[med-svn] r8929 - in trunk/packages: autodock-vina/trunk/debian biomaj/trunk/debian python-pynast/trunk/debian rosetta rosetta/trunk/debian rosetta/trunk/debian/patches snap/trunk/debian

Mon Dec 12 21:31:02 UTC 2011

Author: moeller
Date: 2011-12-12 21:31:02 +0000 (Mon, 12 Dec 2011)
New Revision: 8929

Added:
   trunk/packages/rosetta/trunk-antibody/
Modified:
   trunk/packages/autodock-vina/trunk/debian/changelog
   trunk/packages/autodock-vina/trunk/debian/control
   trunk/packages/autodock-vina/trunk/debian/rules
   trunk/packages/biomaj/trunk/debian/control
   trunk/packages/python-pynast/trunk/debian/README.Debian
   trunk/packages/rosetta/trunk/debian/patches/series
   trunk/packages/rosetta/trunk/debian/rules
   trunk/packages/snap/trunk/debian/changelog
Log:
Series of local changes accidentially left uncommitted before.
 * somewhat neat but unnecessary formatting changes
 * adding uploader from upstream to vina
 * rosetta build instructions
 * pynast more verbose README.Debian
 * snap changelog mentions upload to PPA


Modified: trunk/packages/autodock-vina/trunk/debian/changelog
===================================================================

--- trunk/packages/autodock-vina/trunk/debian/changelog	2011-12-12 17:35:01 UTC (rev 8928)
+++ trunk/packages/autodock-vina/trunk/debian/changelog	2011-12-12 21:31:02 UTC (rev 8929)
@@ -3,6 +3,8 @@
   * debian/copyright: Upstream-Contact changed and DEP5
   * debian/patches/fix_boost.patch: Description of patch incl.
     forewarded upstream
+  [Steffen Moeller]
+  * Added Stefano Forli to uploaders.
 
  -- Andreas Tille <tille at debian.org>  Mon, 28 Nov 2011 13:52:29 +0100
 

Modified: trunk/packages/autodock-vina/trunk/debian/control
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/control	2011-12-12 17:35:01 UTC (rev 8928)
+++ trunk/packages/autodock-vina/trunk/debian/control	2011-12-12 21:31:02 UTC (rev 8929)
@@ -6,7 +6,8 @@
 Uploaders: Steffen Moeller <moeller at debian.org>,
  Yask Gupta <yask.gupta87 at gmail.com>,
  Michael Banck <mbanck at debian.org>,
- Andreas Tille <tille at debian.org>
+ Andreas Tille <tille at debian.org>,
+ Stefano Forli <ntropia at gmail.com>
 Build-Depends: debhelper (>= 8), libboost-all-dev
 Standards-Version: 3.9.2
 Homepage: http://vina.scripps.edu

Modified: trunk/packages/autodock-vina/trunk/debian/rules
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/rules	2011-12-12 17:35:01 UTC (rev 8928)
+++ trunk/packages/autodock-vina/trunk/debian/rules	2011-12-12 21:31:02 UTC (rev 8929)
@@ -6,7 +6,8 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
-CFLAGS=-fpermissive -DBOOST_FILESYSTEM_VERSION=2
+CFLAGS=-fpermissive -DBOOST_FILESYSTEM_VERSION=2 --lto
+LDFLAGS=--lto
 CXXFLAGS=$(CFLAGS)
 
 %:

Modified: trunk/packages/biomaj/trunk/debian/control
===================================================================
--- trunk/packages/biomaj/trunk/debian/control	2011-12-12 17:35:01 UTC (rev 8928)
+++ trunk/packages/biomaj/trunk/debian/control	2011-12-12 21:31:02 UTC (rev 8929)
@@ -18,7 +18,8 @@
 
 Package: biomaj
 Architecture: all
-Depends: openjdk-6-jdk|default-jdk|sun-java6-jdk, ant, libmysql-java, debconf, ${misc:Depends}, ${java:Depends},
+Depends: ${misc:Depends}, ${java:Depends},
+ openjdk-6-jdk|default-jdk|sun-java6-jdk, ant, libmysql-java, debconf, 
  libhsqldb-java,ant-contrib,liblog4j1.2-java,libcommons-net2-java (>= 2.2),libcommons-dbcp-java (>= 1.2),
  libgnumail-java, libcommons-pool-java (>= 1.5), libgnujaf-java, libjgoodies-forms-java (>= 1.2),
  liboro-java (>= 2.0),libregexp-java (>= 1.4),libjcommon-java (>= 1.0),libjsch-java (>= 0.1.42),
@@ -36,7 +37,7 @@
 Architecture: all
 Depends: ${misc:Depends}
 Description: bank properties file examples
- This package contains a set of bank properties that can be used
- as examples for biomaj. It contains many existing banks descriptions
- with or without workflows to transform data.
- Some files may required additional programs for post processes (blast..)
+ This package contains a set of bank properties that can be used as
+ examples for biomaj. It contains many existing banks descriptions
+ with or without workflows to transform data.  Some files may required
+ additional programs for post processes (blast..).

Modified: trunk/packages/python-pynast/trunk/debian/README.Debian
===================================================================
--- trunk/packages/python-pynast/trunk/debian/README.Debian	2011-12-12 17:35:01 UTC (rev 8928)
+++ trunk/packages/python-pynast/trunk/debian/README.Debian	2011-12-12 21:31:02 UTC (rev 8929)
@@ -6,4 +6,12 @@
 alignments. Users who wish to exactly match the results of NAST should
 download PyNAST 1.0.
 
+The package is named 'pynast', not 'nast', since that is the name
+of the python module.
+
+A man page for /usr/bin/pynast is still missing. The package
+was build as a dependency to qiime, so some external help as 
+a contribtion to upstream and this Debian package by a rudimentary
+man page would be appreciated.
+
  -- Andreas Tille <tille at debian.org>  Tue, 29 Nov 2011 11:22:19 +0100

Modified: trunk/packages/rosetta/trunk/debian/patches/series
===================================================================
--- trunk/packages/rosetta/trunk/debian/patches/series	2011-12-12 17:35:01 UTC (rev 8928)
+++ trunk/packages/rosetta/trunk/debian/patches/series	2011-12-12 21:31:02 UTC (rev 8929)
@@ -1,2 +1,3 @@
 #pdbinfo.patch
 #builddoc.patch
+gcc4.6_scons.patch

Modified: trunk/packages/rosetta/trunk/debian/rules
===================================================================
--- trunk/packages/rosetta/trunk/debian/rules	2011-12-12 17:35:01 UTC (rev 8928)
+++ trunk/packages/rosetta/trunk/debian/rules	2011-12-12 21:31:02 UTC (rev 8929)
@@ -8,7 +8,7 @@
 #override_dh_auto_build:
 override_dh_auto_build:
 	#scons cxx=gcc mode=release cxx_ver=4.4 -j 12 bin
-	scons cxx=gcc cxx_ver=4.4 -j 12 bin
+	scons cxx=gcc bin
 	#./BuildDocs.sh
 
 override_dh_install:
@@ -31,6 +31,9 @@
 override_dh_strip:
 	dh_strip --dbg-package rosetta-dbg
 
+override_dh_clean:
+	dh_clean
+	rm -rf build
 
 %:
 	dh $@ 

Modified: trunk/packages/snap/trunk/debian/changelog
===================================================================
--- trunk/packages/snap/trunk/debian/changelog	2011-12-12 17:35:01 UTC (rev 8928)
+++ trunk/packages/snap/trunk/debian/changelog	2011-12-12 21:31:02 UTC (rev 8929)
@@ -1,3 +1,9 @@
+snap (2010-07-28-1~lucid1) lucid; urgency=low
+
+  * Building for Debian PPA
+
+ -- Steffen Moeller <moeller at debian.org>  Fri, 17 Jun 2011 00:52:13 +0200
+
 snap (2010-07-28-1) experimental; urgency=low
 
   * Crude initial release, lacking man pages (Closes: #630753).


