[EMBOSS/f13/master] forgot to update one patch

[Tom Callaway]

commit 6489328ea0ed5c801a4b78805f0874d96380e9ca
Author: Tom "spot" Callaway <tcallawa at redhat.com>
Date:   Wed Nov 10 15:19:45 2010 -0500

    forgot to update one patch

 EMBOSS-6.3.1-system-expat.patch |   52 ++++++++++++++++++++++++---------------
 1 files changed, 32 insertions(+), 20 deletions(-)
---
diff --git a/EMBOSS-6.3.1-system-expat.patch b/EMBOSS-6.3.1-system-expat.patch
index e964356..78fbf58 100644
--- a/EMBOSS-6.3.1-system-expat.patch
+++ b/EMBOSS-6.3.1-system-expat.patch
@@ -1,17 +1,7 @@
-diff -up EMBOSS-6.3.1/ajax/acd/Makefile.am.system-expat EMBOSS-6.3.1/ajax/acd/Makefile.am
-diff -up EMBOSS-6.3.1/ajax/acd/Makefile.in.system-expat EMBOSS-6.3.1/ajax/acd/Makefile.in
-diff -up EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am.system-expat EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am
-diff -up EMBOSS-6.3.1/ajax/ajaxdb/Makefile.in.system-expat EMBOSS-6.3.1/ajax/ajaxdb/Makefile.in
-diff -up EMBOSS-6.3.1/ajax/core/Makefile.am.system-expat EMBOSS-6.3.1/ajax/core/Makefile.am
-diff -up EMBOSS-6.3.1/ajax/core/Makefile.in.system-expat EMBOSS-6.3.1/ajax/core/Makefile.in
-diff -up EMBOSS-6.3.1/ajax/graphics/Makefile.am.system-expat EMBOSS-6.3.1/ajax/graphics/Makefile.am
-diff -up EMBOSS-6.3.1/ajax/graphics/Makefile.in.system-expat EMBOSS-6.3.1/ajax/graphics/Makefile.in
-diff -up EMBOSS-6.3.1/ajax/Makefile.am.system-expat EMBOSS-6.3.1/ajax/Makefile.am
-diff -up EMBOSS-6.3.1/ajax/Makefile.in.system-expat EMBOSS-6.3.1/ajax/Makefile.in
 diff -up EMBOSS-6.3.1/configure.in.system-expat EMBOSS-6.3.1/configure.in
---- EMBOSS-6.3.1/configure.in.system-expat	2010-08-02 17:11:31.000000000 -0400
-+++ EMBOSS-6.3.1/configure.in	2010-08-02 17:12:11.831269942 -0400
-@@ -425,6 +425,7 @@ AC_ARG_ENABLE(systemlibs,
+--- 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 "${enable_systemlibs}" = "yes" ; then
      have_systemlibs=yes
      AC_CHECK_LIB(pcre, pcre_compile)
@@ -19,10 +9,19 @@ diff -up EMBOSS-6.3.1/configure.in.system-expat EMBOSS-6.3.1/configure.in
  fi          
  AM_CONDITIONAL(ESYSTEMLIBS, test "$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	2010-08-02 17:11:31.825142800 -0400
-+++ EMBOSS-6.3.1/configure	2010-08-02 17:14:33.060269076 -0400
-@@ -15339,6 +15339,51 @@ _ACEOF
+--- 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
  
@@ -74,7 +73,20 @@ diff -up EMBOSS-6.3.1/configure.system-expat EMBOSS-6.3.1/configure
  fi
   if test "$have_systemlibs" = "yes"; then
    ESYSTEMLIBS_TRUE=
-diff -up EMBOSS-6.3.1/emboss/Makefile.am.system-expat EMBOSS-6.3.1/emboss/Makefile.am
-diff -up EMBOSS-6.3.1/emboss/Makefile.in.system-expat EMBOSS-6.3.1/emboss/Makefile.in
-diff -up EMBOSS-6.3.1/nucleus/Makefile.am.system-expat EMBOSS-6.3.1/nucleus/Makefile.am
-diff -up EMBOSS-6.3.1/nucleus/Makefile.in.system-expat EMBOSS-6.3.1/nucleus/Makefile.in
+@@ -15299,7 +15344,7 @@ fi
+ 
+ 
+ 
+-ac_config_files="$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="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ajax/zlib/Makefile ajax/core/Makefile ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile ajax/acd/Makefile emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/testdb/Makefile emboss/data/Makefile emboss/data/AAINDEX/Makefile emboss/data/CODONS/Makefile emboss/data/REBASE/Makefile emboss/data/JASPAR_CORE/Makefile emboss/data/JASPAR_FAM/Makefile emboss/data/JASPAR_PHYLOFACTS/Makefile emboss/data/JASPAR_CNE/Makefile emboss/data/JASPAR_POLII/Makefile emboss/data/JASPAR_SPLICE/Makefile emboss/data/JASPAR_PBM/Makefile emboss/data/JASPAR_PBM_HLH/Makefile emboss/data/JASPAR_PBM_HOMEO/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile doc/Makefile doc/manuals/Makefile doc/tutorials/Makefile doc/programs/Makefile doc/programs/html/Makef
 ile doc/programs/text/Makefile jemboss/Makefile jemboss/images/Makefile jemboss/lib/Makefile jemboss/lib/axis/Makefile jemboss/resources/Makefile jemboss/utils/Makefile Makefile"
+ 
+ cat >confcache <<\_ACEOF
+ # This file is a shell script that caches the results of configure
+@@ -16357,7 +16402,6 @@ do
+     "plplot/lib/Makefile") CONFIG_FILES="$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" ;;