[med-svn] r15807 - in trunk/packages/bioperl/tags: . 1.6.923-1/debian

Charles Plessy plessy at moszumanska.debian.org
Sat Jan 18 02:55:53 UTC 2014


Author: plessy
Date: 2014-01-18 02:55:53 +0000 (Sat, 18 Jan 2014)
New Revision: 15807

Added:
   trunk/packages/bioperl/tags/1.6.923-1/
   trunk/packages/bioperl/tags/1.6.923-1/debian/changelog
   trunk/packages/bioperl/tags/1.6.923-1/debian/control
   trunk/packages/bioperl/tags/1.6.923-1/debian/copyright
Removed:
   trunk/packages/bioperl/tags/1.6.923-1/debian/changelog
   trunk/packages/bioperl/tags/1.6.923-1/debian/control
   trunk/packages/bioperl/tags/1.6.923-1/debian/copyright
Log:
[svn-buildpackage] Tagging bioperl 1.6.923-1

Deleted: trunk/packages/bioperl/tags/1.6.923-1/debian/changelog
===================================================================
--- trunk/packages/bioperl/trunk/debian/changelog	2014-01-04 23:48:58 UTC (rev 15725)
+++ trunk/packages/bioperl/tags/1.6.923-1/debian/changelog	2014-01-18 02:55:53 UTC (rev 15807)
@@ -1,324 +0,0 @@
-bioperl (1.6.922-1) unstable; urgency=low
-
-  * New upstream release.
-  * Replaces and Breaks grinder (<< 0.5.3-3~) because of overlaping contents.
-    Closes: #722910
-  * Stop Replacing and Breaking bioperl ( << 1.6.9 ): not needed anymore. 
-
- -- Charles Plessy <plessy at debian.org>  Sun, 22 Sep 2013 13:39:48 +0900
-
-bioperl (1.6.920-1) unstable; urgency=low
-
-  * New upstream release (Closes: #720776)
-  * Adjusted Depends and Recommends (4 additions).
-  * Removed patch ‘fix_berkeleydb3_temp_file_creation’ applied upstream.
-  * Use canonical VCS URLs. 
-
- -- Charles Plessy <plessy at debian.org>  Sun, 08 Sep 2013 20:56:00 +0900
-
-bioperl (1.6.901-4) unstable; urgency=low
-
-  * debian/upstream: Add additional citation data
-  [ Olivier Sallou ]
-  * add missing dependency
-  * Switch to standards 3.9.4
-
- -- Andreas Tille <tille at debian.org>  Tue, 08 May 2012 23:06:09 +0200
-
-bioperl (1.6.901-3) unstable; urgency=low
-
-  * Team upload.
-    [ Olivier Sallou ]
-    + add patch fix_berkeleydb3_temp_file_creation (Closes: #661793).
-      Fixed upstream for next release. 
-    * debian/control: update Standards version
-    * debian/copyright: update Format to latest officiel URL v1.0
-    * debian/patches/fix_examples_perl_location: fix wrong perl location
-    * debian/rules: fix file access rights in dh_install
-
- -- Olivier Sallou <osallou at debian.org>  Fri, 02 Mar 2012 11:10:36 +0100
-
-bioperl (1.6.901-2) unstable; urgency=low
-
-  [ Luca Capello ]
-  * debian/control:
-    + add Recommends: to some libraries already in libbio-perl-perl's
-      for binaries showing help output (Closes: #650412).
-  * debian/README.Debian:
-    + new file with a more detailed explanation about the above.
-
-  [ Andreas Tille ]
-  * debian/source/format: 3.0 (quilt)
-  * Added myself to Uploaders
-
- -- Andreas Tille <tille at debian.org>  Wed, 14 Dec 2011 09:11:41 +0100
-
-bioperl (1.6.901-1) unstable; urgency=low
-
-  * New upstream release.
-  * Point debian/watch to search.cpan.org.
-  * Build using dh and overrides:
-    - Use Debhelper 8 (debian/rules, debian/control).
-    - Simplified debian/rules.
-  * Split into libbio-perl-perl, as discussed with the Debian Perl team.
-    (debian/control, debian/bioperl.install, debian libbio-perl-perl.install)
-  * debian/control:
-    - Incremented Standards-Version to reflect conformance with Policy 3.9.2.
-      No other changes needed.
-    - Vcs-Browser URL made redirectable to viewvc.
-    - Removed useless ‘svn’ in the Vcs-Svn URL.
-
- -- Charles Plessy <plessy at debian.org>  Fri, 17 Jun 2011 13:51:18 +0900
-
-bioperl (1.6.1-2) unstable; urgency=low
-
-  * Removed bibliographic information from the long description
-    (debian/control).
-  * Incremented Standards-Version to reflect conformance with Policy 3.8.4
-    (debian/control, no changes needed).
-  * Build-depends on libxml-sax-expatxs-perl to avoid downloading DTDs during
-    the tests and therefore fail when network is not available
-    (debian/control, Closes: #562442).
-  * Depend on the ${misc:Depends} substvar (debian/control).
-
- -- Charles Plessy <plessy at debian.org>  Fri, 26 Feb 2010 23:52:23 +0900
-
-bioperl (1.6.1-1) unstable; urgency=low
-
-  * New upstream release with new features and many corrections in the
-    test suite (Closes: #533976).
-  * debian/rules: trigger network tests with DEB_MAINTAINER_MODE.
-  * debian/control:
-    - Build-depend on perl-modules >= 5.10.1 to have ExtUtils::Manifest 1.52 or
-      higher, and on libtest-pod-perl.
-    - Added liblist-moreutils-perl, libspreadsheet-writeexcel-perl,
-      libsvg-perl, and libxml-simple-perl, libdbd-pg-perl, libdbd-mysql-perl,
-      libdbd-sqlite3-perl to build and package dependencies (needed by some
-      components of Bioperl, and therefore for the tests).
-
- -- Charles Plessy <plessy at debian.org>  Wed, 30 Sep 2009 18:56:42 +0900
-
-bioperl (1.6.0-3) unstable; urgency=low
-
-  [ David Paleino ]
-  * Removed myself from Uploaders
-
-  [ Charles Plessy ]
-  * debian/control:
-    - Added libdata-stag-perl in bioperl’s Depends field, since it is
-      required in Build.PL.
-    - Added libxml-simple-perl in bioperl’s Recommends and Build-Depends
-      fields, since they are listed in DEPENDENCIES.
-    - Incremented Standards-Version to reflect conformance with Policy 3.8.3
-      (no changes needed).
-  * Collected some informations in debian/upstream-metadata.yaml.
-
- -- Charles Plessy <plessy at debian.org>  Fri, 18 Sep 2009 20:23:51 +0900
-
-bioperl (1.6.0-2) unstable; urgency=low
-
-  * Removed patch system (not used):
-    - removed instructions in debian/rules;
-    - removed quilt from Build-Depends in debian/control.
-  * Re-enabled tests:
-    - uncommented test command in debian/rules;
-    - uncommented previously missing build-dependencies in debian/control.
-    - Re-enabled tests and uncommented build-dependencies accordingly.
-  * Removed libmodule-build-perl and libtest-harness-perl from
-    Build-Depends-Indep (provided by perl-modules).
-  * Better cleaning of empty directories using find -type d -empty -delete
-    instead of rmdir in debian/rules (LP: #324001).
-
- -- Charles Plessy <plessy at debian.org>  Tue, 10 Mar 2009 07:19:11 +0100
-
-bioperl (1.6.0-1) experimental; urgency=low
-
-  [ Charles Plessy ]
-  * debian/control
-    - Updated dependencies according to the new upstream release.
-    - Added the CPAN dependencies of BioPerl to Build-Depends-Indep in order to
-      run the tests at build time.
-    - Added bioperl-run to the recommended packages.
-    - Updated my email address.
-    - Uses Debhelper 7 (debian/compat modified accordingly).
-  * debian/patches: removed as not needed (no downloads by default).
-  * debian/rules:
-    - Uses Build.PL instead of Makefile.PL.
-    - Tests disabled for the experimental upload: not all dependencies are
-      available yet.
-  * debian/README.{Debian,source}: removed as not needed anymore
-  * debian/watch: BioPerl is now mixed case.
-
-  [ David Paleino ]
-  * New upstream stable release:
-    - fixes Bio::AlignIO::next_aln bug (Closes: #266921).
-    - New modules, deprecated modules,… please consult Upstream documents in
-      /usr/share/doc/bioperl.
-  * debian/control:
-    - fields values rewrapped to easily spot diffs in commit mails
-    - dropped B-D-I versioning on perl, since Etch already has a greater 
-      version
-    - Standards-Version bumped to 3.8.0 (no changes needed).
-
- -- Charles Plessy <plessy at debian.org>  Mon, 26 Jan 2009 12:58:28 +0900
-
-bioperl (1.5.2.102-3) unstable; urgency=low
-
-  * debian/control:
-    - Removed MIA Matt Hope (dopey) from the Uploaders field.
-      Thank you for your work, Matt. I hope you are doing well.
-    - Downgraded some recommended package to the 'Suggests' priority,
-      according to the following discussion on Upstream's mail list.
-      http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html
-      (Closes: #448890)
-  * debian/copyright converted to machine-readable format.
-
- -- Charles Plessy <charles-debian-nospam at plessy.org>  Tue, 18 Mar 2008 14:44:57 +0900
-
-bioperl (1.5.2.102-2) unstable; urgency=low
-
-  [ Steffen Moeller ]
-  * Added reference to libsvg-graph-perl (Closes: #342475).
-
-  [ Nelson A. de Oliveira ]
-  * debian/control:
-    - Removed the XS- prefix from Vcs-Browser and Vcs-Svn
-    - Moved debhelper and quilt from Build-Depends-Indep to Build-Depends
-  * Updated debian/copyright
-
-  [ David Paleino ]
-  * debian/control:
-    - updated Recommends (libpostscript-textblock-perl won't exist -
-      the package will be named libpostscript-perl)
-    - fields wrapped at around 80 columns
-    - added myself to Uploaders
-    - added libio-string-perl to Build-Depends-Indep (Closes: #453923)
-    - fixed Vcs-* fields
-    - removed XS- from DM-Upload-Allowed
-  * debian/changelog:
-    - fixing incorrect first line (leading tab)
-  * debian/rules updated
-  * debian/dirs removed (passing arguments to dh_installdirs directly)
-
- -- David Paleino <d.paleino at gmail.com>  Wed, 06 Feb 2008 12:01:15 +0100
-
-bioperl (1.5.2.102-1) unstable; urgency=low
-
-  * Developer release.
-  * Upgraded source package to debhelper 5 and standards-version 3.7.2.
-  * Added libmodule-build-perl and libtest-harness-perl to
-    build-depends-indep.
-  * Disabled automatic CPAN download.
-  * Using quilt instead of .diff.gz to manage modifications.
-  * Updated Recommends list for the binary package.
-  * Moved the "production-quality" scripts to /usr/bin/.
-  * New maintainer: Debian-Med packaging team mailing list.
-  * New uploaders: Charles Plessy and Steffen Moeller.
-  * Updated Depends, Recommends and Suggests.
-  * Imported in Debian-Med's SVN repository on Alioth.
-  * Executing the regression tests during package building.
-  * Moved the Homepage: field out from the package's description.
-  * Updated watch file.
-
- -- Charles Plessy <charles-debian-nospam at plessy.org>  Fri, 21 Sep 2007 22:52:22 +0900
-
-bioperl (1.4-1) unstable; urgency=low
-
-  * New upstream release
-  * Examples and working code are installed by default to usr/bin,
-    this has been moved to usr/share/doc/bioperl/bin
-
- -- Matt Hope <matth at bioinformatics.unsw.edu.au>  Sun, 18 Apr 2004 14:24:11 +1000
-
-bioperl (1.2.1-2) unstable; urgency=low
-
-  * Updated dependencies to libgd-gd2-perl
-    (Closes: Bug#192210)
-  * Same maintainer, different email address
-
- -- Matt Hope <matth at bioinformatics.unsw.edu.au>  Mon, 30 Jun 2003 23:40:59 +1000
-
-bioperl (1.2.1-1) unstable; urgency=low
-
-  * New upstream release
-  * Added more Depends/Recommends.
-  * Added Depend: libio-string-perl
-    (Closes: Bug#188395)
-
- -- Matt Hope <dopey at debian.org>  Sat,  3 May 2003 01:21:54 +1000
-
-bioperl (1.2-1) unstable; urgency=low
-
-  * New upstream release
-
- -- Matt Hope <dopey at debian.org>  Fri, 25 Apr 2003 12:30:10 +1000
-
-bioperl (1.0.2-1) unstable; urgency=low
-
-  * *Another* new upstream release.
-
- -- Matt Hope <dopey at debian.org>  Wed, 17 Jul 2002 09:58:09 +1000
-
-bioperl (1.0.1-1) unstable; urgency=low
-
-  * New upstream release
-
- -- Matt Hope <dopey at debian.org>  Sat, 29 Jun 2002 22:35:08 +1000
-
-bioperl (1.0-1) unstable; urgency=low
-
-  * New upstream release
-
- -- Matt Hope <dopey at debian.org>  Wed, 20 Mar 2002 01:16:30 +1100
-
-bioperl (0.7.2-1) unstable; urgency=low
-
-  * New upstream release.
-  * Adopted by new maintainer; closes: #100208
-  * Fixed lintian errors.
-
- -- Matt Hope <dopey at quickstix.com.au>  Thu, 22 Nov 2001 19:31:26 +1100
-
-bioperl (0.7.1-1) unstable; urgency=low
-
-  * Maintainer set to Debian QA Group <packages at qa.debian.org>.
-  * New upstream release.
-
- -- Adrian Bunk <bunk at fs.tum.de>  Fri, 24 Aug 2001 20:47:57 +0200
-
-bioperl (0.7.0-1) unstable; urgency=low
-
-  * New upstream release; closes: #44245
-
- -- Dr. Guenter Bechly <gbechly at debian.org>  Sat,  5 May 2001 18:35:44 +0200
-
-bioperl (0.05.1-3) unstable; urgency=low
-
-  * Fixed compliance with perl policy; closes: #95880, #95418 
-
- -- Dr. Guenter Bechly <gbechly at debian.org>  Tue,  1 May 2001 08:13:09 +0200
-
-bioperl (0.05.1-2) unstable; urgency=low
-
-  * Adopted by new maintainer; closes: #92806
-  * Updated to latest standards version and added Build-Depends (changed
-    control, copyright, dirs, docs, and rules);
-    closes: #70154, #91121, #91397
-  * Fixed some lintian errors in rules.
-  * Moved package to section non-free/science, because it is a tool that
-    is exclusively useful for molecular biologists.
-
- -- Dr. Guenter Bechly <gbechly at debian.org>  Fri, 20 Apr 2001 19:48:05 +0200
-
-bioperl (0.05.1-1) unstable; urgency=low
-
-  * Complies with the new Perl policy. Closes #40564
-  * New upstream release
-
- -- Stephane Bortzmeyer <bortzmeyer at debian.org>  Wed,  7 Jul 1999 14:49:16 +0200
-
-bioperl (0.05-1) unstable; urgency=low
-
-  * Initial Release.
-
- -- Stephane Bortzmeyer <bortzmeyer at debian.org>  Wed, 19 May 1999 11:35:30 +0200

Copied: trunk/packages/bioperl/tags/1.6.923-1/debian/changelog (from rev 15806, trunk/packages/bioperl/trunk/debian/changelog)
===================================================================
--- trunk/packages/bioperl/tags/1.6.923-1/debian/changelog	                        (rev 0)
+++ trunk/packages/bioperl/tags/1.6.923-1/debian/changelog	2014-01-18 02:55:53 UTC (rev 15807)
@@ -0,0 +1,334 @@
+bioperl (1.6.923-1) unstable; urgency=medium
+
+  * New upstream release.
+  * Does not need non-free libmath-random-perl anymore.
+  * Build-depend on libmodule-build-perl (>= 0.420000).  Despite Lintian's
+    warning that it is useless, the package does not build without.
+  * Conforms to Policy version 3.9.5.
+
+ -- Charles Plessy <plessy at debian.org>  Sat, 18 Jan 2014 11:41:11 +0900
+
+bioperl (1.6.922-1) unstable; urgency=low
+
+  * New upstream release.
+  * Replaces and Breaks grinder (<< 0.5.3-3~) because of overlaping contents.
+    Closes: #722910
+  * Stop Replacing and Breaking bioperl ( << 1.6.9 ): not needed anymore. 
+
+ -- Charles Plessy <plessy at debian.org>  Sun, 22 Sep 2013 13:39:48 +0900
+
+bioperl (1.6.920-1) unstable; urgency=low
+
+  * New upstream release (Closes: #720776)
+  * Adjusted Depends and Recommends (4 additions).
+  * Removed patch ‘fix_berkeleydb3_temp_file_creation’ applied upstream.
+  * Use canonical VCS URLs. 
+
+ -- Charles Plessy <plessy at debian.org>  Sun, 08 Sep 2013 20:56:00 +0900
+
+bioperl (1.6.901-4) unstable; urgency=low
+
+  * debian/upstream: Add additional citation data
+  [ Olivier Sallou ]
+  * add missing dependency
+  * Switch to standards 3.9.4
+
+ -- Andreas Tille <tille at debian.org>  Tue, 08 May 2012 23:06:09 +0200
+
+bioperl (1.6.901-3) unstable; urgency=low
+
+  * Team upload.
+    [ Olivier Sallou ]
+    + add patch fix_berkeleydb3_temp_file_creation (Closes: #661793).
+      Fixed upstream for next release. 
+    * debian/control: update Standards version
+    * debian/copyright: update Format to latest officiel URL v1.0
+    * debian/patches/fix_examples_perl_location: fix wrong perl location
+    * debian/rules: fix file access rights in dh_install
+
+ -- Olivier Sallou <osallou at debian.org>  Fri, 02 Mar 2012 11:10:36 +0100
+
+bioperl (1.6.901-2) unstable; urgency=low
+
+  [ Luca Capello ]
+  * debian/control:
+    + add Recommends: to some libraries already in libbio-perl-perl's
+      for binaries showing help output (Closes: #650412).
+  * debian/README.Debian:
+    + new file with a more detailed explanation about the above.
+
+  [ Andreas Tille ]
+  * debian/source/format: 3.0 (quilt)
+  * Added myself to Uploaders
+
+ -- Andreas Tille <tille at debian.org>  Wed, 14 Dec 2011 09:11:41 +0100
+
+bioperl (1.6.901-1) unstable; urgency=low
+
+  * New upstream release.
+  * Point debian/watch to search.cpan.org.
+  * Build using dh and overrides:
+    - Use Debhelper 8 (debian/rules, debian/control).
+    - Simplified debian/rules.
+  * Split into libbio-perl-perl, as discussed with the Debian Perl team.
+    (debian/control, debian/bioperl.install, debian libbio-perl-perl.install)
+  * debian/control:
+    - Incremented Standards-Version to reflect conformance with Policy 3.9.2.
+      No other changes needed.
+    - Vcs-Browser URL made redirectable to viewvc.
+    - Removed useless ‘svn’ in the Vcs-Svn URL.
+
+ -- Charles Plessy <plessy at debian.org>  Fri, 17 Jun 2011 13:51:18 +0900
+
+bioperl (1.6.1-2) unstable; urgency=low
+
+  * Removed bibliographic information from the long description
+    (debian/control).
+  * Incremented Standards-Version to reflect conformance with Policy 3.8.4
+    (debian/control, no changes needed).
+  * Build-depends on libxml-sax-expatxs-perl to avoid downloading DTDs during
+    the tests and therefore fail when network is not available
+    (debian/control, Closes: #562442).
+  * Depend on the ${misc:Depends} substvar (debian/control).
+
+ -- Charles Plessy <plessy at debian.org>  Fri, 26 Feb 2010 23:52:23 +0900
+
+bioperl (1.6.1-1) unstable; urgency=low
+
+  * New upstream release with new features and many corrections in the
+    test suite (Closes: #533976).
+  * debian/rules: trigger network tests with DEB_MAINTAINER_MODE.
+  * debian/control:
+    - Build-depend on perl-modules >= 5.10.1 to have ExtUtils::Manifest 1.52 or
+      higher, and on libtest-pod-perl.
+    - Added liblist-moreutils-perl, libspreadsheet-writeexcel-perl,
+      libsvg-perl, and libxml-simple-perl, libdbd-pg-perl, libdbd-mysql-perl,
+      libdbd-sqlite3-perl to build and package dependencies (needed by some
+      components of Bioperl, and therefore for the tests).
+
+ -- Charles Plessy <plessy at debian.org>  Wed, 30 Sep 2009 18:56:42 +0900
+
+bioperl (1.6.0-3) unstable; urgency=low
+
+  [ David Paleino ]
+  * Removed myself from Uploaders
+
+  [ Charles Plessy ]
+  * debian/control:
+    - Added libdata-stag-perl in bioperl’s Depends field, since it is
+      required in Build.PL.
+    - Added libxml-simple-perl in bioperl’s Recommends and Build-Depends
+      fields, since they are listed in DEPENDENCIES.
+    - Incremented Standards-Version to reflect conformance with Policy 3.8.3
+      (no changes needed).
+  * Collected some informations in debian/upstream-metadata.yaml.
+
+ -- Charles Plessy <plessy at debian.org>  Fri, 18 Sep 2009 20:23:51 +0900
+
+bioperl (1.6.0-2) unstable; urgency=low
+
+  * Removed patch system (not used):
+    - removed instructions in debian/rules;
+    - removed quilt from Build-Depends in debian/control.
+  * Re-enabled tests:
+    - uncommented test command in debian/rules;
+    - uncommented previously missing build-dependencies in debian/control.
+    - Re-enabled tests and uncommented build-dependencies accordingly.
+  * Removed libmodule-build-perl and libtest-harness-perl from
+    Build-Depends-Indep (provided by perl-modules).
+  * Better cleaning of empty directories using find -type d -empty -delete
+    instead of rmdir in debian/rules (LP: #324001).
+
+ -- Charles Plessy <plessy at debian.org>  Tue, 10 Mar 2009 07:19:11 +0100
+
+bioperl (1.6.0-1) experimental; urgency=low
+
+  [ Charles Plessy ]
+  * debian/control
+    - Updated dependencies according to the new upstream release.
+    - Added the CPAN dependencies of BioPerl to Build-Depends-Indep in order to
+      run the tests at build time.
+    - Added bioperl-run to the recommended packages.
+    - Updated my email address.
+    - Uses Debhelper 7 (debian/compat modified accordingly).
+  * debian/patches: removed as not needed (no downloads by default).
+  * debian/rules:
+    - Uses Build.PL instead of Makefile.PL.
+    - Tests disabled for the experimental upload: not all dependencies are
+      available yet.
+  * debian/README.{Debian,source}: removed as not needed anymore
+  * debian/watch: BioPerl is now mixed case.
+
+  [ David Paleino ]
+  * New upstream stable release:
+    - fixes Bio::AlignIO::next_aln bug (Closes: #266921).
+    - New modules, deprecated modules,… please consult Upstream documents in
+      /usr/share/doc/bioperl.
+  * debian/control:
+    - fields values rewrapped to easily spot diffs in commit mails
+    - dropped B-D-I versioning on perl, since Etch already has a greater 
+      version
+    - Standards-Version bumped to 3.8.0 (no changes needed).
+
+ -- Charles Plessy <plessy at debian.org>  Mon, 26 Jan 2009 12:58:28 +0900
+
+bioperl (1.5.2.102-3) unstable; urgency=low
+
+  * debian/control:
+    - Removed MIA Matt Hope (dopey) from the Uploaders field.
+      Thank you for your work, Matt. I hope you are doing well.
+    - Downgraded some recommended package to the 'Suggests' priority,
+      according to the following discussion on Upstream's mail list.
+      http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html
+      (Closes: #448890)
+  * debian/copyright converted to machine-readable format.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Tue, 18 Mar 2008 14:44:57 +0900
+
+bioperl (1.5.2.102-2) unstable; urgency=low
+
+  [ Steffen Moeller ]
+  * Added reference to libsvg-graph-perl (Closes: #342475).
+
+  [ Nelson A. de Oliveira ]
+  * debian/control:
+    - Removed the XS- prefix from Vcs-Browser and Vcs-Svn
+    - Moved debhelper and quilt from Build-Depends-Indep to Build-Depends
+  * Updated debian/copyright
+
+  [ David Paleino ]
+  * debian/control:
+    - updated Recommends (libpostscript-textblock-perl won't exist -
+      the package will be named libpostscript-perl)
+    - fields wrapped at around 80 columns
+    - added myself to Uploaders
+    - added libio-string-perl to Build-Depends-Indep (Closes: #453923)
+    - fixed Vcs-* fields
+    - removed XS- from DM-Upload-Allowed
+  * debian/changelog:
+    - fixing incorrect first line (leading tab)
+  * debian/rules updated
+  * debian/dirs removed (passing arguments to dh_installdirs directly)
+
+ -- David Paleino <d.paleino at gmail.com>  Wed, 06 Feb 2008 12:01:15 +0100
+
+bioperl (1.5.2.102-1) unstable; urgency=low
+
+  * Developer release.
+  * Upgraded source package to debhelper 5 and standards-version 3.7.2.
+  * Added libmodule-build-perl and libtest-harness-perl to
+    build-depends-indep.
+  * Disabled automatic CPAN download.
+  * Using quilt instead of .diff.gz to manage modifications.
+  * Updated Recommends list for the binary package.
+  * Moved the "production-quality" scripts to /usr/bin/.
+  * New maintainer: Debian-Med packaging team mailing list.
+  * New uploaders: Charles Plessy and Steffen Moeller.
+  * Updated Depends, Recommends and Suggests.
+  * Imported in Debian-Med's SVN repository on Alioth.
+  * Executing the regression tests during package building.
+  * Moved the Homepage: field out from the package's description.
+  * Updated watch file.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Fri, 21 Sep 2007 22:52:22 +0900
+
+bioperl (1.4-1) unstable; urgency=low
+
+  * New upstream release
+  * Examples and working code are installed by default to usr/bin,
+    this has been moved to usr/share/doc/bioperl/bin
+
+ -- Matt Hope <matth at bioinformatics.unsw.edu.au>  Sun, 18 Apr 2004 14:24:11 +1000
+
+bioperl (1.2.1-2) unstable; urgency=low
+
+  * Updated dependencies to libgd-gd2-perl
+    (Closes: Bug#192210)
+  * Same maintainer, different email address
+
+ -- Matt Hope <matth at bioinformatics.unsw.edu.au>  Mon, 30 Jun 2003 23:40:59 +1000
+
+bioperl (1.2.1-1) unstable; urgency=low
+
+  * New upstream release
+  * Added more Depends/Recommends.
+  * Added Depend: libio-string-perl
+    (Closes: Bug#188395)
+
+ -- Matt Hope <dopey at debian.org>  Sat,  3 May 2003 01:21:54 +1000
+
+bioperl (1.2-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Matt Hope <dopey at debian.org>  Fri, 25 Apr 2003 12:30:10 +1000
+
+bioperl (1.0.2-1) unstable; urgency=low
+
+  * *Another* new upstream release.
+
+ -- Matt Hope <dopey at debian.org>  Wed, 17 Jul 2002 09:58:09 +1000
+
+bioperl (1.0.1-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Matt Hope <dopey at debian.org>  Sat, 29 Jun 2002 22:35:08 +1000
+
+bioperl (1.0-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Matt Hope <dopey at debian.org>  Wed, 20 Mar 2002 01:16:30 +1100
+
+bioperl (0.7.2-1) unstable; urgency=low
+
+  * New upstream release.
+  * Adopted by new maintainer; closes: #100208
+  * Fixed lintian errors.
+
+ -- Matt Hope <dopey at quickstix.com.au>  Thu, 22 Nov 2001 19:31:26 +1100
+
+bioperl (0.7.1-1) unstable; urgency=low
+
+  * Maintainer set to Debian QA Group <packages at qa.debian.org>.
+  * New upstream release.
+
+ -- Adrian Bunk <bunk at fs.tum.de>  Fri, 24 Aug 2001 20:47:57 +0200
+
+bioperl (0.7.0-1) unstable; urgency=low
+
+  * New upstream release; closes: #44245
+
+ -- Dr. Guenter Bechly <gbechly at debian.org>  Sat,  5 May 2001 18:35:44 +0200
+
+bioperl (0.05.1-3) unstable; urgency=low
+
+  * Fixed compliance with perl policy; closes: #95880, #95418 
+
+ -- Dr. Guenter Bechly <gbechly at debian.org>  Tue,  1 May 2001 08:13:09 +0200
+
+bioperl (0.05.1-2) unstable; urgency=low
+
+  * Adopted by new maintainer; closes: #92806
+  * Updated to latest standards version and added Build-Depends (changed
+    control, copyright, dirs, docs, and rules);
+    closes: #70154, #91121, #91397
+  * Fixed some lintian errors in rules.
+  * Moved package to section non-free/science, because it is a tool that
+    is exclusively useful for molecular biologists.
+
+ -- Dr. Guenter Bechly <gbechly at debian.org>  Fri, 20 Apr 2001 19:48:05 +0200
+
+bioperl (0.05.1-1) unstable; urgency=low
+
+  * Complies with the new Perl policy. Closes #40564
+  * New upstream release
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org>  Wed,  7 Jul 1999 14:49:16 +0200
+
+bioperl (0.05-1) unstable; urgency=low
+
+  * Initial Release.
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org>  Wed, 19 May 1999 11:35:30 +0200

Deleted: trunk/packages/bioperl/tags/1.6.923-1/debian/control
===================================================================
--- trunk/packages/bioperl/trunk/debian/control	2014-01-04 23:48:58 UTC (rev 15725)
+++ trunk/packages/bioperl/tags/1.6.923-1/debian/control	2014-01-18 02:55:53 UTC (rev 15807)
@@ -1,180 +0,0 @@
-Source: bioperl
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
- Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>,
- Olivier Sallou <osallou at debian.org>
-Build-Depends: debhelper (>= 9)
-Build-Depends-Indep: perl, perl-modules (>= 5.10.1),
- libio-string-perl,
- libdata-stag-perl,
- libtest-most-perl,
-# Recommended in Build.PL (we want them to run the tests)
- libace-perl,
- libalgorithm-munkres-perl,
- libarray-compare-perl,
- libbio-asn1-entrezgene-perl,
- libbio-samtools-perl,
- libclone-perl,
- libconvert-binary-c-perl,
- libdbd-sqlite3-perl,
- libdbd-mysql-perl,
- libdbd-pg-perl,
- libgd-perl,
- libgraph-perl,
- libgraphviz-perl,
- libhtml-parser-perl,
- libhtml-tableextract-perl,
- liblist-moreutils-perl,
-# (non-free) libmath-random-perl,
- libpostscript-perl,
- libset-scalar-perl,
- libsoap-lite-perl,
- libsort-naturally-perl,
- libspreadsheet-parseexcel-perl,
- libspreadsheet-writeexcel-perl,
- libstorable-perl,
- libsvg-perl,
- libsvg-graph-perl,
- libtest-pod-perl,
- liburi-perl,
- libxml-dom-xpath-perl,
- libxml-parser-perl,
- libxml-sax-perl,
- libxml-sax-writer-perl,
- libxml-twig-perl,
- libxml-simple-perl,
- libxml-writer-perl,
- libxml-libxml-perl,
- libwww-perl,
-# Needed to avoid downloading DTDs during the tests and therefore fail when network is not available:
- libxml-sax-expatxs-perl
-Standards-Version: 3.9.4
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/bioperl/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/bioperl/trunk/
-Homepage: http://www.bioperl.org/
-
-Package: bioperl
-Architecture: all
-Depends: libbio-perl-perl ( = ${source:Version} ), ${misc:Depends}, ${perl:Depends}
-Recommends: bioperl-run ( >= 1.6.0 ),
-# for the following see #650412
-# most of `binary -help` outputs
- perl-doc,
-# some libraries already in libbio-perl-perl's Recommends:
-# bp_biofetch_genbank_proxy
- libhttp-message-perl,
- libwww-perl,
- libcache-cache-perl,
-# bp_blast2tree
- libbio-perl-run-perl,
-# bp_bulk_load_gff
- libdbi-perl,
-# bp_chaos_plot
- libgd-gd2-perl,
-# bp_das_server
- libapache-dbi-perl,
-# bp_download_query_genbank
- liburi-perl,
-# bp_einfo
-#	liburi-perl
-#	libhttp-message-perl
- libxml-simple-perl,
-# bp_fast_load_gff
-#	libdbi-perl
-# bp_fetch [not for local indexing]
-# bp_flanks
-#	libhttp-message-perl
-# bp_genbank2gff
-#	libhttp-message-perl
-#	libdbi-perl
-# bp_genbank2gff3
- libyaml-perl,
-# bp_hivq
-#	libhttp-message-perl
-#	libxml-simple-perl
-# bp_meta_gff
-#	libdbi-perl
-# bp_netinstall
-# bp_pairwise_kaks
-#	libbio-perl-run-perl
-# bp_process_wormbase
- libace-perl,
-# bp_query_entrez_taxa
-# bp_remote_blast
-# bp_revtrans-motif
- liblist-moreutils-perl,
-# bp_taxid4species
- libxml-twig-perl,
-# bp_taxonomy2tree
- libset-scalar-perl
-Suggests: groff-base
-Description: Perl tools for computational molecular biology
- The Bioperl project is a coordinated effort to collect computational methods
- routinely used in bioinformatics into a set of standard CPAN-style,
- well-documented, and freely available Perl modules. It is well-accepted
- throughout the community and used in many high-profile projects, e.g.,
- Ensembl.
- .
- The recommended packages are needed to run some of the included
- binaries, for a detailed explanation including the specific Perl
- modules please see README.Debian.
- .
- The suggested package enhances the manual pages.
-
-Package: libbio-perl-perl
-Section: perl
-Architecture: all
-Depends: libio-string-perl, libdata-stag-perl, ${misc:Depends}, ${perl:Depends}
-Replaces: grinder (<< 0.5.3-3~)
-Breaks: grinder (<< 0.5.3-3~)
-# Temporary workaround as bioperl-run has not been split
-Recommends: bioperl-run ( >= 1.6.0 ) | libbio-perl-run-perl ( >= 1.6.0 ),
-# Recommended in Build.PL
- libace-perl,
- libalgorithm-munkres-perl,
- libarray-compare-perl,
- libbio-asn1-entrezgene-perl,
- libclone-perl,
- libconvert-binary-c-perl,
- libdbd-sqlite3-perl,
- libdbd-mysql-perl,
- libdbd-pg-perl,
- libgd-perl,
- libgraph-perl,
- libgraphviz-perl,
- libhtml-parser-perl,
- libhtml-tableextract-perl,
- liblist-moreutils-perl,
-# (non-free) libmath-random-perl,
- libpostscript-perl,
- libset-scalar-perl,
- libsoap-lite-perl,
- libsort-naturally-perl,
- libspreadsheet-parseexcel-perl,
- libspreadsheet-writeexcel-perl,
- libstorable-perl,
- libsvg-perl,
- libsvg-graph-perl,
- liburi-perl,
- libxml-dom-xpath-perl,
- libxml-parser-perl,
- libxml-sax-perl,
- libxml-sax-writer-perl,
- libxml-simple-perl,
- libxml-twig-perl,
- libxml-writer-perl,
- libxml-libxml-perl,
- libwww-perl
-Suggests: bioperl,
- libmath-random-perl,
-# libmath-random-perl is non-free.
- libxml-sax-expatxs-perl
-# Needed to avoid downloading DTDs.
-Description: BioPerl core perl modules
- BioPerl is a toolkit of perl modules useful in building bioinformatics
- solutions in Perl. It is built in an object-oriented manner so that many
- modules depend on each other to achieve a task. The collection of modules in
- libbio-perl-perl consist of the core of the functionality of bioperl.

Copied: trunk/packages/bioperl/tags/1.6.923-1/debian/control (from rev 15806, trunk/packages/bioperl/trunk/debian/control)
===================================================================
--- trunk/packages/bioperl/tags/1.6.923-1/debian/control	                        (rev 0)
+++ trunk/packages/bioperl/tags/1.6.923-1/debian/control	2014-01-18 02:55:53 UTC (rev 15807)
@@ -0,0 +1,178 @@
+Source: bioperl
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <plessy at debian.org>,
+ Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>,
+ Olivier Sallou <osallou at debian.org>
+Build-Depends: debhelper (>= 9)
+Build-Depends-Indep: perl, perl-modules (>= 5.10.1),
+# Unnecessary according to lintian, but building with sbuild shows the contrary.
+ libmodule-build-perl (>= 0.420000),
+ libio-string-perl,
+ libdata-stag-perl,
+ libtest-most-perl,
+# Recommended in Build.PL (we want them to run the tests)
+ libace-perl,
+ libalgorithm-munkres-perl,
+ libarray-compare-perl,
+ libbio-asn1-entrezgene-perl,
+ libbio-samtools-perl,
+ libclone-perl,
+ libconvert-binary-c-perl,
+ libdbd-sqlite3-perl,
+ libdbd-mysql-perl,
+ libdbd-pg-perl,
+ libgd-perl,
+ libgraph-perl,
+ libgraphviz-perl,
+ libhtml-parser-perl,
+ libhtml-tableextract-perl,
+ liblist-moreutils-perl,
+ libpostscript-perl,
+ libset-scalar-perl,
+ libsoap-lite-perl,
+ libsort-naturally-perl,
+ libspreadsheet-parseexcel-perl,
+ libspreadsheet-writeexcel-perl,
+ libstorable-perl,
+ libsvg-perl,
+ libsvg-graph-perl,
+ libtest-pod-perl,
+ liburi-perl,
+ libxml-dom-xpath-perl,
+ libxml-parser-perl,
+ libxml-sax-perl,
+ libxml-sax-writer-perl,
+ libxml-twig-perl,
+ libxml-simple-perl,
+ libxml-writer-perl,
+ libxml-libxml-perl,
+ libwww-perl,
+# Needed to avoid downloading DTDs during the tests and therefore fail when network is not available:
+ libxml-sax-expatxs-perl
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/bioperl/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/bioperl/trunk/
+Homepage: http://www.bioperl.org/
+
+Package: bioperl
+Architecture: all
+Depends: libbio-perl-perl ( = ${source:Version} ), ${misc:Depends}, ${perl:Depends}
+Recommends: bioperl-run ( >= 1.6.0 ),
+# for the following see #650412
+# most of `binary -help` outputs
+ perl-doc,
+# some libraries already in libbio-perl-perl's Recommends:
+# bp_biofetch_genbank_proxy
+ libhttp-message-perl,
+ libwww-perl,
+ libcache-cache-perl,
+# bp_blast2tree
+ libbio-perl-run-perl,
+# bp_bulk_load_gff
+ libdbi-perl,
+# bp_chaos_plot
+ libgd-gd2-perl,
+# bp_das_server
+ libapache-dbi-perl,
+# bp_download_query_genbank
+ liburi-perl,
+# bp_einfo
+#	liburi-perl
+#	libhttp-message-perl
+ libxml-simple-perl,
+# bp_fast_load_gff
+#	libdbi-perl
+# bp_fetch [not for local indexing]
+# bp_flanks
+#	libhttp-message-perl
+# bp_genbank2gff
+#	libhttp-message-perl
+#	libdbi-perl
+# bp_genbank2gff3
+ libyaml-perl,
+# bp_hivq
+#	libhttp-message-perl
+#	libxml-simple-perl
+# bp_meta_gff
+#	libdbi-perl
+# bp_netinstall
+# bp_pairwise_kaks
+#	libbio-perl-run-perl
+# bp_process_wormbase
+ libace-perl,
+# bp_query_entrez_taxa
+# bp_remote_blast
+# bp_revtrans-motif
+ liblist-moreutils-perl,
+# bp_taxid4species
+ libxml-twig-perl,
+# bp_taxonomy2tree
+ libset-scalar-perl
+Suggests: groff-base
+Description: Perl tools for computational molecular biology
+ The Bioperl project is a coordinated effort to collect computational methods
+ routinely used in bioinformatics into a set of standard CPAN-style,
+ well-documented, and freely available Perl modules. It is well-accepted
+ throughout the community and used in many high-profile projects, e.g.,
+ Ensembl.
+ .
+ The recommended packages are needed to run some of the included
+ binaries, for a detailed explanation including the specific Perl
+ modules please see README.Debian.
+ .
+ The suggested package enhances the manual pages.
+
+Package: libbio-perl-perl
+Section: perl
+Architecture: all
+Depends: libio-string-perl, libdata-stag-perl, ${misc:Depends}, ${perl:Depends}
+Replaces: grinder (<< 0.5.3-3~)
+Breaks: grinder (<< 0.5.3-3~)
+# Temporary workaround as bioperl-run has not been split
+Recommends: bioperl-run ( >= 1.6.0 ) | libbio-perl-run-perl ( >= 1.6.0 ),
+# Recommended in Build.PL
+ libace-perl,
+ libalgorithm-munkres-perl,
+ libarray-compare-perl,
+ libbio-asn1-entrezgene-perl,
+ libclone-perl,
+ libconvert-binary-c-perl,
+ libdbd-sqlite3-perl,
+ libdbd-mysql-perl,
+ libdbd-pg-perl,
+ libgd-perl,
+ libgraph-perl,
+ libgraphviz-perl,
+ libhtml-parser-perl,
+ libhtml-tableextract-perl,
+ liblist-moreutils-perl,
+ libpostscript-perl,
+ libset-scalar-perl,
+ libsoap-lite-perl,
+ libsort-naturally-perl,
+ libspreadsheet-parseexcel-perl,
+ libspreadsheet-writeexcel-perl,
+ libstorable-perl,
+ libsvg-perl,
+ libsvg-graph-perl,
+ liburi-perl,
+ libxml-dom-xpath-perl,
+ libxml-parser-perl,
+ libxml-sax-perl,
+ libxml-sax-writer-perl,
+ libxml-simple-perl,
+ libxml-twig-perl,
+ libxml-writer-perl,
+ libxml-libxml-perl,
+ libwww-perl
+Suggests: bioperl,
+ libxml-sax-expatxs-perl
+# Needed to avoid downloading DTDs.
+Description: BioPerl core perl modules
+ BioPerl is a toolkit of perl modules useful in building bioinformatics
+ solutions in Perl. It is built in an object-oriented manner so that many
+ modules depend on each other to achieve a task. The collection of modules in
+ libbio-perl-perl consist of the core of the functionality of bioperl.

Deleted: trunk/packages/bioperl/tags/1.6.923-1/debian/copyright
===================================================================
--- trunk/packages/bioperl/trunk/debian/copyright	2014-01-04 23:48:58 UTC (rev 15725)
+++ trunk/packages/bioperl/tags/1.6.923-1/debian/copyright	2014-01-18 02:55:53 UTC (rev 15807)
@@ -1,221 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Source: http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz
-
-Files: *
-Copyright: The Bioperl developers.
- PRIMARY AUTHORS AND MAJOR CONTRIBUTORS TO BIOPERL
-       Releases co-ordinated and submitted by bioperl core devs.
- .
- .
-       * Ewan Birney <birney at ebi.ac.uk>
-       * Chris Dagdigian <dag at sonsorol.org>
-       * Hilmar Lapp <hlapp at gmx.net>
-       * Heikki Lehväslaiho <heikki at ebi.ac.uk>
-       * Jason Stajich <jason at bioperl.org>
-       * Lincoln Stein <lstein at cshl.org>
- .
-       Previous Bioperl Coordinators:
- .
- .
-       * Steven Brenner <brenner at compbio.berkely.edu>
-       * Georg Fuellen <fuellen at alum.mit.edu>
-       * Steve Chervitz <sac at bioperl.org>
- .
-       Major Contributors
- .
-       * Richard Adams <Richard.Adams at ed.ac.uk>
-       * Shuly Avraham <avraham at cshl.org> - Bio::Graphics::Glyph
-       * Sendu Bala <bix at sendu.me.uk>
-       * Peter Blaiklock <pblaiklo at restrictionmapper.org>
-       * Benjamin Berman <benb at fruitfly.berkeley.edu>
-       * Matthew Betts <Matthew.Betts at ii.uib.no>
-       * David Block <dblock at gnf.org>
-       * Kris Boulez <kris.boulez at algonomics.com>
-       * Tim Bunce <Tim.Bunce at pobox.com> - code optimizations
-       * Scott Cain <cain at cshl.org> - Bio::Graphics::Glyph
-       * Yee Man Chan <ymc at yahoo.com> - Bio::Tools::dpAlign
-       * Brad Chapman <chapmanb at arches.uga.edu>
-       * Michele Clamp <michele at sanger.ac.uk>
-       * Tony Cox <avc at sanger.ac.uk>
-       * James Cuff <james at sanger.ac.uk>
-       * Andrew Dalke <dalke at acm.org>
-       * Allen Day <allenday at ucla.edu>
-       * Jared Fox <jaredfox at ucla.edu> - Bio::SeqIO::interpro
-       * Brian O’Connor <boconnor at ucla.edu> - Bio::TreeIO::svggraph
-       * James Diggans <JDiggans at genelogic.com>
-       * Peter Dimitrov <dimitrov at gnf.org> - Bio::Ontology
-       * Rich Dobson <r.j.dobson at qmul.ac.uk> - Bio::Pop‐Gen::IO::hapmap,phase
-       * Paul Edlefsen <pedlefsen at systemsbiology.org>
-       * Rob Edwards <redwards at utmem.edu> - Bio::Restriction
-       * Arne Elofsson <arne at sbc.su.se>
-       * David Evans <David.Evans at vir.gla.ac.uk>
-       * Christopher Fields <cjfields at uiuc.edu>
-       * Mark Fiers <M.W.E.J.Fiers at plant.wag-ur.nl>
-       * The Fugu Team <fuguteam at fugu-sg.org>
-       * Luc Gauthier <lgauthie at hotmail.com>
-       * James Gilbert <jgrg at sanger.ac.uk>
-       * Nat Goodman
-       * Ed Green <ed at compbio.berkeley.edu>
-       * Matthew Hahn <matthew.hahn at duke.edu>
-       * Roger Hall <roger at iosea.com>
-       * Todd Harris <harris at cshl.org> - SVG support in Bio::Graphics
-       * Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx>
-       * Ian Holmes <ihn at fruitfly.org>
-       * Shawn Hoon <shawnh at fugu-sg.org>
-       * Robert Hubley <rhubley at systemsbiology.org>
-       * Joseph Insana <insana at ebi.ac.uk> - Bio::LiveSeq
-       * Donald Jackson <donald.jackson at bms.com> - SiRNA
-       * Keith James <kdj at sanger.ac.uk> - Bio::Tools::Geneid
-       * Nicolas Joly <njoly at pasteur.fr>
-       * Ian Korf <ikorf at sapiens.wustl.edu>
-       * Dan Kortschak <kortschak at rsbs.anu.edu.au>
-       * Arek Kasprzyk <arek at ebi.ac.uk>
-       * Andreas Kähäri <andreas.kahari at ebi.ac.uk>
-       * Charles C. Kim <cckim at stanford.edu>
-       * Stefan Kirov <skirov at utk.edu> - Bio::Matrix::PSM
-       * Balamurugan Kumarasamy <savikalpa at fugu-sg.org>
-       * Josh Lauricha <laurichj at cs.ucr.edu> - Bio::SeqIO::tigr
-       * Eckhard Lehmann <ecky at e-lehmann.de>
-       * Catherine Letondal <letondal at pasteur.fr>
-       * Philip Lijnzaad <p.lijnzaad at med.uu.nl>
-       * Aaron Mackey <amackey at pcbi.upenn.edu>
-       * Brad Marshall <bradmars at yahoo.com>
-       * Chad Matsalla <chad at dieselwurks.com>
-       * Andrew Macgregor <andrew at anatomy.otago.ac.nz>
-       * Sheldon McKay <mckays at cshl.edu>
-       * Juha Muilu <muilu at ebi.ac.uk>
-       * Chris Mungall <cjm at fruitfly.org>
-       * Giri Narasimhan <giri at cs.fiu.edu>
-       * Brian Osborne <bosborne at alum.mit.edu>
-       * Xiaokang Pan <pan at cshl.org> - Bio::Graphics::Glyph
-       * Jong Park
-       * Matthew Pocock <matthew_pocock at yahoo.co.uk>
-       * Lorenz Pollack <lorenz at ist.org> -- BPlite porting
-       * Richard Resnick -- original Bio::Seq
-       * Todd Richmond <todd at andrew2.stanford.edu>
-       * Peter Schattner <schattner at alum.mit.edu>
-       * Torsten Seemann <torsten.seemann at infotech.monash.edu.au> -- Bio::Tools::Run::StandaloneBlast
-       * Martin Senger <senger at ebi.ac.uk> -- Bio::Biblio
-       * Nigam Shah <nigam at psu.edu>
-       * Shengqiang Shu <sshu at bdgp.lbl.gov> - Bio::Graphics::Glyph
-       * Allen Smith <allens at cpan.org> -- Bio::Matrix and Bio::SimpleAlign fixes
-       * Marc Sohrmann <ms2 at sanger.ac.uk>
-       * Robson Francisco de Souza <rfsouza at citri.iq.usp.br> - Bio::Assem‐bly
-       * Mark Southern <mark_southern at merck.com>
-       * Will Spooner <whs at sanger.ac.uk>
-       * Arne Stabenau <stabenau at ebi.ac.uk>
-       * Elia Stupka <elia at fugu-sg.org>
-       * Gert Thijs <gert.thijs at esat.kuleuven.ac.be>
-       * James Thompson <tex at biosysadmin.com> - Bio::Matrix::PSM protein-related modules.
-       * Charles Tilford <tilfordc at bms.com>
-       * Anthony Underwood <aunderwood at phls.org.uk>
-       * Paul-Christophe Varoutas
-       * Andrew G. Walsh <paeruginosa at hotmail.com>
-       * Kai Wang <tumorimmunology at yahoo.com>
-       * Gary Williams <G.Williams at hgmp.mrc.ac.uk>
-       * Mark Wilkinson <mwilkinson at gene.pbi.nrc.ca>
-       * Helge Weissig <helgew at sdsc.edu>
-       * Juguang Xiao <juguang at tll.org.sg>
-       * Alex Zelensky <alex_zelensky at mac.com> - Bioperl-DB
-       * Peili Zhang <peili at morgan.harvard.edu>
-       * Christian M. Zmasek <czmasek at gnf.org> - Bio::Phenotype & Bio::Ontology
-License: Perl
-Comment:
- Everyone can use it! We don't care if you are academic, corporate, or
- government. BioPerl is licensed under the same terms as Perl itself, which
- means it is dually-licensed under either the Artistic or GPL licenses. The Perl
- Artistic License, or the GNU GPL covers all the legalese and what you can and
- can't do with the source code.
- .
- We do appreciate:
- .
-  * You letting us know you sell or use a product that uses BioPerl. This helps
-    us show people how useful our toolkit is. It also helps us if we seek funding
-    from a government source, to identify the utility of the code to many different
-    groups of users. Add your project and institution to our BioPerl Users page.
- .
-  * If you fix bugs, please let us know about them. Because Bioperl is
-    dual-licensed under the GPL or Artistic licenses, you can choose the Artistic
-    license, which means that you are not required to submit the code fixes, but in
-    the spirit of making a better product we hope you'll contribute back to the
-    community any insight or code improvements.
- . 
-  * Please include the AUTHORS file and ascribe credit to the original BioPerl
-    toolkit where appropriate.
- . 
-  * If you are an academic and you use the software, please cite the article.
-    See the BioPerl publications for a list of papers which describe components in
-    the toolkit. 
-URL: see http://www.bioperl.org/wiki/Licensing_BioPerl
-
-Files: t/lib/Error.pm
-Copyright: © 1997-8 Graham Barr <gbarr at ti.com>
-License: Perl
-
-Files: t/lib/Test/Builder/Tester/Color.pm
-License: Perl
-Copyright: © 2002 Mark Fowler <mark at twoshortplanks.com>
-
-Files: Bio/SeqIO/bsml.pm
-Copyright: © 2001 Charles Tilford <tilfordc at bms.com>
-License: LGPL-2.1+
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
- .
- This library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- Lesser General Public License for more details.
- .
- You should have received a copy of the GNU Lesser General Public
- License along with this library; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
-Comment: On Debian systems, the complete text of the GNU Lesser General Public
- License version 2.1 can be found in ‘/usr/share/common-licenses/LGPL-2.1’.
-
-Files: Bio/SeqIO/msout.pm Bio/SeqIO/mbsout.pm
-Copyright: Public Domain work
-License: public-domain
- This software/database is ``United States Government Work'' under the
- terms of the United States Copyright Act. It was written as part of
- the authors' official duties for the United States Government and thus
- cannot be copyrighted. This software/database is freely available to
- the public for use without a copyright notice. Restrictions cannot
- be placed on its present or future use.
- .
- Although all reasonable efforts have been taken to ensure the accuracy
- and reliability of the software and data, the National Human Genome
- Research Institute (NHGRI) and the U.S. Government does not and cannot
- warrant the performance or results that may be obtained by using this
- software or data.  NHGRI and the U.S. Government disclaims all
- warranties as to performance, merchantability or fitness for any
- particular purpose.
-
-License: Perl
- This program is free software; you can redistribute it and/or modify
- it under the terms of either:
- .
- a) the GNU General Public License as published by the Free Software
-    Foundation; either version 1, or (at your option) any later
-    version, or
- .
- b) the "Artistic License" which comes with Perl.
-Comment: On Debian systems, the complete text of the Artistic License can be
- found in ‘/usr/share/common-licenses/Artistic’, and the complete text of the
- GNU General Public License version 1 can be found in
- ‘/usr/share/common-licenses/GPL-1’.
-
-Files: debian/*
-Copyright: © 1999 Stéphane Bortzmeyer <bortzmeyer at debian.org>
-           © 2001 Dr. Guenter Bechly <gbechly at debian.org>
-	   © 2001 Adrian Bunk <bunk at fs.tum.de>
-	   © 2001—2004 Matt Hope <dopey at debian.org>
-	   © 2007—2011 Charles Plessy <charles-debian-nospam at plessy.org>
-	   © 2008 David Paleino <d.paleino at gmail.com>
-	   © 2008 Nelson A. de Oliveira <naoliv at debian.org>
-License: unclear
- The license under which is placed the work of the earlier contributors is
- unknown. The work of Charles Plessy can be treated as if it were public
- domain.

Copied: trunk/packages/bioperl/tags/1.6.923-1/debian/copyright (from rev 15806, trunk/packages/bioperl/trunk/debian/copyright)
===================================================================
--- trunk/packages/bioperl/tags/1.6.923-1/debian/copyright	                        (rev 0)
+++ trunk/packages/bioperl/tags/1.6.923-1/debian/copyright	2014-01-18 02:55:53 UTC (rev 15807)
@@ -0,0 +1,221 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz
+
+Files: *
+Copyright: The Bioperl developers.
+ PRIMARY AUTHORS AND MAJOR CONTRIBUTORS TO BIOPERL
+       Releases co-ordinated and submitted by bioperl core devs.
+ .
+ .
+       * Ewan Birney <birney at ebi.ac.uk>
+       * Chris Dagdigian <dag at sonsorol.org>
+       * Hilmar Lapp <hlapp at gmx.net>
+       * Heikki Lehväslaiho <heikki at ebi.ac.uk>
+       * Jason Stajich <jason at bioperl.org>
+       * Lincoln Stein <lstein at cshl.org>
+ .
+       Previous Bioperl Coordinators:
+ .
+ .
+       * Steven Brenner <brenner at compbio.berkely.edu>
+       * Georg Fuellen <fuellen at alum.mit.edu>
+       * Steve Chervitz <sac at bioperl.org>
+ .
+       Major Contributors
+ .
+       * Richard Adams <Richard.Adams at ed.ac.uk>
+       * Shuly Avraham <avraham at cshl.org> - Bio::Graphics::Glyph
+       * Sendu Bala <bix at sendu.me.uk>
+       * Peter Blaiklock <pblaiklo at restrictionmapper.org>
+       * Benjamin Berman <benb at fruitfly.berkeley.edu>
+       * Matthew Betts <Matthew.Betts at ii.uib.no>
+       * David Block <dblock at gnf.org>
+       * Kris Boulez <kris.boulez at algonomics.com>
+       * Tim Bunce <Tim.Bunce at pobox.com> - code optimizations
+       * Scott Cain <cain at cshl.org> - Bio::Graphics::Glyph
+       * Yee Man Chan <ymc at yahoo.com> - Bio::Tools::dpAlign
+       * Brad Chapman <chapmanb at arches.uga.edu>
+       * Michele Clamp <michele at sanger.ac.uk>
+       * Tony Cox <avc at sanger.ac.uk>
+       * James Cuff <james at sanger.ac.uk>
+       * Andrew Dalke <dalke at acm.org>
+       * Allen Day <allenday at ucla.edu>
+       * Jared Fox <jaredfox at ucla.edu> - Bio::SeqIO::interpro
+       * Brian O’Connor <boconnor at ucla.edu> - Bio::TreeIO::svggraph
+       * James Diggans <JDiggans at genelogic.com>
+       * Peter Dimitrov <dimitrov at gnf.org> - Bio::Ontology
+       * Rich Dobson <r.j.dobson at qmul.ac.uk> - Bio::Pop‐Gen::IO::hapmap,phase
+       * Paul Edlefsen <pedlefsen at systemsbiology.org>
+       * Rob Edwards <redwards at utmem.edu> - Bio::Restriction
+       * Arne Elofsson <arne at sbc.su.se>
+       * David Evans <David.Evans at vir.gla.ac.uk>
+       * Christopher Fields <cjfields at uiuc.edu>
+       * Mark Fiers <M.W.E.J.Fiers at plant.wag-ur.nl>
+       * The Fugu Team <fuguteam at fugu-sg.org>
+       * Luc Gauthier <lgauthie at hotmail.com>
+       * James Gilbert <jgrg at sanger.ac.uk>
+       * Nat Goodman
+       * Ed Green <ed at compbio.berkeley.edu>
+       * Matthew Hahn <matthew.hahn at duke.edu>
+       * Roger Hall <roger at iosea.com>
+       * Todd Harris <harris at cshl.org> - SVG support in Bio::Graphics
+       * Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx>
+       * Ian Holmes <ihn at fruitfly.org>
+       * Shawn Hoon <shawnh at fugu-sg.org>
+       * Robert Hubley <rhubley at systemsbiology.org>
+       * Joseph Insana <insana at ebi.ac.uk> - Bio::LiveSeq
+       * Donald Jackson <donald.jackson at bms.com> - SiRNA
+       * Keith James <kdj at sanger.ac.uk> - Bio::Tools::Geneid
+       * Nicolas Joly <njoly at pasteur.fr>
+       * Ian Korf <ikorf at sapiens.wustl.edu>
+       * Dan Kortschak <kortschak at rsbs.anu.edu.au>
+       * Arek Kasprzyk <arek at ebi.ac.uk>
+       * Andreas Kähäri <andreas.kahari at ebi.ac.uk>
+       * Charles C. Kim <cckim at stanford.edu>
+       * Stefan Kirov <skirov at utk.edu> - Bio::Matrix::PSM
+       * Balamurugan Kumarasamy <savikalpa at fugu-sg.org>
+       * Josh Lauricha <laurichj at cs.ucr.edu> - Bio::SeqIO::tigr
+       * Eckhard Lehmann <ecky at e-lehmann.de>
+       * Catherine Letondal <letondal at pasteur.fr>
+       * Philip Lijnzaad <p.lijnzaad at med.uu.nl>
+       * Aaron Mackey <amackey at pcbi.upenn.edu>
+       * Brad Marshall <bradmars at yahoo.com>
+       * Chad Matsalla <chad at dieselwurks.com>
+       * Andrew Macgregor <andrew at anatomy.otago.ac.nz>
+       * Sheldon McKay <mckays at cshl.edu>
+       * Juha Muilu <muilu at ebi.ac.uk>
+       * Chris Mungall <cjm at fruitfly.org>
+       * Giri Narasimhan <giri at cs.fiu.edu>
+       * Brian Osborne <bosborne at alum.mit.edu>
+       * Xiaokang Pan <pan at cshl.org> - Bio::Graphics::Glyph
+       * Jong Park
+       * Matthew Pocock <matthew_pocock at yahoo.co.uk>
+       * Lorenz Pollack <lorenz at ist.org> -- BPlite porting
+       * Richard Resnick -- original Bio::Seq
+       * Todd Richmond <todd at andrew2.stanford.edu>
+       * Peter Schattner <schattner at alum.mit.edu>
+       * Torsten Seemann <torsten.seemann at infotech.monash.edu.au> -- Bio::Tools::Run::StandaloneBlast
+       * Martin Senger <senger at ebi.ac.uk> -- Bio::Biblio
+       * Nigam Shah <nigam at psu.edu>
+       * Shengqiang Shu <sshu at bdgp.lbl.gov> - Bio::Graphics::Glyph
+       * Allen Smith <allens at cpan.org> -- Bio::Matrix and Bio::SimpleAlign fixes
+       * Marc Sohrmann <ms2 at sanger.ac.uk>
+       * Robson Francisco de Souza <rfsouza at citri.iq.usp.br> - Bio::Assem‐bly
+       * Mark Southern <mark_southern at merck.com>
+       * Will Spooner <whs at sanger.ac.uk>
+       * Arne Stabenau <stabenau at ebi.ac.uk>
+       * Elia Stupka <elia at fugu-sg.org>
+       * Gert Thijs <gert.thijs at esat.kuleuven.ac.be>
+       * James Thompson <tex at biosysadmin.com> - Bio::Matrix::PSM protein-related modules.
+       * Charles Tilford <tilfordc at bms.com>
+       * Anthony Underwood <aunderwood at phls.org.uk>
+       * Paul-Christophe Varoutas
+       * Andrew G. Walsh <paeruginosa at hotmail.com>
+       * Kai Wang <tumorimmunology at yahoo.com>
+       * Gary Williams <G.Williams at hgmp.mrc.ac.uk>
+       * Mark Wilkinson <mwilkinson at gene.pbi.nrc.ca>
+       * Helge Weissig <helgew at sdsc.edu>
+       * Juguang Xiao <juguang at tll.org.sg>
+       * Alex Zelensky <alex_zelensky at mac.com> - Bioperl-DB
+       * Peili Zhang <peili at morgan.harvard.edu>
+       * Christian M. Zmasek <czmasek at gnf.org> - Bio::Phenotype & Bio::Ontology
+License: Perl
+Comment:
+ Everyone can use it! We don't care if you are academic, corporate, or
+ government. BioPerl is licensed under the same terms as Perl itself, which
+ means it is dually-licensed under either the Artistic or GPL licenses. The Perl
+ Artistic License, or the GNU GPL covers all the legalese and what you can and
+ can't do with the source code.
+ .
+ We do appreciate:
+ .
+  * You letting us know you sell or use a product that uses BioPerl. This helps
+    us show people how useful our toolkit is. It also helps us if we seek funding
+    from a government source, to identify the utility of the code to many different
+    groups of users. Add your project and institution to our BioPerl Users page.
+ .
+  * If you fix bugs, please let us know about them. Because Bioperl is
+    dual-licensed under the GPL or Artistic licenses, you can choose the Artistic
+    license, which means that you are not required to submit the code fixes, but in
+    the spirit of making a better product we hope you'll contribute back to the
+    community any insight or code improvements.
+ . 
+  * Please include the AUTHORS file and ascribe credit to the original BioPerl
+    toolkit where appropriate.
+ . 
+  * If you are an academic and you use the software, please cite the article.
+    See the BioPerl publications for a list of papers which describe components in
+    the toolkit. 
+URL: see http://www.bioperl.org/wiki/Licensing_BioPerl
+
+Files: t/lib/Error.pm
+Copyright: © 1997-8 Graham Barr <gbarr at ti.com>
+License: Perl
+
+Files: t/lib/Test/Builder/Tester/Color.pm
+License: Perl
+Copyright: © 2002 Mark Fowler <mark at twoshortplanks.com>
+
+Files: Bio/SeqIO/bsml.pm
+Copyright: © 2001 Charles Tilford <tilfordc at bms.com>
+License: LGPL-2.1+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ .
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+Comment: On Debian systems, the complete text of the GNU Lesser General Public
+ License version 2.1 can be found in ‘/usr/share/common-licenses/LGPL-2.1’.
+
+Files: Bio/SeqIO/msout.pm Bio/SeqIO/mbsout.pm
+Copyright: Public Domain work
+License: public-domain
+ This software/database is ``United States Government Work'' under the
+ terms of the United States Copyright Act. It was written as part of
+ the authors' official duties for the United States Government and thus
+ cannot be copyrighted. This software/database is freely available to
+ the public for use without a copyright notice. Restrictions cannot
+ be placed on its present or future use.
+ .
+ Although all reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the National Human Genome
+ Research Institute (NHGRI) and the U.S. Government does not and cannot
+ warrant the performance or results that may be obtained by using this
+ software or data.  NHGRI and the U.S. Government disclaims all
+ warranties as to performance, merchantability or fitness for any
+ particular purpose.
+
+License: Perl
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of either:
+ .
+ a) the GNU General Public License as published by the Free Software
+    Foundation; either version 1, or (at your option) any later
+    version, or
+ .
+ b) the "Artistic License" which comes with Perl.
+Comment: On Debian systems, the complete text of the Artistic License can be
+ found in ‘/usr/share/common-licenses/Artistic’, and the complete text of the
+ GNU General Public License version 1 can be found in
+ ‘/usr/share/common-licenses/GPL-1’.
+
+Files: debian/*
+Copyright: © 1999 Stéphane Bortzmeyer <bortzmeyer at debian.org>
+           © 2001 Dr. Guenter Bechly <gbechly at debian.org>
+	   © 2001 Adrian Bunk <bunk at fs.tum.de>
+	   © 2001—2004 Matt Hope <dopey at debian.org>
+	   © 2007—2011 Charles Plessy <charles-debian-nospam at plessy.org>
+	   © 2008 David Paleino <d.paleino at gmail.com>
+	   © 2008 Nelson A. de Oliveira <naoliv at debian.org>
+License: unclear
+ The license under which is placed the work of the earlier contributors is
+ unknown. The work of Charles Plessy can be treated as if it were public
+ domain.




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