[Debian-med-packaging] [SCM] The European Molecular Biology Open Software Suite. branch, master, updated. debian/6.3.1-1-3-g5ffbefa

[Charles Plessy]

The following commit has been merged in the master branch:
commit dd7ba1ed4e8c68e8c8ba958593dc943c614b7f53
Author: Charles Plessy <plessy at debian.org>
Date:   Fri Jul 23 10:27:44 2010 +0900

    First upstream patch for version 6.3.1.

diff --git a/debian/patches/official-upstream-patch.patch b/debian/patches/official-upstream-patch.patch
index 2f63822..fb38271 100644
--- a/debian/patches/official-upstream-patch.patch
+++ b/debian/patches/official-upstream-patch.patch
@@ -1,4 +1,52 @@
 Description: Official upstream patch.
- (none for the moment).
-Origin: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/
+ Fix 1. EMBOSS-6.3.1/configure
+        EMBOSS-6.3.1/m4/mysql.m4
+ .
+ 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
 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
+***************
+*** 14481,14488 ****
+  
+      	    EMBCFLAGS=$CFLAGS
+  	    EMBLDFLAGS=$LDFLAGS
+! 	    CFLAGS=$MYSQL_CFLAGS
+! 	    LDFLAGS=$MYSQL_LDFLAGS
+  
+              cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+  /* end confdefs.h.  */
+--- 14481,14488 ----
+  
+      	    EMBCFLAGS=$CFLAGS
+  	    EMBLDFLAGS=$LDFLAGS
+! 	    CFLAGS="$MYSQL_CFLAGS $EMBCFLAGS"
+! 	    LDFLAGS="$MYSQL_LDFLAGS $EMBLDFLAGS"
+  
+              cat confdefs.h - <<_ACEOF >conftest.$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"]],
diff --git a/debian/patches/series b/debian/patches/series
index 80fc2af..06a3ea4 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,3 @@
-#official-upstream-patch.patch
+official-upstream-patch.patch
 using-pager-in-tfm.patch
 tfm-html.patch

-- 
The European Molecular Biology Open Software Suite.