[med-svn] r14625 - in trunk/packages/bioperl/tags: . 1.6.920-1/debian 1.6.920-1/debian/patches
Charles Plessy
plessy at alioth.debian.org
Sun Sep 8 12:12:10 UTC 2013
Author: plessy
Date: 2013-09-08 12:12:08 +0000 (Sun, 08 Sep 2013)
New Revision: 14625
Added:
trunk/packages/bioperl/tags/1.6.920-1/
trunk/packages/bioperl/tags/1.6.920-1/debian/changelog
trunk/packages/bioperl/tags/1.6.920-1/debian/compat
trunk/packages/bioperl/tags/1.6.920-1/debian/control
trunk/packages/bioperl/tags/1.6.920-1/debian/patches/series
Removed:
trunk/packages/bioperl/tags/1.6.920-1/debian/changelog
trunk/packages/bioperl/tags/1.6.920-1/debian/compat
trunk/packages/bioperl/tags/1.6.920-1/debian/control
trunk/packages/bioperl/tags/1.6.920-1/debian/patches/fix_berkeleydb3_temp_file_creation
trunk/packages/bioperl/tags/1.6.920-1/debian/patches/series
Log:
[svn-buildpackage] Tagging bioperl 1.6.920-1
Deleted: trunk/packages/bioperl/tags/1.6.920-1/debian/changelog
===================================================================
--- trunk/packages/bioperl/trunk/debian/changelog 2013-09-08 01:16:56 UTC (rev 14618)
+++ trunk/packages/bioperl/tags/1.6.920-1/debian/changelog 2013-09-08 12:12:08 UTC (rev 14625)
@@ -1,306 +0,0 @@
-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/1.6.920-1/debian/changelog (from rev 14624, trunk/packages/bioperl/trunk/debian/changelog)
===================================================================
--- trunk/packages/bioperl/tags/1.6.920-1/debian/changelog (rev 0)
+++ trunk/packages/bioperl/tags/1.6.920-1/debian/changelog 2013-09-08 12:12:08 UTC (rev 14625)
@@ -0,0 +1,315 @@
+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/1.6.920-1/debian/compat
===================================================================
--- trunk/packages/bioperl/trunk/debian/compat 2013-09-08 01:16:56 UTC (rev 14618)
+++ trunk/packages/bioperl/tags/1.6.920-1/debian/compat 2013-09-08 12:12:08 UTC (rev 14625)
@@ -1 +0,0 @@
-8
Copied: trunk/packages/bioperl/tags/1.6.920-1/debian/compat (from rev 14623, trunk/packages/bioperl/trunk/debian/compat)
===================================================================
--- trunk/packages/bioperl/tags/1.6.920-1/debian/compat (rev 0)
+++ trunk/packages/bioperl/tags/1.6.920-1/debian/compat 2013-09-08 12:12:08 UTC (rev 14625)
@@ -0,0 +1 @@
+9
Deleted: trunk/packages/bioperl/tags/1.6.920-1/debian/control
===================================================================
--- trunk/packages/bioperl/trunk/debian/control 2013-09-08 01:16:56 UTC (rev 14618)
+++ trunk/packages/bioperl/tags/1.6.920-1/debian/control 2013-09-08 12:12:08 UTC (rev 14625)
@@ -1,175 +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 (>= 8)
-Build-Depends-Indep: perl, perl-modules (>= 5.10.1),
- libio-string-perl,
- libdata-stag-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,
- libgraph-perl,
- libgraphviz-perl,
- libhtml-parser-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://svn.debian.org/viewvc/debian-med/trunk/packages/bioperl/trunk/
-Vcs-Svn: svn://svn.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: bioperl ( << 1.6.9 )
-Breaks: bioperl ( << 1.6.9 )
-# 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,
- libgraph-perl,
- libgraphviz-perl,
- libhtml-parser-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/1.6.920-1/debian/control (from rev 14623, trunk/packages/bioperl/trunk/debian/control)
===================================================================
--- trunk/packages/bioperl/tags/1.6.920-1/debian/control (rev 0)
+++ trunk/packages/bioperl/tags/1.6.920-1/debian/control 2013-09-08 12:12:08 UTC (rev 14625)
@@ -0,0 +1,180 @@
+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: bioperl ( << 1.6.9 )
+Breaks: bioperl ( << 1.6.9 )
+# 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.
Deleted: trunk/packages/bioperl/tags/1.6.920-1/debian/patches/fix_berkeleydb3_temp_file_creation
===================================================================
--- trunk/packages/bioperl/trunk/debian/patches/fix_berkeleydb3_temp_file_creation 2013-09-08 01:16:56 UTC (rev 14618)
+++ trunk/packages/bioperl/tags/1.6.920-1/debian/patches/fix_berkeleydb3_temp_file_creation 2013-09-08 12:12:08 UTC (rev 14625)
@@ -1,17 +0,0 @@
-Subject: wrong order in file creation
-Description: tie operation has flags and mode in the wrong order.
- Fixed upstream with commit 2b0daf196e0f2acf373c2bc8f0bf2449c36edf40.
- Patch should be removed with next upstream release.
-Author: Olivier Sallou <olivier.sallou at irisa.fr
-Last-Updated: 02/03/2012
---- a/Bio/DB/SeqFeature/Store/berkeleydb3.pm
-+++ b/Bio/DB/SeqFeature/Store/berkeleydb3.pm
-@@ -497,7 +497,7 @@
- my $numeric_cmp = DB_File::BTREEINFO->new;
- $numeric_cmp->{compare} = sub { $_[0] <=> $_[1] };
- $numeric_cmp->{flags} = R_DUP;
-- my $s = tie %sort,'DB_File',$name,0666,O_CREAT|O_RDWR,$numeric_cmp
-+ my $s = tie %sort,'DB_File',$name,O_CREAT|O_RDWR,0666,$numeric_cmp
- or $self->throw("Couldn't create temporary file for sorting: $!");
-
- my $index = $self->index_db('locations');
Deleted: trunk/packages/bioperl/tags/1.6.920-1/debian/patches/series
===================================================================
--- trunk/packages/bioperl/trunk/debian/patches/series 2013-09-08 01:16:56 UTC (rev 14618)
+++ trunk/packages/bioperl/tags/1.6.920-1/debian/patches/series 2013-09-08 12:12:08 UTC (rev 14625)
@@ -1,2 +0,0 @@
-fix_examples_perl_location
-fix_berkeleydb3_temp_file_creation
Copied: trunk/packages/bioperl/tags/1.6.920-1/debian/patches/series (from rev 14621, trunk/packages/bioperl/trunk/debian/patches/series)
===================================================================
--- trunk/packages/bioperl/tags/1.6.920-1/debian/patches/series (rev 0)
+++ trunk/packages/bioperl/tags/1.6.920-1/debian/patches/series 2013-09-08 12:12:08 UTC (rev 14625)
@@ -0,0 +1,2 @@
+fix_examples_perl_location
+#fix_berkeleydb3_temp_file_creation
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