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velvet (1.2.10+dfsg1-7) unstable; urgency=medium
* velvet-examples: Depends: velvet-tests
Closes: #929563
-- Andreas Tille <tille@debian.org> Sat, 07 Dec 2019 21:28:03 +0100
velvet (1.2.10+dfsg1-6) unstable; urgency=medium
* Use 2to3 to port to Python3
Closes: #945743
* debhelper-compat 12
* Standards-Version: 4.4.1
* Secure URI in copyright format
* Remove trailing whitespace in debian/changelog
* Remove trailing whitespace in debian/control
* autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
* Use secure URI in Homepage field.
* Set upstream metadata fields: Repository-Browse.
* Remove obsolete fields Contact, Name from debian/upstream/metadata.
-- Andreas Tille <tille@debian.org> Mon, 02 Dec 2019 13:40:35 +0100
velvet (1.2.10+dfsg1-5) unstable; urgency=medium
[ Steffen Moeller ]
* debian/upstream/metadata: Added references to registries.
[ Andreas Tille ]
* drop unneeded get-orig-source target
* debhelper 11 (--no-parallel needed)
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
* d/control: Drop unnecessary Testsuite field
* Provide manpages for versions with MAXKMERLENGTH = 127
* Try better hardening but failed (hints are welcome)
* Fix spelling
* Secure URI in watch file
* Remove unused lintian override
-- Andreas Tille <tille@debian.org> Thu, 05 Jul 2018 10:17:41 +0200
velvet (1.2.10+dfsg1-4) experimental; urgency=medium
* Add version with MAXKMERLENGTH=127
-- Andreas Tille <tille@debian.org> Fri, 24 Feb 2017 10:10:36 +0100
velvet (1.2.10+dfsg1-3) unstable; urgency=medium
* Moved from SVN to Git
* Do not mention files in d/copyright that are not part of the source
* Lintian override for false positives
-- Andreas Tille <tille@debian.org> Thu, 10 Dec 2015 09:02:23 +0100
velvet (1.2.10+dfsg1-2) unstable; urgency=medium
* Fix gcc-5 build issue by adapting upstream patch
Closes: #778161
* cme fix dpkg-control
-- Andreas Tille <tille@debian.org> Sat, 27 Jun 2015 11:44:54 +0200
velvet (1.2.10+dfsg1-1) unstable; urgency=medium
* Drop more stuff from upstream source via Files-Excluded
* cme fix dpkg-control
* Do not pack example data into another archive
* add autopkgtest (using new binary package velvet-tests)
* do not create manpages at package build time (which is error prone anyway
but rather prepare them before using debian/createmanpages script
-- Andreas Tille <tille@debian.org> Mon, 30 Jun 2014 13:56:46 +0200
velvet (1.2.10+dfsg-1biolinux6) trusty; urgency=medium
[ Andreas Tille ]
* Moved debian/upstream to debian/upstream/metadata
* Base get-orig-source target on recent uscan that understands
Files-Excluded
* debian/rules: no need to explicitly force xz compression any more
[ Tim Booth ]
* Remove MeteVelvet and VelvetOptimiser in dh_clean, not dh_install
* Include example_data.tar.xz in -example package
-- Tim Booth <tbooth@ceh.ac.uk> Mon, 30 Jun 2014 11:39:24 +0100
velvet (1.2.10+dfsg-1biolinux5) trusty; urgency=low
* Rebuild for Ubuntu Trusty
* Fold in some chages from Bio-Linux
* Add velvet-long package as suggested by upstream
* Fix TeX deps so manual still builds
* Add .c/.h and .pl files to dh_compress exclusions
* Ensure that MetaVelvet and VelvetOptimiser sources are excluded
as they don't belong in -examples
-- Tim Booth <tbooth@ceh.ac.uk> Fri, 27 Jun 2014 13:52:48 +0100
velvet (1.2.10+dfsg-1) unstable; urgency=low
* New upstream version (+adapted patch)
* debian/watch: cope with +dfsg suffix (in addition to old ~nozlibcopy)
* debian/get-orig-source:
- Enable simple changing of suffix for repackaged source
- Check for existence of enhanced uscan and use it if available for
easier repackaging
* debian/control:
- cme fix dpkg-control
- no explicit quilt Build-Depends (also removed from rules)
- bumped python from Recommends to Depends because there are
Python scripts installed in velvet/contrib
- use anonscm in Vcs fields
* debian/copyright:
Add Files-Excluded to document what was removed from original source
* rename debian/{docs,install} to debian/velvet.{docs,install} which
is more safe in the case of multibinary package
* debian/velvet.install: shuffle* files are in contrib directory now
* debhelper 9 (control+compat) to enable hardening options
* debian/rules: propagate hardening options
* debian/copyright:
- Files-Excluded: Exclude MAXOS internal files cruft from upstream archive
- Adapt Source location
* debian/README.source: Updated explanation for repackaging, droped some
outdated information
* debian/rules:
- Do not try to rmdir nonexisting directory
- Remove extra copies of GPL
* debian/velvet-examples.install: use install instead of examples to move
the examples into /usr/share/doc/velvet directly. Also all contrib stuff
was moved here to not bloat main velvet binary package with potentially
unused stuff in /usr/share
* debian/README.Debian: document move of contrib stuff
-- Andreas Tille <tille@debian.org> Thu, 01 Aug 2013 14:33:28 +0200
velvet (1.2.03~nozlibcopy-1) unstable; urgency=low
* New upstream release.
* Updated debian/patches/include_debians_zlib.patch.
-- Charles Plessy <plessy@debian.org> Thu, 16 Feb 2012 13:37:19 +0900
velvet (1.1.07~nozlibcopy-1) unstable; urgency=low
* New upstream release (Closes: #647415).
* debian/contol:
- Pre-Depends on dpkg (>= 1.15.6) for Ubuntu LTS.
- Removed Multi-Arch: foreign.
-- Charles Plessy <plessy@debian.org> Fri, 09 Dec 2011 14:07:58 +0900
velvet (1.1.06~nozlibcopy-1) unstable; urgency=low
[ Andreas Tille ]
* New upstream version
* debian/copyright: Revised
* debian/get-orig-source: Do not remove MetaVelvet
* debian/control:
Build-Depends: texlive-latex-base
[ Charles Plessy ]
* Corrected VCS URLs in debian/control.
* Compress source and binary packages with xz
(debian/rules, debian/get-orig-source).
* Turn on multithreading with OpenMP (debian/rules).
* Remove empty directory contrib/MetaVelvet-v0.3.1/obj (debian/rules).
-- Charles Plessy <plessy@debian.org> Tue, 27 Sep 2011 15:12:41 +0900
velvet (1.1.05-1ubuntu4) lucid; urgency=low
* Moved from CDBS to DH
* New upstream. Still includes a copy of Zlib but the default
is now to use the system version, so removed relevant patch.
* Modified build to work on unmodified upstream (still works on
pruned upstream).
-- Tim Booth <tbooth@ceh.ac.uk> Thu, 11 Aug 2011 13:34:46 +0100
velvet (1.1.02~nozlibcopy-1) unstable; urgency=low
* New upstream version
upgraded patches, tweak $(LIBS) into Z_LIB_FILES variable
of Makefile which makes patch more robust against upstream
changes
* Debhelper 8 (control+compat)
* debian/rules: Leave out Z_LIB_FILES in parameter list
* debian/get-orig-source: Once we are rebuilding the original
tarball anyway it makes sense to remove an outdated copy of
MetaVelvet and replace it rather by a hint to the currently
maintained source in README.source
* Standards-Version: 3.9.2 (no changes needed)
-- Andreas Tille <tille@debian.org> Fri, 15 Apr 2011 10:51:16 +0200
velvet (1.0.18~nozlibcopy-1) unstable; urgency=low
* New upstream version
* debian/get-orig-source: Make sure MD5sum stays the same for different
download
-- Andreas Tille <tille@debian.org> Wed, 19 Jan 2011 08:48:19 +0100
velvet (1.0.15~nozlibcopy-2) unstable; urgency=low
* Fix FTBFS with ld --as-needed (thanks for the patch to
Matthias Klose)
Closes: #607535
-- Andreas Tille <tille@debian.org> Mon, 20 Dec 2010 08:43:16 +0100
velvet (1.0.15~nozlibcopy-1) unstable; urgency=low
* New upstream source
* Standards-Version: 3.9.1 (no changes needed)
* debian/get-upstream-source: Remove precompiled *.o files and
.DS_Store files once we are repackaging anyway
* debian/patches/fix-perl-path.patch: Fix Perl path
-- Andreas Tille <tille@debian.org> Wed, 24 Nov 2010 15:42:33 +0100
velvet (1.0.02~nozlibcopy-1) unstable; urgency=low
* New upstream version
* Source format 3.0 (quilt)
* debian/control:
- Recommends: python (some new scripts in /usr/share/velvet/contrib
are Python scripts)
- Build-Depends: quilt
* debian/rules:
include /usr/share/cdbs/1/rules/patchsys-quilt.mk
(instead of simple-patchsys)
* debian/patches: Switch to quilt
* debian/patches/shuffleSequences_fasta.patch:
Add interpreter to Python script
-- Andreas Tille <tille@debian.org> Thu, 24 Jun 2010 15:41:53 +0200
velvet (0.7.61~nozlibcopy-1) unstable; urgency=low
* New upstream version
* debian/get-orig-source, debian/rules: Strip zlib copy from
upstream tarball
-- Andreas Tille <tille@debian.org> Mon, 22 Mar 2010 15:41:53 +0100
velvet (0.7.59~nozlibcopy-1) unstable; urgency=low
* New upstream release
[ Charles Plessy ]
* Incremented Standard-Version in debian/control to reflect conformance
with Policy 3.8.4 (no changes needed).
[ Andreas Tille ]
* Fixed watch file to make sure it is not supporting newer upstream
-- Charles Plessy <plessy@debian.org> Sat, 20 Feb 2010 13:00:13 +0900
velvet (0.7.56~nozlibcopy-1) unstable; urgency=low
* New upstream version.
* Repackaged the upstream directory to remove the convenience copy
of the zlib. Documented this in ‘debian/README.source’.
Closes: #561433.
* Updated debian/copyright.
* Added ‘include_debians_zlib.patch’ to enforce the use of
/usr/include/zlib.h. This patch is applied using CDBS, see
‘debian/rules’ and ‘debian/README.source’.
* Renamed ‘debian/reference’ ‘debian/upstream-metadata.yaml’ and
centralised upstream-specific information there.
-- Charles Plessy <plessy@debian.org> Mon, 25 Jan 2010 13:03:06 +0900
velvet (0.7.55-1) unstable; urgency=low
* New upstream version
-- Andreas Tille <tille@debian.org> Fri, 25 Sep 2009 14:52:41 +0200
velvet (0.7.53-1) unstable; urgency=low
* New upstream release:
- Ignored reads in Pebble corrected
- Added automatic measure of median coverage and median insert length
- Updated manual to cover the above
-- Charles Plessy <plessy@debian.org> Fri, 04 Sep 2009 13:42:22 +0900
velvet (0.7.52-1) unstable; urgency=low
* New upstream release:
V 0.7.51
- Small parsing bug
- Correction to the observed-insert-length script
- Verified strncpy calls
- NCBI friendly 10bp N-gaps
V 0.7.52
- Crashing bug when parsing fa.gz files
- Crashing bug with tiny Graph files
- Bug when loading FASTA files with short lines
- Corrected snp_view.pl script to write reverse strand reads in
snp_view_reads file
- Corrected snp_view.pl script to behave better near the edges of contigs
- Updated observed_insert_length to compute the standard deviation of
the set
- Corrected observed_insert_length script so that it does not crash on
empty libraries
- Crashing bug when providing an odd number of paired reads
- Mapping bug of reads during tour bus correction
* Replaced the UNRELEASED tag by ‘unstable’ in debian/changelog as
0.7.50-1 was really uploaded and accepted by the archive.
-- Charles Plessy <plessy@debian.org> Thu, 03 Sep 2009 20:00:54 +0900
velvet (0.7.50-1) unstable; urgency=low
* New upstream release:
V 0.7.49
- Added the optional output of unused reads
- Added David Studholme's FastA -> AGP script
V 0.7.50
- Added the extractContigReads script
- Updated the FastA -> AGP script
- Added the observed-insert-length script
- Small parsing bug in simplified read import
* Incremented Standards-Version in debian/control to reflect conformance
with Policy 3.8.3 (no changes needed).
-- Charles Plessy <plessy@debian.org> Wed, 19 Aug 2009 21:58:49 +0900
velvet (0.7.48-1) unstable; urgency=low
* New upstream release:
- Accelerated concatenation (pre-graph and graph)
- Unlimited contig size
- Bug in parsing FASTA files with very long lines
- Parsing bug in snp_view.pl script
-- Charles Plessy <plessy@debian.org> Tue, 11 Aug 2009 19:54:03 +0900
velvet (0.7.47-1) unstable; urgency=low
* New upstream release correcting bugs and enhancing documentation.
* Multi-Arch support (‘foreign’) in debian/control.
* Corrected debian/install to avoid ugly ‘contrib/contrib’ location.
-- Charles Plessy <plessy@debian.org> Thu, 30 Jul 2009 13:43:13 +0900
velvet (0.7.44-1) unstable; urgency=low
* 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.
-- Charles Plessy <plessy@debian.org> Sun, 12 Jul 2009 00:24:56 +0900
velvet (0.7.37-1) unstable; urgency=low
* 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.
-- Charles Plessy <plessy@debian.org> Sat, 27 Jun 2009 12:27:27 +0900
velvet (0.7.34-1) unstable; urgency=low
* 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).
-- Charles Plessy <plessy@debian.org> Tue, 09 Jun 2009 21:28:03 +0900
velvet (0.7.31-1) unstable; urgency=low
* New upstream version
* Standards-Version: 3.8.1 (no changes needed)
* Create manpages using help2man
* Move third-party/layout and third-party/afg_handling to examples
because these scripts are actually not to run velvet but for
the convenience of users - in /urs/share/velvet these scripts
seem to be perfectly hidden and in /usr/share/doc/velvet might
create users attendance
* Added missing quilt entry in debian/rules
-- Andreas Tille <tille@debian.org> Fri, 27 Mar 2009 13:23:32 +0100
velvet (0.7.24-1) unstable; urgency=low
* Initial release (Closes: #487026)
-- Charles Plessy <plessy@debian.org> Wed, 09 Jul 2008 14:06:55 +0900
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