Log of /trunk/packages/velvet

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Revision 9849 - Directory Listing
Modified Fri Mar 2 00:07:41 2012 UTC (15 months, 2 weeks ago) by plessy

Corrected the files that did not validate with YAML::XS.

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Revision 9702 - Directory Listing
Modified Sat Feb 18 01:23:39 2012 UTC (16 months ago) by plessy

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

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Revision 9675 - Directory Listing
Modified Thu Feb 16 04:43:03 2012 UTC (16 months ago) by plessy

[svn-buildpackage] Tagging velvet 1.2.03~nozlibcopy-1

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Revision 9674 - Directory Listing
Modified Thu Feb 16 04:41:45 2012 UTC (16 months ago) by plessy

velvet (1.2.03~nozlibcopy-1) unstable; urgency=low

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Revision 9673 - Directory Listing
Modified Thu Feb 16 04:36:30 2012 UTC (16 months ago) by plessy

Updated debian/patches/include_debians_zlib.patch.

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Revision 9672 - Directory Listing
Modified Thu Feb 16 04:35:42 2012 UTC (16 months ago) by plessy

Using 1.0 URL for the machine-readable Debian copyright format.

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Revision 9671 - Directory Listing
Modified Thu Feb 16 04:33:00 2012 UTC (16 months ago) by plessy

New upstream release, with one more copyright holder.

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Revision 9492 - Directory Listing
Modified Sun Jan 29 03:35:57 2012 UTC (16 months, 2 weeks ago) by plessy

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

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Revision 8859 - Directory Listing
Modified Fri Dec 9 05:41:40 2011 UTC (18 months, 1 week ago) by plessy

[svn-buildpackage] Tagging velvet 1.1.07~nozlibcopy-1

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Revision 8858 - Directory Listing
Modified Fri Dec 9 05:39:36 2011 UTC (18 months, 1 week ago) by plessy

Uploaded new upstream release after removing Multi-Arch: foreign.

No new copyright notice nor license statement.

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Revision 8857 - Directory Listing
Modified Fri Dec 9 04:48:47 2011 UTC (18 months, 1 week ago) by plessy

Pre-Depends on dpkg (>= 1.15.6) for Ubuntu LTS.

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Revision 7947 - Directory Listing
Modified Tue Sep 27 06:43:14 2011 UTC (20 months, 3 weeks ago) by plessy

[svn-buildpackage] Tagging velvet 1.1.06~nozlibcopy-1

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Revision 7946 - Directory Listing
Modified Tue Sep 27 06:42:22 2011 UTC (20 months, 3 weeks ago) by plessy

Remove empty directory contrib/MetaVelvet-v0.3.1/obj

Uploaded after this last change.

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Revision 7945 - Directory Listing
Modified Tue Sep 27 05:28:49 2011 UTC (20 months, 3 weeks ago) by plessy

Turn on multithreading with OpenMP.

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Revision 7944 - Directory Listing
Modified Tue Sep 27 04:06:31 2011 UTC (20 months, 3 weeks ago) by plessy

Compress source package with xz.

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Revision 7932 - Directory Listing
Modified Mon Sep 26 10:43:31 2011 UTC (20 months, 3 weeks ago) by plessy

Compress binary packages with xz.

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Revision 7931 - Directory Listing
Modified Mon Sep 26 10:34:48 2011 UTC (20 months, 3 weeks ago) by plessy

New upstream release changing only contrib/VelvetOptimiser.

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Revision 7930 - Directory Listing
Modified Mon Sep 26 10:27:40 2011 UTC (20 months, 3 weeks ago) by plessy

Corrected VCS URLs.

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Revision 7435 - Directory Listing
Modified Sat Aug 13 03:08:12 2011 UTC (22 months ago) by plessy

Validated and reformatted with ‘config-edit -application dpkg-copyright’.

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Revision 7431 - Directory Listing
Modified Fri Aug 12 14:08:19 2011 UTC (22 months, 1 week ago) by tille

Build-Depends: texlive-latex-base

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Revision 7430 - Directory Listing
Modified Fri Aug 12 13:36:05 2011 UTC (22 months, 1 week ago) by tille

Do not remove MetaVelvet any more, do not leave dangling symlink behind

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Revision 7429 - Directory Listing
Modified Fri Aug 12 13:29:51 2011 UTC (22 months, 1 week ago) by tille

Revised velvet copyright, remove entries for zlib again because it turns out to be too complicated to mention all those different copyrights :-(

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Revision 7427 - Directory Listing
Modified Thu Aug 11 16:02:44 2011 UTC (22 months, 1 week ago) by tbooth-guest

Shifted from CDBS to DH.  Confirmed that the resulting DEB is identical to the
one produced before, apart from some file size difference due to switch from '-O2'
to '-O3' compiler flag.  I'm not sure why the two build systems have different defaults?

The issue with MetaVelvet seems to have gone away - upstream have cleaned up the build
system a lot since Andreas was struggling with it.

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Revision 7424 - Directory Listing
Modified Thu Aug 11 12:59:52 2011 UTC (22 months, 1 week ago) by tbooth-guest

New upstream, now uses system Zlib by default, so removed one unneedded patch.

I was having trouble with the get-orig-source and the modified tarball.
After reading #561433 I decided it was easier to modify the build to work on a
pristine tarball and add the short Copyright statement from
/usr/share/doc/zlib1g/copyright to the copyright file.

Only tested to compile on Ubuntu Lucid

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Revision 6575 - Directory Listing
Modified Fri Apr 15 09:10:31 2011 UTC (2 years, 2 months ago) by tille

Tagged latest version, marked version in squeeze, removed some older tags

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Revision 6574 - Directory Listing
Modified Fri Apr 15 09:02:16 2011 UTC (2 years, 2 months ago) by tille

Bumped STandards-Version and upload to unstable

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Revision 6573 - Directory Listing
Modified Fri Apr 15 08:56:06 2011 UTC (2 years, 2 months ago) by tille

Once we are rebuilding the original tarball anyway, it seems simpler to remove the outdated MetaVelvet code rather than adapting the build system.  If MetaVelvet is needed it should be packaged separately.  The issue is documented in README.source.

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Revision 6463 - Directory Listing
Modified Tue Apr 5 13:54:26 2011 UTC (2 years, 2 months ago) by tille

New upstream version, adapted patches to this new version; debhlper 8; prepare building of meta-velvet (whatever this is - needs to be clarified); TODO: exclude contrib/MetaVelvet-v0.3.1 directory from binary package ... and clarify the sense of meta-velvet (separate binary package????)

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Revision 5789 - Directory Listing
Modified Sat Jan 29 22:52:19 2011 UTC (2 years, 4 months ago) by tille

Typo

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Revision 5681 - Directory Listing
Modified Wed Jan 19 08:00:40 2011 UTC (2 years, 4 months ago) by tille

Tagged 1.0.18~nozlibcopy-1

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Revision 5680 - Directory Listing
Modified Wed Jan 19 07:57:26 2011 UTC (2 years, 4 months ago) by tille

New upstream version

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Revision 5607 - Directory Listing
Modified Mon Dec 20 10:39:46 2010 UTC (2 years, 5 months ago) by tille

Tagged 1.0.15~nozlibcopy-2

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Revision 5606 - Directory Listing
Modified Mon Dec 20 10:38:44 2010 UTC (2 years, 5 months ago) by tille

FIx ld -as-needed FTBFS issue (thanks for the patch to Matthias Klose)

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Revision 5487 - Directory Listing
Modified Wed Nov 24 15:01:42 2010 UTC (2 years, 6 months ago) by tille

Tagged 1.0.15~nozlibcopy-1; removed several older tags

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Revision 5486 - Directory Listing
Modified Wed Nov 24 14:59:49 2010 UTC (2 years, 6 months ago) by tille

New upstream source

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Revision 4911 - Directory Listing
Modified Thu Jun 24 14:23:27 2010 UTC (2 years, 11 months ago) by tille

Tagged 1.0.02~nozlibcopy-1

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Revision 4910 - Directory Listing
Modified Thu Jun 24 14:18:52 2010 UTC (2 years, 11 months ago) by tille

New upstream version, source format 3.0 (quilt), switched from simple-patchsys to quilt

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Revision 4674 - Directory Listing
Modified Mon Mar 22 14:52:19 2010 UTC (3 years, 2 months ago) by tille

Tagged 0.7.61~nozlibcopy-1

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Revision 4673 - Directory Listing
Modified Mon Mar 22 14:50:35 2010 UTC (3 years, 2 months ago) by tille

New upstream version, get-orig-source target to strip zlib copy

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Revision 4626 - Directory Listing
Modified Sat Feb 20 04:49:12 2010 UTC (3 years, 3 months ago) by plessy

[svn-buildpackage] Tagging velvet (0.7.59~nozlibcopy-1)

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Revision 4625 - Directory Listing
Modified Sat Feb 20 04:48:37 2010 UTC (3 years, 3 months ago) by plessy

New upstream release.

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Revision 4584 - Directory Listing
Modified Tue Jan 26 10:47:11 2010 UTC (3 years, 4 months ago) by tille

Fixed watch file to reflect ~nozlibcopy extension

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Revision 4583 - Directory Listing
Modified Mon Jan 25 04:59:21 2010 UTC (3 years, 4 months ago) by plessy

[svn-buildpackage] Tagging velvet (0.7.56~nozlibcopy-1)

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Revision 4582 - Directory Listing
Modified Mon Jan 25 04:58:06 2010 UTC (3 years, 4 months ago) by plessy

New upstream release. Zlib convenience copy removed from Debian source package.

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Revision 4021 - Directory Listing
Modified Fri Sep 25 13:15:05 2009 UTC (3 years, 8 months ago) by tille

Tagged 0.7.55-1

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Revision 4020 - Directory Listing
Modified Fri Sep 25 13:13:44 2009 UTC (3 years, 8 months ago) by tille

New upstream version; ignore two minor lintian warnings for this upload but asked author about fixing the issues upstream; seems to be actively maintained so we might expext an update soon.

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Revision 3876 - Directory Listing
Modified Fri Sep 4 06:47:46 2009 UTC (3 years, 9 months ago) by plessy

[svn-buildpackage] Tagging velvet (0.7.53-1)

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Revision 3875 - Directory Listing
Modified Fri Sep 4 06:45:25 2009 UTC (3 years, 9 months ago) by plessy

New upstream release.

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Revision 3870 - Directory Listing
Modified Thu Sep 3 11:41:33 2009 UTC (3 years, 9 months ago) by plessy

[svn-buildpackage] Tagging velvet (0.7.52-1)

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Revision 3869 - Directory Listing
Modified Thu Sep 3 11:40:54 2009 UTC (3 years, 9 months ago) by plessy

New upstream release.

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Revision 3800 - Directory Listing
Modified Fri Aug 21 04:21:07 2009 UTC (3 years, 9 months ago) by plessy

Corrected broken changelog.

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Revision 3799 - Directory Listing
Modified Fri Aug 21 04:18:28 2009 UTC (3 years, 9 months ago) by plessy

[svn-buildpackage] Tagging velvet (0.7.50-1)

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Revision 3795 - Directory Listing
Modified Wed Aug 19 13:29:38 2009 UTC (3 years, 10 months ago) by plessy

Uploaded.

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Revision 3794 - Directory Listing
Modified Wed Aug 19 13:20:19 2009 UTC (3 years, 10 months ago) by plessy

New upstream release available. Will upload soon.

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Revision 3758 - Directory Listing
Modified Tue Aug 11 11:13:49 2009 UTC (3 years, 10 months ago) by plessy

[svn-buildpackage] Tagging velvet (0.7.48-1)

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Revision 3757 - Directory Listing
Modified Tue Aug 11 11:12:57 2009 UTC (3 years, 10 months ago) by plessy

New upstream release.

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Revision 3714 - Directory Listing
Modified Thu Jul 30 05:00:44 2009 UTC (3 years, 10 months ago) by plessy

[svn-buildpackage] Tagging velvet (0.7.47-1)

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Revision 3713 - Directory Listing
Modified Thu Jul 30 04:59:07 2009 UTC (3 years, 10 months ago) by plessy

New upstream release correcting bugs and enhancing documentation.

Packaging changes:
  * Multi-Arch support (‘foreign’) in debian/control.
  * Corrected debian/install to avoid ugly ‘contrib/contrib’ location.

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Revision 3615 - Directory Listing
Modified Sat Jul 11 15:38:50 2009 UTC (3 years, 11 months ago) by plessy

[svn-buildpackage] Tagging velvet (0.7.44-1)

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Revision 3614 - Directory Listing
Modified Sat Jul 11 15:34:53 2009 UTC (3 years, 11 months ago) by plessy

New upstream release and packaging polishing.

  * New upstream release.
  * Added bibliographic information in BibTeX format in debian/references.
  * debian/rules: touch zlib to avoid third-party zlib to be built.
  * Removed ‘debian/patches/20_external_zlib.patch’. Passing apropriate
    variables in debian/rules is enough to build dynamically on Debian's
    zlib.
  * Removed the quilt patch system (debian/control, debian/README.source
    debian/rules).
  * Incremented Standards-Version in debian/control to reflect conformance
    with Policy 3.8.2 (no changes needed).
  * Corrected the installation of files that were moved from the
    ‘third-party’ directory to the ‘contrib’ directory.
  * Experimentation on debian/copyright.

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Revision 3566 - Directory Listing
Modified Sat Jun 27 03:39:52 2009 UTC (3 years, 11 months ago) by plessy

[svn-buildpackage] Tagging velvet (0.7.37-1)

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Revision 3565 - Directory Listing
Modified Sat Jun 27 03:38:05 2009 UTC (3 years, 11 months ago) by plessy

New upstream release.

   - Small formatting change to error messages
   - K > 31 now possible
   - --help option corrected for velvetg
   - Acceleration of k-mer operations (comparable to 64bit int performance)
   - Fixed variable lengths
   - Reordered struct declaration for more efficent memory alignment
 * debian/rules:
   - Restored manpage generation for velvetg*.
   - Added forgotten CFLAGS for the colorspace building.

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Revision 3477 - Directory Listing
Modified Wed Jun 10 02:46:06 2009 UTC (4 years ago) by plessy

[svn-buildpackage] Tagging velvet (0.7.34-1)

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Revision 3476 - Directory Listing
Modified Wed Jun 10 02:44:18 2009 UTC (4 years ago) by plessy

New upstream release; minor trouble to autogenerate the manpages.

 * New upstream release correcting multiple bugs, changing the stats output,
   allowing optional scaffolding and multiple rounds of Pebble.
 * Added the programs velveth_de and velvetg_de to the package in /usr/bin,
   and the scripts shuffleSequences_fasta.pl and shuffleSequences_fastq.pl in
   /usr/share/velvet (debian/rules, debian/install).
 * Refreshed debian/copyright. 
 * Temporarly disabled the manpage generation of velvetg* because the --help
   option is not available (debian/rules).

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Revision 3217 - Directory Listing
Modified Fri Mar 27 12:58:58 2009 UTC (4 years, 2 months ago) by tille

Tagged 0.7.31-1

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Revision 3216 - Directory Listing
Modified Fri Mar 27 12:55:09 2009 UTC (4 years, 2 months ago) by tille

Added missing quilt entry in debian/rules

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Revision 3215 - Directory Listing
Modified Fri Mar 27 12:32:48 2009 UTC (4 years, 2 months ago) by tille

New version, use help2man to create man pages, moved third party contrib stuff to /usr/share/doc/velvet/examples to make it more visible for users.

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Revision 3152 - Directory Listing
Modified Fri Mar 6 15:37:01 2009 UTC (4 years, 3 months ago) by tille

New upstream version.  Hopefully ftpmaster will be able to work down NEW queue soon ...

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Revision 2969 - Directory Listing
Modified Mon Jan 12 15:22:54 2009 UTC (4 years, 5 months ago) by plessy

[svn-buildpackage] Tagging velvet (0.7.24-1)

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Revision 2968 - Directory Listing
Modified Mon Jan 12 15:12:04 2009 UTC (4 years, 5 months ago) by plessy

Forgot to add README.source for Policy 3.8.0.

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Revision 2967 - Directory Listing
Modified Mon Jan 12 15:06:59 2009 UTC (4 years, 5 months ago) by plessy

Polished copyright file, fixed minor errors; ready for upload.

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Revision 2799 - Directory Listing
Modified Mon Dec 15 21:18:52 2008 UTC (4 years, 6 months ago) by tille

Machine readable copyrigh

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Revision 2798 - Directory Listing
Modified Mon Dec 15 21:12:04 2008 UTC (4 years, 6 months ago) by tille

Do not use third-party/zlib stuff.  Patch should be suggested upstream.  Remark: The #ifdef (Windows) condition does not work because the inclulde path mentioned there does not exist.

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Revision 2776 - Directory Listing
Modified Sat Dec 13 01:42:20 2008 UTC (4 years, 6 months ago) by plessy

Unset OPT as DEB_BUILD_OPTIONS does the job (thanks to D. Leidert).

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Revision 2775 - Directory Listing
Modified Fri Dec 12 10:18:14 2008 UTC (4 years, 6 months ago) by plessy

-O2 is the default in Debian, and often -O3 does not make the program faster.

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Revision 2774 - Directory Listing
Modified Thu Dec 11 14:22:55 2008 UTC (4 years, 6 months ago) by plessy

Reverted Andreases patch, and added a velvet-example package.

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Revision 2773 - Directory Listing
Modified Thu Dec 11 13:39:09 2008 UTC (4 years, 6 months ago) by tille

It is "Uploader_s_" and bumped policy version.

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Revision 2772 - Directory Listing
Modified Thu Dec 11 13:37:27 2008 UTC (4 years, 6 months ago) by tille

Do not touch third-party/zlib-1.2.3 at all.  The patch for src/readSet.c might be a little bit rude and perhaps we should suggest a better #ifdef EXTERNAL_ZLIB magic to upstream instead of this.

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Revision 2771 - Directory Listing
Modified Thu Dec 11 10:41:34 2008 UTC (4 years, 6 months ago) by tille

We also have interest in velvet - tried to fix the watch file but failed.  I guess we have to ask upstream for help ....

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Revision 2769 - Directory Listing
Modified Thu Dec 11 09:49:02 2008 UTC (4 years, 6 months ago) by plessy

The patches were not necessary in the end.

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Revision 2074 - Directory Listing
Modified Fri Jun 20 02:31:51 2008 UTC (5 years ago) by plessy

Preliminary package

I do not plan to upload this package before Lenny is released, but I am very
open to fast-track requests. Upstream has to be contacted to release the
sources of the PDF manual.

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Revision 2073 - Directory Listing
Modified Fri Jun 20 02:19:30 2008 UTC (5 years ago) by plessy

[svn-inject] Applying Debian modifications to trunk

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Revision 2072 - Directory Listing
Modified Fri Jun 20 02:19:11 2008 UTC (5 years ago) by plessy

Creating trunk directory

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Revision 2071 - Directory Listing
Added Fri Jun 20 02:18:38 2008 UTC (5 years ago) by plessy

Creating velvet/tags/ directory.