry -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for IceConnectionNumber in -lICE" >&5 -+$as_echo_n "checking for IceConnectionNumber in -lICE... " >&6; } -+if test "${ac_cv_lib_ICE_IceConnectionNumber+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-lICE $X_EXTRA_LIBS $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$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 IceConnectionNumber (); -+int -+main () -+{ -+return IceConnectionNumber (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_ICE_IceConnectionNumber=yes -+else -+ ac_cv_lib_ICE_IceConnectionNumber=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_ICE_IceConnectionNumber" >&5 -+$as_echo "$ac_cv_lib_ICE_IceConnectionNumber" >&6; } -+if test "x$ac_cv_lib_ICE_IceConnectionNumber" = x""yes; then : -+ X_PRE_LIBS="$X_PRE_LIBS -lSM -lICE" -+fi -+ -+ LDFLAGS=$ac_save_LDFLAGS -+ -+fi -+ -+ac_header_dirent=no -+for ac_hdr in dirent.h sys/ndir.h sys/dir.h ndir.h; do -+ as_ac_Header=`$as_echo "ac_cv_header_dirent_$ac_hdr" | $as_tr_sh` -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_hdr that defines DIR" >&5 -+$as_echo_n "checking for $ac_hdr that defines DIR... " >&6; } -+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then : -+ $as_echo_n "(cached) " >&6 -+else -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+#include -+#include <$ac_hdr> -+ -+int -+main () -+{ -+if ((DIR *) 0) -+return 0; -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_compile "$LINENO"; then : -+ eval "$as_ac_Header=yes" -+else -+ eval "$as_ac_Header=no" -+fi -+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext -+fi -+eval ac_res=\$$as_ac_Header -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 -+$as_echo "$ac_res" >&6; } -+eval as_val=\$$as_ac_Header -+ if test "x$as_val" = x""yes; then : -+ cat >>confdefs.h <<_ACEOF -+@%:@define `$as_echo "HAVE_$ac_hdr" | $as_tr_cpp` 1 -+_ACEOF -+ -+ac_header_dirent=$ac_hdr; break -+fi -+ -+done -+# Two versions of opendir et al. are in -ldir and -lx on SCO Xenix. -+if test $ac_header_dirent = dirent.h; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing opendir" >&5 -+$as_echo_n "checking for library containing opendir... " >&6; } -+if test "${ac_cv_search_opendir+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_func_search_save_LIBS=$LIBS -+cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+ -+/* Override any GCC internal prototype to avoid an error. -+ Use char because int might match the return type of a GCC -+ builtin and then its argument prototype would still apply. */ -+#ifdef __cplusplus -+extern "C" -+#endif -+char opendir (); -+int -+main () -+{ -+return opendir (); -+ ; -+ return 0; -+} -+_ACEOF -+for ac_lib in '' dir; do -+ if test -z "$ac_lib"; then -+ ac_res="none required" -+ else -+ ac_res=-l$ac_lib -+ LIBS="-l$ac_lib $ac_func_search_save_LIBS" -+ fi -+ if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_search_opendir=$ac_res -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext -+ if test "${ac_cv_search_opendir+set}" = set; then : -+ break -+fi -+done -+if test "${ac_cv_search_opendir+set}" = set; then : -+ -+else -+ ac_cv_search_opendir=no -+fi -+rm conftest.$ac_ext -+LIBS=$ac_func_search_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_opendir" >&5 -+$as_echo "$ac_cv_search_opendir" >&6; } -+ac_res=$ac_cv_search_opendir -+if test "$ac_res" != no; then : -+ test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" -+ -+fi -+ -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing opendir" >&5 -+$as_echo_n "checking for library containing opendir... " >&6; } -+if test "${ac_cv_search_opendir+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_func_search_save_LIBS=$LIBS -+cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+ -+/* Override any GCC internal prototype to avoid an error. -+ Use char because int might match the return type of a GCC -+ builtin and then its argument prototype would still apply. */ -+#ifdef __cplusplus -+extern "C" -+#endif -+char opendir (); -+int -+main () -+{ -+return opendir (); -+ ; -+ return 0; -+} -+_ACEOF -+for ac_lib in '' x; do -+ if test -z "$ac_lib"; then -+ ac_res="none required" -+ else -+ ac_res=-l$ac_lib -+ LIBS="-l$ac_lib $ac_func_search_save_LIBS" -+ fi -+ if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_search_opendir=$ac_res -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext -+ if test "${ac_cv_search_opendir+set}" = set; then : -+ break -+fi -+done -+if test "${ac_cv_search_opendir+set}" = set; then : -+ -+else -+ ac_cv_search_opendir=no -+fi -+rm conftest.$ac_ext -+LIBS=$ac_func_search_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_opendir" >&5 -+$as_echo "$ac_cv_search_opendir" >&6; } -+ac_res=$ac_cv_search_opendir -+if test "$ac_res" != no; then : -+ test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" -+ -+fi -+ -+fi -+ -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5 -+$as_echo_n "checking for ANSI C header files... " >&6; } -+if test "${ac_cv_header_stdc+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+#include -+#include -+#include -+#include -+ -+int -+main () -+{ -+ -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_compile "$LINENO"; then : -+ ac_cv_header_stdc=yes -+else -+ ac_cv_header_stdc=no -+fi -+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext -+ -+if test $ac_cv_header_stdc = yes; then -+ # SunOS 4.x string.h does not declare mem*, contrary to ANSI. -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+#include -+ -+_ACEOF -+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | -+ $EGREP "memchr" >/dev/null 2>&1; then : -+ -+else -+ ac_cv_header_stdc=no -+fi -+rm -f conftest* -+ -+fi -+ -+if test $ac_cv_header_stdc = yes; then -+ # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+#include -+ -+_ACEOF -+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | -+ $EGREP "free" >/dev/null 2>&1; then : -+ -+else -+ ac_cv_header_stdc=no -+fi -+rm -f conftest* -+ -+fi -+ -+if test $ac_cv_header_stdc = yes; then -+ # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. -+ if test "$cross_compiling" = yes; then : -+ : -+else -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+#include -+#include -+#if ((' ' & 0x0FF) == 0x020) -+# define ISLOWER(c) ('a' <= (c) && (c) <= 'z') -+# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) -+#else -+# define ISLOWER(c) \ -+ (('a' <= (c) && (c) <= 'i') \ -+ || ('j' <= (c) && (c) <= 'r') \ -+ || ('s' <= (c) && (c) <= 'z')) -+# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) -+#endif -+ -+#define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) -+int -+main () -+{ -+ int i; -+ for (i = 0; i < 256; i++) -+ if (XOR (islower (i), ISLOWER (i)) -+ || toupper (i) != TOUPPER (i)) -+ return 2; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_run "$LINENO"; then : -+ -+else -+ ac_cv_header_stdc=no -+fi -+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ -+ conftest.$ac_objext conftest.beam conftest.$ac_ext -+fi -+ -+fi -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5 -+$as_echo "$ac_cv_header_stdc" >&6; } -+if test $ac_cv_header_stdc = yes; then -+ -+$as_echo "@%:@define STDC_HEADERS 1" >>confdefs.h -+ -+fi -+ -+ -+for ac_header in unistd.h TargetConfig.h -+do : -+ as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` -+ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default" -+eval as_val=\$$as_ac_Header -+ if test "x$as_val" = x""yes; then : -+ cat >>confdefs.h <<_ACEOF -+@%:@define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 -+_ACEOF -+ -+fi -+ -+done -+ -+#as# AC_CHECK_HEADERS([arpa/inet.h fcntl.h float.h limits.h \ -+#as# malloc.h memory.h netdb.h netinet/in.h \ -+#as# shadow.h stddef.h stdint.h stdlib.h string.h strings.h \ -+#as# sys/file.h sys/ioctl.h sys/param.h sys/socket.h sys/time.h \ -+#as# termios.h unistd.h]) -+ -+# Checks for typedefs, structures, and compiler characteristics. -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for an ANSI C-conforming const" >&5 -+$as_echo_n "checking for an ANSI C-conforming const... " >&6; } -+if test "${ac_cv_c_const+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+ -+int -+main () -+{ -+/* FIXME: Include the comments suggested by Paul. */ -+#ifndef __cplusplus -+ /* Ultrix mips cc rejects this. */ -+ typedef int charset[2]; -+ const charset cs; -+ /* SunOS 4.1.1 cc rejects this. */ -+ char const *const *pcpcc; -+ char **ppc; -+ /* NEC SVR4.0.2 mips cc rejects this. */ -+ struct point {int x, y;}; -+ static struct point const zero = {0,0}; -+ /* AIX XL C 1.02.0.0 rejects this. -+ It does not let you subtract one const X* pointer from another in -+ an arm of an if-expression whose if-part is not a constant -+ expression */ -+ const char *g = "string"; -+ pcpcc = &g + (g ? g-g : 0); -+ /* HPUX 7.0 cc rejects these. */ -+ ++pcpcc; -+ ppc = (char**) pcpcc; -+ pcpcc = (char const *const *) ppc; -+ { /* SCO 3.2v4 cc rejects this. */ -+ char *t; -+ char const *s = 0 ? (char *) 0 : (char const *) 0; -+ -+ *t++ = 0; -+ if (s) return 0; -+ } -+ { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */ -+ int x[] = {25, 17}; -+ const int *foo = &x[0]; -+ ++foo; -+ } -+ { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */ -+ typedef const int *iptr; -+ iptr p = 0; -+ ++p; -+ } -+ { /* AIX XL C 1.02.0.0 rejects this saying -+ "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */ -+ struct s { int j; const int *ap[3]; }; -+ struct s *b; b->j = 5; -+ } -+ { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */ -+ const int foo = 10; -+ if (!foo) return 0; -+ } -+ return !cs[0] && !zero.x; -+#endif -+ -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_compile "$LINENO"; then : -+ ac_cv_c_const=yes -+else -+ ac_cv_c_const=no -+fi -+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_const" >&5 -+$as_echo "$ac_cv_c_const" >&6; } -+if test $ac_cv_c_const = no; then -+ -+$as_echo "@%:@define const /**/" >>confdefs.h -+ -+fi -+ -+#as# AC_HEADER_STDBOOL -+#as# AC_TYPE_UID_T -+#as# AC_C_INLINE -+#as# AC_TYPE_INT32_T -+ac_fn_c_check_type "$LINENO" "pid_t" "ac_cv_type_pid_t" "$ac_includes_default" -+if test "x$ac_cv_type_pid_t" = x""yes; then : -+ -+else -+ -+cat >>confdefs.h <<_ACEOF -+@%:@define pid_t int -+_ACEOF -+ -+fi -+ -+ac_fn_c_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default" -+if test "x$ac_cv_type_size_t" = x""yes; then : -+ -+else -+ -+cat >>confdefs.h <<_ACEOF -+@%:@define size_t unsigned int -+_ACEOF -+ -+fi -+ -+#as# AC_STRUCT_TIMEZONE -+#as# AC_TYPE_UINT32_T -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether struct tm is in sys/time.h or time.h" >&5 -+$as_echo_n "checking whether struct tm is in sys/time.h or time.h... " >&6; } -+if test "${ac_cv_struct_tm+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+#include -+#include -+ -+int -+main () -+{ -+struct tm tm; -+ int *p = &tm.tm_sec; -+ return !p; -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_compile "$LINENO"; then : -+ ac_cv_struct_tm=time.h -+else -+ ac_cv_struct_tm=sys/time.h -+fi -+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_struct_tm" >&5 -+$as_echo "$ac_cv_struct_tm" >&6; } -+if test $ac_cv_struct_tm = sys/time.h; then -+ -+$as_echo "@%:@define TM_IN_SYS_TIME 1" >>confdefs.h -+ -+fi -+ -+ -+#as# AC_CHECK_TYPES([ptrdiff_t]) -+ -+ -+ -+#AC_FUNC_ERROR_AT_LINE -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether getpgrp requires zero arguments" >&5 -+$as_echo_n "checking whether getpgrp requires zero arguments... " >&6; } -+if test "${ac_cv_func_getpgrp_void+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ # Use it with a single arg. -+cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+$ac_includes_default -+int -+main () -+{ -+getpgrp (0); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_compile "$LINENO"; then : -+ ac_cv_func_getpgrp_void=no -+else -+ ac_cv_func_getpgrp_void=yes -+fi -+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext -+ -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_getpgrp_void" >&5 -+$as_echo "$ac_cv_func_getpgrp_void" >&6; } -+if test $ac_cv_func_getpgrp_void = yes; then -+ -+$as_echo "@%:@define GETPGRP_VOID 1" >>confdefs.h -+ -+fi -+ -+for ac_func in strftime -+do : -+ ac_fn_c_check_func "$LINENO" "strftime" "ac_cv_func_strftime" -+if test "x$ac_cv_func_strftime" = x""yes; then : -+ cat >>confdefs.h <<_ACEOF -+@%:@define HAVE_STRFTIME 1 -+_ACEOF -+ -+else -+ # strftime is in -lintl on SCO UNIX. -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for strftime in -lintl" >&5 -+$as_echo_n "checking for strftime in -lintl... " >&6; } -+if test "${ac_cv_lib_intl_strftime+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-lintl $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$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 strftime (); -+int -+main () -+{ -+return strftime (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_intl_strftime=yes -+else -+ ac_cv_lib_intl_strftime=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_intl_strftime" >&5 -+$as_echo "$ac_cv_lib_intl_strftime" >&6; } -+if test "x$ac_cv_lib_intl_strftime" = x""yes; then : -+ $as_echo "@%:@define HAVE_STRFTIME 1" >>confdefs.h -+ -+LIBS="-lintl $LIBS" -+fi -+ -+fi -+done -+ -+for ac_header in vfork.h -+do : -+ ac_fn_c_check_header_mongrel "$LINENO" "vfork.h" "ac_cv_header_vfork_h" "$ac_includes_default" -+if test "x$ac_cv_header_vfork_h" = x""yes; then : -+ cat >>confdefs.h <<_ACEOF -+@%:@define HAVE_VFORK_H 1 -+_ACEOF -+ -+fi -+ -+done -+ -+for ac_func in fork vfork -+do : -+ as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` -+ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var" -+eval as_val=\$$as_ac_var -+ if test "x$as_val" = x""yes; then : -+ cat >>confdefs.h <<_ACEOF -+@%:@define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 -+_ACEOF -+ -+fi -+done -+ -+if test "x$ac_cv_func_fork" = xyes; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for working fork" >&5 -+$as_echo_n "checking for working fork... " >&6; } -+if test "${ac_cv_func_fork_works+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test "$cross_compiling" = yes; then : -+ ac_cv_func_fork_works=cross -+else -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+$ac_includes_default -+int -+main () -+{ -+ -+ /* By Ruediger Kuhlmann. */ -+ return fork () < 0; -+ -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_run "$LINENO"; then : -+ ac_cv_func_fork_works=yes -+else -+ ac_cv_func_fork_works=no -+fi -+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ -+ conftest.$ac_objext conftest.beam conftest.$ac_ext -+fi -+ -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_fork_works" >&5 -+$as_echo "$ac_cv_func_fork_works" >&6; } -+ -+else -+ ac_cv_func_fork_works=$ac_cv_func_fork -+fi -+if test "x$ac_cv_func_fork_works" = xcross; then -+ case $host in -+ *-*-amigaos* | *-*-msdosdjgpp*) -+ # Override, as these systems have only a dummy fork() stub -+ ac_cv_func_fork_works=no -+ ;; -+ *) -+ ac_cv_func_fork_works=yes -+ ;; -+ esac -+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: result $ac_cv_func_fork_works guessed because of cross compilation" >&5 -+$as_echo "$as_me: WARNING: result $ac_cv_func_fork_works guessed because of cross compilation" >&2;} -+fi -+ac_cv_func_vfork_works=$ac_cv_func_vfork -+if test "x$ac_cv_func_vfork" = xyes; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for working vfork" >&5 -+$as_echo_n "checking for working vfork... " >&6; } -+if test "${ac_cv_func_vfork_works+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test "$cross_compiling" = yes; then : -+ ac_cv_func_vfork_works=cross -+else -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+/* Thanks to Paul Eggert for this test. */ -+$ac_includes_default -+#include -+#ifdef HAVE_VFORK_H -+# include -+#endif -+/* On some sparc systems, changes by the child to local and incoming -+ argument registers are propagated back to the parent. The compiler -+ is told about this with #include , but some compilers -+ (e.g. gcc -O) don't grok . Test for this by using a -+ static variable whose address is put into a register that is -+ clobbered by the vfork. */ -+static void -+#ifdef __cplusplus -+sparc_address_test (int arg) -+# else -+sparc_address_test (arg) int arg; -+#endif -+{ -+ static pid_t child; -+ if (!child) { -+ child = vfork (); -+ if (child < 0) { -+ perror ("vfork"); -+ _exit(2); -+ } -+ if (!child) { -+ arg = getpid(); -+ write(-1, "", 0); -+ _exit (arg); -+ } -+ } -+} -+ -+int -+main () -+{ -+ pid_t parent = getpid (); -+ pid_t child; -+ -+ sparc_address_test (0); -+ -+ child = vfork (); -+ -+ if (child == 0) { -+ /* Here is another test for sparc vfork register problems. This -+ test uses lots of local variables, at least as many local -+ variables as main has allocated so far including compiler -+ temporaries. 4 locals are enough for gcc 1.40.3 on a Solaris -+ 4.1.3 sparc, but we use 8 to be safe. A buggy compiler should -+ reuse the register of parent for one of the local variables, -+ since it will think that parent can't possibly be used any more -+ in this routine. Assigning to the local variable will thus -+ munge parent in the parent process. */ -+ pid_t -+ p = getpid(), p1 = getpid(), p2 = getpid(), p3 = getpid(), -+ p4 = getpid(), p5 = getpid(), p6 = getpid(), p7 = getpid(); -+ /* Convince the compiler that p..p7 are live; otherwise, it might -+ use the same hardware register for all 8 local variables. */ -+ if (p != p1 || p != p2 || p != p3 || p != p4 -+ || p != p5 || p != p6 || p != p7) -+ _exit(1); -+ -+ /* On some systems (e.g. IRIX 3.3), vfork doesn't separate parent -+ from child file descriptors. If the child closes a descriptor -+ before it execs or exits, this munges the parent's descriptor -+ as well. Test for this by closing stdout in the child. */ -+ _exit(close(fileno(stdout)) != 0); -+ } else { -+ int status; -+ struct stat st; -+ -+ while (wait(&status) != child) -+ ; -+ return ( -+ /* Was there some problem with vforking? */ -+ child < 0 -+ -+ /* Did the child fail? (This shouldn't happen.) */ -+ || status -+ -+ /* Did the vfork/compiler bug occur? */ -+ || parent != getpid() -+ -+ /* Did the file descriptor bug occur? */ -+ || fstat(fileno(stdout), &st) != 0 -+ ); -+ } -+} -+_ACEOF -+if ac_fn_c_try_run "$LINENO"; then : -+ ac_cv_func_vfork_works=yes -+else -+ ac_cv_func_vfork_works=no -+fi -+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ -+ conftest.$ac_objext conftest.beam conftest.$ac_ext -+fi -+ -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_vfork_works" >&5 -+$as_echo "$ac_cv_func_vfork_works" >&6; } -+ -+fi; -+if test "x$ac_cv_func_fork_works" = xcross; then -+ ac_cv_func_vfork_works=$ac_cv_func_vfork -+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: result $ac_cv_func_vfork_works guessed because of cross compilation" >&5 -+$as_echo "$as_me: WARNING: result $ac_cv_func_vfork_works guessed because of cross compilation" >&2;} -+fi -+ -+if test "x$ac_cv_func_vfork_works" = xyes; then -+ -+$as_echo "@%:@define HAVE_WORKING_VFORK 1" >>confdefs.h -+ -+else -+ -+$as_echo "@%:@define vfork fork" >>confdefs.h -+ -+fi -+if test "x$ac_cv_func_fork_works" = xyes; then -+ -+$as_echo "@%:@define HAVE_WORKING_FORK 1" >>confdefs.h -+ -+fi -+ -+for ac_func in vprintf -+do : -+ ac_fn_c_check_func "$LINENO" "vprintf" "ac_cv_func_vprintf" -+if test "x$ac_cv_func_vprintf" = x""yes; then : -+ cat >>confdefs.h <<_ACEOF -+@%:@define HAVE_VPRINTF 1 -+_ACEOF -+ -+ac_fn_c_check_func "$LINENO" "_doprnt" "ac_cv_func__doprnt" -+if test "x$ac_cv_func__doprnt" = x""yes; then : -+ -+$as_echo "@%:@define HAVE_DOPRNT 1" >>confdefs.h -+ -+fi -+ -+fi -+done -+ -+ -+#as# AC_FUNC_MALLOC -+#as# AC_FUNC_MKTIME -+#as# AC_FUNC_REALLOC -+#as# AC_FUNC_STRTOD -+ -+for ac_func in memmove -+do : -+ ac_fn_c_check_func "$LINENO" "memmove" "ac_cv_func_memmove" -+if test "x$ac_cv_func_memmove" = x""yes; then : -+ cat >>confdefs.h <<_ACEOF -+@%:@define HAVE_MEMMOVE 1 -+_ACEOF -+ -+fi -+done -+ -+#as# AC_CHECK_FUNCS([alarm atexit bzero dup2 floor \ -+#as# getcwd gethostbyname getspnam gettimeofday inet_ntoa \ -+#as# localtime_r memmove memset mkdir modf pow regcomp rint \ -+#as# select socket sqrt strchr strcspn strdup strerror strpbrk \ -+#as# strrchr strspn strstr strtol]) -+ -+if test "${with_x}" != "no" ; then -+ -+ CFLAGS="$CFLAGS $X_CFLAGS" -+if test "`uname`" != "IRIX64" && test "`uname`" != "IRIX" ; then -+ XLIB="$X_LIBS -lX11 $X_EXTRA_LIBS" -+else -+ XLIB="-lX11 $X_EXTRA_LIBS" -+fi -+ -+ -+ac_fn_c_check_header_mongrel "$LINENO" "X11/Xlib.h" "ac_cv_header_X11_Xlib_h" "$ac_includes_default" -+if test "x$ac_cv_header_X11_Xlib_h" = x""yes; then : -+ -+ $as_echo "@%:@define PLD_xwin 1" >>confdefs.h -+ -+ -+else -+ -+ echo "" -+ echo "X11 graphics have been selected but no X11 header files" -+ echo "have been found." -+ echo "" -+ echo "This error usually happens on Linux/MacOSX distributions" -+ echo "where the optional X11 development files have not been installed." -+ echo "On Linux RPM systems this package is usually called something" -+ echo "like xorg-x11-proto-devel whereas on Debian/Ubuntu it may" -+ echo "be called x-dev. On MacOSX installation DVDs the X11 files" -+ echo "can usually be found as an explicitly named optional" -+ echo "installation." -+ echo "" -+ echo "After installing the X11 development files you should do a" -+ echo "'make clean' and perform the configure stage again." -+ echo "" -+ echo "Alternatively, to install EMBOSS without X11 support, you can add" -+ echo "the --without-x switch to the configure command." -+ echo "" -+ exit $? -+ -+fi -+ -+ -+ -+ -+fi -+ -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for socket in -lc" >&5 -+$as_echo_n "checking for socket in -lc... " >&6; } -+if test "${ac_cv_lib_c_socket+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-lc $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$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 socket (); -+int -+main () -+{ -+return socket (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_c_socket=yes -+else -+ ac_cv_lib_c_socket=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_c_socket" >&5 -+$as_echo "$ac_cv_lib_c_socket" >&6; } -+if test "x$ac_cv_lib_c_socket" = x""yes; then : -+ LIBS="$LIBS" -+else -+ LIBS="$LIBS -lsocket" -+fi -+ -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lm" >&5 -+$as_echo_n "checking for main in -lm... " >&6; } -+if test "${ac_cv_lib_m_main+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-lm $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+ -+ -+int -+main () -+{ -+return main (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_m_main=yes -+else -+ ac_cv_lib_m_main=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_main" >&5 -+$as_echo "$ac_cv_lib_m_main" >&6; } -+if test "x$ac_cv_lib_m_main" = x""yes; then : -+ cat >>confdefs.h <<_ACEOF -+@%:@define HAVE_LIBM 1 -+_ACEOF -+ -+ LIBS="-lm $LIBS" -+ -+fi -+ -+ -+if test "`uname`" = "FreeBSD" && ${with_pngdriver} != "no"; then -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -liconv" >&5 -+$as_echo_n "checking for main in -liconv... " >&6; } -+if test "${ac_cv_lib_iconv_main+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-liconv $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+ -+ -+int -+main () -+{ -+return main (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_iconv_main=yes -+else -+ ac_cv_lib_iconv_main=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_iconv_main" >&5 -+$as_echo "$ac_cv_lib_iconv_main" >&6; } -+if test "x$ac_cv_lib_iconv_main" = x""yes; then : -+ LIBS="$LIBS" -+else -+ LIBS="-liconv $LIBS" -+fi -+ -+fi -+ -+ if false; then -+ AMPNG_TRUE= -+ AMPNG_FALSE='#' -+else -+ AMPNG_TRUE='#' -+ AMPNG_FALSE= -+fi -+ -+ if false; then -+ AMPDF_TRUE= -+ AMPDF_FALSE='#' -+else -+ AMPDF_TRUE='#' -+ AMPDF_FALSE= -+fi -+ -+ -+# -+# Handle general setup e.g. documentation directory -+# -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if docroot is given" >&5 -+$as_echo_n "checking if docroot is given... " >&6; } -+ -+@%:@ Check whether --with-docroot was given. -+if test "${with_docroot+set}" = set; then : -+ withval=$with_docroot; if test "$withval" != no ; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -+$as_echo "yes" >&6; } -+ CPPFLAGS="$CPPFLAGS -DDOC_ROOT=\\\"$withval\\\"" -+fi -+else -+ -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+ -+fi -+ -+ -+ -+ -+# GCC profiling -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if gcc profiling is selected" >&5 -+$as_echo_n "checking if gcc profiling is selected... " >&6; } -+ -+@%:@ Check whether --with-gccprofile was given. -+if test "${with_gccprofile+set}" = set; then : -+ withval=$with_gccprofile; if test "$withval" != no ; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -+$as_echo "yes" >&6; } -+ CFLAGS="$CFLAGS -g -pg" -+ LDFLAGS="$LDFLAGS -pg" -+fi -+else -+ -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+ -+fi -+ -+ -+ -+ -+# -+# Handle user hints -+# -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if java include directory given" >&5 -+$as_echo_n "checking if java include directory given... " >&6; } -+ -+@%:@ Check whether --with-java was given. -+if test "${with_java+set}" = set; then : -+ withval=$with_java; if test "$withval" != no ; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -+$as_echo "yes" >&6; } -+ JALT_HOME="$withval" -+ if test -d $withval ; then -+ echo "Java directory $withval exists" -+ else -+ echo "Java directory $withval does not exist" -+ exit 0 -+ fi -+ -+ JALT_HOME="${JALT_HOME} -DHAVE_JAVA" -+ # Extract the first word of "javac", so it can be a program name with args. -+set dummy javac; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_havejavac+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$havejavac"; then -+ ac_cv_prog_havejavac="$havejavac" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_havejavac=""yes"" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+ test -z "$ac_cv_prog_havejavac" && ac_cv_prog_havejavac=""no"" -+fi -+fi -+havejavac=$ac_cv_prog_havejavac -+if test -n "$havejavac"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $havejavac" >&5 -+$as_echo "$havejavac" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+ if test "${havejavac}" != yes ; then -+ echo "Error: Either JAVA not installed or 'javac' not in your PATH" -+ exit 1 -+ fi -+ if test -f /etc/debian_release || test -f /etc/debian_version ; then -+ CFLAGS="$CFLAGS -DDEBIAN" -+ fi -+ JAVA_OK=yes -+ -+else -+ JAVA_OK=no -+ -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+ -+fi -+else -+ -+ -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+ -+ -+fi -+ -+ -+if test -n "${JALT_HOME}" -+then -+ CFLAGS="$CFLAGS -I${JALT_HOME}" -+fi -+ -+ -+# -+# Handle user hints -+# -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if java OS include directory given" >&5 -+$as_echo_n "checking if java OS include directory given... " >&6; } -+ -+@%:@ Check whether --with-javaos was given. -+if test "${with_javaos+set}" = set; then : -+ withval=$with_javaos; if test "$withval" != no ; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -+$as_echo "yes" >&6; } -+ if test -d $withval ; then -+ echo "Javaos directory $withval exists" -+ else -+ echo "Javaos directory $withval does not exist" -+ exit 0 -+ fi -+ ALT_HOMEOS="$withval" -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+else -+ -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+ if test "$JAVA_OK" = "yes" ; then -+ echo "Error: --with-java=dir unspecified" -+ exit 0 -+ fi -+ -+fi -+ -+ -+if test -n "${ALT_HOMEOS}" -+then -+ CFLAGS="$CFLAGS -I${ALT_HOMEOS}" -+fi -+ -+ -+ -+# -+# Handle user hints -+# -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to look for pdf support" >&5 -+$as_echo_n "checking whether to look for pdf support... 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" >&6; } -+ if pkg-config --exists plplotd; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -+$as_echo "yes" >&6; } -+ PLPLOT_CFLAGS=`pkg-config --cflags plplotd` -+ PLPLOT_LIBS=`pkg-config --libs plplotd` -+ -+$as_echo "@%:@define PLPLOT_H \"plplot.h\"" >>confdefs.h -+ -+ -+$as_echo "@%:@define PLPLOTP_H \"plplotP.h\"" >>confdefs.h -+ -+ check_plplotpkg_ok=yes -+ else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+ fi -+fi -+if test x$check_plplotpkg_ok = xno; then -+ if test x = x; then -+ ac_fn_c_check_header_mongrel "$LINENO" "plplot.h" "ac_cv_header_plplot_h" "$ac_includes_default" -+if test "x$ac_cv_header_plplot_h" = x""yes; then : -+ check_plplothead_ok=yes -+else -+ check_plplothead_ok=no -+fi -+ -+ -+ if test x$check_plplothead_ok = xyes; then -+ -+$as_echo "@%:@define PLPLOT_H \"plplot.h\"" >>confdefs.h -+ -+ -+$as_echo "@%:@define PLPLOTP_H \"plplotP.h\"" >>confdefs.h -+ -+ else -+ ac_fn_c_check_header_mongrel "$LINENO" "plplot/plplot.h" "ac_cv_header_plplot_plplot_h" "$ac_includes_default" -+if test "x$ac_cv_header_plplot_plplot_h" = x""yes; then : -+ check_plplothead_ok=yes -+else -+ check_plplothead_ok=no -+fi -+ -+ -+ if test x$check_plplothead_ok = xyes; then -+ -+$as_echo "@%:@define PLPLOT_H \"plplot/plplot.h\"" >>confdefs.h -+ -+ -+$as_echo "@%:@define PLPLOTP_H \"plplot/plplotP.h\"" >>confdefs.h -+ -+ else -+ check_plplot_ok=no -+ fi -+ fi -+ else -+ ac_fn_c_check_header_mongrel "$LINENO" "/plplot.h" "ac_cv_header__plplot_h" "$ac_includes_default" -+if test "x$ac_cv_header__plplot_h" = x""yes; then : -+ check_plplothead_ok=yes -+else -+ check_plplothead_ok=no -+fi -+ -+ -+ if test x$check_plplothead_ok = xyes; then -+ -+$as_echo "@%:@define PLPLOT_H \"plplot.h\"" >>confdefs.h -+ -+ -+$as_echo "@%:@define PLPLOTP_H \"plplotP.h\"" >>confdefs.h -+ -+ PLPLOT_CFLAGS="-I" -+ else -+ check_plplot_ok=no -+ fi -+ fi -+ if test x = x; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for c_plinit in -lplplotd" >&5 -+$as_echo_n "checking for c_plinit in -lplplotd... 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" >&6; } -+ -+@%:@ Check whether --with-pngdriver was given. -+if test "${with_pngdriver+set}" = set; then : -+ withval=$with_pngdriver; if test "$withval" != no ; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -+$as_echo "yes" >&6; } -+ ALT_HOME="$withval" -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+else -+ -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -+$as_echo "yes" >&6; } -+ALT_HOME=/usr -+ -+fi -+ -+ -+ -+# -+# Locate png/gd/zlib, if wanted -+# -+if test -d "${ALT_HOME}" -+then -+ -+# -+# Keep a copy if it fails -+# -+ ALT_LDFLAGS="$LDFLAGS" -+ ALT_CPPFLAGS="$CPPFLAGS" -+ -+# -+# Set -+# -+ LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib" -+ CPPFLAGS="$CPPFLAGS -I$ALT_HOME/include" -+ -+ ICCHECK=0 -+ if test "`uname`" = "SunOS"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for libiconv_close in -liconv" >&5 -+$as_echo_n "checking for libiconv_close in -liconv... 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" >&6; } -+if test "${ac_cv_lib_gd_gdImageCreateFromPng+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-lgd -L${ALT_HOME}/lib -lgd -lpng -lz -lm $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$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 gdImageCreateFromPng (); -+int -+main () -+{ -+return gdImageCreateFromPng (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_gd_gdImageCreateFromPng=yes -+else -+ ac_cv_lib_gd_gdImageCreateFromPng=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_gd_gdImageCreateFromPng" >&5 -+$as_echo "$ac_cv_lib_gd_gdImageCreateFromPng" >&6; } -+if test "x$ac_cv_lib_gd_gdImageCreateFromPng" = x""yes; then : -+ CHECK=1 -+else -+ CHECK=0 -+fi -+ -+ if test $CHECK = "0"; then -+ echo need to upgrade gd for png driver for plplot -+ fi -+ fi -+# -+# If everything found okay then proceed to include png driver in config. -+# -+ if test $CHECK = "1" ; then -+ LIBS="$LIBS -lgd -lpng -lz -lm" -+ -+ if test $ICCHECK = "1" ; then -+ LIBS="$LIBS -liconv" -+ fi -+ -+ if test "`uname`" = "SunOS"; then -+ LDFLAGS="$LDFLAGS -R$ALT_HOME/lib" -+ fi -+ -+ $as_echo "@%:@define PLD_png 1" >>confdefs.h -+ -+ if true; then -+ AMPNG_TRUE= -+ AMPNG_FALSE='#' -+else -+ AMPNG_TRUE='#' -+ AMPNG_FALSE= -+fi -+ -+ echo PNG libraries found -+ if test $ALT_HOME = "/usr" ; then -+ LDFLAGS="$ALT_LDFLAGS" -+ CPPFLAGS="$ALT_CPPFLAGS" -+ fi -+ else -+# -+# If not okay then reset FLAGS. -+# -+ if false; then -+ AMPNG_TRUE= -+ AMPNG_FALSE='#' -+else -+ AMPNG_TRUE='#' -+ AMPNG_FALSE= -+fi -+ -+ LDFLAGS="$ALT_LDFLAGS" -+ CPPFLAGS="$ALT_CPPFLAGS" -+ echo No png driver will be made due to librarys missing/old. -+ fi -+# echo PNG STUFF FOLLOWS!!! -+# echo CHECK = $CHECK -+# echo LIBS = $LIBS -+# echo LDFLAGS = $LDFLAGS -+# echo CPPFLAGS = $CPPFLAGS -+ -+ -+else -+ if test $withval != "no"; then -+ echo "Directory $ALT_HOME does not exist" -+ exit 0 -+ fi -+fi -+ -+# -+# Handle user authorisation -+# -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if any authorisation type is given" >&5 -+$as_echo_n "checking if any authorisation type is given... " >&6; } -+ -+@%:@ Check whether --with-auth was given. -+if test "${with_auth+set}" = set; then : -+ withval=$with_auth; if test "$withval" != no ; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -+$as_echo "yes" >&6; } -+ -+ ALT_AUTHTYPE="-D${withval}" -+ -+ if test "$withval" = "yes" ; then -+ ALT_AUTHTYPE="-DPAM" -+ fi -+ if test "$withval" = "pam" ; then -+ ALT_AUTHTYPE="-DPAM" -+ fi -+ if test "$withval" = "shadow" ; then -+ ALT_AUTHTYPE="-DN_SHADOW" -+ fi -+ if test "$withval" = "rshadow" ; then -+ ALT_AUTHTYPE="-DR_SHADOW" -+ fi -+ if test "$withval" = "noshadow" ; then -+ ALT_AUTHTYPE="-DNO_SHADOW" -+ fi -+ if test "$withval" = "rnoshadow" ; then -+ ALT_AUTHTYPE="-DRNO_SHADOW" -+ fi -+ if test "$withval" = "aixshadow" ; then -+ ALT_AUTHTYPE="-DAIX_SHADOW" -+ fi -+ if test "$withval" = "hpuxshadow" ; then -+ ALT_AUTHTYPE="-DHPUX_SHADOW" -+ fi -+if test "`uname`" != "IRIX64" && test "`uname`" != "IRIX" ; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lcrypt" >&5 -+$as_echo_n "checking for main in -lcrypt... " >&6; } -+if test "${ac_cv_lib_crypt_main+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-lcrypt $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+ -+ -+int -+main () -+{ -+return main (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_crypt_main=yes -+else -+ ac_cv_lib_crypt_main=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_crypt_main" >&5 -+$as_echo "$ac_cv_lib_crypt_main" >&6; } -+if test "x$ac_cv_lib_crypt_main" = x""yes; then : -+ LDFLAGS="$LDFLAGS -lcrypt" -+else -+ LDFLAGS="$LDFLAGS" -+fi -+ -+fi -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lpam" >&5 -+$as_echo_n "checking for main in -lpam... " >&6; } -+if test "${ac_cv_lib_pam_main+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-lpam $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+ -+ -+int -+main () -+{ -+return main (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_pam_main=yes -+else -+ ac_cv_lib_pam_main=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_pam_main" >&5 -+$as_echo "$ac_cv_lib_pam_main" >&6; } -+if test "x$ac_cv_lib_pam_main" = x""yes; then : -+ LDFLAGS="$LDFLAGS -lpam" -+else -+ LDFLAGS="$LDFLAGS" -+fi -+ -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+else -+ -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+# if test "$JAVA_OK" = "yes" ; then -+# echo "Error: --with-java=dir unspecified" -+# exit 0 -+# fi -+ -+fi -+ -+ -+if test -n "${ALT_AUTHTYPE}" -+then -+ CFLAGS="$CFLAGS ${ALT_AUTHTYPE}" -+else -+ CFLAGS="$CFLAGS -DNO_AUTH" -+fi -+ -+ -+ -+# -+# -+# -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if Linux x86_64" >&5 -+$as_echo_n "checking if Linux x86_64... " >&6; } -+ -+ -+if test "`uname -a | grep Linux`"; then -+ if test "`uname -a | grep x86_64`"; then -+ CFLAGS="${CFLAGS} -D__amd64__" -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -+$as_echo "yes" >&6; } -+ else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+ fi -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+ -+ -+ -+@%:@ Check whether --with-mysql was given. -+if test "${with_mysql+set}" = set; then : -+ withval=$with_mysql; -+ if test "$withval" = "no"; then -+ want_mysql="no" -+ elif test "$withval" = "yes"; then -+ want_mysql="yes" -+ else -+ want_mysql="yes" -+ MYSQL_CONFIG="$withval" -+ fi -+ -+else -+ want_mysql="yes" -+ -+fi -+ -+ -+ MYSQL_CFLAGS="" -+ MYSQL_LDFLAGS="" -+ MYSQL_VERSION="" -+ -+ -+ if test "$want_mysql" = "yes"; then -+ -+ if test -z "$MYSQL_CONFIG" -o test; then -+ # Extract the first word of "mysql_config", so it can be a program name with args. -+set dummy mysql_config; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_path_MYSQL_CONFIG+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ case $MYSQL_CONFIG in -+ [\\/]* | ?:[\\/]*) -+ ac_cv_path_MYSQL_CONFIG="$MYSQL_CONFIG" # Let the user override the test with a path. -+ ;; -+ *) -+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_path_MYSQL_CONFIG="$as_dir/$ac_word$ac_exec_ext" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+ test -z "$ac_cv_path_MYSQL_CONFIG" && ac_cv_path_MYSQL_CONFIG="no" -+ ;; -+esac -+fi -+MYSQL_CONFIG=$ac_cv_path_MYSQL_CONFIG -+if test -n "$MYSQL_CONFIG"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MYSQL_CONFIG" >&5 -+$as_echo "$MYSQL_CONFIG" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+ fi -+ -+ if test "$MYSQL_CONFIG" != "no"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for MySQL libraries" >&5 -+$as_echo_n "checking for MySQL libraries... " >&6; } -+ -+ MYSQL_CFLAGS="`$MYSQL_CONFIG --include`" -+ MYSQL_LDFLAGS="`$MYSQL_CONFIG --libs`" -+ -+ MYSQL_VERSION=`$MYSQL_CONFIG --version` -+ -+ -+ EMBCFLAGS=$CFLAGS -+ EMBLDFLAGS=$LDFLAGS -+ CFLAGS="$MYSQL_CFLAGS $EMBCFLAGS" -+ LDFLAGS="$MYSQL_LDFLAGS $EMBLDFLAGS" -+ -+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext -+/* end confdefs.h. */ -+#include -+ #include "mysql.h" -+int -+main () -+{ -+mysql_info(NULL) -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ havemysql=yes -+else -+ havemysql=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+ -+ CFLAGS=$EMBCFLAGS -+ LDFLAGS=$EMBLDFLAGS -+ -+ if test "$havemysql" = yes; then -+ -+$as_echo "@%:@define HAVE_MYSQL 1" >>confdefs.h -+ -+ found_mysql="yes" -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -+$as_echo "yes" >&6; } -+ else -+ MYSQL_CFLAGS="" -+ MYSQL_LDFLAGS="" -+ found_mysql="no" -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+ fi -+ else -+ found_mysql="no" -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+ fi -+ fi -+ -+ -+ -+ mysql_version_req= -+ -+ if test "$found_mysql" = "yes" -a -n "$mysql_version_req"; then -+ -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if MySQL version is >= $mysql_version_req" >&5 -+$as_echo_n "checking if MySQL version is >= $mysql_version_req... " >&6; } -+ -+ mysql_version_req_major=`expr $mysql_version_req : '\([0-9]*\)'` -+ mysql_version_req_minor=`expr $mysql_version_req : '[0-9]*\.\([0-9]*\)'` -+ mysql_version_req_micro=`expr $mysql_version_req : '[0-9]*\.[0-9]*\.\([0-9]*\)'` -+ if test "x$mysql_version_req_micro" = "x"; then -+ mysql_version_req_micro="0" -+ fi -+ -+ mysql_version_req_number=`expr $mysql_version_req_major \* 1000000 \ -+ \+ $mysql_version_req_minor \* 1000 \ -+ \+ $mysql_version_req_micro` -+ -+ mysql_version_major=`expr $MYSQL_VERSION : '\([0-9]*\)'` -+ mysql_version_minor=`expr $MYSQL_VERSION : '[0-9]*\.\([0-9]*\)'` -+ mysql_version_micro=`expr $MYSQL_VERSION : '[0-9]*\.[0-9]*\.\([0-9]*\)'` -+ if test "x$mysql_version_micro" = "x"; then -+ mysql_version_micro="0" -+ fi -+ -+ mysql_version_number=`expr $mysql_version_major \* 1000000 \ -+ \+ $mysql_version_minor \* 1000 \ -+ \+ $mysql_version_micro` -+ -+ mysql_version_check=`expr $mysql_version_number \>\= $mysql_version_req_number` -+ if test "$mysql_version_check" = "1"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -+$as_echo "yes" >&6; } -+ else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+ fi -+ fi -+ -+ -+ -+ -+ -+ -+ -+@%:@ Check whether --with-postgresql was given. -+if test "${with_postgresql+set}" = set; then : -+ withval=$with_postgresql; -+ if test "$withval" = "no"; then -+ want_postgresql="no" -+ elif test "$withval" = "yes"; then -+ want_postgresql="yes" -+ else -+ want_postgresql="yes" -+ PG_CONFIG="$withval" -+ fi -+ -+else -+ want_postgresql="yes" -+ -+fi -+ -+ -+ POSTGRESQL_CFLAGS="" -+ POSTGRESQL_LDFLAGS="" -+ POSTGRESQL_POSTGRESQL="" -+ -+ -+ if test "$want_postgresql" = "yes"; then -+ -+ if test -z "$PG_CONFIG" -o test; then -+ # Extract the first word of "pg_config", so it can be a program name with args. -+set dummy pg_config; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_path_PG_CONFIG+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ case $PG_CONFIG in -+ [\\/]* | ?:[\\/]*) -+ ac_cv_path_PG_CONFIG="$PG_CONFIG" # Let the user override the test with a path. -+ ;; -+ *) -+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_path_PG_CONFIG="$as_dir/$ac_word$ac_exec_ext" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+ test -z "$ac_cv_path_PG_CONFIG" && ac_cv_path_PG_CONFIG="no" -+ ;; -+esac -+fi -+PG_CONFIG=$ac_cv_path_PG_CONFIG -+if test -n "$PG_CONFIG"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PG_CONFIG" >&5 -+$as_echo "$PG_CONFIG" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+ fi -+ -+ if test "$PG_CONFIG" != "no"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for PostgreSQL libraries" >&5 -+$as_echo_n "checking for PostgreSQL libraries... " >&6; } -+ -+ POSTGRESQL_CFLAGS="-I`$PG_CONFIG --includedir`" -+ POSTGRESQL_LDFLAGS="-L`$PG_CONFIG --libdir` -lpq" -+ -+ POSTGRESQL_VERSION=`$PG_CONFIG --version | sed -e 's#PostgreSQL ##'` -+ -+ -+$as_echo "@%:@define HAVE_POSTGRESQL 1" >>confdefs.h -+ -+ -+ found_postgresql="yes" -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -+$as_echo "yes" >&6; } -+ else -+ found_postgresql="no" -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: Not configuring for PostgreSQL" >&5 -+$as_echo "Not configuring for PostgreSQL" >&6; } -+ fi -+ fi -+ -+ -+ -+ postgresql_version_req= -+ -+ if test "$found_postgresql" = "yes" -a -n "$postgresql_version_req"; then -+ -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if PostgreSQL version is >= $postgresql_version_req" >&5 -+$as_echo_n "checking if PostgreSQL version is >= $postgresql_version_req... " >&6; } -+ -+ postgresql_version_req_major=`expr $postgresql_version_req : '\([0-9]*\)'` -+ postgresql_version_req_minor=`expr $postgresql_version_req : '[0-9]*\.\([0-9]*\)'` -+ postgresql_version_req_micro=`expr $postgresql_version_req : '[0-9]*\.[0-9]*\.\([0-9]*\)'` -+ if test "x$postgresql_version_req_micro" = "x"; then -+ postgresql_version_req_micro="0" -+ fi -+ -+ postgresql_version_req_number=`expr $postgresql_version_req_major \* 1000000 \ -+ \+ $postgresql_version_req_minor \* 1000 \ -+ \+ $postgresql_version_req_micro` -+ -+ postgresql_version_major=`expr $POSTGRESQL_VERSION : '\([0-9]*\)'` -+ postgresql_version_minor=`expr $POSTGRESQL_VERSION : '[0-9]*\.\([0-9]*\)'` -+ postgresql_version_micro=`expr $POSTGRESQL_VERSION : '[0-9]*\.[0-9]*\.\([0-9]*\)'` -+ if test "x$postgresql_version_micro" = "x"; then -+ postgresql_version_micro="0" -+ fi -+ -+ postgresql_version_number=`expr $postgresql_version_major \* 1000000 \ -+ \+ $postgresql_version_minor \* 1000 \ -+ \+ $postgresql_version_micro` -+ -+ postgresql_version_check=`expr $postgresql_version_number \>\= $postgresql_version_req_number` -+ if test "$postgresql_version_check" = "1"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -+$as_echo "yes" >&6; } -+ else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+ fi -+ fi -+ -+ -+ -+ -+ -+ -+CFLAGS="$CFLAGS $MYSQL_CFLAGS" -+LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS" -+ -+CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS" -+LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS" -+ -+ -+ -+# Extract the first word of "javac", so it can be a program name with args. -+set dummy javac; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_javac_in_path+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$javac_in_path"; then -+ ac_cv_prog_javac_in_path="$javac_in_path" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_javac_in_path="true" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+ test -z "$ac_cv_prog_javac_in_path" && ac_cv_prog_javac_in_path="false" -+fi -+fi -+javac_in_path=$ac_cv_prog_javac_in_path -+if test -n "$javac_in_path"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $javac_in_path" >&5 -+$as_echo "$javac_in_path" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+# Extract the first word of "ant", so it can be a program name with args. -+set dummy ant; ac_word=$2 -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -+$as_echo_n "checking for $ac_word... " >&6; } -+if test "${ac_cv_prog_ant_in_path+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ if test -n "$ant_in_path"; then -+ ac_cv_prog_ant_in_path="$ant_in_path" # Let the user override the test. -+else -+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -+for as_dir in $PATH -+do -+ IFS=$as_save_IFS -+ test -z "$as_dir" && as_dir=. -+ for ac_exec_ext in '' $ac_executable_extensions; do -+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then -+ ac_cv_prog_ant_in_path="true" -+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 -+ break 2 -+ fi -+done -+ done -+IFS=$as_save_IFS -+ -+ test -z "$ac_cv_prog_ant_in_path" && ac_cv_prog_ant_in_path="false" -+fi -+fi -+ant_in_path=$ac_cv_prog_ant_in_path -+if test -n "$ant_in_path"; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ant_in_path" >&5 -+$as_echo "$ant_in_path" >&6; } -+else -+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -+$as_echo "no" >&6; } -+fi -+ -+ -+ if test "$ant_in_path" = "true" && "$javac_in_path" = "true"; then -+ EHAVEANT_TRUE= -+ EHAVEANT_FALSE='#' -+else -+ EHAVEANT_TRUE='#' -+ EHAVEANT_FALSE= -+fi -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+ -+#dnl Test if --enable-corba is given -+#AC_ARG_ENABLE(corba, -+# AS_HELP_STRING([--enable-corba], [corba (need glib and orbit)])) -+#if test "${enable_corba}" = "yes" ; then -+#AC_MSG_CHECKING(for ORBit and glib) -+#CPPFLAGS="$CPPFLAGS -I/usr/lib/glib/include -I/usr/local/lib/glib/include" -+# -+#AC_CHECK_HEADERS(glib.h) -+#AC_CHECK_HEADERS(orb/orbit.h) -+#AC_CHECK_LIB(glib, main) -+# -+#AC_CHECK_LIB(ORBitutil, main) -+#AC_CHECK_LIB(IIOP, main) -+#AC_CHECK_LIB(ORBit, main) -+#fi -+ -+@%:@ Check whether --enable-debug was given. -+if test "${enable_debug+set}" = set; then : -+ enableval=$enable_debug; -+fi -+ -+if test "${enable_debug}" = "yes" ; then -+ CFLAGS="$CFLAGS -g" -+fi -+ -+ -+if test "`uname`" = "IRIX" || test "`uname`" = "IRIX64"; then -+CFLAGS="-Wl,-LD_MSG:off=85:off=84:off=16:off=134 $CFLAGS" -+fi -+ -+ -+ -+ -+if test "${enable_large+set}" != set; then -+enable_large=yes -+fi -+ -+ -+@%:@ Check whether --enable-large was given. -+if test "${enable_large+set}" = set; then : -+ enableval=$enable_large; -+fi -+ -+if test "${enable_large}" = "yes" ; then -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for large file support" >&5 -+$as_echo_n "checking for large file support... 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"$delay_single_quote_subst"`' -+hardcode_automatic='`$ECHO "X$hardcode_automatic" | $Xsed -e "$delay_single_quote_subst"`' -+inherit_rpath='`$ECHO "X$inherit_rpath" | $Xsed -e "$delay_single_quote_subst"`' -+link_all_deplibs='`$ECHO "X$link_all_deplibs" | $Xsed -e "$delay_single_quote_subst"`' -+fix_srcfile_path='`$ECHO "X$fix_srcfile_path" | $Xsed -e "$delay_single_quote_subst"`' -+always_export_symbols='`$ECHO "X$always_export_symbols" | $Xsed -e "$delay_single_quote_subst"`' -+export_symbols_cmds='`$ECHO "X$export_symbols_cmds" | $Xsed -e "$delay_single_quote_subst"`' -+exclude_expsyms='`$ECHO "X$exclude_expsyms" | $Xsed -e "$delay_single_quote_subst"`' -+include_expsyms='`$ECHO "X$include_expsyms" | $Xsed -e "$delay_single_quote_subst"`' -+prelink_cmds='`$ECHO "X$prelink_cmds" | $Xsed -e "$delay_single_quote_subst"`' -+file_list_spec='`$ECHO "X$file_list_spec" | $Xsed -e "$delay_single_quote_subst"`' -+variables_saved_for_relink='`$ECHO "X$variables_saved_for_relink" | $Xsed -e "$delay_single_quote_subst"`' -+need_lib_prefix='`$ECHO "X$need_lib_prefix" | $Xsed -e "$delay_single_quote_subst"`' -+need_version='`$ECHO "X$need_version" | $Xsed -e "$delay_single_quote_subst"`' -+version_type='`$ECHO "X$version_type" | $Xsed -e "$delay_single_quote_subst"`' -+runpath_var='`$ECHO "X$runpath_var" | $Xsed -e "$delay_single_quote_subst"`' -+shlibpath_var='`$ECHO "X$shlibpath_var" | $Xsed -e "$delay_single_quote_subst"`' -+shlibpath_overrides_runpath='`$ECHO "X$shlibpath_overrides_runpath" | $Xsed -e "$delay_single_quote_subst"`' -+libname_spec='`$ECHO "X$libname_spec" | $Xsed -e "$delay_single_quote_subst"`' -+library_names_spec='`$ECHO "X$library_names_spec" | $Xsed -e "$delay_single_quote_subst"`' -+soname_spec='`$ECHO "X$soname_spec" | $Xsed -e "$delay_single_quote_subst"`' -+postinstall_cmds='`$ECHO "X$postinstall_cmds" | $Xsed -e "$delay_single_quote_subst"`' -+postuninstall_cmds='`$ECHO "X$postuninstall_cmds" | $Xsed -e "$delay_single_quote_subst"`' -+finish_cmds='`$ECHO "X$finish_cmds" | $Xsed -e "$delay_single_quote_subst"`' -+finish_eval='`$ECHO "X$finish_eval" | $Xsed -e "$delay_single_quote_subst"`' -+hardcode_into_libs='`$ECHO "X$hardcode_into_libs" | $Xsed -e "$delay_single_quote_subst"`' -+sys_lib_search_path_spec='`$ECHO "X$sys_lib_search_path_spec" | $Xsed -e "$delay_single_quote_subst"`' -+sys_lib_dlsearch_path_spec='`$ECHO "X$sys_lib_dlsearch_path_spec" | $Xsed -e "$delay_single_quote_subst"`' -+hardcode_action='`$ECHO "X$hardcode_action" | $Xsed -e "$delay_single_quote_subst"`' -+enable_dlopen='`$ECHO "X$enable_dlopen" | $Xsed -e "$delay_single_quote_subst"`' -+enable_dlopen_self='`$ECHO "X$enable_dlopen_self" | $Xsed -e "$delay_single_quote_subst"`' -+enable_dlopen_self_static='`$ECHO "X$enable_dlopen_self_static" | $Xsed -e "$delay_single_quote_subst"`' -+old_striplib='`$ECHO "X$old_striplib" | $Xsed -e "$delay_single_quote_subst"`' -+striplib='`$ECHO "X$striplib" | $Xsed -e "$delay_single_quote_subst"`' -+ -+LTCC='$LTCC' -+LTCFLAGS='$LTCFLAGS' -+compiler='$compiler_DEFAULT' -+ -+# Quote evaled strings. -+for var in SED \ -+GREP \ -+EGREP \ -+FGREP \ -+LD \ -+NM \ -+LN_S \ -+lt_SP2NL \ -+lt_NL2SP \ -+reload_flag \ -+OBJDUMP \ -+deplibs_check_method \ -+file_magic_cmd \ -+AR \ -+AR_FLAGS \ -+STRIP \ -+RANLIB \ -+CC \ -+CFLAGS \ -+compiler \ -+lt_cv_sys_global_symbol_pipe \ -+lt_cv_sys_global_symbol_to_cdecl \ -+lt_cv_sys_global_symbol_to_c_name_address \ -+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix \ -+SHELL \ -+ECHO \ -+lt_prog_compiler_no_builtin_flag \ -+lt_prog_compiler_wl \ -+lt_prog_compiler_pic \ -+lt_prog_compiler_static \ -+lt_cv_prog_compiler_c_o \ -+need_locks \ -+DSYMUTIL \ -+NMEDIT \ -+LIPO \ -+OTOOL \ -+OTOOL64 \ -+shrext_cmds \ -+export_dynamic_flag_spec \ -+whole_archive_flag_spec \ -+compiler_needs_object \ -+with_gnu_ld \ -+allow_undefined_flag \ -+no_undefined_flag \ -+hardcode_libdir_flag_spec \ -+hardcode_libdir_flag_spec_ld \ -+hardcode_libdir_separator \ -+fix_srcfile_path \ -+exclude_expsyms \ -+include_expsyms \ -+file_list_spec \ -+variables_saved_for_relink \ -+libname_spec \ -+library_names_spec \ -+soname_spec \ -+finish_eval \ -+old_striplib \ -+striplib; do -+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in -+ *[\\\\\\\`\\"\\\$]*) -+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$sed_quote_subst\\"\\\`\\\\\\"" -+ ;; -+ *) -+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\"" -+ ;; -+ esac -+done -+ -+# Double-quote double-evaled strings. -+for var in reload_cmds \ -+old_postinstall_cmds \ -+old_postuninstall_cmds \ -+old_archive_cmds \ -+extract_expsyms_cmds \ -+old_archive_from_new_cmds \ -+old_archive_from_expsyms_cmds \ -+archive_cmds \ -+archive_expsym_cmds \ -+module_cmds \ -+module_expsym_cmds \ -+export_symbols_cmds \ -+prelink_cmds \ -+postinstall_cmds \ -+postuninstall_cmds \ -+finish_cmds \ -+sys_lib_search_path_spec \ -+sys_lib_dlsearch_path_spec; do -+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in -+ *[\\\\\\\`\\"\\\$]*) -+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$double_quote_subst\\" -e \\"\\\$sed_quote_subst\\" -e \\"\\\$delay_variable_subst\\"\\\`\\\\\\"" -+ ;; -+ *) -+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\"" -+ ;; -+ esac -+done -+ -+# Fix-up fallback echo if it was mangled by the above quoting rules. -+case \$lt_ECHO in -+*'\\\$0 --fallback-echo"') lt_ECHO=\`\$ECHO "X\$lt_ECHO" | \$Xsed -e 's/\\\\\\\\\\\\\\\$0 --fallback-echo"\$/\$0 --fallback-echo"/'\` -+ ;; -+esac -+ -+ac_aux_dir='$ac_aux_dir' -+xsi_shell='$xsi_shell' -+lt_shell_append='$lt_shell_append' -+ -+# See if we are running on zsh, and set the options which allow our -+# commands through without removal of \ escapes INIT. -+if test -n "\${ZSH_VERSION+set}" ; then -+ setopt NO_GLOB_SUBST -+fi -+ -+ -+ PACKAGE='$PACKAGE' -+ VERSION='$VERSION' -+ TIMESTAMP='$TIMESTAMP' -+ RM='$RM' -+ ofile='$ofile' -+ -+ -+ -+ -+_ACEOF -+ -+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 -+ -+# Handling of arguments. -+for ac_config_target in $ac_config_targets -+do -+ case $ac_config_target in -+ "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; -+ "libtool") CONFIG_COMMANDS="$CONFIG_COMMANDS libtool" ;; -+ "nucleus/Makefile") CONFIG_FILES="$CONFIG_FILES nucleus/Makefile" ;; -+ "ajax/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/Makefile" ;; -+ "ajax/core/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/core/Makefile" ;; -+ "ajax/graphics/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/graphics/Makefile" ;; -+ "ajax/ensembl/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/ensembl/Makefile" ;; -+ "ajax/ajaxdb/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/ajaxdb/Makefile" ;; -+ "ajax/acd/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/acd/Makefile" ;; -+ "emboss/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/Makefile" ;; -+ "emboss/acd/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/acd/Makefile" ;; -+ "test/Makefile") CONFIG_FILES="$CONFIG_FILES test/Makefile" ;; -+ "test/data/Makefile") CONFIG_FILES="$CONFIG_FILES test/data/Makefile" ;; -+ "test/embl/Makefile") CONFIG_FILES="$CONFIG_FILES test/embl/Makefile" ;; -+ "test/genbank/Makefile") CONFIG_FILES="$CONFIG_FILES test/genbank/Makefile" ;; -+ "test/pir/Makefile") CONFIG_FILES="$CONFIG_FILES test/pir/Makefile" ;; -+ "test/swiss/Makefile") CONFIG_FILES="$CONFIG_FILES test/swiss/Makefile" ;; -+ "test/swnew/Makefile") CONFIG_FILES="$CONFIG_FILES test/swnew/Makefile" ;; -+ "test/testdb/Makefile") CONFIG_FILES="$CONFIG_FILES test/testdb/Makefile" ;; -+ "emboss/data/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/Makefile" ;; -+ "emboss/data/AAINDEX/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/AAINDEX/Makefile" ;; -+ "emboss/data/CODONS/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/CODONS/Makefile" ;; -+ "emboss/data/REBASE/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/REBASE/Makefile" ;; -+ "emboss/data/JASPAR_CORE/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/JASPAR_CORE/Makefile" ;; -+ "emboss/data/JASPAR_FAM/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/JASPAR_FAM/Makefile" ;; -+ "emboss/data/JASPAR_PHYLOFACTS/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/JASPAR_PHYLOFACTS/Makefile" ;; -+ "emboss/data/JASPAR_CNE/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/JASPAR_CNE/Makefile" ;; -+ "emboss/data/JASPAR_POLII/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/JASPAR_POLII/Makefile" ;; -+ "emboss/data/JASPAR_SPLICE/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/JASPAR_SPLICE/Makefile" ;; -+ "emboss/data/JASPAR_PBM/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/JASPAR_PBM/Makefile" ;; -+ "emboss/data/JASPAR_PBM_HLH/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/JASPAR_PBM_HLH/Makefile" ;; -+ "emboss/data/JASPAR_PBM_HOMEO/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/JASPAR_PBM_HOMEO/Makefile" ;; -+ "emboss/data/PRINTS/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/PRINTS/Makefile" ;; -+ "emboss/data/PROSITE/Makefile") CONFIG_FILES="$CONFIG_FILES emboss/data/PROSITE/Makefile" ;; -+ "doc/Makefile") CONFIG_FILES="$CONFIG_FILES doc/Makefile" ;; -+ "doc/manuals/Makefile") CONFIG_FILES="$CONFIG_FILES doc/manuals/Makefile" ;; -+ "doc/tutorials/Makefile") CONFIG_FILES="$CONFIG_FILES doc/tutorials/Makefile" ;; -+ "doc/programs/Makefile") CONFIG_FILES="$CONFIG_FILES doc/programs/Makefile" ;; -+ "doc/programs/html/Makefile") CONFIG_FILES="$CONFIG_FILES doc/programs/html/Makefile" ;; -+ "doc/programs/text/Makefile") CONFIG_FILES="$CONFIG_FILES doc/programs/text/Makefile" ;; -+ "jemboss/Makefile") CONFIG_FILES="$CONFIG_FILES jemboss/Makefile" ;; -+ "jemboss/images/Makefile") CONFIG_FILES="$CONFIG_FILES jemboss/images/Makefile" ;; -+ "jemboss/lib/Makefile") CONFIG_FILES="$CONFIG_FILES jemboss/lib/Makefile" ;; -+ "jemboss/lib/axis/Makefile") CONFIG_FILES="$CONFIG_FILES jemboss/lib/axis/Makefile" ;; -+ "jemboss/resources/Makefile") CONFIG_FILES="$CONFIG_FILES jemboss/resources/Makefile" ;; -+ 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Make it in the build tree -+# simply because there is no reason against having it here, and in addition, -+# creating and moving files from /tmp can sometimes cause problems. -+# Hook for its removal unless debugging. -+# Note that there is a small window in which the directory will not be cleaned: -+# after its creation but before its name has been assigned to `$tmp'. -+$debug || -+{ -+ tmp= -+ trap 'exit_status=$? -+ { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status -+' 0 -+ trap 'as_fn_exit 1' 1 2 13 15 -+} -+# Create a (secure) tmp directory for tmp files. -+ -+{ -+ tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` && -+ test -n "$tmp" && test -d "$tmp" -+} || -+{ -+ tmp=./conf$$-$RANDOM -+ (umask 077 && mkdir "$tmp") -+} || as_fn_error "cannot create a temporary directory in ." 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This must work even if \$libdir does not exist. -+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld -+ -+# Whether we need a single "-rpath" flag with a separated argument. -+hardcode_libdir_separator=$lt_hardcode_libdir_separator -+ -+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes -+# DIR into the resulting binary. -+hardcode_direct=$hardcode_direct -+ -+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes -+# DIR into the resulting binary and the resulting library dependency is -+# "absolute",i.e impossible to change by setting \${shlibpath_var} if the -+# library is relocated. -+hardcode_direct_absolute=$hardcode_direct_absolute -+ -+# Set to "yes" if using the -LDIR flag during linking hardcodes DIR -+# into the resulting binary. -+hardcode_minus_L=$hardcode_minus_L -+ -+# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR -+# into the resulting binary. -+hardcode_shlibpath_var=$hardcode_shlibpath_var -+ -+# Set to "yes" if building a shared library automatically hardcodes DIR -+# into the library and all subsequent libraries and executables linked -+# against it. -+hardcode_automatic=$hardcode_automatic -+ -+# Set to yes if linker adds runtime paths of dependent libraries -+# to runtime path list. -+inherit_rpath=$inherit_rpath -+ -+# Whether libtool must link a program against all its dependency libraries. -+link_all_deplibs=$link_all_deplibs -+ -+# Fix the shell variable \$srcfile for the compiler. -+fix_srcfile_path=$lt_fix_srcfile_path -+ -+# Set to "yes" if exported symbols are required. -+always_export_symbols=$always_export_symbols -+ -+# The commands to list exported symbols. -+export_symbols_cmds=$lt_export_symbols_cmds -+ -+# Symbols that should not be listed in the preloaded symbols. -+exclude_expsyms=$lt_exclude_expsyms -+ -+# Symbols that must always be exported. -+include_expsyms=$lt_include_expsyms -+ -+# Commands necessary for linking programs (against libraries) with templates. -+prelink_cmds=$lt_prelink_cmds -+ -+# Specify filename containing input files. -+file_list_spec=$lt_file_list_spec -+ -+# How to hardcode a shared library path into an executable. -+hardcode_action=$hardcode_action -+ -+# ### END LIBTOOL CONFIG -+ -+_LT_EOF -+ -+ case $host_os in -+ aix3*) -+ cat <<\_LT_EOF >> "$cfgfile" -+# AIX sometimes has problems with the GCC collect2 program. For some -+# reason, if we set the COLLECT_NAMES environment variable, the problems -+# vanish in a puff of smoke. -+if test "X${COLLECT_NAMES+set}" != Xset; then -+ COLLECT_NAMES= -+ export COLLECT_NAMES -+fi -+_LT_EOF -+ ;; -+ esac -+ -+ -+ltmain="$ac_aux_dir/ltmain.sh" -+ -+ -+ # We use sed instead of cat because bash on DJGPP gets confused if -+ # if finds mixed CR/LF and LF-only lines. Since sed operates in -+ # text mode, it properly converts lines to CR/LF. This bash problem -+ # is reportedly fixed, but why not run on old versions too? -+ sed '/^# Generated shell functions inserted here/q' "$ltmain" >> "$cfgfile" \ -+ || (rm -f "$cfgfile"; exit 1) -+ -+ case $xsi_shell in -+ yes) -+ cat << \_LT_EOF >> "$cfgfile" -+ -+# func_dirname file append nondir_replacement -+# Compute the dirname of FILE. If nonempty, add APPEND to the result, -+# otherwise set result to NONDIR_REPLACEMENT. -+func_dirname () -+{ -+ case ${1} in -+ */*) func_dirname_result="${1%/*}${2}" ;; -+ * ) func_dirname_result="${3}" ;; -+ esac -+} -+ -+# func_basename file -+func_basename () -+{ -+ func_basename_result="${1##*/}" -+} -+ -+# func_dirname_and_basename file append nondir_replacement -+# perform func_basename and func_dirname in a single function -+# call: -+# dirname: Compute the dirname of FILE. If nonempty, -+# add APPEND to the result, otherwise set result -+# to NONDIR_REPLACEMENT. -+# value returned in "$func_dirname_result" -+# basename: Compute filename of FILE. -+# value retuned in "$func_basename_result" -+# Implementation must be kept synchronized with func_dirname -+# and func_basename. For efficiency, we do not delegate to -+# those functions but instead duplicate the functionality here. -+func_dirname_and_basename () -+{ -+ case ${1} in -+ */*) func_dirname_result="${1%/*}${2}" ;; -+ * ) func_dirname_result="${3}" ;; -+ esac -+ func_basename_result="${1##*/}" -+} -+ -+# func_stripname prefix suffix name -+# strip PREFIX and SUFFIX off of NAME. -+# PREFIX and SUFFIX must not contain globbing or regex special -+# characters, hashes, percent signs, but SUFFIX may contain a leading -+# dot (in which case that matches only a dot). -+func_stripname () -+{ -+ # pdksh 5.2.14 does not do ${X%$Y} correctly if both X and Y are -+ # positional parameters, so assign one to ordinary parameter first. -+ func_stripname_result=${3} -+ func_stripname_result=${func_stripname_result#"${1}"} -+ func_stripname_result=${func_stripname_result%"${2}"} -+} -+ -+# func_opt_split -+func_opt_split () -+{ -+ func_opt_split_opt=${1%%=*} -+ func_opt_split_arg=${1#*=} -+} -+ -+# func_lo2o object -+func_lo2o () -+{ -+ case ${1} in -+ *.lo) func_lo2o_result=${1%.lo}.${objext} ;; -+ *) func_lo2o_result=${1} ;; -+ esac -+} -+ -+# func_xform libobj-or-source -+func_xform () -+{ -+ func_xform_result=${1%.*}.lo -+} -+ -+# func_arith arithmetic-term... -+func_arith () -+{ -+ func_arith_result=$(( $* )) -+} -+ -+# func_len string -+# STRING may not start with a hyphen. -+func_len () -+{ -+ func_len_result=${#1} -+} -+ -+_LT_EOF -+ ;; -+ *) # Bourne compatible functions. -+ cat << \_LT_EOF >> "$cfgfile" -+ -+# func_dirname file append nondir_replacement -+# Compute the dirname of FILE. If nonempty, add APPEND to the result, -+# otherwise set result to NONDIR_REPLACEMENT. -+func_dirname () -+{ -+ # Extract subdirectory from the argument. -+ func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"` -+ if test "X$func_dirname_result" = "X${1}"; then -+ func_dirname_result="${3}" -+ else -+ func_dirname_result="$func_dirname_result${2}" -+ fi -+} -+ -+# func_basename file -+func_basename () -+{ -+ func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"` -+} -+ -+ -+# func_stripname prefix suffix name -+# strip PREFIX and SUFFIX off of NAME. -+# PREFIX and SUFFIX must not contain globbing or regex special -+# characters, hashes, percent signs, but SUFFIX may contain a leading -+# dot (in which case that matches only a dot). -+# func_strip_suffix prefix name -+func_stripname () -+{ -+ case ${2} in -+ .*) func_stripname_result=`$ECHO "X${3}" \ -+ | $Xsed -e "s%^${1}%%" -e "s%\\\\${2}\$%%"`;; -+ *) func_stripname_result=`$ECHO "X${3}" \ -+ | $Xsed -e "s%^${1}%%" -e "s%${2}\$%%"`;; -+ esac -+} -+ -+# sed scripts: -+my_sed_long_opt='1s/^\(-[^=]*\)=.*/\1/;q' -+my_sed_long_arg='1s/^-[^=]*=//' -+ -+# func_opt_split -+func_opt_split () -+{ -+ func_opt_split_opt=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_opt"` -+ func_opt_split_arg=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_arg"` -+} -+ -+# func_lo2o object -+func_lo2o () -+{ -+ func_lo2o_result=`$ECHO "X${1}" | $Xsed -e "$lo2o"` -+} -+ -+# func_xform libobj-or-source -+func_xform () -+{ -+ func_xform_result=`$ECHO "X${1}" | $Xsed -e 's/\.[^.]*$/.lo/'` -+} -+ -+# func_arith arithmetic-term... -+func_arith () -+{ -+ func_arith_result=`expr "$@"` -+} -+ -+# func_len string -+# STRING may not start with a hyphen. -+func_len () -+{ -+ func_len_result=`expr "$1" : ".*" 2>/dev/null || echo $max_cmd_len` -+} -+ -+_LT_EOF -+esac -+ -+case $lt_shell_append in -+ yes) -+ cat << \_LT_EOF >> "$cfgfile" -+ -+# func_append var value -+# Append VALUE to the end of shell variable VAR. -+func_append () -+{ -+ eval "$1+=\$2" -+} -+_LT_EOF -+ ;; -+ *) -+ cat << \_LT_EOF >> "$cfgfile" -+ -+# func_append var value -+# Append VALUE to the end of shell variable VAR. -+func_append () -+{ -+ eval "$1=\$$1\$2" -+} -+ -+_LT_EOF -+ ;; -+ esac -+ -+ -+ sed -n '/^# Generated shell functions inserted here/,$p' "$ltmain" >> "$cfgfile" \ -+ || (rm -f "$cfgfile"; exit 1) -+ -+ mv -f "$cfgfile" "$ofile" || -+ (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile") -+ chmod +x "$ofile" -+ -+ ;; -+ -+ esac -+done # for ac_tag -+ -+ -+as_fn_exit 0 -+_ACEOF -+ac_clean_files=$ac_clean_files_save -+ -+test $ac_write_fail = 0 || -+ as_fn_error "write failure creating $CONFIG_STATUS" "$LINENO" 5 -+ -+ -+# configure is writing to config.log, and then calls config.status. -+# config.status does its own redirection, appending to config.log. -+# Unfortunately, on DOS this fails, as config.log is still kept open -+# by configure, so config.status won't be able to write to it; its -+# output is simply discarded. So we exec the FD to /dev/null, -+# effectively closing config.log, so it can be properly (re)opened and -+# appended to by config.status. When coming back to configure, we -+# need to make the FD available again. -+if test "$no_create" != yes; then -+ ac_cs_success=: -+ ac_config_status_args= -+ test "$silent" = yes && -+ ac_config_status_args="$ac_config_status_args --quiet" -+ exec 5>/dev/null -+ $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false -+ exec 5>>config.log -+ # Use ||, not &&, to avoid exiting from the if with $? = 1, which -+ # would make configure fail if this is the last instruction. -+ $ac_cs_success || as_fn_exit $? -+fi -+if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then -+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 -+$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} -+fi -+ -diff -urP EMBOSS-6.3.1.orig/autom4te.cache/requests EMBOSS-6.3.1/autom4te.cache/requests ---- EMBOSS-6.3.1.orig/autom4te.cache/requests 1969-12-31 19:00:00.000000000 -0500 -+++ EMBOSS-6.3.1/autom4te.cache/requests 2010-08-02 17:23:22.949268306 -0400 -@@ -0,0 +1,68 @@ -+# This file was generated. -+# It contains the lists of macros which have been traced. -+# It can be safely removed. -+ -+@request = ( -+ bless( [ -+ '0', -+ 1, -+ [ -+ '/usr/share/autoconf' -+ ], -+ [ -+ '/usr/share/autoconf/autoconf/autoconf.m4f', -+ 'aclocal.m4', -+ 'configure.in' -+ ], -+ { -+ 'AM_PROG_F77_C_O' => 1, -+ '_LT_AC_TAGCONFIG' => 1, -+ 'm4_pattern_forbid' => 1, -+ 'AC_INIT' => 1, -+ '_AM_COND_IF' => 1, -+ 'AC_CANONICAL_TARGET' => 1, -+ 'AC_SUBST' => 1, -+ 'AC_CONFIG_LIBOBJ_DIR' => 1, -+ 'AC_FC_SRCEXT' => 1, -+ 'AC_CANONICAL_HOST' => 1, -+ 'AC_PROG_LIBTOOL' => 1, -+ 'AM_INIT_AUTOMAKE' => 1, -+ 'AC_CONFIG_SUBDIRS' => 1, -+ 'AM_AUTOMAKE_VERSION' => 1, -+ 'LT_CONFIG_LTDL_DIR' => 1, -+ 'AC_REQUIRE_AUX_FILE' => 1, -+ 'AC_CONFIG_LINKS' => 1, -+ 'LT_SUPPORTED_TAG' => 1, -+ 'm4_sinclude' => 1, -+ 'AM_MAINTAINER_MODE' => 1, -+ 'AM_GNU_GETTEXT_INTL_SUBDIR' => 1, -+ '_m4_warn' => 1, -+ 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_AM_SUBST_NOTMAKE([am__EXEEXT_FALSE]) -+m4trace:configure.in:664: -1- _m4_warn([obsolete], [AC_C_BIGENDIAN should be used with AC_CONFIG_HEADERS], []) -+m4trace:configure.in:664: -1- AC_SUBST_TRACE([top_builddir]) -+m4trace:configure.in:664: -1- AC_SUBST_TRACE([top_build_prefix]) -+m4trace:configure.in:664: -1- AC_SUBST_TRACE([srcdir]) -+m4trace:configure.in:664: -1- AC_SUBST_TRACE([abs_srcdir]) -+m4trace:configure.in:664: -1- AC_SUBST_TRACE([top_srcdir]) -+m4trace:configure.in:664: -1- AC_SUBST_TRACE([abs_top_srcdir]) -+m4trace:configure.in:664: -1- AC_SUBST_TRACE([builddir]) -+m4trace:configure.in:664: -1- AC_SUBST_TRACE([abs_builddir]) -+m4trace:configure.in:664: -1- AC_SUBST_TRACE([abs_top_builddir]) -+m4trace:configure.in:664: -1- AC_SUBST_TRACE([INSTALL]) -+m4trace:configure.in:664: -1- AC_SUBST_TRACE([MKDIR_P]) -+m4trace:configure.in:664: -1- AC_REQUIRE_AUX_FILE([ltmain.sh]) -diff -urP EMBOSS-6.3.1.orig/doc/Makefile.in EMBOSS-6.3.1/doc/Makefile.in ---- EMBOSS-6.3.1.orig/doc/Makefile.in 2010-07-19 07:55:40.000000000 -0400 -+++ EMBOSS-6.3.1/doc/Makefile.in 2010-08-02 17:23:23.593142800 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -167,6 +167,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -253,9 +255,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits doc/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu doc/Makefile -+ $(AUTOMAKE) --gnits doc/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/doc/manuals/Makefile.in EMBOSS-6.3.1/doc/manuals/Makefile.in ---- EMBOSS-6.3.1.orig/doc/manuals/Makefile.in 2010-07-19 07:55:40.000000000 -0400 -+++ EMBOSS-6.3.1/doc/manuals/Makefile.in 2010-08-02 17:23:23.661142730 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -241,9 +243,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/manuals/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits doc/manuals/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu doc/manuals/Makefile -+ $(AUTOMAKE) --gnits doc/manuals/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/doc/programs/html/Makefile.in EMBOSS-6.3.1/doc/programs/html/Makefile.in ---- EMBOSS-6.3.1.orig/doc/programs/html/Makefile.in 2010-07-19 07:55:40.000000000 -0400 -+++ EMBOSS-6.3.1/doc/programs/html/Makefile.in 2010-08-02 17:23:23.811143149 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -352,9 +354,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/programs/html/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits doc/programs/html/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu doc/programs/html/Makefile -+ $(AUTOMAKE) --gnits doc/programs/html/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/doc/programs/Makefile.in EMBOSS-6.3.1/doc/programs/Makefile.in ---- EMBOSS-6.3.1.orig/doc/programs/Makefile.in 2010-07-19 07:55:40.000000000 -0400 -+++ EMBOSS-6.3.1/doc/programs/Makefile.in 2010-08-02 17:23:23.730143289 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -167,6 +167,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -253,9 +255,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/programs/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits doc/programs/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu doc/programs/Makefile -+ $(AUTOMAKE) --gnits doc/programs/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/doc/programs/text/Makefile.in EMBOSS-6.3.1/doc/programs/text/Makefile.in ---- EMBOSS-6.3.1.orig/doc/programs/text/Makefile.in 2010-07-19 07:55:40.000000000 -0400 -+++ EMBOSS-6.3.1/doc/programs/text/Makefile.in 2010-08-02 17:23:23.888142800 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -298,9 +300,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/programs/text/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits doc/programs/text/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu doc/programs/text/Makefile -+ $(AUTOMAKE) --gnits doc/programs/text/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/doc/tutorials/Makefile.in EMBOSS-6.3.1/doc/tutorials/Makefile.in ---- EMBOSS-6.3.1.orig/doc/tutorials/Makefile.in 2010-07-19 07:55:40.000000000 -0400 -+++ EMBOSS-6.3.1/doc/tutorials/Makefile.in 2010-08-02 17:23:23.956143149 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -239,9 +241,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/tutorials/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits doc/tutorials/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu doc/tutorials/Makefile -+ $(AUTOMAKE) --gnits doc/tutorials/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/acd/Makefile.in EMBOSS-6.3.1/emboss/acd/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/acd/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/acd/Makefile.in 2010-08-02 17:23:24.995143010 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -152,6 +152,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -308,9 +310,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/acd/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/acd/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/acd/Makefile -+ $(AUTOMAKE) --gnits emboss/acd/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/AAINDEX/Makefile.in EMBOSS-6.3.1/emboss/data/AAINDEX/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/AAINDEX/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/AAINDEX/Makefile.in 2010-08-02 17:23:25.066142730 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -237,9 +239,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/AAINDEX/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/AAINDEX/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/AAINDEX/Makefile -+ $(AUTOMAKE) --gnits emboss/data/AAINDEX/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/CODONS/Makefile.in EMBOSS-6.3.1/emboss/data/CODONS/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/CODONS/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/CODONS/Makefile.in 2010-08-02 17:23:25.144143079 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -296,9 +298,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/CODONS/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/CODONS/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/CODONS/Makefile -+ $(AUTOMAKE) --gnits emboss/data/CODONS/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/JASPAR_CNE/Makefile.in EMBOSS-6.3.1/emboss/data/JASPAR_CNE/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/JASPAR_CNE/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/JASPAR_CNE/Makefile.in 2010-08-02 17:23:25.214143219 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -237,9 +239,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/JASPAR_CNE/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/JASPAR_CNE/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/JASPAR_CNE/Makefile -+ $(AUTOMAKE) --gnits emboss/data/JASPAR_CNE/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/JASPAR_CORE/Makefile.in EMBOSS-6.3.1/emboss/data/JASPAR_CORE/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/JASPAR_CORE/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/JASPAR_CORE/Makefile.in 2010-08-02 17:23:25.283143010 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -237,9 +239,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/JASPAR_CORE/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/JASPAR_CORE/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/JASPAR_CORE/Makefile -+ $(AUTOMAKE) --gnits emboss/data/JASPAR_CORE/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/JASPAR_FAM/Makefile.in EMBOSS-6.3.1/emboss/data/JASPAR_FAM/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/JASPAR_FAM/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/JASPAR_FAM/Makefile.in 2010-08-02 17:23:25.353143778 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -237,9 +239,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/JASPAR_FAM/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/JASPAR_FAM/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/JASPAR_FAM/Makefile -+ $(AUTOMAKE) --gnits emboss/data/JASPAR_FAM/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/JASPAR_PBM/Makefile.in EMBOSS-6.3.1/emboss/data/JASPAR_PBM/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/JASPAR_PBM/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/JASPAR_PBM/Makefile.in 2010-08-02 17:23:25.422143149 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -237,9 +239,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/JASPAR_PBM/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/JASPAR_PBM/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/JASPAR_PBM/Makefile -+ $(AUTOMAKE) --gnits emboss/data/JASPAR_PBM/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/JASPAR_PBM_HLH/Makefile.in EMBOSS-6.3.1/emboss/data/JASPAR_PBM_HLH/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/JASPAR_PBM_HLH/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/JASPAR_PBM_HLH/Makefile.in 2010-08-02 17:23:25.492142870 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -237,9 +239,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/JASPAR_PBM_HLH/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/JASPAR_PBM_HLH/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/JASPAR_PBM_HLH/Makefile -+ $(AUTOMAKE) --gnits emboss/data/JASPAR_PBM_HLH/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/JASPAR_PBM_HOMEO/Makefile.in EMBOSS-6.3.1/emboss/data/JASPAR_PBM_HOMEO/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/JASPAR_PBM_HOMEO/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/JASPAR_PBM_HOMEO/Makefile.in 2010-08-02 17:23:25.561143149 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -237,9 +239,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/JASPAR_PBM_HOMEO/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/JASPAR_PBM_HOMEO/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/JASPAR_PBM_HOMEO/Makefile -+ $(AUTOMAKE) --gnits emboss/data/JASPAR_PBM_HOMEO/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/JASPAR_PHYLOFACTS/Makefile.in EMBOSS-6.3.1/emboss/data/JASPAR_PHYLOFACTS/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/JASPAR_PHYLOFACTS/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/JASPAR_PHYLOFACTS/Makefile.in 2010-08-02 17:23:25.630143079 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -237,9 +239,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/JASPAR_PHYLOFACTS/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/JASPAR_PHYLOFACTS/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/JASPAR_PHYLOFACTS/Makefile -+ $(AUTOMAKE) --gnits emboss/data/JASPAR_PHYLOFACTS/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/JASPAR_POLII/Makefile.in EMBOSS-6.3.1/emboss/data/JASPAR_POLII/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/JASPAR_POLII/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/JASPAR_POLII/Makefile.in 2010-08-02 17:23:25.704143778 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -237,9 +239,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/JASPAR_POLII/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/JASPAR_POLII/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/JASPAR_POLII/Makefile -+ $(AUTOMAKE) --gnits emboss/data/JASPAR_POLII/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/JASPAR_SPLICE/Makefile.in EMBOSS-6.3.1/emboss/data/JASPAR_SPLICE/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/JASPAR_SPLICE/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/JASPAR_SPLICE/Makefile.in 2010-08-02 17:23:25.777143568 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -237,9 +239,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/JASPAR_SPLICE/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/JASPAR_SPLICE/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/JASPAR_SPLICE/Makefile -+ $(AUTOMAKE) --gnits emboss/data/JASPAR_SPLICE/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/Makefile.in EMBOSS-6.3.1/emboss/data/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/Makefile.in 2010-08-02 17:23:25.863143219 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -191,6 +191,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -318,9 +320,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/Makefile -+ $(AUTOMAKE) --gnits emboss/data/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/PRINTS/Makefile.in EMBOSS-6.3.1/emboss/data/PRINTS/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/PRINTS/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/PRINTS/Makefile.in 2010-08-02 17:23:25.935143359 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -237,9 +239,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/PRINTS/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/PRINTS/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/PRINTS/Makefile -+ $(AUTOMAKE) --gnits emboss/data/PRINTS/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/PROSITE/Makefile.in EMBOSS-6.3.1/emboss/data/PROSITE/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/PROSITE/Makefile.in 2010-07-19 07:55:41.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/PROSITE/Makefile.in 2010-08-02 17:23:26.007143918 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -237,9 +239,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/PROSITE/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/PROSITE/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/PROSITE/Makefile -+ $(AUTOMAKE) --gnits emboss/data/PROSITE/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/data/REBASE/Makefile.in EMBOSS-6.3.1/emboss/data/REBASE/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/data/REBASE/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/emboss/data/REBASE/Makefile.in 2010-08-02 17:23:26.080143359 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -237,9 +239,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu emboss/data/REBASE/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits emboss/data/REBASE/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu emboss/data/REBASE/Makefile -+ $(AUTOMAKE) --gnits emboss/data/REBASE/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/emboss/Makefile.in EMBOSS-6.3.1/emboss/Makefile.in ---- EMBOSS-6.3.1.orig/emboss/Makefile.in 2010-08-02 17:23:03.949267957 -0400 -+++ EMBOSS-6.3.1/emboss/Makefile.in 2010-08-02 17:23:24.902143429 -0400 -@@ -120,9 +120,8 @@ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ - $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -- $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -137,7 +136,7 @@ - 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/core/libajax.la $(EXTRA_LDS) $(am__DEPENDENCIES_1) \ - $(am__DEPENDENCIES_1) - am_abiview_OBJECTS = abiview.$(OBJEXT) - abiview_OBJECTS = $(am_abiview_OBJECTS) -@@ -145,23 +144,21 @@ - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_acdc_OBJECTS = acdc.$(OBJEXT) - acdc_OBJECTS = $(am_acdc_OBJECTS) - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_acdgalaxy_OBJECTS = acdgalaxy.$(OBJEXT) - acdgalaxy_OBJECTS = $(am_acdgalaxy_OBJECTS) - 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/core/libajax.la $(EXTRA_LDS) $(am__DEPENDENCIES_1) \ - $(am__DEPENDENCIES_1) - am_acdlog_OBJECTS = acdlog.$(OBJEXT) - acdlog_OBJECTS = $(am_acdlog_OBJECTS) -@@ -169,15 +166,14 @@ - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_acdpretty_OBJECTS = acdpretty.$(OBJEXT) - acdpretty_OBJECTS = $(am_acdpretty_OBJECTS) - 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/core/libajax.la $(EXTRA_LDS) $(am__DEPENDENCIES_1) \ - $(am__DEPENDENCIES_1) - am_acdrelations_OBJECTS = acdrelations.$(OBJEXT) - acdrelations_OBJECTS = $(am_acdrelations_OBJECTS) -@@ -185,7 +181,7 @@ - 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/core/libajax.la $(EXTRA_LDS) $(am__DEPENDENCIES_1) \ - $(am__DEPENDENCIES_1) - am_acdtable_OBJECTS = acdtable.$(OBJEXT) - acdtable_OBJECTS = $(am_acdtable_OBJECTS) -@@ -193,47 +189,42 @@ - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_acdtrace_OBJECTS = acdtrace.$(OBJEXT) - acdtrace_OBJECTS = $(am_acdtrace_OBJECTS) - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_acdvalid_OBJECTS = acdvalid.$(OBJEXT) - acdvalid_OBJECTS = $(am_acdvalid_OBJECTS) - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_acdxsd_OBJECTS = acdxsd.$(OBJEXT) - acdxsd_OBJECTS = $(am_acdxsd_OBJECTS) - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_ajtest_OBJECTS = ajtest.$(OBJEXT) - ajtest_OBJECTS = $(am_ajtest_OBJECTS) - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_aligncopy_OBJECTS = aligncopy.$(OBJEXT) - aligncopy_OBJECTS = $(am_aligncopy_OBJECTS) - 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/core/libajax.la $(EXTRA_LDS) $(am__DEPENDENCIES_1) \ - $(am__DEPENDENCIES_1) - am_aligncopypair_OBJECTS = aligncopypair.$(OBJEXT) - aligncopypair_OBJECTS = $(am_aligncopypair_OBJECTS) -@@ -241,7 +232,7 @@ - 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/core/libajax.la $(EXTRA_LDS) $(am__DEPENDENCIES_1) \ - $(am__DEPENDENCIES_1) - am_antigenic_OBJECTS = antigenic.$(OBJEXT) - antigenic_OBJECTS = $(am_antigenic_OBJECTS) -@@ -249,7 +240,7 @@ - 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/core/libajax.la $(EXTRA_LDS) $(am__DEPENDENCIES_1) \ - $(am__DEPENDENCIES_1) - am_backtranambig_OBJECTS = backtranambig.$(OBJEXT) - backtranambig_OBJECTS = $(am_backtranambig_OBJECTS) -@@ -257,7 +248,7 @@ - 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/core/libajax.la $(EXTRA_LDS) $(am__DEPENDENCIES_1) \ - $(am__DEPENDENCIES_1) - am_backtranseq_OBJECTS = backtranseq.$(OBJEXT) - backtranseq_OBJECTS = $(am_backtranseq_OBJECTS) -@@ -265,7 +256,7 @@ - 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) \ -+ 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../ajax/core/libajax.la \ -- $(EXTRA_LDS) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_trimspace_OBJECTS = trimspace.$(OBJEXT) - trimspace_OBJECTS = $(am_trimspace_OBJECTS) - 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/core/libajax.la $(EXTRA_LDS) $(am__DEPENDENCIES_1) \ - $(am__DEPENDENCIES_1) - am_twofeat_OBJECTS = twofeat.$(OBJEXT) - twofeat_OBJECTS = $(am_twofeat_OBJECTS) -@@ -1921,23 +1781,21 @@ - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_union_OBJECTS = union.$(OBJEXT) - union_OBJECTS = $(am_union_OBJECTS) - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_vectorstrip_OBJECTS = vectorstrip.$(OBJEXT) - vectorstrip_OBJECTS = $(am_vectorstrip_OBJECTS) - 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/core/libajax.la $(EXTRA_LDS) $(am__DEPENDENCIES_1) \ - $(am__DEPENDENCIES_1) - am_water_OBJECTS = water.$(OBJEXT) - water_OBJECTS = $(am_water_OBJECTS) -@@ -1945,31 +1803,28 @@ - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_whichdb_OBJECTS = whichdb.$(OBJEXT) - whichdb_OBJECTS = $(am_whichdb_OBJECTS) - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_wobble_OBJECTS = wobble.$(OBJEXT) - wobble_OBJECTS = $(am_wobble_OBJECTS) - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_wordcount_OBJECTS = wordcount.$(OBJEXT) - wordcount_OBJECTS = $(am_wordcount_OBJECTS) - 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/core/libajax.la $(EXTRA_LDS) $(am__DEPENDENCIES_1) \ - $(am__DEPENDENCIES_1) - am_wordfinder_OBJECTS = wordfinder.$(OBJEXT) - wordfinder_OBJECTS = $(am_wordfinder_OBJECTS) -@@ -1977,7 +1832,7 @@ - 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/core/libajax.la $(EXTRA_LDS) $(am__DEPENDENCIES_1) \ - $(am__DEPENDENCIES_1) - am_wordmatch_OBJECTS = wordmatch.$(OBJEXT) - wordmatch_OBJECTS = $(am_wordmatch_OBJECTS) -@@ -1985,7 +1840,7 @@ - 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/core/libajax.la $(EXTRA_LDS) $(am__DEPENDENCIES_1) \ - $(am__DEPENDENCIES_1) - am_wossname_OBJECTS = wossname.$(OBJEXT) - wossname_OBJECTS = $(am_wossname_OBJECTS) -@@ -1993,16 +1848,14 @@ - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - am_yank_OBJECTS = yank.$(OBJEXT) - yank_OBJECTS = $(am_yank_OBJECTS) - 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) \ -- $(am__DEPENDENCIES_1) -+ $(EXTRA_LDS) $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) - DEFAULT_INCLUDES = -I.@am__isrc@ - depcomp = $(SHELL) $(top_srcdir)/depcomp - am__depfiles_maybe = depfiles -@@ -2285,6 +2138,8 @@ - EXEEXT = @EXEEXT@ - FGREP = @FGREP@ - GREP = @GREP@ -+HAVE_MEMMOVE = @HAVE_MEMMOVE@ -+HAVE_STRERROR = @HAVE_STRERROR@ - INSTALL = @INSTALL@ - INSTALL_DATA = @INSTALL_DATA@ - INSTALL_PROGRAM = @INSTALL_PROGRAM@ -diff -urP EMBOSS-6.3.1.orig/jemboss/images/Makefile.in EMBOSS-6.3.1/jemboss/images/Makefile.in ---- EMBOSS-6.3.1.orig/jemboss/images/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/jemboss/images/Makefile.in 2010-08-02 17:23:26.349152370 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -241,9 +243,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu jemboss/images/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits jemboss/images/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu jemboss/images/Makefile -+ $(AUTOMAKE) --gnits jemboss/images/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/jemboss/lib/axis/Makefile.in EMBOSS-6.3.1/jemboss/lib/axis/Makefile.in ---- EMBOSS-6.3.1.orig/jemboss/lib/axis/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/jemboss/lib/axis/Makefile.in 2010-08-02 17:23:26.561143289 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -240,9 +242,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu jemboss/lib/axis/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits jemboss/lib/axis/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu jemboss/lib/axis/Makefile -+ $(AUTOMAKE) --gnits jemboss/lib/axis/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/jemboss/lib/Makefile.in EMBOSS-6.3.1/jemboss/lib/Makefile.in ---- EMBOSS-6.3.1.orig/jemboss/lib/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/jemboss/lib/Makefile.in 2010-08-02 17:23:26.489268446 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -191,6 +191,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -280,9 +282,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu jemboss/lib/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits jemboss/lib/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu jemboss/lib/Makefile -+ $(AUTOMAKE) --gnits jemboss/lib/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/jemboss/Makefile.in EMBOSS-6.3.1/jemboss/Makefile.in ---- EMBOSS-6.3.1.orig/jemboss/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/jemboss/Makefile.in 2010-08-02 17:23:26.161144127 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -191,6 +191,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -diff -urP EMBOSS-6.3.1.orig/jemboss/resources/Makefile.in EMBOSS-6.3.1/jemboss/resources/Makefile.in ---- EMBOSS-6.3.1.orig/jemboss/resources/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/jemboss/resources/Makefile.in 2010-08-02 17:23:26.634144057 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -244,9 +246,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu jemboss/resources/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits jemboss/resources/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu jemboss/resources/Makefile -+ $(AUTOMAKE) --gnits jemboss/resources/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/jemboss/utils/Makefile.in EMBOSS-6.3.1/jemboss/utils/Makefile.in ---- EMBOSS-6.3.1.orig/jemboss/utils/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/jemboss/utils/Makefile.in 2010-08-02 17:23:26.712212083 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -239,9 +241,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu jemboss/utils/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits jemboss/utils/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu jemboss/utils/Makefile -+ $(AUTOMAKE) --gnits jemboss/utils/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/Makefile.in EMBOSS-6.3.1/Makefile.in ---- EMBOSS-6.3.1.orig/Makefile.in 2010-08-02 17:23:03.950268376 -0400 -+++ EMBOSS-6.3.1/Makefile.in 2010-08-02 17:23:27.458268375 -0400 -@@ -43,9 +43,8 @@ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ - $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -- $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \ -diff -urP EMBOSS-6.3.1.orig/nucleus/Makefile.in EMBOSS-6.3.1/nucleus/Makefile.in ---- EMBOSS-6.3.1.orig/nucleus/Makefile.in 2010-08-02 17:23:03.951268237 -0400 -+++ EMBOSS-6.3.1/nucleus/Makefile.in 2010-08-02 17:23:26.813142660 -0400 -@@ -43,9 +43,8 @@ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ - $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -- $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -135,6 +134,8 @@ - EXEEXT = @EXEEXT@ - FGREP = @FGREP@ - GREP = @GREP@ -+HAVE_MEMMOVE = @HAVE_MEMMOVE@ -+HAVE_STRERROR = @HAVE_STRERROR@ - INSTALL = @INSTALL@ - INSTALL_DATA = @INSTALL_DATA@ - INSTALL_PROGRAM = @INSTALL_PROGRAM@ -diff -urP EMBOSS-6.3.1.orig/test/data/Makefile.in EMBOSS-6.3.1/test/data/Makefile.in ---- EMBOSS-6.3.1.orig/test/data/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/test/data/Makefile.in 2010-08-02 17:23:26.956142939 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -255,9 +257,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/data/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits test/data/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu test/data/Makefile -+ $(AUTOMAKE) --gnits test/data/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/test/embl/Makefile.in EMBOSS-6.3.1/test/embl/Makefile.in ---- EMBOSS-6.3.1.orig/test/embl/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/test/embl/Makefile.in 2010-08-02 17:23:27.028142869 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -242,9 +244,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/embl/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits test/embl/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu test/embl/Makefile -+ $(AUTOMAKE) --gnits test/embl/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/test/genbank/Makefile.in EMBOSS-6.3.1/test/genbank/Makefile.in ---- EMBOSS-6.3.1.orig/test/genbank/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/test/genbank/Makefile.in 2010-08-02 17:23:27.101268096 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -242,9 +244,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/genbank/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits test/genbank/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu test/genbank/Makefile -+ $(AUTOMAKE) --gnits test/genbank/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/test/Makefile.in EMBOSS-6.3.1/test/Makefile.in ---- EMBOSS-6.3.1.orig/test/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/test/Makefile.in 2010-08-02 17:23:26.884143009 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -167,6 +167,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -253,9 +255,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits test/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu test/Makefile -+ $(AUTOMAKE) --gnits test/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/test/pir/Makefile.in EMBOSS-6.3.1/test/pir/Makefile.in ---- EMBOSS-6.3.1.orig/test/pir/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/test/pir/Makefile.in 2010-08-02 17:23:27.172268026 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -245,9 +247,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/pir/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits test/pir/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu test/pir/Makefile -+ $(AUTOMAKE) --gnits test/pir/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/test/swiss/Makefile.in EMBOSS-6.3.1/test/swiss/Makefile.in ---- EMBOSS-6.3.1.orig/test/swiss/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/test/swiss/Makefile.in 2010-08-02 17:23:27.241267677 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -240,9 +242,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/swiss/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits test/swiss/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu test/swiss/Makefile -+ $(AUTOMAKE) --gnits test/swiss/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/test/swnew/Makefile.in EMBOSS-6.3.1/test/swnew/Makefile.in ---- EMBOSS-6.3.1.orig/test/swnew/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/test/swnew/Makefile.in 2010-08-02 17:23:27.311267887 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -241,9 +243,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/swnew/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits test/swnew/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu test/swnew/Makefile -+ $(AUTOMAKE) --gnits test/swnew/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ -diff -urP EMBOSS-6.3.1.orig/test/testdb/Makefile.in EMBOSS-6.3.1/test/testdb/Makefile.in ---- EMBOSS-6.3.1.orig/test/testdb/Makefile.in 2010-07-19 07:55:42.000000000 -0400 -+++ EMBOSS-6.3.1/test/testdb/Makefile.in 2010-08-02 17:23:27.381267677 -0400 -@@ -39,9 +39,9 @@ - am__aclocal_m4_deps = $(top_srcdir)/m4/amd64.m4 \ - $(top_srcdir)/m4/general.m4 $(top_srcdir)/m4/hpdf.m4 \ - $(top_srcdir)/m4/java.m4 $(top_srcdir)/m4/lf_x11.m4 \ -- $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/pngdriver.m4 \ -- $(top_srcdir)/m4/postgresql.m4 $(top_srcdir)/m4/sgi.m4 \ -- $(top_srcdir)/configure.in -+ $(top_srcdir)/m4/mysql.m4 $(top_srcdir)/m4/plplot.m4 \ -+ $(top_srcdir)/m4/pngdriver.m4 $(top_srcdir)/m4/postgresql.m4 \ -+ $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in - am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ - $(ACLOCAL_M4) - mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs -@@ -151,6 +151,8 @@ - PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ - PCRE_VERSION = @PCRE_VERSION@ - PG_CONFIG = @PG_CONFIG@ -+PLPLOT_CFLAGS = @PLPLOT_CFLAGS@ -+PLPLOT_LIBS = @PLPLOT_LIBS@ - POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - POSTGRESQL_CFLAGS = @POSTGRESQL_CFLAGS@ - POSTGRESQL_LDFLAGS = @POSTGRESQL_LDFLAGS@ -@@ -239,9 +241,9 @@ - exit 1;; \ - esac; \ - done; \ -- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/testdb/Makefile'; \ -+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnits test/testdb/Makefile'; \ - $(am__cd) $(top_srcdir) && \ -- $(AUTOMAKE) --gnu test/testdb/Makefile -+ $(AUTOMAKE) --gnits test/testdb/Makefile - .PRECIOUS: Makefile - Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status - @case '$?' in \ diff --git a/EMBOSS-6.3.1-system-expat.patch b/EMBOSS-6.3.1-system-expat.patch deleted file mode 100644 index 78fbf58..0000000 --- a/EMBOSS-6.3.1-system-expat.patch +++ /dev/null @@ -1,92 +0,0 @@ -diff -up EMBOSS-6.3.1/configure.in.system-expat EMBOSS-6.3.1/configure.in ---- EMBOSS-6.3.1/configure.in.system-expat 2010-11-09 15:05:50.600682002 -0500 -+++ EMBOSS-6.3.1/configure.in 2010-11-09 15:06:25.101681999 -0500 -@@ -424,6 +424,7 @@ AC_ARG_ENABLE(systemlibs, - if test "${enable_systemlibs}" = "yes" ; then - have_systemlibs=yes - AC_CHECK_LIB(pcre, pcre_compile) -+ AC_CHECK_LIB(expat, XML_ParserCreate) - fi - AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes") - AC_SUBST(ESYSTEMLIBS) -@@ -660,7 +661,7 @@ CHECK_THREADS - - - AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile --ajax/expat/Makefile ajax/zlib/Makefile ajax/core/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-expat EMBOSS-6.3.1/configure ---- EMBOSS-6.3.1/configure.system-expat 2010-11-09 15:05:50.603682002 -0500 -+++ EMBOSS-6.3.1/configure 2010-11-09 15:06:59.620682003 -0500 -@@ -14946,6 +14946,51 @@ _ACEOF - - fi - -+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for XML_ParserCreate in -lexpat" >&5 -+$as_echo_n "checking for XML_ParserCreate in -lexpat... " >&6; } -+if test "${ac_cv_lib_expat_XML_ParserCreate+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-lexpat $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$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 XML_ParserCreate (); -+int -+main () -+{ -+return XML_ParserCreate (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_expat_XML_ParserCreate=yes -+else -+ ac_cv_lib_expat_XML_ParserCreate=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_expat_XML_ParserCreate" >&5 -+$as_echo "$ac_cv_lib_expat_XML_ParserCreate" >&6; } -+if test "x$ac_cv_lib_expat_XML_ParserCreate" = x""yes; then : -+ cat >>confdefs.h <<_ACEOF -+#define HAVE_LIBEXPAT 1 -+_ACEOF -+ -+ LIBS="-lexpat $LIBS" -+ -+fi -+ - fi - if test "$have_systemlibs" = "yes"; then - ESYSTEMLIBS_TRUE= -@@ -15299,7 +15344,7 @@ fi - - - --ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile ajax/acd/Makefile emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/testdb/Makefile emboss/data/Makefile emboss/data/AAINDEX/Makefile emboss/data/CODONS/Makefile emboss/data/REBASE/Makefile emboss/data/JASPAR_CORE/Makefile emboss/data/JASPAR_FAM/Makefile emboss/data/JASPAR_PHYLOFACTS/Makefile emboss/data/JASPAR_CNE/Makefile emboss/data/JASPAR_POLII/Makefile emboss/data/JASPAR_SPLICE/Makefile emboss/data/JASPAR_PBM/Makefile emboss/data/JASPAR_PBM_HLH/Makefile emboss/data/JASPAR_PBM_HOMEO/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile doc/Makefile doc/manuals/Makefile doc/tutorials/Makefile doc/programs/Makefile doc/programs/html/Makefile doc/programs/text/Makefile jemboss/Makefile jemboss/images/Makefile jemboss/lib/Makefile jemboss/lib/axis/Makefile jemboss/resources/Makefile jemboss/utils/Makefile Makefile" -+ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/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 -@@ -16357,7 +16402,6 @@ do - "plplot/lib/Makefile") CONFIG_FILES="$CONFIG_FILES plplot/lib/Makefile" ;; - "nucleus/Makefile") CONFIG_FILES="$CONFIG_FILES nucleus/Makefile" ;; - "ajax/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/Makefile" ;; -- "ajax/expat/Makefile") CONFIG_FILES="$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" ;; - "ajax/graphics/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/graphics/Makefile" ;; diff --git a/EMBOSS-6.3.1-system-hack.patch b/EMBOSS-6.3.1-system-hack.patch deleted file mode 100644 index 0407e7f..0000000 --- a/EMBOSS-6.3.1-system-hack.patch +++ /dev/null @@ -1,23 +0,0 @@ -diff -up EMBOSS-6.3.1/ajax/Makefile.am.system EMBOSS-6.3.1/ajax/Makefile.am ---- EMBOSS-6.3.1/ajax/Makefile.am.system 2010-08-02 17:26:39.537175842 -0400 -+++ EMBOSS-6.3.1/ajax/Makefile.am 2010-08-02 17:26:50.081151953 -0400 -@@ -1,6 +1,4 @@ - ## Process this file with automake to produce Makefile.in --if !ESYSTEMLIBS --EXTRA_DIRS = expat zlib pcre --endif -+EXTRA_DIRS = - - SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd -diff -up EMBOSS-6.3.1/ajax/Makefile.in.system EMBOSS-6.3.1/ajax/Makefile.in ---- EMBOSS-6.3.1/ajax/Makefile.in.system 2010-08-02 17:27:13.560269914 -0400 -+++ EMBOSS-6.3.1/ajax/Makefile.in 2010-08-02 17:27:24.406144161 -0400 -@@ -242,7 +242,7 @@ target_alias = @target_alias@ - top_build_prefix = @top_build_prefix@ - top_builddir = @top_builddir@ - top_srcdir = @top_srcdir@ --@ESYSTEMLIBS_FALSE@EXTRA_DIRS = expat zlib pcre -+@ESYSTEMLIBS_FALSE@EXTRA_DIRS = - SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd - all: all-recursive - diff --git a/EMBOSS-6.3.1-system-pcre.patch b/EMBOSS-6.3.1-system-pcre.patch deleted file mode 100644 index 615a8c0..0000000 --- a/EMBOSS-6.3.1-system-pcre.patch +++ /dev/null @@ -1,2776 +0,0 @@ -diff -up EMBOSS-6.3.1/ajax/acd/Makefile.am.system-pcre EMBOSS-6.3.1/ajax/acd/Makefile.am ---- EMBOSS-6.3.1/ajax/acd/Makefile.am.system-pcre 2010-06-16 07:36:00.000000000 -0400 -+++ EMBOSS-6.3.1/ajax/acd/Makefile.am 2010-08-02 15:53:45.289153815 -0400 -@@ -13,10 +13,10 @@ CYGWIN_LDACD = -L../../plplot -L../pcre - endif - - if !ESYSTEMLIBS --EXTRA_INCLUDES = -I$(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 -+#include - - #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$${pid}_.err &2; bad=1; fi; \ -+ done; \ -+ done; rm -f c$${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 \ diff --git a/EMBOSS-6.3.1-system-zlib.patch b/EMBOSS-6.3.1-system-zlib.patch deleted file mode 100644 index a50a2a3..0000000 --- a/EMBOSS-6.3.1-system-zlib.patch +++ /dev/null @@ -1,92 +0,0 @@ -diff -up EMBOSS-6.3.1/configure.in.system-zlib EMBOSS-6.3.1/configure.in ---- EMBOSS-6.3.1/configure.in.system-zlib 2010-11-10 08:49:30.735682003 -0500 -+++ EMBOSS-6.3.1/configure.in 2010-11-10 08:49:30.745682003 -0500 -@@ -425,6 +425,7 @@ if test "${enable_systemlibs}" = "yes" ; - have_systemlibs=yes - AC_CHECK_LIB(pcre, pcre_compile) - AC_CHECK_LIB(expat, XML_ParserCreate) -+ AC_CHECK_LIB(z, compress) - fi - AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes") - AC_SUBST(ESYSTEMLIBS) -@@ -661,7 +662,7 @@ CHECK_THREADS - - - AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile --ajax/zlib/Makefile ajax/core/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-zlib EMBOSS-6.3.1/configure ---- EMBOSS-6.3.1/configure.system-zlib 2010-11-10 08:50:26.740682011 -0500 -+++ EMBOSS-6.3.1/configure 2010-11-10 08:50:58.823682003 -0500 -@@ -14991,6 +14991,51 @@ _ACEOF - - fi - -+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for compress in -lz" >&5 -+$as_echo_n "checking for compress in -lz... " >&6; } -+if test "${ac_cv_lib_z_compress+set}" = set; then : -+ $as_echo_n "(cached) " >&6 -+else -+ ac_check_lib_save_LIBS=$LIBS -+LIBS="-lz $LIBS" -+cat confdefs.h - <<_ACEOF >conftest.$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 compress (); -+int -+main () -+{ -+return compress (); -+ ; -+ return 0; -+} -+_ACEOF -+if ac_fn_c_try_link "$LINENO"; then : -+ ac_cv_lib_z_compress=yes -+else -+ ac_cv_lib_z_compress=no -+fi -+rm -f core conftest.err conftest.$ac_objext \ -+ conftest$ac_exeext conftest.$ac_ext -+LIBS=$ac_check_lib_save_LIBS -+fi -+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_z_compress" >&5 -+$as_echo "$ac_cv_lib_z_compress" >&6; } -+if test "x$ac_cv_lib_z_compress" = x""yes; then : -+ cat >>confdefs.h <<_ACEOF -+#define HAVE_LIBZ 1 -+_ACEOF -+ -+ LIBS="-lz $LIBS" -+ -+fi -+ - fi - if test "$have_systemlibs" = "yes"; then - ESYSTEMLIBS_TRUE= -@@ -15344,7 +15389,7 @@ fi - - - --ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ajax/zlib/Makefile ajax/core/Makefile ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile ajax/acd/Makefile emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/testdb/Makefile emboss/data/Makefile emboss/data/AAINDEX/Makefile emboss/data/CODONS/Makefile emboss/data/REBASE/Makefile emboss/data/JASPAR_CORE/Makefile emboss/data/JASPAR_FAM/Makefile emboss/data/JASPAR_PHYLOFACTS/Makefile emboss/data/JASPAR_CNE/Makefile emboss/data/JASPAR_POLII/Makefile emboss/data/JASPAR_SPLICE/Makefile emboss/data/JASPAR_PBM/Makefile emboss/data/JASPAR_PBM_HLH/Makefile emboss/data/JASPAR_PBM_HOMEO/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile doc/Makefile doc/manuals/Makefile doc/tutorials/Makefile doc/programs/Makefile doc/programs/html/Makefile doc/programs/text/Makefile jemboss/Makefile jemboss/images/Makefile jemboss/lib/Makefile jemboss/lib/axis/Makefile jemboss/resources/Makefile jemboss/utils/Makefile Makefile" -+ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ajax/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 -@@ -16402,7 +16447,6 @@ do - "plplot/lib/Makefile") CONFIG_FILES="$CONFIG_FILES plplot/lib/Makefile" ;; - "nucleus/Makefile") CONFIG_FILES="$CONFIG_FILES nucleus/Makefile" ;; - "ajax/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/Makefile" ;; -- "ajax/zlib/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/zlib/Makefile" ;; - "ajax/core/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/core/Makefile" ;; - "ajax/graphics/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/graphics/Makefile" ;; - "ajax/ensembl/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/ensembl/Makefile" ;; diff --git a/EMBOSS-6.4.0-system-expat.patch b/EMBOSS-6.4.0-system-expat.patch new file mode 100644 index 0000000..8010fa1 --- /dev/null +++ b/EMBOSS-6.4.0-system-expat.patch @@ -0,0 +1,20 @@ +diff -up EMBOSS-6.4.0/configure.in.system-expat EMBOSS-6.4.0/configure.in +--- EMBOSS-6.4.0/configure.in.system-expat 2011-11-23 17:06:08.000000000 +0100 ++++ EMBOSS-6.4.0/configure.in 2011-11-23 17:07:00.615161077 +0100 +@@ -643,6 +643,7 @@ AC_ARG_ENABLE([systemlibs], + if test "${enable_systemlibs}" = "yes" ; then + have_systemlibs=yes + AC_CHECK_LIB(pcre, pcre_compile) ++ AC_CHECK_LIB(expat, XML_ParserCreate) + fi + AM_CONDITIONAL([ESYSTEMLIBS], [test "$have_systemlibs" = "yes"]) + AC_SUBST([ESYSTEMLIBS]) +@@ -806,7 +807,6 @@ AC_CONFIG_FILES([Makefile + ajax/ajaxdb/Makefile + ajax/core/Makefile + ajax/ensembl/Makefile +- ajax/expat/Makefile + ajax/graphics/Makefile + ajax/zlib/Makefile + doc/Makefile +diff -up EMBOSS-6.4.0/configure.system-expat EMBOSS-6.4.0/configure diff --git a/EMBOSS-6.4.0-system-hack.patch b/EMBOSS-6.4.0-system-hack.patch new file mode 100644 index 0000000..6360411 --- /dev/null +++ b/EMBOSS-6.4.0-system-hack.patch @@ -0,0 +1,11 @@ +diff -up EMBOSS-6.4.0/ajax/Makefile.am.system-hack EMBOSS-6.4.0/ajax/Makefile.am +--- EMBOSS-6.4.0/ajax/Makefile.am.system-hack 2011-11-23 17:14:51.094999577 +0100 ++++ EMBOSS-6.4.0/ajax/Makefile.am 2011-11-23 17:14:51.116999682 +0100 +@@ -1,6 +1,4 @@ + ## Process this file with automake to produce Makefile.in +-if !ESYSTEMLIBS +-EXTRA_DIRS = expat zlib pcre +-endif ++EXTRA_DIRS = + + SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd diff --git a/EMBOSS-6.4.0-system-pcre.patch b/EMBOSS-6.4.0-system-pcre.patch new file mode 100644 index 0000000..4136704 --- /dev/null +++ b/EMBOSS-6.4.0-system-pcre.patch @@ -0,0 +1,234 @@ +diff -up EMBOSS-6.4.0/ajax/acd/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/acd/Makefile.am +--- EMBOSS-6.4.0/ajax/acd/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200 ++++ EMBOSS-6.4.0/ajax/acd/Makefile.am 2011-11-23 17:03:07.033953627 +0100 +@@ -13,11 +13,11 @@ CYGWIN_LDACD = -L../../plplot -L../pcre + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(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 + + AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \ +--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ ++-I$(top_srcdir)/plplot \ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/graphics \ + -I$(top_srcdir)/ajax/ensembl \ +diff -up EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am +--- EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200 ++++ EMBOSS-6.4.0/ajax/ajaxdb/Makefile.am 2011-11-23 17:03:07.033953627 +0100 +@@ -13,13 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pc + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(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 + + + AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \ + -I$(top_srcdir)/plplot \ +--I$(top_srcdir)/ajax/pcre \ + $(EXTRA_INCLUDES) \ + $(AXIS2C_CPPFLAGS) \ + -I$(top_srcdir)/ajax/ensembl +diff -up EMBOSS-6.4.0/ajax/core/ajreg.h.system-pcre EMBOSS-6.4.0/ajax/core/ajreg.h +--- EMBOSS-6.4.0/ajax/core/ajreg.h.system-pcre 2010-04-14 09:44:20.000000000 +0200 ++++ EMBOSS-6.4.0/ajax/core/ajreg.h 2011-11-23 17:03:07.034953633 +0100 +@@ -16,9 +16,8 @@ extern "C" + #define ajreg_h + + #include "ajax.h" +-#include "pcre_config.h" +-#include "pcre_internal.h" +-#include "pcreposix.h" ++#include ++#include + + #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-6.4.0/ajax/core/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/core/Makefile.am +--- EMBOSS-6.4.0/ajax/core/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200 ++++ EMBOSS-6.4.0/ajax/core/Makefile.am 2011-11-23 17:03:07.035953639 +0100 +@@ -12,14 +12,14 @@ 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$(top_srcdir)/ajax/pcre + endif + + + AM_CPPFLAGS = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \ + -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \ + $(MYSQL_CPPFLAGS) $(POSTGRESQL_CPPFLAGS) \ +--I. -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES) ++-I. -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) + + AJAXSRC = ajalign.c ajarr.c \ + ajassem.c ajassemread.c ajassemwrite.c \ +diff -up EMBOSS-6.4.0/ajax/ensembl/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/ensembl/Makefile.am +--- EMBOSS-6.4.0/ajax/ensembl/Makefile.am.system-pcre 2011-07-07 00:01:27.000000000 +0200 ++++ EMBOSS-6.4.0/ajax/ensembl/Makefile.am 2011-11-23 17:03:07.035953639 +0100 +@@ -10,14 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../e + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/pcre + endif + + + AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \ + -I$(top_srcdir)/plplot \ +-$(EXTRA_INCLUDES) \ +--I$(top_srcdir)/ajax/pcre ++$(EXTRA_INCLUDES) + + ENSEMBLSRC = \ + ensalign.c \ +diff -up EMBOSS-6.4.0/ajax/graphics/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/graphics/Makefile.am +--- EMBOSS-6.4.0/ajax/graphics/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200 ++++ EMBOSS-6.4.0/ajax/graphics/Makefile.am 2011-11-23 17:03:07.036953645 +0100 +@@ -10,13 +10,12 @@ CYGWIN_LDAJAXG = -L../../plplot -L../exp + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/pcre + endif + + + AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \ + -I$(top_srcdir)/plplot \ +--I$(top_srcdir)/ajax/pcre \ + $(EXTRA_INCLUDES) + + AJAXGSRC = ajgraph.c ajhist.c +diff -up EMBOSS-6.4.0/ajax/Makefile.am.system-pcre EMBOSS-6.4.0/ajax/Makefile.am +--- EMBOSS-6.4.0/ajax/Makefile.am.system-pcre 2010-06-16 12:26:45.000000000 +0200 ++++ EMBOSS-6.4.0/ajax/Makefile.am 2011-11-23 17:03:07.037953651 +0100 +@@ -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 = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd +diff -up EMBOSS-6.4.0/configure.in.system-pcre EMBOSS-6.4.0/configure.in +--- EMBOSS-6.4.0/configure.in.system-pcre 2011-06-23 20:47:57.000000000 +0200 ++++ EMBOSS-6.4.0/configure.in 2011-11-23 17:05:22.496688169 +0100 +@@ -459,31 +459,6 @@ esac + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR=7 +-PCRE_MINOR=9 +-PCRE_DATE=11-Apr-2009 +-PCRE_VERSION=${PCRE_MAJOR}.${PCRE_MINOR} +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD=-DPOSIX_MALLOC_THRESHOLD=10 +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION=0:1:0 +-PCRE_POSIXLIB_VERSION=0:0:0 +- +- + dnl Define where the EMBOSS package is located + AC_SUBST([AJAX_FIXED_ROOT]) + AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" +@@ -667,6 +642,7 @@ AC_ARG_ENABLE([systemlibs], + [AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])]) + if test "${enable_systemlibs}" = "yes" ; then + have_systemlibs=yes ++ AC_CHECK_LIB(pcre, pcre_compile) + fi + AM_CONDITIONAL([ESYSTEMLIBS], [test "$have_systemlibs" = "yes"]) + AC_SUBST([ESYSTEMLIBS]) +@@ -832,7 +808,6 @@ AC_CONFIG_FILES([Makefile + ajax/ensembl/Makefile + ajax/expat/Makefile + ajax/graphics/Makefile +- ajax/pcre/Makefile + ajax/zlib/Makefile + doc/Makefile + doc/manuals/Makefile +diff -up EMBOSS-6.4.0/emboss/Makefile.am.system-pcre EMBOSS-6.4.0/emboss/Makefile.am +--- EMBOSS-6.4.0/emboss/Makefile.am.system-pcre 2011-07-08 18:46:55.000000000 +0200 ++++ EMBOSS-6.4.0/emboss/Makefile.am 2011-11-23 17:03:07.038953657 +0100 +@@ -102,12 +102,11 @@ wossdata wossinput wossname wossoperatio + yank + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(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 + + AM_CPPFLAGS = -I$(top_srcdir)/ajax/core \ + -I$(top_srcdir)/nucleus \ +- -I$(top_srcdir)/ajax/pcre \ + $(EXTRA_INCLUDES) \ + $(AXIS2C_CPPFLAGS) \ + -I$(top_srcdir)/ajax/graphics \ +@@ -399,14 +398,14 @@ 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 + + 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 = $(EXTRA_DIST) +diff -up EMBOSS-6.4.0/nucleus/Makefile.am.system-pcre EMBOSS-6.4.0/nucleus/Makefile.am +--- EMBOSS-6.4.0/nucleus/Makefile.am.system-pcre 2011-06-14 10:36:34.000000000 +0200 ++++ EMBOSS-6.4.0/nucleus/Makefile.am 2011-11-23 17:03:07.039953663 +0100 +@@ -19,14 +19,14 @@ CYGWIN_LIBS = -L../plplot -L../ajax/pcre + -lezlib -leplplot + else + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(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 + + + AM_CPPFLAGS = -I$(top_srcdir)/ajax/core -I$(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/graphics \ + -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ diff --git a/EMBOSS-6.4.0-system-zlib.patch b/EMBOSS-6.4.0-system-zlib.patch new file mode 100644 index 0000000..a2f7a59 --- /dev/null +++ b/EMBOSS-6.4.0-system-zlib.patch @@ -0,0 +1,20 @@ +diff -up EMBOSS-6.4.0/configure.in.system-zlib EMBOSS-6.4.0/configure.in +--- EMBOSS-6.4.0/configure.in.system-zlib 2011-11-23 17:07:55.000000000 +0100 ++++ EMBOSS-6.4.0/configure.in 2011-11-23 17:08:36.848586027 +0100 +@@ -644,6 +644,7 @@ if test "${enable_systemlibs}" = "yes" ; + have_systemlibs=yes + AC_CHECK_LIB(pcre, pcre_compile) + AC_CHECK_LIB(expat, XML_ParserCreate) ++ AC_CHECK_LIB(z, compress) + fi + AM_CONDITIONAL([ESYSTEMLIBS], [test "$have_systemlibs" = "yes"]) + AC_SUBST([ESYSTEMLIBS]) +@@ -808,7 +809,6 @@ AC_CONFIG_FILES([Makefile + ajax/core/Makefile + ajax/ensembl/Makefile + ajax/graphics/Makefile +- ajax/zlib/Makefile + doc/Makefile + doc/manuals/Makefile + doc/programs/Makefile +diff -up EMBOSS-6.4.0/configure.system-zlib EMBOSS-6.4.0/configure diff --git a/EMBOSS.spec b/EMBOSS.spec index 760997c..9bb4fb2 100644 --- a/EMBOSS.spec +++ b/EMBOSS.spec @@ -17,8 +17,8 @@ %define emhome %{_datadir}/EMBOSS Name: EMBOSS -Version: 6.3.1 -Release: 11%{?dist} +Version: 6.4.0 +Release: 1%{?dist} Summary: The European Molecular Biology Open Software Suite Group: Applications/Engineering @@ -38,40 +38,33 @@ Source1: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README.fixes Source2: jemboss.desktop %endif # Upstream patch -Patch0: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-4.gz -# Use system-wide pcre. Sent upstream. -Patch1: EMBOSS-6.3.1-system-pcre.patch +Patch0: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-24.gz +# Use system-wide pcre. Sent upstream. Updated patch created on 2011-11-23. +Patch1: EMBOSS-6.4.0-system-pcre.patch # Use system-wide plplot -# Patch3: EMBOSS-6.3.1-system-plplot.patch -# Use system-wide expat -Patch4: EMBOSS-6.3.1-system-expat.patch -# Use system-wide zlib -Patch5: EMBOSS-6.3.1-system-zlib.patch -# Fix x86_64 check to be finer grained, eliminate koji false positive -# Sent upstream 2010-11-10 -Patch6: EMBOSS-6.3.1-fix-amd64-check.patch - -#Fedora-specific. Not sent upstream. -Patch7: %{name}-fedora.patch -Patch8: EMBOSS-6.3.1-system-hack.patch +# Patch3: EMBOSS-6.3.1-system-plplot.patch +# Use system-wide expat. Updated patch created on 2011-11-23. +Patch4: EMBOSS-6.4.0-system-expat.patch +# Use system-wide zlib. Updated patch created on 2011-11-23. +Patch5: EMBOSS-6.4.0-system-zlib.patch -# Sent upstream on 2010-10-27 -# Cleaner version generated on 2010-11-04 -# Upstream's final version received on 2010-11-10 -Patch9: EMBOSS-6.3.1-new-fix-doc-finding.patch +# Fedora-specific. Not sent upstream. +Patch7: %{name}-fedora.patch +# Updated patch created on 2011-11-23. +Patch8: EMBOSS-6.4.0-system-hack.patch BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) BuildRequires: gd-devel BuildRequires: pam-devel BuildRequires: pcre-devel -BuildRequires: zlib-devel -# BuildRequires: plplot-devel -BuildRequires: expat-devel -BuildRequires: libharu-devel -BuildRequires: postgresql-devel -BuildRequires: mysql-devel -BuildRequires: libtool, autoconf +BuildRequires: zlib-devel +# BuildRequires: plplot-devel +BuildRequires: expat-devel +BuildRequires: libharu-devel +BuildRequires: postgresql-devel +BuildRequires: mysql-devel +BuildRequires: libtool, autoconf %if %{with jemboss} BuildRequires: ant BuildRequires: desktop-file-utils @@ -86,7 +79,7 @@ Requires: jdk = 2000:1.6.0_17-fcs %endif # We need this to force updates across minor releases where sonames do not change -Requires: %{name}-libs = %{version}-%{release} +Requires: %{name}-libs = %{version}-%{release} %description EMBOSS is a new, free Open Source software analysis package specially @@ -107,7 +100,7 @@ Trends in Genetics June 2000, vol 16, No 6. pp.276-277 Summary: Development tools for programs which will use the %{name} library Group: Development/Libraries Requires: %{name}-libs = %{version}-%{release} -Requires: libeplplot-devel = %{version}-%{release} +Requires: libeplplot-devel = %{version}-%{release} %description devel The %{name}-devel package includes the header files and static libraries @@ -150,9 +143,9 @@ Group: System Environment/Libraries A modified version of plplot used by EMBOSS. %package -n libeplplot-devel -Summary: Development files for eplplot -Group: Development/Libraries -Requires: libeplplot = %{version}-%{release} +Summary: Development files for eplplot +Group: Development/Libraries +Requires: libeplplot = %{version}-%{release} %description -n libeplplot-devel The libeplplot-devel package includes the header files and libraries @@ -166,17 +159,15 @@ necessary for developing programs which will use the eplplot library. # %%patch3 -p1 -b .system-plplot %patch4 -p1 -b .system-expat %patch5 -p1 -b .system-zlib -%patch6 -p1 -b .fix-amd64-check %patch7 -p0 -b .fedora -%patch8 -p1 -b .system -%patch9 -p1 -b .fix-doc-finding +%patch8 -p1 -b .system-hack # Remove bundled expat, pcre and zlib to make sure that system versions are used rm -rf ajax/{expat,pcre,zlib} #install the patch readme -#install -pm 644 %{SOURCE1} README.fixes +install -pm 644 %{SOURCE1} README.fixes #these files were executable for some reason chmod 644 emboss/prettyplot.c emboss/polydot.c emboss/supermatcher.c @@ -300,7 +291,7 @@ rm -rf $RPM_BUILD_ROOT %files %defattr(-,root,root,-) -%doc AUTHORS ChangeLog FAQ INSTALL NEWS README THANKS +%doc AUTHORS ChangeLog FAQ INSTALL NEWS README README.fixes THANKS %{_bindir}/* %exclude %{_bindir}/runJemboss.csh %exclude %{_bindir}/jembossctl @@ -339,6 +330,12 @@ rm -rf $RPM_BUILD_ROOT %{_includedir}/EMBOSS/eplplot/ %changelog +* Wed Nov 23 2011 Julian Sikorski - 6.4.0-1 +- Updated to 6.4.0 +- Dropped included new-fix-doc-finding and fix-amd64-check patches +- Updated system libs patches +- tabs → spaces to satisfy rpmlint + * Wed Mar 23 2011 Dan Horák - 6.3.1-11 - rebuilt for mysql 5.5.10 (soname bump in libmysqlclient) diff --git a/README.fixes b/README.fixes index d732848..3c1d2ee 100644 --- a/README.fixes +++ b/README.fixes @@ -1,39 +1,191 @@ The files in this directory are bugfix replacements for files in -the EMBOSS-6.3.1 distribution. Just drop the replacement files in +the EMBOSS-6.4.0 distribution. Just drop the replacement files in the location shown and redo the 'make install.' -Fix 1. EMBOSS-6.3.1/configure - EMBOSS-6.3.1/m4/mysql.m4 +Fix 1. EMBOSS-6.4.0/emboss/dbiflat.c + EMBOSS-6.4.0/emboss/dbxflat.c -21 Jul 2010: Addresses a problem whereby, in some circumstances, inclusion of - hpdf support prevented inclusion of MySQL support. - Using the mysql.m4 from this patch may cause a libtool - error during compilation if you have a version of libtool - greater than 2.2.6b on your system. If this happens type - "autoreconf -fi" after adding the file. Note that you - do not need to use the mysql.m4 file and it is probably - safer not to; just use the configure file. +10-Aug-2011: The SwissProt description line format includes addtional + tags which interfere with the EMBL parser used in + previous releases. The fix replaces this with a SwissProt + parser that strips out the extra tags. After patching the + release, any existing SwissProt description index files + should be reindexed. Other indexes are unchanged. -Fix 2. EMBOSS-6.3.1/configure +Fix 2. EMBOSS-6.4.0/ajax/core/ajquery.c -6 Aug 2010: This is exactly the same as Fix 1 above, but the associated - file in the patches directory does not contain the - mysql.m4 file - it is unnecessary for the operation of the - EMBOSS distribution. Using this patch will not cause the - libtool problem described above. +10-Aug-2011: For databases with more than one valid format (examples + include the EBI dbfetch server) this fix allows the + format to be specified with a qualifier on the command + line. In the original release only a format in the query + string was used. -Fix 3. EMBOSS-6.3.1/ajax/graphics/ajgraph.c +Fix 3. EMBOSS-6.4.0/ajax/core/ajfeatread.c -9 Aug 2010: Fix potential crash using -debug +10-Aug-2011: When parsing GFF3 format input, long feature tags (for + example extremely long translations) exceeded limits in + regular expression parsing. Ths fix decouples testing for + escaped quotes from the main task of finding quoted + strings. -Fix 4. EMBOSS-6.3.1/ajax/ensembl/ensregistry.c - EMBOSS-6.3.1/ajax/ajaxdb/ajseqdb.c.c +Fix 4. EMBOSS-6.4.0/emboss/data/Etcode.dat + +10-Aug-2001: The local data file used by application tcode had a missing + parameter line. + + +Fix 5. EMBOSS-6.4.0/ajax/core/ajrange.c + +10-Aug-2011: When sequence ranges (and possible highlighting for + showalign) were in a list file the parser overwrote + string values. + + +Fix 5. EMBOSS-6.4.0/ajax/core/ajseqabi.c + +10-Aug-2011: Sample names in ABI format files were stored in + incompletely defined strings. This fix corrects the + string object. The sample name is also used as the + sequence name. + + +Fix 6. EMBOSS-6.4.0/emboss/dbxresource.c + +10-Aug-2011: A future change to the format of Data Resource Catalogue + entries in DRCAT.dat requires an update to the parsing of + category lines. The current version is not affected. + + +Fix 7. EMBOSS-6.4.0/emboss/server.ensemblgenomes + EMBOSS-6.4.0/emboss/cacheensembl.c + EMBOSS-6.4.0/ajax/ensembl/ensregistry.c + EMBOSS-6.4.0/ajax/ensembl/ensregistry.c + EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.c + EMBOSS-6.4.0/ajax/ensembl/ensdatabaseadaptor.h + +10-Aug-2011: Microbial genomes use an enumerated species code which + must be added to the query for data retrieval. This fix + adds the species code to the comment field. In the next + release a more complete solution will be implemented. + + +Fix 8. EMBOSS-6.4.0/ajax/core/ajarch.h + +10-Aug-2011: Corrects the size of long integers on Windows systems only. + + +Fix 9. EMBOSS-6.4.0/emboss/cirdna.c + +10-Aug-2011: Cirdna prints text inside solid blocks invisibly. When + printed outside the text scaling was too small. The text + scale is now adjusted for the radius and sequence length + so that labels should be readable outside the box. + + +Fix 10. EMBOSS-6.4.0/ajax/core/ajpat.c + +10-Aug-2011: Fuzznuc, fuzzpro and fuzztran using a pattern file + ignored the command line -mismatch qualifier for the + first pattern. The default mismatch is now set to this + value at the start of the pattern matching loop in the + library. + + +Fix 11. EMBOSS-6.4.0/ajax/core/ajfmt.c + +11-Aug-2011: ajFmtScanF handled va_list incorrectly. Only noticeable by code + developers. + + +Fix 12. EMBOSS-6.4.0/nucleus/embgroup.c + +18-Aug-2011: An internal string variable should be initialised as NULL. + + +Fix 13. EMBOSS-6.4.0/ajax/core/ajseqread.c + +18-Aug-2011: Reading protein GFF3 files ignored the EMBOSS type comment. + This appears to be the only way to detect a protein GFF3 file. + +Fix 14. EMBOSS-6.4.0/emboss/data/Efeatures.gff3protein + +18-Aug-2011: In writing GFF3 protein file, uses the current term name + from the Sequence Ontology to clear errors from the GFF3 + online validator. + +Fix 15. EMBOSS-6.4.0/ajax/core/ajfeatwrite.c + +18-Aug-2011: When writing GFF3 format, tags names are explicitly + converted to lower case as required by the GFF3 + standard. This includes EC_number and /PCR_conditions in + EMBL/GenBank/DDBJ and several RefseqP tags. The score is + written using g format to represent very low values. + +Fix 16. EMBOSS-6.4.0/ajax/core/ajnexus.c + EMBOSS-6.4.0/ajax/core/ajseqread.c + +22-Aug-2011: When reading nexus data format with no taxlabels block + the attempt to read the taxa (sequence names) from the + matrix block failed. + +Fix 17. EMBOSS-6.4.0/ajax/ajaxdb/ajtextdb.c + +22-Aug-2011: The SRS access method added a stray '+' character to the + getz command line. + +Fix 18. EMBOSS-6.4.0/ajax/core/ajquery.c + +25-Aug-2011: In some cases a query using a simple identifier + could try to test an undefined "sv" field. + +Fix 19. EMBOSS-6.4.0/ajax/core/ajseqread.c + +02-Sep-2011: Reading "raw" sequence format failed when piped from + standard input. In release 6.4.0 "raw" format was + redefined as a binary format to catch binary files that + start with one or more sequence characters followed by a + NULL character. This fix continues to check binary files, + but has to drop the check for data piped through standard + input which is read as text and cannot be reread as + binary. + +Fix 20. EMBOSS-6.4.0/ajax/core/ajnam.c + +02-Sep-2011: Complex database definitions with more than one type or + format are allowed in 6.4.0 but caused an error message + from showdb when the type and format were tested. + +Fix 21. EMBOSS-6.4.0/emboss/drfinddata.c + EMBOSS-6.4.0/emboss/drfindformat.c + EMBOSS-6.4.0/emboss/drfindid.c + EMBOSS-6.4.0/emboss/drfindresource.c + +02-Sep-2011: Running with -debug fails. Debug calls used obsolete datatype + for data resource internals. Without -debug there was no problem. + +Fix 22. EMBOSS-6.4.0/emboss/diffseq.c + EMBOSS-6.4.0/ajax/core/ajreport.c + +14-Sep-2011: Diffseq reports insertions in the second sequence with a + length 2 reversed region in the first sequence instead of + a length 0 empty sequence. This bug was introduced in + release 6.0.0 when reversed sequence features were updated. + +Fix 23. EMBOSS-6.4.0/ajax/core/ajindex.c + +04-Oct-2011: Dbx index files from earlier releases do not include a + type parameter to indicate an Identifier or Secondary + index. The code to test index field names failed to + define id and acc fields as Identifiers. This fix allows + old indexes to work with EMBOSS 6.4.0. + +Fix 24. EMBOSS-6.4.0/ajax/core/ajfileio.c + +05-Oct-2011: Trimming carriage control from the ends of lines in a + buffer failed when MacOSX-style characters are used and + the line buffer is a reference counted string. An example + on non-MacOSX systems was processing the data returned by + the NCBI Entrez server. -9 Aug 2010: Allow two Ensembl sequences to be loaded without re-registering. - Fix Ensembl Genomes registration. - Fix Ensembl Genomes identifiers for species without stable - identifiers. If the identifier does not obey a stable identifier - pattern, it is matched against Exons, Transcripts and - Translations in exactly that order. diff --git a/sources b/sources index ffa09ed..39e789e 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -04d1179b6261103a77e396d54f8ac38e EMBOSS-6.3.1.tar.gz -7a42594c5eda4adc6457f33e4ab0d8f2 patch-1-4.gz +54993a22064222b01bd4fc8086f7684d EMBOSS-6.4.0.tar.gz +0b84d6012076308f544505379834e630 patch-1-24.gz