[EMBOSS] - Updated the upstream patch to 1-4

[belegdol]

commit 5466a51052888b9015571fe453ab9a3eb0211930
Author: Julian Sikorski <belegdol at gmail.com>
Date:   Tue Aug 10 21:21:26 2010 +0200

    - Updated the upstream patch to 1-4

 .gitignore   |    2 +-
 EMBOSS.spec  |    7 +++++--
 README.fixes |   30 ++++++++++++++++++++++++++++++
 sources      |    2 +-
 4 files changed, 37 insertions(+), 4 deletions(-)
---
diff --git a/.gitignore b/.gitignore
index c613538..666ef37 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,2 @@
-patch-1-1.gz
 EMBOSS-6.3.1.tar.gz
+patch-1-4.gz
diff --git a/EMBOSS.spec b/EMBOSS.spec
index fcfb294..9c3fd7a 100644
--- a/EMBOSS.spec
+++ b/EMBOSS.spec
@@ -18,7 +18,7 @@
 
 Name:           EMBOSS
 Version:        6.3.1
-Release:        1%{?dist}
+Release:        2%{?dist}
 Summary:        The European Molecular Biology Open Software Suite
 
 Group:          Applications/Engineering
@@ -38,7 +38,7 @@ 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-1-1.gz
+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
 # Use system-wide plplot
@@ -293,6 +293,9 @@ rm -rf $RPM_BUILD_ROOT
 
 
 %changelog
+* Tue Aug 10 2010 Julian Sikorski <belegdol at fedoraproject.org> - 6.3.1-2
+- Updated the upstream patch to 1-4
+
 * Mon Aug 02 2010 Tom "spot" Callaway <tcallawa at redhat.com> - 6.3.1-1
 - update to 6.3.1
 
diff --git a/README.fixes b/README.fixes
index 3c56d79..d732848 100644
--- a/README.fixes
+++ b/README.fixes
@@ -7,3 +7,33 @@ Fix 1. EMBOSS-6.3.1/configure
 
 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.
+
+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.
+
+
+Fix 3. EMBOSS-6.3.1/ajax/graphics/ajgraph.c
+
+9 Aug 2010: Fix potential crash using -debug
+
+
+Fix 4. EMBOSS-6.3.1/ajax/ensembl/ensregistry.c
+       EMBOSS-6.3.1/ajax/ajaxdb/ajseqdb.c.c
+
+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 4e461f9..ffa09ed 100644
--- a/sources
+++ b/sources
@@ -1,2 +1,2 @@
-4d4cc882ce44ad5e44c38231c9f3ae53  patch-1-1.gz
 04d1179b6261103a77e396d54f8ac38e  EMBOSS-6.3.1.tar.gz
+7a42594c5eda4adc6457f33e4ab0d8f2  patch-1-4.gz