[med-svn] r18212 - in trunk/packages/mafft/tags: . 7.187-1/debian
Charles Plessy
plessy at moszumanska.debian.org
Sun Oct 5 00:24:11 UTC 2014
Author: plessy
Date: 2014-10-05 00:24:10 +0000 (Sun, 05 Oct 2014)
New Revision: 18212
Added:
trunk/packages/mafft/tags/7.187-1/
trunk/packages/mafft/tags/7.187-1/debian/changelog
trunk/packages/mafft/tags/7.187-1/debian/control
trunk/packages/mafft/tags/7.187-1/debian/copyright
Removed:
trunk/packages/mafft/tags/7.187-1/debian/changelog
trunk/packages/mafft/tags/7.187-1/debian/control
trunk/packages/mafft/tags/7.187-1/debian/copyright
Log:
[svn-buildpackage] Tagging mafft 7.187-1
Deleted: trunk/packages/mafft/tags/7.187-1/debian/changelog
===================================================================
--- trunk/packages/mafft/trunk/debian/changelog 2014-10-04 22:32:58 UTC (rev 18210)
+++ trunk/packages/mafft/tags/7.187-1/debian/changelog 2014-10-05 00:24:10 UTC (rev 18212)
@@ -1,247 +0,0 @@
-mafft (7.164-1) unstable; urgency=medium
-
- * New upstream version
-
- -- Andreas Tille <tille at debian.org> Mon, 04 Aug 2014 15:04:10 +0200
-
-mafft (7.158-1) unstable; urgency=medium
-
- * New upstream release.
-
- -- Charles Plessy <plessy at debian.org> Sun, 13 Jul 2014 20:26:22 +0900
-
-mafft (7.157-1) unstable; urgency=medium
-
- * New upstream release.
- * debian/control
- - Added substitution variable ${perl:Depends}, used by Debhelper.
- - Recommend libwww-perl used by the script ‘seekquencer_premafft.pl’.
-
- -- Charles Plessy <plessy at debian.org> Wed, 18 Jun 2014 08:10:02 +0900
-
-mafft (7.149-1) unstable; urgency=medium
-
- * New upstream release.
-
- -- Charles Plessy <plessy at debian.org> Sat, 12 Apr 2014 13:46:13 +0900
-
-mafft (7.147-1) unstable; urgency=medium
-
- * New upstream release.
-
- -- Charles Plessy <plessy at debian.org> Sun, 30 Mar 2014 19:40:37 +0900
-
-mafft (7.130-1) unstable; urgency=low
-
- * New upstream release.
- * Correct ‘XS-Testsuite’ to ‘Testsuite’ in debian/control.
-
- -- Charles Plessy <plessy at debian.org> Sun, 19 Jan 2014 08:25:50 +0900
-
-mafft (7.127-1) unstable; urgency=low
-
- * New upstream release.
- * debian/tests/with-example-data: Don't write progress to stderr on success.
- Closes: #728190, thanks to Martin Pitt <martin.pitt at ubuntu.com>.
- * Conforms with Policy 3.9.5.
- * Pass CPPFLAGS within CFLAGS.
-
- -- Charles Plessy <plessy at debian.org> Sat, 30 Nov 2013 17:30:14 +0900
-
-mafft (7.123-1) unstable; urgency=low
-
- * New upstream version.
- * Correct watch file, which was downloading the non-free version.
- This error did not affect the current stable release of Debian.
- * debian/tests/with-example-data: disable multithreading to stabilise output.
-
- -- Charles Plessy <plessy at debian.org> Wed, 16 Oct 2013 08:22:20 +0900
-
-mafft (7.058-1) unstable; urgency=low
-
- * New upstream version incorporated debian/patches
- Closes: #715827, #715830, #715831, #715847, #715881
-
- -- Andreas Tille <tille at debian.org> Sun, 04 Aug 2013 08:51:10 +0200
-
-mafft (7.055-1) unstable; urgency=low
-
- [ Charles Plessy ]
- * Signal the use of autopkgtest in debian/control (closes: #692683).
-
- [ Andreas Tille ]
- * New upstream version
- * debian/README.source: removed because redundant
- * debian/patches/hardening.patch: Enable propagation of hardening
- options
- * debian/control: use anonscm in Vcs fields
-
- -- Andreas Tille <tille at debian.org> Tue, 30 Jul 2013 13:39:43 +0200
-
-mafft (6.940-1) unstable; urgency=low
-
- [ Charles Plessy ]
- * New upstream release (no new license nor copyright statement).
- * Removed unnecessary build-dependance on quilt.
- * Test for regressions with autopkgtest insted of doing it at build time.
- (debian/control, debian/tests/control, debian/tests/with-example-data)
- * debian/control:
- - Removed 'Pre-Depends: dpkg (>= 1.15.6)' now that Ubuntu LTS 12.04 is out.
- - Increment Standards-Version to show conformance with Policy 3.9.4.
- - Removed DM-Upload-Allowed field.
- - Normalised with the command cme fix dpkg-control.
- - Use Debhelper 9 (also debian/compat).
- * Pass dpkg build flags in debian/rules.
-
- [ Andreas Tille ]
- * debian/upstream:
- - Single Reference field instead of Reference-*
- - Add additional reference from tasks file
- - Authors in BibTeX conform format
-
- -- Charles Plessy <plessy at debian.org> Sun, 14 Oct 2012 15:42:54 +0900
-
-mafft (6.864-1) unstable; urgency=low
-
- * New upstream release.
- * Pre-Depends on dpkg (>= 1.15.6) for xz compression support (debian/control).
- * Renamed debian/README.Debian debian/README.test.
- * Track the new website in debian/watch.
-
- -- Charles Plessy <plessy at debian.org> Thu, 12 Jan 2012 19:00:31 +0900
-
-mafft (6.860-1) unstable; urgency=low
-
- * New upstream release.
- * Simplified debian/watch.
- * Updated Homepage (debian/control).
- * Compress binary package with xz (debian/control).
-
- -- Charles Plessy <plessy at debian.org> Sun, 18 Sep 2011 14:43:10 +0900
-
-mafft (6.859-1) unstable; urgency=low
-
- * New upstream release.
- * Converted debian/copyright to machine-readable (DEP 5) format.
-
- -- Charles Plessy <plessy at debian.org> Sat, 27 Aug 2011 12:06:00 +0900
-
-mafft (6.857-1) unstable; urgency=low
-
- * New upstream version.
- * Enable multithread, correct FHS path (debian/rules).
- * Removed extra manpage copies instead of patching Makefile and
- installing via debhleper (debian/patches, debian/rules, debian/manpages).
- * Removed debian/dirs, not needed anymore.
- * Run the tests after installation, and allow them to fail (debian/rules).
- * Build when running debian/rules build (override typo, Closes: #636634).
- * Corrected VCS fields in debian/control.
- * Incremented Standards-Version to reflect conformance wiht Policy 3.9.2
- (debian/control, no changes needed).
-
- -- Charles Plessy <plessy at debian.org> Fri, 05 Aug 2011 09:54:09 +0900
-
-mafft (6.850-1) unstable; urgency=low
-
- * New upstream version
- * Adapted patch to new upstream
- * Debhelper 8 (control + compat)
- * debian/rules: Switch to dh
- * debian/links: override broken symlinks created in Makefile
-
- -- Andreas Tille <tille at debian.org> Sat, 12 Mar 2011 00:02:43 +0100
-
-mafft (6.833-1) unstable; urgency=low
-
- * New upstream version
-
- -- Andreas Tille <tille at debian.org> Wed, 17 Nov 2010 13:51:28 +0100
-
-mafft (6.815-1) unstable; urgency=low
-
- * New upstream version
- * Switch to source format 3.0 (quilt)
- * Standards-Version: 3.9.1 (no changes needed)
-
- -- Andreas Tille <tille at debian.org> Thu, 05 Aug 2010 10:29:50 +0200
-
-mafft (6.811-1) unstable; urgency=low
-
- * New upstream version
- * Standards-Version: 3.8.4 (no changes needed)
-
- -- Andreas Tille <tille at debian.org> Thu, 24 Jun 2010 13:08:06 +0200
-
-mafft (6.717-1) unstable; urgency=low
-
- * New upstream version
- * Added a few informations about Upstream in debian/upstream-metadata.yaml.
- * Documented how this package is tested in debian/README.Debian.
- * Refreshed debian/copyright, using the verbatim upstream license,
- indented with a tabulation.
-
- -- Charles Plessy <plessy at debian.org> Mon, 14 Dec 2009 13:02:59 +0900
-
-mafft (6.716-1) unstable; urgency=low
-
- * New upstream version
-
- -- Andreas Tille <tille at debian.org> Tue, 03 Nov 2009 12:39:12 +0100
-
-mafft (6.713-1) unstable; urgency=low
-
- [ David Paleino ]
- * debian/control:
- - removed myself from Uploaders
-
- [ Andreas Tille ]
- * New upstream version
- * debian/control:
- - Standards-Version: 3.8.3 (no changes needed)
- - s/Debian-Med/Debian Med/
- - Recommends: blast2, lynx, ruby (instead of Suggests - we have a Ruby
- script in /usr/bin using blast and lynx.
- * debhelper 7
- * No need for debian/patches/Securisation-by-mktemp-usage.patch any more
- * debian/watch: Handle -with.*-extensions naming - we are dealing
- with the without-extensions tarball in Debian
-
- -- Andreas Tille <tille at debian.org> Mon, 28 Sep 2009 09:02:30 +0200
-
-mafft (6.240-2) unstable; urgency=high
-
- [ Charles Plessy ]
- * debian/control:
- - Moved the Homepage: field out from the package's description.
- - Enhances: t-coffee.
- * Updated my email address.
- * Securisation of the temorary files of mafft-homologs:
- - debian/control: build-depend on quilt.
- - debian/rules: modified to use quilt.
- - debian/README.source: signals that the package uses quilt.
- - debian/patches: added a patch to use non-guessable temporary files
- (Closes: #496366). Thanks to Dmitry E. Oboukhov for finding the bug, Thijs
- Kinkhorst for preliminary, Kazutaka Katoh for the final implementation,
- and Michael Schutte for the final review.
- - debian/mafft-homologs.1*, debian/README.Debian: document that the
- program is patched.
-
- [ David Paleino ]
- * debian/mafft.1, debian/mafft-homologs.1 added - manpages built statically.
- * debian/control:
- - B-D updated (see above)
- - added myself to Uploaders
- - moved XS-Vcs-* fields to Vcs-*
- - Updated to Standards-Version 3.7.3 (no changes needed)
- * debian/rules:
- - reflecting static build of manpages
- - minor changes
-
- -- Charles Plessy <plessy at debian.org> Mon, 25 Aug 2008 23:30:20 +0900
-
-mafft (6.240-1) unstable; urgency=low
-
- * Initial release (Closes: #409640)
-
- -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 9 Jun 2007 12:06:43 +0900
-
Copied: trunk/packages/mafft/tags/7.187-1/debian/changelog (from rev 18211, trunk/packages/mafft/trunk/debian/changelog)
===================================================================
--- trunk/packages/mafft/tags/7.187-1/debian/changelog (rev 0)
+++ trunk/packages/mafft/tags/7.187-1/debian/changelog 2014-10-05 00:24:10 UTC (rev 18212)
@@ -0,0 +1,254 @@
+mafft (7.187-1) unstable; urgency=medium
+
+ * New upstream release.
+ * Conforms to Policy 3.9.6.
+
+ -- Charles Plessy <plessy at debian.org> Sun, 05 Oct 2014 09:00:33 +0900
+
+mafft (7.164-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Mon, 04 Aug 2014 15:04:10 +0200
+
+mafft (7.158-1) unstable; urgency=medium
+
+ * New upstream release.
+
+ -- Charles Plessy <plessy at debian.org> Sun, 13 Jul 2014 20:26:22 +0900
+
+mafft (7.157-1) unstable; urgency=medium
+
+ * New upstream release.
+ * debian/control
+ - Added substitution variable ${perl:Depends}, used by Debhelper.
+ - Recommend libwww-perl used by the script ‘seekquencer_premafft.pl’.
+
+ -- Charles Plessy <plessy at debian.org> Wed, 18 Jun 2014 08:10:02 +0900
+
+mafft (7.149-1) unstable; urgency=medium
+
+ * New upstream release.
+
+ -- Charles Plessy <plessy at debian.org> Sat, 12 Apr 2014 13:46:13 +0900
+
+mafft (7.147-1) unstable; urgency=medium
+
+ * New upstream release.
+
+ -- Charles Plessy <plessy at debian.org> Sun, 30 Mar 2014 19:40:37 +0900
+
+mafft (7.130-1) unstable; urgency=low
+
+ * New upstream release.
+ * Correct ‘XS-Testsuite’ to ‘Testsuite’ in debian/control.
+
+ -- Charles Plessy <plessy at debian.org> Sun, 19 Jan 2014 08:25:50 +0900
+
+mafft (7.127-1) unstable; urgency=low
+
+ * New upstream release.
+ * debian/tests/with-example-data: Don't write progress to stderr on success.
+ Closes: #728190, thanks to Martin Pitt <martin.pitt at ubuntu.com>.
+ * Conforms with Policy 3.9.5.
+ * Pass CPPFLAGS within CFLAGS.
+
+ -- Charles Plessy <plessy at debian.org> Sat, 30 Nov 2013 17:30:14 +0900
+
+mafft (7.123-1) unstable; urgency=low
+
+ * New upstream version.
+ * Correct watch file, which was downloading the non-free version.
+ This error did not affect the current stable release of Debian.
+ * debian/tests/with-example-data: disable multithreading to stabilise output.
+
+ -- Charles Plessy <plessy at debian.org> Wed, 16 Oct 2013 08:22:20 +0900
+
+mafft (7.058-1) unstable; urgency=low
+
+ * New upstream version incorporated debian/patches
+ Closes: #715827, #715830, #715831, #715847, #715881
+
+ -- Andreas Tille <tille at debian.org> Sun, 04 Aug 2013 08:51:10 +0200
+
+mafft (7.055-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * Signal the use of autopkgtest in debian/control (closes: #692683).
+
+ [ Andreas Tille ]
+ * New upstream version
+ * debian/README.source: removed because redundant
+ * debian/patches/hardening.patch: Enable propagation of hardening
+ options
+ * debian/control: use anonscm in Vcs fields
+
+ -- Andreas Tille <tille at debian.org> Tue, 30 Jul 2013 13:39:43 +0200
+
+mafft (6.940-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * New upstream release (no new license nor copyright statement).
+ * Removed unnecessary build-dependance on quilt.
+ * Test for regressions with autopkgtest insted of doing it at build time.
+ (debian/control, debian/tests/control, debian/tests/with-example-data)
+ * debian/control:
+ - Removed 'Pre-Depends: dpkg (>= 1.15.6)' now that Ubuntu LTS 12.04 is out.
+ - Increment Standards-Version to show conformance with Policy 3.9.4.
+ - Removed DM-Upload-Allowed field.
+ - Normalised with the command cme fix dpkg-control.
+ - Use Debhelper 9 (also debian/compat).
+ * Pass dpkg build flags in debian/rules.
+
+ [ Andreas Tille ]
+ * debian/upstream:
+ - Single Reference field instead of Reference-*
+ - Add additional reference from tasks file
+ - Authors in BibTeX conform format
+
+ -- Charles Plessy <plessy at debian.org> Sun, 14 Oct 2012 15:42:54 +0900
+
+mafft (6.864-1) unstable; urgency=low
+
+ * New upstream release.
+ * Pre-Depends on dpkg (>= 1.15.6) for xz compression support (debian/control).
+ * Renamed debian/README.Debian debian/README.test.
+ * Track the new website in debian/watch.
+
+ -- Charles Plessy <plessy at debian.org> Thu, 12 Jan 2012 19:00:31 +0900
+
+mafft (6.860-1) unstable; urgency=low
+
+ * New upstream release.
+ * Simplified debian/watch.
+ * Updated Homepage (debian/control).
+ * Compress binary package with xz (debian/control).
+
+ -- Charles Plessy <plessy at debian.org> Sun, 18 Sep 2011 14:43:10 +0900
+
+mafft (6.859-1) unstable; urgency=low
+
+ * New upstream release.
+ * Converted debian/copyright to machine-readable (DEP 5) format.
+
+ -- Charles Plessy <plessy at debian.org> Sat, 27 Aug 2011 12:06:00 +0900
+
+mafft (6.857-1) unstable; urgency=low
+
+ * New upstream version.
+ * Enable multithread, correct FHS path (debian/rules).
+ * Removed extra manpage copies instead of patching Makefile and
+ installing via debhleper (debian/patches, debian/rules, debian/manpages).
+ * Removed debian/dirs, not needed anymore.
+ * Run the tests after installation, and allow them to fail (debian/rules).
+ * Build when running debian/rules build (override typo, Closes: #636634).
+ * Corrected VCS fields in debian/control.
+ * Incremented Standards-Version to reflect conformance wiht Policy 3.9.2
+ (debian/control, no changes needed).
+
+ -- Charles Plessy <plessy at debian.org> Fri, 05 Aug 2011 09:54:09 +0900
+
+mafft (6.850-1) unstable; urgency=low
+
+ * New upstream version
+ * Adapted patch to new upstream
+ * Debhelper 8 (control + compat)
+ * debian/rules: Switch to dh
+ * debian/links: override broken symlinks created in Makefile
+
+ -- Andreas Tille <tille at debian.org> Sat, 12 Mar 2011 00:02:43 +0100
+
+mafft (6.833-1) unstable; urgency=low
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Wed, 17 Nov 2010 13:51:28 +0100
+
+mafft (6.815-1) unstable; urgency=low
+
+ * New upstream version
+ * Switch to source format 3.0 (quilt)
+ * Standards-Version: 3.9.1 (no changes needed)
+
+ -- Andreas Tille <tille at debian.org> Thu, 05 Aug 2010 10:29:50 +0200
+
+mafft (6.811-1) unstable; urgency=low
+
+ * New upstream version
+ * Standards-Version: 3.8.4 (no changes needed)
+
+ -- Andreas Tille <tille at debian.org> Thu, 24 Jun 2010 13:08:06 +0200
+
+mafft (6.717-1) unstable; urgency=low
+
+ * New upstream version
+ * Added a few informations about Upstream in debian/upstream-metadata.yaml.
+ * Documented how this package is tested in debian/README.Debian.
+ * Refreshed debian/copyright, using the verbatim upstream license,
+ indented with a tabulation.
+
+ -- Charles Plessy <plessy at debian.org> Mon, 14 Dec 2009 13:02:59 +0900
+
+mafft (6.716-1) unstable; urgency=low
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Tue, 03 Nov 2009 12:39:12 +0100
+
+mafft (6.713-1) unstable; urgency=low
+
+ [ David Paleino ]
+ * debian/control:
+ - removed myself from Uploaders
+
+ [ Andreas Tille ]
+ * New upstream version
+ * debian/control:
+ - Standards-Version: 3.8.3 (no changes needed)
+ - s/Debian-Med/Debian Med/
+ - Recommends: blast2, lynx, ruby (instead of Suggests - we have a Ruby
+ script in /usr/bin using blast and lynx.
+ * debhelper 7
+ * No need for debian/patches/Securisation-by-mktemp-usage.patch any more
+ * debian/watch: Handle -with.*-extensions naming - we are dealing
+ with the without-extensions tarball in Debian
+
+ -- Andreas Tille <tille at debian.org> Mon, 28 Sep 2009 09:02:30 +0200
+
+mafft (6.240-2) unstable; urgency=high
+
+ [ Charles Plessy ]
+ * debian/control:
+ - Moved the Homepage: field out from the package's description.
+ - Enhances: t-coffee.
+ * Updated my email address.
+ * Securisation of the temorary files of mafft-homologs:
+ - debian/control: build-depend on quilt.
+ - debian/rules: modified to use quilt.
+ - debian/README.source: signals that the package uses quilt.
+ - debian/patches: added a patch to use non-guessable temporary files
+ (Closes: #496366). Thanks to Dmitry E. Oboukhov for finding the bug, Thijs
+ Kinkhorst for preliminary, Kazutaka Katoh for the final implementation,
+ and Michael Schutte for the final review.
+ - debian/mafft-homologs.1*, debian/README.Debian: document that the
+ program is patched.
+
+ [ David Paleino ]
+ * debian/mafft.1, debian/mafft-homologs.1 added - manpages built statically.
+ * debian/control:
+ - B-D updated (see above)
+ - added myself to Uploaders
+ - moved XS-Vcs-* fields to Vcs-*
+ - Updated to Standards-Version 3.7.3 (no changes needed)
+ * debian/rules:
+ - reflecting static build of manpages
+ - minor changes
+
+ -- Charles Plessy <plessy at debian.org> Mon, 25 Aug 2008 23:30:20 +0900
+
+mafft (6.240-1) unstable; urgency=low
+
+ * Initial release (Closes: #409640)
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 9 Jun 2007 12:06:43 +0900
+
Deleted: trunk/packages/mafft/tags/7.187-1/debian/control
===================================================================
--- trunk/packages/mafft/trunk/debian/control 2014-10-04 22:32:58 UTC (rev 18210)
+++ trunk/packages/mafft/tags/7.187-1/debian/control 2014-10-05 00:24:10 UTC (rev 18212)
@@ -1,42 +0,0 @@
-Source: mafft
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
-Section: science
-Testsuite: autopkgtest
-Priority: optional
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.5
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mafft/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mafft/trunk/
-Homepage: http://mafft.cbrc.jp/alignment/software/
-
-Package: mafft
-Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${perl:Depends}
-Recommends: blast2,
- libwww-perl,
- lynx,
- ruby
-Enhances: t-coffee
-Description: Multiple alignment program for amino acid or nucleotide sequences
- MAFFT is a multiple sequence alignment program which offers three
- accuracy-oriented methods:
- * L-INS-i (probably most accurate; recommended for <200 sequences;
- iterative refinement method incorporating local pairwise alignment
- information),
- * G-INS-i (suitable for sequences of similar lengths; recommended for
- <200 sequences; iterative refinement method incorporating global
- pairwise alignment information),
- * E-INS-i (suitable for sequences containing large unalignable regions;
- recommended for <200 sequences),
- and five speed-oriented methods:
- * FFT-NS-i (iterative refinement method; two cycles only),
- * FFT-NS-i (iterative refinement method; max. 1000 iterations),
- * FFT-NS-2 (fast; progressive method),
- * FFT-NS-1 (very fast; recommended for >2000 sequences; progressive
- method with a rough guide tree),
- * NW-NS-PartTree-1 (recommended for ∼50,000 sequences; progressive
- method with the PartTree algorithm).
Copied: trunk/packages/mafft/tags/7.187-1/debian/control (from rev 18211, trunk/packages/mafft/trunk/debian/control)
===================================================================
--- trunk/packages/mafft/tags/7.187-1/debian/control (rev 0)
+++ trunk/packages/mafft/tags/7.187-1/debian/control 2014-10-05 00:24:10 UTC (rev 18212)
@@ -0,0 +1,42 @@
+Source: mafft
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
+Section: science
+Testsuite: autopkgtest
+Priority: optional
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mafft/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mafft/trunk/
+Homepage: http://mafft.cbrc.jp/alignment/software/
+
+Package: mafft
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ${perl:Depends}
+Recommends: blast2,
+ libwww-perl,
+ lynx,
+ ruby
+Enhances: t-coffee
+Description: Multiple alignment program for amino acid or nucleotide sequences
+ MAFFT is a multiple sequence alignment program which offers three
+ accuracy-oriented methods:
+ * L-INS-i (probably most accurate; recommended for <200 sequences;
+ iterative refinement method incorporating local pairwise alignment
+ information),
+ * G-INS-i (suitable for sequences of similar lengths; recommended for
+ <200 sequences; iterative refinement method incorporating global
+ pairwise alignment information),
+ * E-INS-i (suitable for sequences containing large unalignable regions;
+ recommended for <200 sequences),
+ and five speed-oriented methods:
+ * FFT-NS-i (iterative refinement method; two cycles only),
+ * FFT-NS-i (iterative refinement method; max. 1000 iterations),
+ * FFT-NS-2 (fast; progressive method),
+ * FFT-NS-1 (very fast; recommended for >2000 sequences; progressive
+ method with a rough guide tree),
+ * NW-NS-PartTree-1 (recommended for ∼50,000 sequences; progressive
+ method with the PartTree algorithm).
Deleted: trunk/packages/mafft/tags/7.187-1/debian/copyright
===================================================================
--- trunk/packages/mafft/trunk/debian/copyright 2014-10-04 22:32:58 UTC (rev 18210)
+++ trunk/packages/mafft/tags/7.187-1/debian/copyright 2014-10-05 00:24:10 UTC (rev 18212)
@@ -1,47 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Source: http://mafft.cbrc.jp/alignment/software/mafft-7.158-without-extensions-src.tgz
-Comment: Debian only distributes MAFFT without its extensions.
- The mafft-*-with-extensions-src.tgz upstream packages have an ‘extensions’
- directory, which contains code from the Vienna RNA package, that does not allow
- commercial use and is therefore unsuitable for Debian.
-
-Files: *
-Copyright: © 2009–2014 Kazutaka Katoh
-License: mafft
- Redistribution and use in source and binary forms,
- with or without modification, are permitted provided
- that the following conditions are met:
- .
- Redistributions of source code must retain the
- above copyright notice, this list of conditions
- and the following disclaimer. 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.
- .
- The name of the author may not be used to endorse
- or promote products derived from this software without
- specific prior written permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE AUTHOR "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 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: debian/*
-Copyright: (C) 2009 Andreas Tille <tille at debian.org>
-License: same-as-mafft
- See above
-
Copied: trunk/packages/mafft/tags/7.187-1/debian/copyright (from rev 18211, trunk/packages/mafft/trunk/debian/copyright)
===================================================================
--- trunk/packages/mafft/tags/7.187-1/debian/copyright (rev 0)
+++ trunk/packages/mafft/tags/7.187-1/debian/copyright 2014-10-05 00:24:10 UTC (rev 18212)
@@ -0,0 +1,47 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://mafft.cbrc.jp/alignment/software/mafft-7.187-without-extensions-src.tgz
+Comment: Debian only distributes MAFFT without its extensions.
+ The mafft-*-with-extensions-src.tgz upstream packages have an ‘extensions’
+ directory, which contains code from the Vienna RNA package, that does not allow
+ commercial use and is therefore unsuitable for Debian.
+
+Files: *
+Copyright: © 2009–2014 Kazutaka Katoh
+License: mafft
+ Redistribution and use in source and binary forms,
+ with or without modification, are permitted provided
+ that the following conditions are met:
+ .
+ Redistributions of source code must retain the
+ above copyright notice, this list of conditions
+ and the following disclaimer. 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.
+ .
+ The name of the author may not be used to endorse
+ or promote products derived from this software without
+ specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR "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 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: debian/*
+Copyright: (C) 2009 Andreas Tille <tille at debian.org>
+License: same-as-mafft
+ See above
+
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