[med-svn] r9861 - in trunk/packages/bioperl/tags: . 1.6.901-3/debian 1.6.901-3/debian/patches
olivier sallou
osallou-guest at alioth.debian.org
Fri Mar 2 15:40:05 UTC 2012
Author: osallou-guest
Date: 2012-03-02 15:40:04 +0000 (Fri, 02 Mar 2012)
New Revision: 9861
Added:
trunk/packages/bioperl/tags/1.6.901-3/
trunk/packages/bioperl/tags/1.6.901-3/debian/changelog
trunk/packages/bioperl/tags/1.6.901-3/debian/control
trunk/packages/bioperl/tags/1.6.901-3/debian/copyright
trunk/packages/bioperl/tags/1.6.901-3/debian/patches/
trunk/packages/bioperl/tags/1.6.901-3/debian/patches/fix_examples_perl_location
trunk/packages/bioperl/tags/1.6.901-3/debian/patches/series
trunk/packages/bioperl/tags/1.6.901-3/debian/rules
Removed:
trunk/packages/bioperl/tags/1.6.901-3/debian/changelog
trunk/packages/bioperl/tags/1.6.901-3/debian/control
trunk/packages/bioperl/tags/1.6.901-3/debian/copyright
trunk/packages/bioperl/tags/1.6.901-3/debian/patches/series
trunk/packages/bioperl/tags/1.6.901-3/debian/rules
Log:
[svn-buildpackage] Tagging bioperl 1.6.901-3
Deleted: trunk/packages/bioperl/tags/1.6.901-3/debian/changelog
===================================================================
--- trunk/packages/bioperl/trunk/debian/changelog 2012-03-02 05:25:32 UTC (rev 9851)
+++ trunk/packages/bioperl/tags/1.6.901-3/debian/changelog 2012-03-02 15:40:04 UTC (rev 9861)
@@ -1,284 +0,0 @@
-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/1.6.901-3/debian/changelog (from rev 9858, trunk/packages/bioperl/trunk/debian/changelog)
===================================================================
--- trunk/packages/bioperl/tags/1.6.901-3/debian/changelog (rev 0)
+++ trunk/packages/bioperl/tags/1.6.901-3/debian/changelog 2012-03-02 15:40:04 UTC (rev 9861)
@@ -0,0 +1,297 @@
+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/1.6.901-3/debian/control
===================================================================
--- trunk/packages/bioperl/trunk/debian/control 2012-03-02 05:25:32 UTC (rev 9851)
+++ trunk/packages/bioperl/tags/1.6.901-3/debian/control 2012-03-02 15:40:04 UTC (rev 9861)
@@ -1,174 +0,0 @@
-Source: bioperl
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Charles Plessy <plessy at debian.org>,
- Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille 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,
- 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: 3.9.2
-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/1.6.901-3/debian/control (from rev 9854, trunk/packages/bioperl/trunk/debian/control)
===================================================================
--- trunk/packages/bioperl/tags/1.6.901-3/debian/control (rev 0)
+++ trunk/packages/bioperl/tags/1.6.901-3/debian/control 2012-03-02 15:40:04 UTC (rev 9861)
@@ -0,0 +1,174 @@
+Source: bioperl
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy at debian.org>,
+ Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille 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,
+ 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: 3.9.3
+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.
Deleted: trunk/packages/bioperl/tags/1.6.901-3/debian/copyright
===================================================================
--- trunk/packages/bioperl/trunk/debian/copyright 2012-03-02 05:25:32 UTC (rev 9851)
+++ trunk/packages/bioperl/tags/1.6.901-3/debian/copyright 2012-03-02 15:40:04 UTC (rev 9861)
@@ -1,221 +0,0 @@
-Format: http://dep.debian.net/deps/dep5/
-Source: http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.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/1.6.901-3/debian/copyright (from rev 9853, trunk/packages/bioperl/trunk/debian/copyright)
===================================================================
--- trunk/packages/bioperl/tags/1.6.901-3/debian/copyright (rev 0)
+++ trunk/packages/bioperl/tags/1.6.901-3/debian/copyright 2012-03-02 15:40:04 UTC (rev 9861)
@@ -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-1.6.901.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/1.6.901-3/debian/patches/fix_examples_perl_location (from rev 9859, trunk/packages/bioperl/trunk/debian/patches/fix_examples_perl_location)
===================================================================
--- trunk/packages/bioperl/tags/1.6.901-3/debian/patches/fix_examples_perl_location (rev 0)
+++ trunk/packages/bioperl/tags/1.6.901-3/debian/patches/fix_examples_perl_location 2012-03-02 15:40:04 UTC (rev 9861)
@@ -0,0 +1,60 @@
+Subject: fix perl location
+Description: wrong shebang perl location
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 02/03/2012
+--- a/examples/db/getGenBank.pl
++++ b/examples/db/getGenBank.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ #
+ # How to retrieve GenBank entries over the Web
+ #
+--- a/examples/db/get_seqs.pl
++++ b/examples/db/get_seqs.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use vars qw($USAGE);
+ use Carp;
+--- a/examples/generate_random_seq.pl
++++ b/examples/generate_random_seq.pl
+@@ -1,4 +1,4 @@
+-#!/bin/perl
++#!/usr/bin/perl
+ use strict;
+ use vars qw($USAGE);
+
+--- a/examples/searchio/psiblast_features.pl
++++ b/examples/searchio/psiblast_features.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ # Example usage of a SearchIO::psiblast parser of traditional format Blast
+ # and PSI-Blast reports.
+--- a/examples/structure/structure-io.pl
++++ b/examples/structure/structure-io.pl
+@@ -1,4 +1,4 @@
+-#!/bin/perl
++#!/usr/bin/perl
+ # Getting Entry, Chain, Residue, and Atom objects given a PDB file
+
+ use Bio::Structure::IO;
+--- a/examples/tk/hitdisplay.pl
++++ b/examples/tk/hitdisplay.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ #
+ # PROGRAM : hitdisplay.pl
+ # PURPOSE : Demonstrate Bio::Tk::HitDisplay
+--- a/examples/tools/gb_to_gff.pl
++++ b/examples/tools/gb_to_gff.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ use strict;
+
+ use Bio::Tools::GFF;
Deleted: trunk/packages/bioperl/tags/1.6.901-3/debian/patches/series
===================================================================
--- trunk/packages/bioperl/trunk/debian/patches/series 2012-03-02 10:43:54 UTC (rev 9852)
+++ trunk/packages/bioperl/tags/1.6.901-3/debian/patches/series 2012-03-02 15:40:04 UTC (rev 9861)
@@ -1 +0,0 @@
-fix_berkeleydb3_temp_file_creation
Copied: trunk/packages/bioperl/tags/1.6.901-3/debian/patches/series (from rev 9858, trunk/packages/bioperl/trunk/debian/patches/series)
===================================================================
--- trunk/packages/bioperl/tags/1.6.901-3/debian/patches/series (rev 0)
+++ trunk/packages/bioperl/tags/1.6.901-3/debian/patches/series 2012-03-02 15:40:04 UTC (rev 9861)
@@ -0,0 +1,2 @@
+fix_examples_perl_location
+fix_berkeleydb3_temp_file_creation
Deleted: trunk/packages/bioperl/tags/1.6.901-3/debian/rules
===================================================================
--- trunk/packages/bioperl/trunk/debian/rules 2012-03-02 05:25:32 UTC (rev 9851)
+++ trunk/packages/bioperl/tags/1.6.901-3/debian/rules 2012-03-02 15:40:04 UTC (rev 9861)
@@ -1,27 +0,0 @@
-#!/usr/bin/make -f
-
-ifneq (,$(DEB_MAINTAINER_MODE))
-NETWORK = --network
-endif
-
-%:
- dh $@
-
-override_dh_auto_configure:
- dh_auto_configure -- $(NETWORK)
-
-override_dh_clean:
- dh_clean build-stamp install-stamp bioperl.conf biodatabases.pod \
- biodesign.pod bioperl.pod bioscripts.pod
-
-override_dh_install:
- dh_install
- # prename is the rename utility written in perl usually available as /usr/bin/rename in Debian.
- prename s/.pl$$// debian/bioperl/usr/bin/*pl
- prename s/.pl.1p$$/.1p/ debian/bioperl/usr/share/man/man1/*1p
-
-override_dh_installchangelogs:
- dh_installchangelogs Changes
-
-override_dh_installexamples:
- dh_installexamples examples/*
Copied: trunk/packages/bioperl/tags/1.6.901-3/debian/rules (from rev 9860, trunk/packages/bioperl/trunk/debian/rules)
===================================================================
--- trunk/packages/bioperl/tags/1.6.901-3/debian/rules (rev 0)
+++ trunk/packages/bioperl/tags/1.6.901-3/debian/rules 2012-03-02 15:40:04 UTC (rev 9861)
@@ -0,0 +1,28 @@
+#!/usr/bin/make -f
+
+ifneq (,$(DEB_MAINTAINER_MODE))
+NETWORK = --network
+endif
+
+%:
+ dh $@
+
+override_dh_auto_configure:
+ dh_auto_configure -- $(NETWORK)
+
+override_dh_clean:
+ dh_clean build-stamp install-stamp bioperl.conf biodatabases.pod \
+ biodesign.pod bioperl.pod bioscripts.pod
+
+override_dh_install:
+ dh_install
+ # prename is the rename utility written in perl usually available as /usr/bin/rename in Debian.
+ prename s/.pl$$// debian/bioperl/usr/bin/*pl
+ prename s/.pl.1p$$/.1p/ debian/bioperl/usr/share/man/man1/*1p
+ chmod 644 debian/libbio-perl-perl/usr/share/perl5/Bio/DB/HIV/lanl-schema.xml
+
+override_dh_installchangelogs:
+ dh_installchangelogs Changes
+
+override_dh_installexamples:
+ dh_installexamples examples/*
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