[med-svn] r2119 - in trunk/packages/clustalw/trunk: . debian debian/patches

Wed Jul 2 02:06:41 UTC 2008

Author: plessy
Date: 2008-07-02 02:06:40 +0000 (Wed, 02 Jul 2008)
New Revision: 2119

Added:
   trunk/packages/clustalw/trunk/debian/compat
Removed:
   trunk/packages/clustalw/trunk/debian/patches/series
   trunk/packages/clustalw/trunk/debian/patches/to_build_with_g++-4.3.patch
Modified:
   trunk/packages/clustalw/trunk/CHANGELOG
   trunk/packages/clustalw/trunk/debian/changelog
   trunk/packages/clustalw/trunk/debian/clustalw.1
   trunk/packages/clustalw/trunk/debian/clustalw.1.xml
   trunk/packages/clustalw/trunk/debian/control
   trunk/packages/clustalw/trunk/debian/copyright
Log:
New upstream release integrating the g++ patch.

  * debian/patches/to_build_with_g++-4.3.patch was accepted upstream
    and therefore removed here.
  * debian/copyright: added a disclaimer clarifying that this package is not
    part of the Debian operating system (requirement of Policy 3.8.0).
  * debian/control:  
    - Updated Standards-Version to 3.8.0.
    - Enhances: emboss (EMBOSS has a wrapper for clustalw, `emma'.)
  * debian/clustaw.1*: incremented version number


Modified: trunk/packages/clustalw/trunk/CHANGELOG
===================================================================

--- trunk/packages/clustalw/trunk/CHANGELOG	2008-07-01 19:54:32 UTC (rev 2118)
+++ trunk/packages/clustalw/trunk/CHANGELOG	2008-07-02 02:06:40 UTC (rev 2119)
@@ -1,4 +1,25 @@
 ----------------------------------------------------------------------
+Version 2.0.9
+----------------------------------------------------------------------
+
+* GUI now responding and giving feedback during alignment
+
+* automatic automake os detection
+
+* new OS_ define (set by clustalw/configure clustalx/clustalx.pro)
+
+* got rid of qt3 dependencies
+
+* removed QScrollArea bug workaround (fixed in Qt 4.3)
+
+* Fixed bug 135: Last sequence and last residue not displayed on MacOSX
+
+* Fixed bug 123: secondary structure profile alignment in clustalX on Mac
+
+* Fixed g++-4.3 build error (include climits.h)
+
+
+----------------------------------------------------------------------
 Version 2.0.8
 ----------------------------------------------------------------------
 

Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog	2008-07-01 19:54:32 UTC (rev 2118)
+++ trunk/packages/clustalw/trunk/debian/changelog	2008-07-02 02:06:40 UTC (rev 2119)
@@ -1,3 +1,17 @@
+clustalw (2.0.9-1) unstable; urgency=low
+
+  * New upstream release.
+  * debian/patches/to_build_with_g++-4.3.patch was accepted upstream
+    and therefore removed here.
+  * debian/copyright: added a disclaimer clarifying that this package is not
+    part of the Debian operating system (requirement of Policy 3.8.0).
+  * debian/control:  
+    - Updated Standards-Version to 3.8.0.
+    - Enhances: emboss (EMBOSS has a wrapper for clustalw, `emma'.)
+  * debian/clustaw.1*: incremented version number.
+
+ -- Charles Plessy <plessy at debian.org>  Tue, 24 Jun 2008 13:28:22 +0900
+
 clustalw (2.0.8-1) unstable; urgency=low
 
   * New upstream release.

Modified: trunk/packages/clustalw/trunk/debian/clustalw.1
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1	2008-07-01 19:54:32 UTC (rev 2118)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1	2008-07-02 02:06:40 UTC (rev 2119)
@@ -1,11 +1,11 @@
 .\"     Title: CLUSTALW
 .\"    Author: Des Higgins
 .\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\"      Date: 06/04/2008
+.\"      Date: 06/24/2008
 .\"    Manual: Clustal Manual
-.\"    Source: Clustal 2.0.8
+.\"    Source: Clustal 2.0.9
 .\"
-.TH "CLUSTALW" "1" "06/04/2008" "Clustal 2.0.8" "Clustal Manual"
+.TH "CLUSTALW" "1" "06/24/2008" "Clustal 2.0.9" "Clustal Manual"
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)

Modified: trunk/packages/clustalw/trunk/debian/clustalw.1.xml
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1.xml	2008-07-01 19:54:32 UTC (rev 2118)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1.xml	2008-07-02 02:06:40 UTC (rev 2119)
@@ -18,7 +18,7 @@
   <!ENTITY dhsurname   "Plessy">
   <!ENTITY dhemail     "plessy at debian.org">
   <!ENTITY dhusername  "&dhfirstname; &dhsurname;">
-  <!ENTITY dhrelease   "2.0.8">
+  <!ENTITY dhrelease   "2.0.9">
   <!ENTITY dhtitle     "Clustal Manual">
   <!ENTITY dhucpackage "CLUSTALW">
   <!ENTITY dhpackage   "clustalw">

Added: trunk/packages/clustalw/trunk/debian/compat
===================================================================
--- trunk/packages/clustalw/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/clustalw/trunk/debian/compat	2008-07-02 02:06:40 UTC (rev 2119)
@@ -0,0 +1 @@
+5

Modified: trunk/packages/clustalw/trunk/debian/control
===================================================================
--- trunk/packages/clustalw/trunk/debian/control	2008-07-01 19:54:32 UTC (rev 2118)
+++ trunk/packages/clustalw/trunk/debian/control	2008-07-02 02:06:40 UTC (rev 2119)
@@ -5,7 +5,7 @@
 DM-Upload-Allowed: yes
 Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>
 Build-Depends: debhelper (>= 5), cdbs, autotools-dev
-Standards-Version: 3.7.3
+Standards-Version: 3.8.0
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/clustalw/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/clustalw/trunk/
 XS-Autobuild: yes
@@ -15,7 +15,7 @@
 Architecture: any
 Depends: ${shlibs:Depends}
 Suggests: clustalx, seaview
-Enhances: t-coffee
+Enhances: emboss, t-coffee
 Description: global multiple nucleotide or peptide sequence alignment
  This program performs an alignment of multiple nucleotide or amino acid
  sequences. It recognizes the format of input sequences and whether the

Modified: trunk/packages/clustalw/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalw/trunk/debian/copyright	2008-07-01 19:54:32 UTC (rev 2118)
+++ trunk/packages/clustalw/trunk/debian/copyright	2008-07-02 02:06:40 UTC (rev 2119)
@@ -2,7 +2,15 @@
 Upstream-Author: Des Higgins, Julie Thompson and Toby Gibson
 Packaged-By: Stephane Bortzmeyer <bortzmeyer at debian.org>
 Packaged-Date: Fri, 28 Aug 1998 16:09:48 +0200
-Original-Source-Location: http://www.clustal.org/download/current/clustalw-2.0.7-src.tar.gz
+Original-Source-Location: http://www.clustal.org/download/current/clustalw-2.0.9-src.tar.gz
+
+X-Non-Free-Disclamer: This package is not part of the Debian operating system.
+ The clustalw source and binary Debian packages are part of the "non-free" area
+ in our archive. The packages in this area are not part of the Debian system,
+ although they have been configured for use with Debian. We nevertheless
+ support the use of the clustalw source and binary Debian pacakges and provide
+ infrastructure for non-free packages (such as our bug tracking system and
+ mailing lists). 
 X-Non-Free-Autobuild: yes
   The licence does not forbid Debian from using autobuilders to create binary
   packages.

Deleted: trunk/packages/clustalw/trunk/debian/patches/series
===================================================================
--- trunk/packages/clustalw/trunk/debian/patches/series	2008-07-01 19:54:32 UTC (rev 2118)
+++ trunk/packages/clustalw/trunk/debian/patches/series	2008-07-02 02:06:40 UTC (rev 2119)
@@ -1 +0,0 @@
-to_build_with_g++-4.3.patch

Deleted: trunk/packages/clustalw/trunk/debian/patches/to_build_with_g++-4.3.patch
===================================================================
--- trunk/packages/clustalw/trunk/debian/patches/to_build_with_g++-4.3.patch	2008-07-01 19:54:32 UTC (rev 2118)
+++ trunk/packages/clustalw/trunk/debian/patches/to_build_with_g++-4.3.patch	2008-07-02 02:06:40 UTC (rev 2119)
@@ -1,15 +0,0 @@
-Author: Charles Plessy <plessy at debian.org>
-Forwarded: clustalw at ucd.ie
-Description: Adds a header necessary to g++-4.3
- This patch has been accepted upstream and will be removed with clustalw 2.0.9.
-License: Use, copy, modify, distribute as if in public domain.
---- clustalw-2.0.8.orig/src/general/UserParameters.cpp
-+++ clustalw-2.0.8/src/general/UserParameters.cpp
-@@ -14,6 +14,7 @@
- #include <stdlib.h>
- #include <exception>
- #include <iostream>
-+#include <climits>
- //#include <limits>
- #include <iomanip>
- #include <fstream>


