[med-svn] r18715 - in trunk/packages/vsearch/trunk/debian: . tests

Sun Feb 1 15:12:53 UTC 2015

Author: tille
Date: 2015-02-01 15:12:52 +0000 (Sun, 01 Feb 2015)
New Revision: 18715

Added:
   trunk/packages/vsearch/trunk/debian/README.test
Modified:
   trunk/packages/vsearch/trunk/debian/README.source
   trunk/packages/vsearch/trunk/debian/changelog
   trunk/packages/vsearch/trunk/debian/control
   trunk/packages/vsearch/trunk/debian/copyright
   trunk/packages/vsearch/trunk/debian/tests/run-unit-test
   trunk/packages/vsearch/trunk/debian/vsearch-data.install
   trunk/packages/vsearch/trunk/debian/vsearch.docs
Log:
Commit as uploaded


Modified: trunk/packages/vsearch/trunk/debian/README.source
===================================================================

--- trunk/packages/vsearch/trunk/debian/README.source	2015-02-01 15:07:53 UTC (rev 18714)
+++ trunk/packages/vsearch/trunk/debian/README.source	2015-02-01 15:12:52 UTC (rev 18715)
@@ -14,5 +14,13 @@
 The same is true for data/PR2-18S-rRNA-V4.fsa which is just an
 uncompressed copy of data/PR2-18S-rRNA-V4.fsa.bz2
 
+Regarding the remaining data files here is the explanation requested by
+ftpmaster according to
+  http://lists.debian.org/debian-devel/2013/09/msg00332.html
+
+Files: data/*
+The files and their origin are described in data/README.md
+
+
  -- Andreas Tille <tille at debian.org>  Wed, 14 Jan 2015 10:40:22 +0000
 

Added: trunk/packages/vsearch/trunk/debian/README.test
===================================================================
--- trunk/packages/vsearch/trunk/debian/README.test	                        (rev 0)
+++ trunk/packages/vsearch/trunk/debian/README.test	2015-02-01 15:12:52 UTC (rev 18715)
@@ -0,0 +1,9 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+To run the unit tests for vsearch you need to install the data provided
+in vsearch-data.  After installing this package simply run
+
+   sh run-unit-test
+
+in this directory.

Modified: trunk/packages/vsearch/trunk/debian/changelog
===================================================================
--- trunk/packages/vsearch/trunk/debian/changelog	2015-02-01 15:07:53 UTC (rev 18714)
+++ trunk/packages/vsearch/trunk/debian/changelog	2015-02-01 15:12:52 UTC (rev 18715)
@@ -1,8 +1,9 @@
-vsearch (1.0.7+dfsg-1) UNRELEASED; urgency=medium
+vsearch (1.0.7+dfsg-1) unstable; urgency=medium
 
   * Initial Debian release
+    Closes: #775820
 
- -- Andreas Tille <tille at debian.org>  Wed, 14 Jan 2015 10:40:22 +0000
+ -- Andreas Tille <tille at debian.org>  Tue, 20 Jan 2015 14:10:55 +0100
 
 vsearch (1.0.7-0biolinux1) trusty; urgency=low
 

Modified: trunk/packages/vsearch/trunk/debian/control
===================================================================
--- trunk/packages/vsearch/trunk/debian/control	2015-02-01 15:07:53 UTC (rev 18714)
+++ trunk/packages/vsearch/trunk/debian/control	2015-02-01 15:12:52 UTC (rev 18715)
@@ -30,7 +30,7 @@
   - be as fast or faster than usearch
 
 Package: vsearch-data
-Architecture: any
+Architecture: all
 Depends: ${shlibs:Depends},
          ${misc:Depends}
 Description: example data for vsearch tool for processing metagenomic sequences

Modified: trunk/packages/vsearch/trunk/debian/copyright
===================================================================
--- trunk/packages/vsearch/trunk/debian/copyright	2015-02-01 15:07:53 UTC (rev 18714)
+++ trunk/packages/vsearch/trunk/debian/copyright	2015-02-01 15:12:52 UTC (rev 18715)
@@ -1,6 +1,6 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: VSEARCH
-Upstream-Contact: Torbjørn Rognes <torognes at ifi.uio.no>
+Upstream-Contact: Torbjørn Rognes
 Source: https://github.com/torognes/vsearch/
 Files-Excluded: bin/*
                 data/BioMarKs.fsa.gz
@@ -13,7 +13,7 @@
          an uncompressed copy of data/PR2-18S-rRNA-V4.fsa.bz2
 
 Files: *
-Copyright: © 2014-2015 Torbjørn Rognes & Tomas Flouri
+Copyright: © 2014-2015 Torbjorn Rognes & Tomas Flouri
 License: Affero-GPL-3
                     GNU AFFERO GENERAL PUBLIC LICENSE
                        Version 3, 19 November 2007
@@ -677,6 +677,27 @@
  For more information on this, and how to apply and follow the GNU AGPL, see
  <http://www.gnu.org/licenses/>.
 
+Files: src/cityhash/*
+Copyright: 2011 Google, Inc. (Geoff Pike and Jyrki Alakuijala)
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
 Files: debian/*
 Copyright: © 2014-2015 Tim Booth <tbooth at ceh.ac.uk>
            © 2015 Andreas Tille <tille at debian.org>

Modified: trunk/packages/vsearch/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/vsearch/trunk/debian/tests/run-unit-test	2015-02-01 15:07:53 UTC (rev 18714)
+++ trunk/packages/vsearch/trunk/debian/tests/run-unit-test	2015-02-01 15:12:52 UTC (rev 18715)
@@ -2,7 +2,7 @@
 
 pkg=vsearch
 if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=`mktemp -d /var/tmp/${pkg}-test.XXXXXX`
+  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
 fi
 cd $ADTTMP
 mkdir -p data

Modified: trunk/packages/vsearch/trunk/debian/vsearch-data.install
===================================================================
--- trunk/packages/vsearch/trunk/debian/vsearch-data.install	2015-02-01 15:07:53 UTC (rev 18714)
+++ trunk/packages/vsearch/trunk/debian/vsearch-data.install	2015-02-01 15:12:52 UTC (rev 18715)
@@ -1,9 +1,9 @@
-data/simm.tar.gz		usr/share/doc/vsearch/examples
-data/BioMarKs50k.fsa		usr/share/doc/vsearch/examples
-data/BioMarKs.fsa.*		usr/share/doc/vsearch/examples
-data/PR2-18S-rRNA-V4.fsa*	usr/share/doc/vsearch/examples
-data/Rfam_11_0.*		usr/share/doc/vsearch/examples
-data/Rfam_9_1.fasta		usr/share/doc/vsearch/examples
-data/README.html		usr/share/doc/vsearch/examples
-eval/*.pl			usr/share/doc/vsearch/tests/eval
-eval/*.txt			usr/share/doc/vsearch/tests/eval
+data/simm.tar.gz	usr/share/doc/vsearch/examples
+data/BioMarKs50k.fsa	usr/share/doc/vsearch/examples
+data/BioMarKs.fsa.*	usr/share/doc/vsearch/examples
+data/PR2-18S-rRNA-V4*	usr/share/doc/vsearch/examples
+data/Rfam_11_0.*	usr/share/doc/vsearch/examples
+data/Rfam_9_1.fasta	usr/share/doc/vsearch/examples
+data/README.html	usr/share/doc/vsearch/examples
+eval/*.pl		usr/share/doc/vsearch/tests/eval
+eval/*.txt		usr/share/doc/vsearch/tests/eval

Modified: trunk/packages/vsearch/trunk/debian/vsearch.docs
===================================================================
--- trunk/packages/vsearch/trunk/debian/vsearch.docs	2015-02-01 15:07:53 UTC (rev 18714)
+++ trunk/packages/vsearch/trunk/debian/vsearch.docs	2015-02-01 15:12:52 UTC (rev 18715)
@@ -1,2 +1,3 @@
 *.html
 doc/*.pdf
+debian/tests/run-unit-test


