[med-svn] r12528 - in trunk/packages/mafft/tags: . 6.940-1/debian

Charles Plessy plessy at alioth.debian.org
Fri Nov 9 00:04:30 UTC 2012


Author: plessy
Date: 2012-11-09 00:04:29 +0000 (Fri, 09 Nov 2012)
New Revision: 12528

Added:
   trunk/packages/mafft/tags/6.940-1/
   trunk/packages/mafft/tags/6.940-1/debian/changelog
   trunk/packages/mafft/tags/6.940-1/debian/compat
   trunk/packages/mafft/tags/6.940-1/debian/control
   trunk/packages/mafft/tags/6.940-1/debian/copyright
   trunk/packages/mafft/tags/6.940-1/debian/rules
   trunk/packages/mafft/tags/6.940-1/debian/tests/
Removed:
   trunk/packages/mafft/tags/6.940-1/debian/changelog
   trunk/packages/mafft/tags/6.940-1/debian/compat
   trunk/packages/mafft/tags/6.940-1/debian/control
   trunk/packages/mafft/tags/6.940-1/debian/copyright
   trunk/packages/mafft/tags/6.940-1/debian/rules
Log:
[svn-buildpackage] Tagging mafft 6.940-1

Deleted: trunk/packages/mafft/tags/6.940-1/debian/changelog
===================================================================
--- trunk/packages/mafft/trunk/debian/changelog	2012-10-14 04:10:59 UTC (rev 12407)
+++ trunk/packages/mafft/tags/6.940-1/debian/changelog	2012-11-09 00:04:29 UTC (rev 12528)
@@ -1,153 +0,0 @@
-mafft (6.864-2) UNRELEASED; urgency=low
-
-  * debian/upstream:
-     - Single Reference field instead of Reference-*
-     - Add additional reference from tasks file
-     - Authors in BibTeX conform format
-
- -- Andreas Tille <tille at debian.org>  Wed, 07 Mar 2012 23:30:03 +0100
-
-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/6.940-1/debian/changelog (from rev 12527, trunk/packages/mafft/trunk/debian/changelog)
===================================================================
--- trunk/packages/mafft/tags/6.940-1/debian/changelog	                        (rev 0)
+++ trunk/packages/mafft/tags/6.940-1/debian/changelog	2012-11-09 00:04:29 UTC (rev 12528)
@@ -0,0 +1,167 @@
+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/6.940-1/debian/compat
===================================================================
--- trunk/packages/mafft/trunk/debian/compat	2012-10-14 04:10:59 UTC (rev 12407)
+++ trunk/packages/mafft/tags/6.940-1/debian/compat	2012-11-09 00:04:29 UTC (rev 12528)
@@ -1 +0,0 @@
-8

Copied: trunk/packages/mafft/tags/6.940-1/debian/compat (from rev 12423, trunk/packages/mafft/trunk/debian/compat)
===================================================================
--- trunk/packages/mafft/tags/6.940-1/debian/compat	                        (rev 0)
+++ trunk/packages/mafft/tags/6.940-1/debian/compat	2012-11-09 00:04:29 UTC (rev 12528)
@@ -0,0 +1 @@
+9

Deleted: trunk/packages/mafft/tags/6.940-1/debian/control
===================================================================
--- trunk/packages/mafft/trunk/debian/control	2012-10-14 04:10:59 UTC (rev 12407)
+++ trunk/packages/mafft/tags/6.940-1/debian/control	2012-11-09 00:04:29 UTC (rev 12528)
@@ -1,39 +0,0 @@
-Source: mafft
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 8), quilt (>= 0.47)
-Standards-Version: 3.9.2
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mafft/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mafft/trunk/
-Homepage: http://mafft.cbrc.jp/alignment/software/
-
-Package: mafft
-Architecture: any
-# Needed until after Ubuntu 12.04 LTS.
-Pre-Depends: dpkg (>= 1.15.6)
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: blast2, 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/6.940-1/debian/control (from rev 12423, trunk/packages/mafft/trunk/debian/control)
===================================================================
--- trunk/packages/mafft/tags/6.940-1/debian/control	                        (rev 0)
+++ trunk/packages/mafft/tags/6.940-1/debian/control	2012-11-09 00:04:29 UTC (rev 12528)
@@ -0,0 +1,40 @@
+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
+Priority: optional
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.4
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mafft/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mafft/trunk/
+Homepage: http://mafft.cbrc.jp/alignment/software/
+
+Package: mafft
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Recommends: blast2,
+            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/6.940-1/debian/copyright
===================================================================
--- trunk/packages/mafft/trunk/debian/copyright	2012-10-14 04:10:59 UTC (rev 12407)
+++ trunk/packages/mafft/tags/6.940-1/debian/copyright	2012-11-09 00:04:29 UTC (rev 12528)
@@ -1,48 +0,0 @@
-Format: http://dep.debian.net/deps/dep5/
-Source: http://mafft.cbrc.jp/alignment/software/mafft-6.864-without-extensions-src.tgz
-Comment: Debian only distributes MAFFT without its extensions.
- The mafft-6.x-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 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) 2007 Charles Plessy <charles at debian.org>,
-           (C) 2009 Andreas Tille <tille at debian.org>
-License: same-as-mafft
- See above
-

Copied: trunk/packages/mafft/tags/6.940-1/debian/copyright (from rev 12416, trunk/packages/mafft/trunk/debian/copyright)
===================================================================
--- trunk/packages/mafft/tags/6.940-1/debian/copyright	                        (rev 0)
+++ trunk/packages/mafft/tags/6.940-1/debian/copyright	2012-11-09 00:04:29 UTC (rev 12528)
@@ -0,0 +1,48 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://mafft.cbrc.jp/alignment/software/mafft-6.940-without-extensions-src.tgz
+Comment: Debian only distributes MAFFT without its extensions.
+ The mafft-6.x-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: © 2009-2012 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) 2007 Charles Plessy <charles at debian.org>,
+           (C) 2009 Andreas Tille <tille at debian.org>
+License: same-as-mafft
+ See above
+

Deleted: trunk/packages/mafft/tags/6.940-1/debian/rules
===================================================================
--- trunk/packages/mafft/trunk/debian/rules	2012-10-14 04:10:59 UTC (rev 12407)
+++ trunk/packages/mafft/tags/6.940-1/debian/rules	2012-11-09 00:04:29 UTC (rev 12528)
@@ -1,33 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-# Build rules for the Debian package mafft.
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-%:
-	dh $@ --with quilt
-
-override_dh_auto_build:
-	$(MAKE) -C core PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft
-
-override_dh_clean:
-	[ ! -f core/Makefile ] || $(MAKE) -C core clean
-	rm -rf binaries/* scripts/*
-	dh_clean
-
-MAFFT = MAFFT_BINARIES=$(CURDIR)/binaries scripts/mafft
-
-override_dh_install:
-	$(MAKE) -C core PREFIX=$(CURDIR)/debian/mafft/usr/lib/mafft MANDIR=$(CURDIR)/debian/mafft/usr/share/man/man1 LIBDIR=$(CURDIR)/debian/mafft/usr/lib/mafft/lib/mafft install
-	rm $(CURDIR)/debian/mafft/usr/lib/mafft/lib/mafft/*.1
-	# Testing Mafft…
-	$(MAFFT) 				test/sample | diff test/sample.fftns2 -
-	$(MAFFT) --maxiterate 100 		test/sample | diff test/sample.fftnsi -
-	$(MAFFT) --globalpair 			test/sample | diff test/sample.gins1 -
-	$(MAFFT) --globalpair --maxiterate 100	test/sample | diff test/sample.ginsi -
-	$(MAFFT) --localpair			test/sample | diff test/sample.lins1 -
-	$(MAFFT) --localpair --maxiterate 100	test/sample | diff test/sample.linsi -
-
-override_dh_builddeb:
-	dh_builddeb -- -Z xz

Copied: trunk/packages/mafft/tags/6.940-1/debian/rules (from rev 12527, trunk/packages/mafft/trunk/debian/rules)
===================================================================
--- trunk/packages/mafft/tags/6.940-1/debian/rules	                        (rev 0)
+++ trunk/packages/mafft/tags/6.940-1/debian/rules	2012-11-09 00:04:29 UTC (rev 12528)
@@ -0,0 +1,29 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Build rules for the Debian package mafft.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+	dh $@
+
+override_dh_auto_build:
+	$(MAKE) -C core PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft CFLAGS="$(shell dpkg-buildflags --get CFLAGS)" CPPFLAGS="$(shell dpkg-buildflags --get CPPFLAGS)" CXXFLAGS="$(shell dpkg-buildflags --get CXXFLAGS)" LDFLAGS="$(shell dpkg-buildflags --get LDFLAGS)"
+
+override_dh_clean:
+	[ ! -f core/Makefile ] || $(MAKE) -C core clean
+	rm -rf binaries/* scripts/*
+	dh_clean
+
+MAFFT = MAFFT_BINARIES=$(CURDIR)/binaries scripts/mafft
+
+override_dh_install:
+	$(MAKE) -C core PREFIX=$(CURDIR)/debian/mafft/usr/lib/mafft MANDIR=$(CURDIR)/debian/mafft/usr/share/man/man1 LIBDIR=$(CURDIR)/debian/mafft/usr/lib/mafft/lib/mafft install
+	rm $(CURDIR)/debian/mafft/usr/lib/mafft/lib/mafft/*.1
+
+override_dh_compress:
+	dh_compress -X test/sample
+
+override_dh_builddeb:
+	dh_builddeb -- -Z xz




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