[Debian-med-packaging] [SCM] The European Molecular Biology Open Software Suite. branch, master, updated. debian/6.3.1-3-2-g2de3ab8

[Charles Plessy]

The following commit has been merged in the master branch:
commit 4e840f70e4fa76f34b946bb32fbe0d0574a226cf
Author: Charles Plessy <plessy at debian.org>
Date:   Sat Aug 7 21:19:15 2010 +0900

     # New upstream patch.
    
    URL: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-2.gz

diff --git a/debian/changelog b/debian/changelog
index 8499b09..2da22f8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+emboss (6.3.1-4) unstable; urgency=low
+
+  * New upstream patch, version 1-2.
+
+ -- Charles Plessy <plessy at debian.org>  Sat, 07 Aug 2010 21:18:18 +0900
+
 emboss (6.3.1-3) unstable; urgency=low
 
   * Use default Java instead of OpenJDK (debian/control, debian/rules,
diff --git a/debian/patches/official-upstream-patch.patch b/debian/patches/official-upstream-patch.patch
index fb38271..fd8e550 100644
--- a/debian/patches/official-upstream-patch.patch
+++ b/debian/patches/official-upstream-patch.patch
@@ -4,11 +4,25 @@ Description: Official upstream patch.
  .
  21 Jul 2010: Addresses a problem whereby, in some circumstances, inclusion of
               hpdf support prevented inclusion of MySQL support.
-Origin: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-1.gz
+              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.
+ .
+ Fix 2. EMBOSS-6.3.1/configure
+ .
+ 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.
+Origin: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-2.gz
 Forwarded: not-needed
 diff -c -N --recursive -a EMBOSS-6.3.1old/configure EMBOSS-6.3.1/configure
 *** EMBOSS-6.3.1old/configure	2010-07-19 12:55:36.000000000 +0100
---- EMBOSS-6.3.1/configure	2010-07-21 09:46:12.000000000 +0100
+--- EMBOSS-6.3.1/configure	2010-08-06 09:06:53.000000000 +0100
 ***************
 *** 14481,14488 ****
   
@@ -28,25 +42,3 @@ diff -c -N --recursive -a EMBOSS-6.3.1old/configure EMBOSS-6.3.1/configure
   
               cat confdefs.h - <<_ACEOF >conftest.$ac_ext
   /* end confdefs.h.  */
-diff -c -N --recursive -a EMBOSS-6.3.1old/m4/mysql.m4 EMBOSS-6.3.1/m4/mysql.m4
-*** EMBOSS-6.3.1old/m4/mysql.m4	2010-05-18 23:12:06.000000000 +0100
---- EMBOSS-6.3.1/m4/mysql.m4	2010-07-21 09:45:46.000000000 +0100
-***************
-*** 96,103 ****
-  
-      	    EMBCFLAGS=$CFLAGS
-  	    EMBLDFLAGS=$LDFLAGS
-! 	    CFLAGS=$MYSQL_CFLAGS
-! 	    LDFLAGS=$MYSQL_LDFLAGS
-  
-              AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
-                                                #include "mysql.h"]],
---- 96,103 ----
-  
-      	    EMBCFLAGS=$CFLAGS
-  	    EMBLDFLAGS=$LDFLAGS
-! 	    CFLAGS="$MYSQL_CFLAGS $EMBCFLAGS"
-! 	    LDFLAGS="$MYSQL_LDFLAGS $EMBLDFLAGS"
-  
-              AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
-                                                #include "mysql.h"]],

-- 
The European Molecular Biology Open Software Suite.