Author: plessy Date: 2012-02-16 04:43:03 +0000 (Thu, 16 Feb 2012) New Revision: 9675
Added: trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/ trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/changelog trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/copyright trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/patches/include_debians_zlib.patch Removed: trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/changelog trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/copyright trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/patches/include_debians_zlib.patch Log: [svn-buildpackage] Tagging velvet 1.2.03~nozlibcopy-1 Deleted: trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/changelog =================================================================== --- trunk/packages/velvet/trunk/debian/changelog 2012-02-15 16:26:47 UTC (rev 9670) +++ trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/changelog 2012-02-16 04:43:03 UTC (rev 9675) @@ -1,272 +0,0 @@ -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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Mon, 25 Jan 2010 13:03:06 +0900 - -velvet (0.7.55-1) unstable; urgency=low - - * New upstream version - - -- Andreas Tille <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Fri, 27 Mar 2009 13:23:32 +0100 - -velvet (0.7.24-1) unstable; urgency=low - - * Initial release (Closes: #487026) - - -- Charles Plessy <[email protected]> Wed, 09 Jul 2008 14:06:55 +0900 Copied: trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/changelog (from rev 9674, trunk/packages/velvet/trunk/debian/changelog) =================================================================== --- trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/changelog (rev 0) +++ trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/changelog 2012-02-16 04:43:03 UTC (rev 9675) @@ -0,0 +1,279 @@ +velvet (1.2.03~nozlibcopy-1) unstable; urgency=low + + * New upstream release. + * Updated debian/patches/include_debians_zlib.patch. + + -- Charles Plessy <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Mon, 25 Jan 2010 13:03:06 +0900 + +velvet (0.7.55-1) unstable; urgency=low + + * New upstream version + + -- Andreas Tille <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Fri, 27 Mar 2009 13:23:32 +0100 + +velvet (0.7.24-1) unstable; urgency=low + + * Initial release (Closes: #487026) + + -- Charles Plessy <[email protected]> Wed, 09 Jul 2008 14:06:55 +0900 Deleted: trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/copyright =================================================================== --- trunk/packages/velvet/trunk/debian/copyright 2012-02-15 16:26:47 UTC (rev 9670) +++ trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/copyright 2012-02-16 04:43:03 UTC (rev 9675) @@ -1,92 +0,0 @@ -Format: http://dep.debian.net/deps/dep5/ -Upstream-Name: Velvet -Upstream-Contact: Daniel Zerbino <[email protected]> -Source: http://www.ebi.ac.uk/~zerbino/velvet/ - -Files: * -Copyright: © 2006-2011 Daniel Zerbino <[email protected]> - © 2000-2005 Guy St.C. Slater <[email protected]> - © 2009 John Marshall <[email protected]> - © 2009 David Studholme <[email protected]> -License: GPL-2+ - -Files: src/fibpriv.h - src/dfib.c - src/fib.h - src/fib.c - src/dfib.h - src/dfibpriv.h -Copyright: © 1997, 1999-2003 John-Mark Gurney. -License: FreeBSD-like - Redistribution and use in source and binary forms, with or without - . - are met: - 1. Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. - 2. Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer in the - documentation and/or other materials provided with the distribution. - . - THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND - ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE - IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE - ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE - FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL - DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS - OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) - HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT - LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY - OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF - SUCH DAMAGE. - -Files: contrib/afg_handling/* contrib/VelvetOptimiser/* -Copyright: © 2008,2009 Simon Gladman <[email protected]> -License: GPL-2+ - -Files: contrib/layout/* -Copyright: © 2008 Paul Harrison ([email protected]) -License: GPL-2+ - -Files: contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl contrib/observed-insert-length.pl/observed-insert-length.pl contrib/show_repeats/show_repeats.pl -Copyright: 2009, Torsten Seemann - 2009, Daniel Zerbino -License: GPL-3+ - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - . - This program 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 General Public License for more details. - . - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. -Comment: On Debian systems, the complete text of the GNU General Public - License version 3 can be found in ‘/usr/share/common-licenses/GPL-3’. - -Files: debian/* -Copyright: 2008-2009 Charles Plessy <[email protected]> - 2008-2011 Andreas Tille <[email protected]> - 2011 Tim Booth <[email protected]> -License: Same - The packaging work is licensed under the same terms as Velvet itself. - -License: GPL-2+ - Velvet is free software; you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. - . - Velvet 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 General Public License for more details. - . - You should have received a copy of the GNU General Public License - along with Velvet; 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 General Public - License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. - Copied: trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/copyright (from rev 9672, trunk/packages/velvet/trunk/debian/copyright) =================================================================== --- trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/copyright (rev 0) +++ trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/copyright 2012-02-16 04:43:03 UTC (rev 9675) @@ -0,0 +1,95 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: Velvet +Upstream-Contact: Daniel Zerbino <[email protected]> +Source: http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.03.tgz + Upstream sources are modified by removing the “third-party” directory, + which contains a convenience copy of the Zlib. + +Files: * +Copyright: © 2006-2011 Daniel Zerbino <[email protected]> + © 2000-2005 Guy St.C. Slater <[email protected]> + © 2009 John Marshall <[email protected]> + © 2009 David Studholme <[email protected]> + © 2011 Convey Computer Corporation ([email protected]) +License: GPL-2+ + +Files: src/fibpriv.h + src/dfib.c + src/fib.h + src/fib.c + src/dfib.h + src/dfibpriv.h +Copyright: © 1997, 1999-2003 John-Mark Gurney. +License: FreeBSD-like + Redistribution and use in source and binary forms, with or without + . + are met: + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + . + THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND + ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE + FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL + DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS + OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) + HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT + LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY + OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + +Files: contrib/afg_handling/* contrib/VelvetOptimiser/* +Copyright: © 2008,2009 Simon Gladman <[email protected]> +License: GPL-2+ + +Files: contrib/layout/* +Copyright: © 2008 Paul Harrison ([email protected]) +License: GPL-2+ + +Files: contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl contrib/observed-insert-length.pl/observed-insert-length.pl contrib/show_repeats/show_repeats.pl +Copyright: 2009, Torsten Seemann + 2009, Daniel Zerbino +License: GPL-3+ + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + . + This program 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 General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. +Comment: On Debian systems, the complete text of the GNU General Public + License version 3 can be found in ‘/usr/share/common-licenses/GPL-3’. + +Files: debian/* +Copyright: 2008-2009 Charles Plessy <[email protected]> + 2008-2011 Andreas Tille <[email protected]> + 2011 Tim Booth <[email protected]> +License: Same + The packaging work is licensed under the same terms as Velvet itself. + +License: GPL-2+ + Velvet is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + . + Velvet 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 General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with Velvet; 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 General Public + License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. + Deleted: trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/patches/include_debians_zlib.patch =================================================================== --- trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch 2012-02-15 16:26:47 UTC (rev 9670) +++ trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/patches/include_debians_zlib.patch 2012-02-16 04:43:03 UTC (rev 9675) @@ -1,14 +0,0 @@ -Description: Use the zlib distributed by Debian, not the one in third-party/zlib-1.2.3/. -Author: Charles Plessy <[email protected]> -Forwarded: no ---- a/src/readSet.c -+++ b/src/readSet.c -@@ -35,7 +35,7 @@ - #elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32) - #include "../third-party/zlib-1.2.3/Win32/include/zlib.h" - #else --#include "../third-party/zlib-1.2.3/zlib.h" -+#include <zlib.h> - #endif - - #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__) Copied: trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/patches/include_debians_zlib.patch (from rev 9673, trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch) =================================================================== --- trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/patches/include_debians_zlib.patch (rev 0) +++ trunk/packages/velvet/tags/1.2.03~nozlibcopy-1/debian/patches/include_debians_zlib.patch 2012-02-16 04:43:03 UTC (rev 9675) @@ -0,0 +1,27 @@ +Description: Use the zlib distributed by Debian, not the one in third-party/zlib-1.2.3/. +Author: Charles Plessy <[email protected]> +Forwarded: no +--- a/src/readSet.c ++++ b/src/readSet.c +@@ -35,7 +35,7 @@ + #elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32) + #include "../third-party/zlib-1.2.3/Win32/include/zlib.h" + #else +-#include "../third-party/zlib-1.2.3/zlib.h" ++#include <zlib.h> + #endif + + #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__) +Index: velvet-1.2.03~nozlibcopy/src/binarySequences.c +=================================================================== +--- velvet-1.2.03~nozlibcopy.orig/src/binarySequences.c 2012-02-16 13:27:43.832843704 +0900 ++++ velvet-1.2.03~nozlibcopy/src/binarySequences.c 2012-02-16 13:28:04.176843708 +0900 +@@ -34,7 +34,7 @@ + #if defined(_WIN32) || defined(__WIN32__) || defined(WIN32) + #include "../third-party/zlib-1.2.3/Win32/include/zlib.h" + #else +-#include "../third-party/zlib-1.2.3/zlib.h" ++#include <zlib.h> + #endif + + #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
