Log of /trunk/packages/bioperl

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Revision 9861 - Directory Listing
Modified Fri Mar 2 15:40:04 2012 UTC (14 months, 2 weeks ago) by osallou-guest

[svn-buildpackage] Tagging bioperl 1.6.901-3

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Revision 9860 - Directory Listing
Modified Fri Mar 2 12:34:14 2012 UTC (14 months, 2 weeks ago) by osallou-guest

fix wrong path in debian build

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Revision 9859 - Directory Listing
Modified Fri Mar 2 12:21:48 2012 UTC (14 months, 2 weeks ago) by osallou-guest

fix perl path in examples

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Revision 9858 - Directory Listing
Modified Fri Mar 2 12:21:10 2012 UTC (14 months, 2 weeks ago) by osallou-guest

fix perl path in examples

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Revision 9857 - Directory Listing
Modified Fri Mar 2 12:20:53 2012 UTC (14 months, 2 weeks ago) by osallou-guest

fix file access right

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Revision 9856 - Directory Listing
Modified Fri Mar 2 12:05:00 2012 UTC (14 months, 2 weeks ago) by osallou-guest

fix email address of changelog

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Revision 9855 - Directory Listing
Modified Fri Mar 2 11:53:39 2012 UTC (14 months, 2 weeks ago) by osallou-guest

add changes info

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Revision 9854 - Directory Listing
Modified Fri Mar 2 11:52:37 2012 UTC (14 months, 2 weeks ago) by osallou-guest

change standards version to 5.9.3

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Revision 9853 - Directory Listing
Modified Fri Mar 2 11:51:38 2012 UTC (14 months, 2 weeks ago) by osallou-guest

change copyright format from DEP5 to new offical v1.0

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Revision 9852 - Directory Listing
Modified Fri Mar 2 10:43:54 2012 UTC (14 months, 2 weeks ago) by osallou-guest

add patch fix_berkeleydb3_temp_file_creation to fix 661793

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Revision 9702 - Directory Listing
Modified Sat Feb 18 01:23:39 2012 UTC (15 months ago) by plessy

debian/upstream: Moved DOI and PMID to the Reference namespace.

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Revision 9492 - Directory Listing
Modified Sun Jan 29 03:35:57 2012 UTC (15 months, 3 weeks ago) by plessy

Renamed debian/upstream-metadata.yaml to debian/upstream.

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Revision 8949 - Directory Listing
Modified Wed Dec 14 11:08:52 2011 UTC (17 months ago) by tille

Tagged 1.6.901-2 and removed historical tags

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Revision 8948 - Directory Listing
Modified Wed Dec 14 09:06:32 2011 UTC (17 months ago) by tille

Applied patch by Luca Capello, source format 3.0 (quilt)

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Revision 7070 - Directory Listing
Modified Fri Jun 17 08:36:14 2011 UTC (23 months ago) by plessy

[svn-buildpackage] Tagging bioperl 1.6.901-1

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Revision 7069 - Directory Listing
Modified Fri Jun 17 08:35:02 2011 UTC (23 months ago) by plessy

Break and replace bioperl accordingly; Uploaded to NEW.

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Revision 7063 - Directory Listing
Modified Fri Jun 17 04:22:05 2011 UTC (23 months ago) by plessy

Found public domain work in the debdiff with version 1.6.1.

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Revision 7060 - Directory Listing
Modified Fri Jun 17 03:58:59 2011 UTC (23 months ago) by plessy

Removed useless ‘svn’ in the Vcs-Svn URL.

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Revision 7059 - Directory Listing
Modified Fri Jun 17 03:56:02 2011 UTC (23 months ago) by plessy

Incremented Standards-Version and modified Vcs-Browser.

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Revision 7058 - Directory Listing
Modified Fri Jun 17 03:53:44 2011 UTC (23 months ago) by plessy

Deleted debian/reference and updated debian/upstream-metadata.yaml.

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Revision 7057 - Directory Listing
Modified Fri Jun 17 00:34:49 2011 UTC (23 months ago) by plessy

Split into libbio-perl-perl, as discussed with the Debian Perl team.

See ‘http://lists.debian.org/debian-perl/2010/02/msg00074.html’.

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Revision 7054 - Directory Listing
Modified Thu Jun 16 23:19:10 2011 UTC (23 months ago) by plessy

Depend and build-depend on libsort-naturally-perl, recommended in “Build.PL”.

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Revision 7053 - Directory Listing
Modified Thu Jun 16 23:05:30 2011 UTC (23 months ago) by plessy

New upstream release again.

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Revision 6949 - Directory Listing
Modified Wed Jun 8 20:59:35 2011 UTC (23 months, 1 week ago) by plessy

Note about DEB_MAINTAINER_MODE.

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Revision 6800 - Directory Listing
Modified Mon May 9 22:45:27 2011 UTC (2 years ago) by plessy

Build using dh and overrides.

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Revision 6799 - Directory Listing
Modified Mon May 9 22:07:48 2011 UTC (2 years ago) by plessy

Converted to DEP-5 and valdiated with ‘config-edit -application dpkg-copyright -ui none’.

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Revision 6798 - Directory Listing
Modified Mon May 9 21:43:29 2011 UTC (2 years ago) by plessy

New bugtracker for BioPerl at OBF.

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Revision 6797 - Directory Listing
Modified Mon May 9 14:08:10 2011 UTC (2 years ago) by plessy

Point debian/watch to search.cpan.org.

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Revision 5177 - Directory Listing
Modified Fri Aug 20 22:57:12 2010 UTC (2 years, 9 months ago) by moeller

Updating version of bioperl1.2.3.

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Revision 4638 - Directory Listing
Modified Fri Feb 26 14:55:00 2010 UTC (3 years, 2 months ago) by plessy

Uploaded.

  * 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).

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Revision 4634 - Directory Listing
Modified Wed Feb 24 04:08:58 2010 UTC (3 years, 2 months ago) by plessy

Added contact information for BioPerl from its README file.

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Revision 4633 - Directory Listing
Modified Wed Feb 24 04:06:59 2010 UTC (3 years, 2 months ago) by plessy

Preparing the upload of either a patched version or a new upstream release.

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Revision 4632 - Directory Listing
Modified Wed Feb 24 03:57:04 2010 UTC (3 years, 2 months ago) by plessy

Revert accidental reversion of compatibility change from version 1.6.0-1.

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Revision 4533 - Directory Listing
Modified Fri Jan 8 14:18:17 2010 UTC (3 years, 4 months ago) by plessy

Fixed a nasty indentation bug.

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Revision 4532 - Directory Listing
Modified Fri Jan 8 13:54:13 2010 UTC (3 years, 4 months ago) by plessy

Corrected another syntax error.

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Revision 4531 - Directory Listing
Modified Fri Jan 8 13:35:23 2010 UTC (3 years, 4 months ago) by plessy

Corrected a syntax error.

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Revision 4508 - Directory Listing
Modified Sun Jan 3 15:18:35 2010 UTC (3 years, 4 months ago) by plessy

Syntax corrections.

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Revision 4187 - Directory Listing
Modified Thu Oct 8 05:03:07 2009 UTC (3 years, 7 months ago) by naoliv

s/Debian-Med/Debian Med

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Revision 4116 - Directory Listing
Modified Fri Oct 2 04:28:53 2009 UTC (3 years, 7 months ago) by plessy

[svn-buildpackage] Tagging bioperl (1.6.1-1)

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Revision 4086 - Directory Listing
Modified Wed Sep 30 10:09:43 2009 UTC (3 years, 7 months ago) by plessy

Last addition to the build-deps (for the tests), spellchecked changelog, and uploaded.

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Revision 4082 - Directory Listing
Modified Wed Sep 30 04:08:05 2009 UTC (3 years, 7 months ago) by plessy

Version 1.6.1 released this morning, waiting for Perl 5.10.1 to be
available in Sid build chroots.

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Revision 4014 - Directory Listing
Modified Wed Sep 23 00:29:08 2009 UTC (3 years, 7 months ago) by plessy

Tested alpha 3 release.

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Revision 4010 - Directory Listing
Modified Tue Sep 22 08:41:11 2009 UTC (3 years, 7 months ago) by plessy

Restored other changes that were reverted by inadvertance.

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Revision 4009 - Directory Listing
Modified Tue Sep 22 08:38:39 2009 UTC (3 years, 7 months ago) by plessy

Added a dependancy removed by mistake.

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Revision 4008 - Directory Listing
Modified Tue Sep 22 08:37:26 2009 UTC (3 years, 7 months ago) by plessy

New upstream release in preparation, adding some new dependancies.

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Revision 4007 - Directory Listing
Modified Tue Sep 22 08:23:20 2009 UTC (3 years, 7 months ago) by plessy

Use DEB_MAINTAINER_MODE to run the network tests.

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Revision 4003 - Directory Listing
Modified Fri Sep 18 11:46:09 2009 UTC (3 years, 8 months ago) by plessy

[svn-buildpackage] Tagging bioperl (1.6.0-3)

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Revision 4002 - Directory Listing
Modified Fri Sep 18 11:45:34 2009 UTC (3 years, 8 months ago) by plessy

Update adding missing dependancies and metadata for experimental purposes.

  * 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).

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Revision 3424 - Directory Listing
Modified Sat May 23 12:52:36 2009 UTC (3 years, 11 months ago) by hanska-guest

Oops, back to UNRELEASED

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Revision 3367 - Directory Listing
Modified Tue May 5 19:05:12 2009 UTC (4 years ago) by hanska-guest

Removed myself from Uploaders

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Revision 3167 - Directory Listing
Modified Tue Mar 10 07:24:16 2009 UTC (4 years, 2 months ago) by plessy

[svn-buildpackage] Tagging bioperl (1.6.0-2)

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Revision 3166 - Directory Listing
Modified Tue Mar 10 07:23:19 2009 UTC (4 years, 2 months ago) by plessy

Uploaded after minor correction of the dependancies.

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Revision 3095 - Directory Listing
Modified Mon Feb 9 04:01:20 2009 UTC (4 years, 3 months ago) by plessy

It was noticed in Ubuntu that 1.6.0-1 actually fails to build from source.

There is a stupid hardcoding in a path, that contains 'powerpc' in its name and
causes a `rm' command to fail on other architectures. This is solved in
1.6.0-2.

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Revision 3059 - Directory Listing
Modified Mon Jan 26 10:36:12 2009 UTC (4 years, 3 months ago) by plessy

Preparation of the non-experimental update.

To be uploaded when all missing build-dependancies will be ready.

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Revision 3058 - Directory Listing
Modified Mon Jan 26 10:15:08 2009 UTC (4 years, 3 months ago) by plessy

[svn-buildpackage] Tagging bioperl (1.6.0-1)

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Revision 3057 - Directory Listing
Modified Mon Jan 26 08:20:47 2009 UTC (4 years, 3 months ago) by plessy

Simplification of build process. Tests disabled and some build-deps removed for experimental upload.

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Revision 3023 - Directory Listing
Modified Mon Jan 19 15:49:10 2009 UTC (4 years, 4 months ago) by plessy

Added libxml-libxml-perl, and tested RC3 (all tests passed).

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Revision 2998 - Directory Listing
Modified Fri Jan 16 10:49:17 2009 UTC (4 years, 4 months ago) by plessy

Sorting out dependancies, reenabling tests, and a bit of cleaning.

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Revision 2991 - Directory Listing
Modified Thu Jan 15 10:28:42 2009 UTC (4 years, 4 months ago) by plessy

Beginning to reorganise the dependancies.

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Revision 2952 - Directory Listing
Modified Sat Jan 10 20:17:35 2009 UTC (4 years, 4 months ago) by hanska-guest

Really add the file. D'oh!

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Revision 2951 - Directory Listing
Modified Sat Jan 10 20:15:17 2009 UTC (4 years, 4 months ago) by hanska-guest

  - Standards-Version bumped to 3.8.0:
    + debian/README.source added

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Revision 2950 - Directory Listing
Modified Sat Jan 10 20:01:41 2009 UTC (4 years, 4 months ago) by hanska-guest

dropped B-D-I versioning on perl, since Etch already has a greater 
version

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Revision 2949 - Directory Listing
Modified Sat Jan 10 20:00:43 2009 UTC (4 years, 4 months ago) by hanska-guest

* debian/control:
  - fields values rewrapped to easily spot diffs in commit mails

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Revision 2948 - Directory Listing
Modified Sat Jan 10 19:52:55 2009 UTC (4 years, 4 months ago) by hanska-guest

TODO: run installation interactively and figure out new dependancies.
  - fixes Bio::AlignIO::next_aln bug (Closes: #266921)

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Revision 2947 - Directory Listing
Modified Sat Jan 10 19:48:49 2009 UTC (4 years, 4 months ago) by hanska-guest

New upstream release

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Revision 2941 - Directory Listing
Modified Sat Jan 10 08:36:46 2009 UTC (4 years, 4 months ago) by plessy

Updated to detect newer versions.

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Revision 2785 - Directory Listing
Modified Mon Dec 15 11:46:53 2008 UTC (4 years, 5 months ago) by plessy

Unclean commit that starts to prepare the 1.6.0 release.

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Revision 2474 - Directory Listing
Modified Thu Sep 11 06:47:42 2008 UTC (4 years, 8 months ago) by plessy

Preparing experimental release of a nightly build version (needed for GBrowse).

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Revision 1813 - Directory Listing
Modified Sun Apr 27 08:15:54 2008 UTC (5 years ago) by plessy

Updated my email address.

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Revision 1707 - Directory Listing
Modified Tue Apr 8 13:35:28 2008 UTC (5 years, 1 month ago) by naoliv

Tagging release 1.5.2.102-3

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Revision 1706 - Directory Listing
Modified Tue Apr 8 13:34:40 2008 UTC (5 years, 1 month ago) by naoliv

Uploaded

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Revision 1701 - Directory Listing
Modified Tue Apr 8 05:27:01 2008 UTC (5 years, 1 month ago) by charles-guest

Corrected redundant entries in the dependancy fields, improved explanation and fixed typo.

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Revision 1649 - Directory Listing
Modified Sat Mar 22 05:16:54 2008 UTC (5 years, 2 months ago) by charles-guest

Downgraded most recommended package to the lower priority, and converted debian/copyright to a machine-readable format.

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Revision 1648 - Directory Listing
Modified Sat Mar 22 04:17:37 2008 UTC (5 years, 2 months ago) by charles-guest

repository cleanup

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Revision 1624 - Directory Listing
Modified Tue Mar 18 05:48:54 2008 UTC (5 years, 2 months ago) by charles-guest

Removed MIA maintainer from Uploaders.

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Revision 1623 - Directory Listing
Modified Tue Mar 18 02:30:47 2008 UTC (5 years, 2 months ago) by naoliv

Tagging release 1.5.2.102-2

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Revision 1622 - Directory Listing
Modified Tue Mar 18 02:28:48 2008 UTC (5 years, 2 months ago) by naoliv

Some more updates in debian/copyright and uploaded

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Revision 1619 - Directory Listing
Modified Tue Mar 18 00:55:11 2008 UTC (5 years, 2 months ago) by naoliv

Still needs to include Copyright and update Upstream authors

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Revision 1604 - Directory Listing
Modified Mon Mar 17 03:06:59 2008 UTC (5 years, 2 months ago) by naoliv

Work in progress.

Needs to finish the copyright file (and take a look at Bio/SeqIO/bsml.pm, t/lib/Error.pm, t/lib/Test/Builder/Tester/Color.pm, as they have a different license, according to licensecheck);

Needs to verify if it's necessary to have /usr/lib/perl5/auto/Bio/ (it's an empty directory)

Forward manpage warnings to upstream (as they seem to be all autogenerated, and some contain errors)

[I will be back in 9 hours more or less, so if someone wants to play with some of these "needs" :-) ]

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Revision 1310 - Directory Listing
Modified Wed Feb 6 11:48:02 2008 UTC (5 years, 3 months ago) by hanska-guest

* Using DM-Upload-Allowed instead of XS-DM-Upload-Allowed
* Added ?rev=0&sc=0 to Vcs-Browser fields
* Sanitized Vcs-* fields

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Revision 1306 - Directory Listing
Modified Wed Feb 6 11:02:02 2008 UTC (5 years, 3 months ago) by hanska-guest

  - fixed Vcs-* fields
  - removed XS- from DM-Upload-Allowed

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Revision 1207 - Directory Listing
Modified Mon Jan 28 01:34:04 2008 UTC (5 years, 3 months ago) by charles-guest

Fixing case mistake

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Revision 1203 - Directory Listing
Modified Sun Jan 27 17:01:17 2008 UTC (5 years, 3 months ago) by hanska-guest

Sorry, forgot to commit it. See previous log for details

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Revision 1202 - Directory Listing
Modified Sun Jan 27 17:00:35 2008 UTC (5 years, 3 months ago) by hanska-guest

Closing 453923 + other small fixes

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Revision 884 - Directory Listing
Modified Sun Dec 9 13:25:23 2007 UTC (5 years, 5 months ago) by charles-guest

+XS-DM-Upload-Allowed: Yes

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Revision 859 - Directory Listing
Modified Fri Nov 23 16:06:33 2007 UTC (5 years, 5 months ago) by smoe-guest

Adding reference to publication.

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Revision 755 - Directory Listing
Modified Sat Nov 3 22:07:16 2007 UTC (5 years, 6 months ago) by naoliv

Small cleanups

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Revision 754 - Directory Listing
Modified Sat Nov 3 20:49:03 2007 UTC (5 years, 6 months ago) by hanska-guest

* 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
* debian/changelog:
  - fixing incorrect first line (leading tab)

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Revision 749 - Directory Listing
Modified Sat Nov 3 17:29:16 2007 UTC (5 years, 6 months ago) by smoe-guest

I had forgotten about this one in my prior upload.

Cheers,

Steffen

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Revision 738 - Directory Listing
Modified Mon Oct 29 20:01:11 2007 UTC (5 years, 6 months ago) by smoe-guest

I am fairly happy with the BioPerl package now as it was just successfully passing
its run through pbuilder. The following lintian warning remain. If someone
has any idea what to do about them ... please go for it.

Many thanks go to Charles for all his work on this!

Steffen

W: bioperl: manpage-has-bad-whatis-entry usr/share/man/man1/bp_make_mrna_protein.1p.gz
W: bioperl: manpage-has-bad-whatis-entry usr/share/man/man1/bp_search2BSML.1p.gz
W: bioperl: manpage-has-bad-whatis-entry usr/share/man/man1/bp_search2gff.1p.gz
W: bioperl: manpage-has-bad-whatis-entry usr/share/man/man1/bp_search2tribe.1p.gz
W: bioperl: manpage-has-bad-whatis-entry usr/share/man/man3/Bio::DB::GFF::Adaptor::biofetch.3pm.gz
W: bioperl: manpage-has-bad-whatis-entry usr/share/man/man3/Bio::SeqIO::agave.3pm.gz
W: bioperl: manpage-has-errors-from-man usr/share/man/man3/Bio::SeqIO::bsml.3pm.gz 409: warning [p 4, 0.3i]: can't break line
W: bioperl: manpage-has-errors-from-man usr/share/man/man3/Bio::Tools::Geneid.3pm.gz 159: warning: can't find numbered character 243
W: bioperl: manpage-has-errors-from-man usr/share/man/man3/Bio::Tools::GuessSeqFormat.3pm.gz 276: warning: can't find numbered character 228
W: bioperl: binary-without-manpage usr/bin/bp_seqfeature_load

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Revision 734 - Directory Listing
Modified Thu Oct 25 02:39:37 2007 UTC (5 years, 6 months ago) by charles-guest

Disabled the tests, which try to access internet.

It seems that sequence ontology is needed for the tests, and
there are attempts to donwload them from internet. Not only the
ressource is error 500 today, but anyway the buildds do not give
net access to the packages being built.

Maybe we can package SO and build-depend on it if we want the tests
in the build logs...

http://song.cvs.sourceforge.net/song/ontology/

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Revision 733 - Directory Listing
Modified Thu Oct 25 02:14:07 2007 UTC (5 years, 6 months ago) by charles-guest

Updated watch file

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Revision 732 - Directory Listing
Modified Sun Oct 21 20:13:25 2007 UTC (5 years, 7 months ago) by smoe-guest

[bioperl]

* added me as an uploader
* would have uploaded if the libmodule-build-perl problem
  would not have resurfaced (fixed in upcoming -0.2 release)

[tm-align]

* Debian-Med official maintainer

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Revision 441 - Directory Listing
Modified Fri Sep 21 14:36:11 2007 UTC (5 years, 8 months ago) by charles-guest

Moving Homepage: field out from the package description.

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Revision 336 - Directory Listing
Modified Sat Jun 16 04:36:40 2007 UTC (5 years, 11 months ago) by charles-guest

many other packages provide sequences usable for tests

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Revision 335 - Directory Listing
Modified Sat Jun 16 04:33:56 2007 UTC (5 years, 11 months ago) by charles-guest

adding one suggested dependancy

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Revision 334 - Directory Listing
Modified Sat Jun 16 04:33:10 2007 UTC (5 years, 11 months ago) by charles-guest

enabling tests

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Revision 333 - Directory Listing
Modified Fri Jun 15 04:33:19 2007 UTC (5 years, 11 months ago) by charles-guest

using prename instead of rename, which is usually a symlink to prename.

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Revision 332 - Directory Listing
Modified Fri Jun 15 02:40:21 2007 UTC (5 years, 11 months ago) by charles-guest

SVN management

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Revision 331 - Directory Listing
Modified Fri Jun 15 02:37:21 2007 UTC (5 years, 11 months ago) by charles-guest

using quilt instead of diff.gz

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Revision 330 - Directory Listing
Modified Fri Jun 15 02:36:12 2007 UTC (5 years, 11 months ago) by charles-guest

Adding Matt Hope as uploader, using quilt instead of diff.gz

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Revision 325 - Directory Listing
Modified Fri Jun 15 00:03:23 2007 UTC (5 years, 11 months ago) by charles-guest

[svn-inject] Applying Debian modifications to trunk

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Revision 324 - Directory Listing
Modified Fri Jun 15 00:02:59 2007 UTC (5 years, 11 months ago) by charles-guest

[svn-inject] Forking bioperl source to Trunk

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Revision 323 - Directory Listing
Modified Fri Jun 15 00:02:52 2007 UTC (5 years, 11 months ago) by charles-guest

[svn-inject] Tagging upstream source version of bioperl

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Revision 322 - Directory Listing
Added Fri Jun 15 00:02:45 2007 UTC (5 years, 11 months ago) by charles-guest

[svn-inject] Installing original source of bioperl