[med-svn] r4047 - in trunk/packages/clustalw/trunk: . debian

[Charles Plessy]

Author: plessy
Date: 2009-09-28 07:03:32 +0000 (Mon, 28 Sep 2009)
New Revision: 4047

Modified:
   trunk/packages/clustalw/trunk/CHANGELOG
   trunk/packages/clustalw/trunk/debian/changelog
   trunk/packages/clustalw/trunk/debian/control
   trunk/packages/clustalw/trunk/debian/copyright
   trunk/packages/clustalw/trunk/debian/watch
Log:
Lifting up the package for the new upstream release.

(Still a few things to polish).


Modified: trunk/packages/clustalw/trunk/CHANGELOG
===================================================================
--- trunk/packages/clustalw/trunk/CHANGELOG	2009-09-28 06:32:49 UTC (rev 4046)
+++ trunk/packages/clustalw/trunk/CHANGELOG	2009-09-28 07:03:32 UTC (rev 4047)
@@ -1,4 +1,59 @@
 ----------------------------------------------------------------------
+Version 2.0.12
+----------------------------------------------------------------------
+
+* Fixed bug 189 "Fixed filename used for iteration":
+Now Creating temporary file and added error check
+
+* Fixed bug 180 "Pairwise NJ tree: final bracket missing"
+
+* Fixed bug 178 "Seg-fault on 64bit when -quicktree -upgma for sequences with high identity":
+  Using relative error now to avoid unsafe comparison which led to
+  incorrect branching
+
+* Fixed Bug 176 "iteration doesn't iterate if -usetree is used as well"
+
+* Fixed bug 162 "percent identity file option in clustalW not working":
+Added -pim as command line option. See help
+
+* Fixed bug 155 "upgma trees cannot be read"
+
+* Fixed bug 147 "report duplicate sequences":
+ "ClustalW/X now report offending sequences which are empty, duplicates etc
+
+* Fixed bug 134 "Exit when encountering unrecognized cmdline params":
+ClustalW now exits when encountering invalid values for command line
+arguments instead of just reverting to default values
+
+* Fixed bug 185 "clustal alignments differ between interactive and commandline mode"
+window-gap and ktuple initialisation now fixed and made the same
+between commandline and interactive mode
+
+* Fixed bug 184 "error messages are send to stdout"
+
+* Fixed bug when weights are 0, and nseq > INT_SCALE_FACTOR in UPGMA
+  code (see RootedGuideTree.cpp)
+
+* General code cleanup
+- Introduced return values where control reached end of non-void function
+- Removed unused variables 
+- Removed comparison between signed and unsigned integer expressions
+- Removed deprecated conversion from string constant to char*
+
+
+
+----------------------------------------------------------------------
+Version 2.0.11
+----------------------------------------------------------------------
+
+* fixed file extension bug 166 in interactive mode
+
+* Fixed bug 169, memory violation for DNA/RNA k-tuple
+
+* Cut down distance calculation, symmetric matrix
+
+
+----------------------------------------------------------------------
 Version 2.0.10
 ----------------------------------------------------------------------
 

Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog	2009-09-28 06:32:49 UTC (rev 4046)
+++ trunk/packages/clustalw/trunk/debian/changelog	2009-09-28 07:03:32 UTC (rev 4047)
@@ -1,3 +1,13 @@
+clustalw (2.0.12-1) UNRELEASED; urgency=low
+
+  * New upstream release fixing many bugs
+    (see /usr/share/doc/clustalw CHANGELOG).
+  * Updated debian/watch to latest upstream names.
+  * debian/control:
+    - Added ${misc:Depends} substitition variable.
+
+ -- Charles Plessy <plessy at debian.org>  Mon, 28 Sep 2009 15:56:36 +0900
+
 clustalw (2.0.10-1) unstable; urgency=low
 
   * New upstream release:

Modified: trunk/packages/clustalw/trunk/debian/control
===================================================================
--- trunk/packages/clustalw/trunk/debian/control	2009-09-28 06:32:49 UTC (rev 4046)
+++ trunk/packages/clustalw/trunk/debian/control	2009-09-28 07:03:32 UTC (rev 4047)
@@ -13,7 +13,7 @@
 
 Package: clustalw
 Architecture: any
-Depends: ${shlibs:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}
 Suggests: clustalx, seaview
 Enhances: bioperl-run, emboss, t-coffee
 Description: global multiple nucleotide or peptide sequence alignment

Modified: trunk/packages/clustalw/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalw/trunk/debian/copyright	2009-09-28 06:32:49 UTC (rev 4046)
+++ trunk/packages/clustalw/trunk/debian/copyright	2009-09-28 07:03:32 UTC (rev 4047)
@@ -2,7 +2,7 @@
 Upstream-Author: Des Higgins, Julie Thompson and Toby Gibson
 X-Packaged-By: Stephane Bortzmeyer <bortzmeyer at debian.org>
 X-Packaged-Date: Fri, 28 Aug 1998 16:09:48 +0200
-Original-Source-Location: http://www.clustal.org/download/current/clustalw-2.0.10-src.tar.gz
+Original-Source-Location: http://www.clustal.org/download/current/clustalw-2.0.12.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

Modified: trunk/packages/clustalw/trunk/debian/watch
===================================================================
--- trunk/packages/clustalw/trunk/debian/watch	2009-09-28 06:32:49 UTC (rev 4046)
+++ trunk/packages/clustalw/trunk/debian/watch	2009-09-28 07:03:32 UTC (rev 4047)
@@ -1,2 +1,2 @@
 version=3
-http://www.clustal.org/download/current/clustalw-(.*)-src.tar.gz
+http://www.clustal.org/download/current/clustalw-([\.\d]*).tar.gz