Author: plessy
Date: 2009-12-14 05:15:41 +0000 (Mon, 14 Dec 2009)
New Revision: 4447
Modified:
trunk/packages/mafft/trunk/debian/README.Debian
trunk/packages/mafft/trunk/debian/changelog
trunk/packages/mafft/trunk/debian/copyright
Log:
New usptream version, and various minor packaging changes.
* 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.
Modified: trunk/packages/mafft/trunk/debian/README.Debian
===================================================================
--- trunk/packages/mafft/trunk/debian/README.Debian 2009-12-13 18:21:13 UTC
(rev 4446)
+++ trunk/packages/mafft/trunk/debian/README.Debian 2009-12-14 05:15:41 UTC
(rev 4447)
@@ -1,26 +1,19 @@
mafft for Debian
----------------
-Some test are available:
+The mafft program is tested when we assemble our binary packages in our build
+network. The following commands are run and compared to a reference output:
-% cd /usr/share/doc/mafft/test
-% mafft sample > test.fftns2 # FFT-NS-2
-% mafft --maxiterate 100 sample > test.fftnsi # FFT-NS-i
-% mafft --globalpair sample > test.gins1 # G-INS-1
-% mafft --globalpair --maxiterate 100 sample > test.ginsi # G-INS-i
-% mafft --localpair sample > test.lins1 # L-INS-1
-% mafft --localpair --maxiterate 100 sample > test.linsi # L-INS-i
-% diff test.fftns2 sample.fftns2
-% diff test.fftnsi sample.fftnsi
-% diff test.gins1 sample.gins1
-% diff test.ginsi sample.ginsi
-% diff test.lins1 sample.lins1
-% diff test.linsi sample.linsi
+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 -
+The test sample and the reference output are distributed compressed in the
+mafft binary package in the ‘/usr/share/doc/mafft/test’ directory. You can copy
+this directory to a temporary place, uncompress the files and run the above
+commands to reproduce the tests on your local installation.
-The programs mafft and mafft-homologs have been patched to enhance the security
-of the temporary files they create. You can consult the patch in the Debian
-source package. It has been reviewed and amended by Kazutaka Katoh, the
-upstream author of MAFFT.
-
- -- Charles Plessy <[email protected]> Mon, 25 Aug 2008
23:29:19 +0900
+ -- Charles Plessy <[email protected]> Mon, 14 Dec 2009 12:43:21 +0900
Modified: trunk/packages/mafft/trunk/debian/changelog
===================================================================
--- trunk/packages/mafft/trunk/debian/changelog 2009-12-13 18:21:13 UTC (rev
4446)
+++ trunk/packages/mafft/trunk/debian/changelog 2009-12-14 05:15:41 UTC (rev
4447)
@@ -1,8 +1,12 @@
-mafft (6.716-2) UNRELEASED; urgency=low
+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 <[email protected]> Tue, 01 Dec 2009 15:25:04 +0900
+ -- Charles Plessy <[email protected]> Mon, 14 Dec 2009 13:02:59 +0900
mafft (6.716-1) unstable; urgency=low
Modified: trunk/packages/mafft/trunk/debian/copyright
===================================================================
--- trunk/packages/mafft/trunk/debian/copyright 2009-12-13 18:21:13 UTC (rev
4446)
+++ trunk/packages/mafft/trunk/debian/copyright 2009-12-14 05:15:41 UTC (rev
4447)
@@ -1,42 +1,49 @@
-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-Upstream-Author: Kazutaka Katoh <[email protected]>
-Packaged-By: Charles Plessy <[email protected]>,
- Andreas Tille <[email protected]>
-Packaged-Date: Wed, 7 Feb 2007 21:44:40 +0900
-Upstream-Source: http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html
+Name : MAFFT
+Contact : Kazutaka Katoh <[email protected]>
+Source :
http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.717-without-extensions-src.tgz
-Files: *
-Copyright: (C) 2006-2009 Kazutaka Katoh
-License: BSD-like
- 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.
-X-Comment: There are two tarballs provided by upstream:
- mafft-6.713-with-extensions-src.tgz and mafft-6.713-without-extensions-src.tgz
- We are using the *without-extensions* tarball because the extensions are
- non-free.
+Comment : Debian only distributes MAFFT without its extensions.
+ The mafft-6.6xx-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.
+
+Copyright: (c) 2009 Kazutaka Katoh
+License: Similar to BSD.
+
+ 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 <[email protected]>,
(C) 2009 Andreas Tille <[email protected]>
License: Same as mafft
-
\ No newline at end of file
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