[med-svn] r18105 - in trunk/packages/wise/tags: . 2.4.1-17/debian 2.4.1-17/debian/tests
Charles Plessy
plessy at moszumanska.debian.org
Tue Sep 23 12:54:01 UTC 2014
Author: plessy
Date: 2014-09-23 12:54:00 +0000 (Tue, 23 Sep 2014)
New Revision: 18105
Added:
trunk/packages/wise/tags/2.4.1-17/
trunk/packages/wise/tags/2.4.1-17/debian/changelog
trunk/packages/wise/tags/2.4.1-17/debian/control
trunk/packages/wise/tags/2.4.1-17/debian/tests/control
trunk/packages/wise/tags/2.4.1-17/debian/tests/run-unit-test
Removed:
trunk/packages/wise/tags/2.4.1-17/debian/changelog
trunk/packages/wise/tags/2.4.1-17/debian/control
trunk/packages/wise/tags/2.4.1-17/debian/tests/control
trunk/packages/wise/tags/2.4.1-17/debian/tests/run-unit-test
Log:
[svn-buildpackage] Tagging wise 2.4.1-17
Deleted: trunk/packages/wise/tags/2.4.1-17/debian/changelog
===================================================================
--- trunk/packages/wise/trunk/debian/changelog 2014-09-23 10:38:00 UTC (rev 18098)
+++ trunk/packages/wise/tags/2.4.1-17/debian/changelog 2014-09-23 12:54:00 UTC (rev 18105)
@@ -1,216 +0,0 @@
-wise (2.4.1-16) unstable; urgency=medium
-
- * Make sure package builds also for arch only builds
- Closes: #757275
-
- -- Andreas Tille <tille at debian.org> Thu, 07 Aug 2014 09:49:11 +0200
-
-wise (2.4.1-15) unstable; urgency=medium
-
- * Move debian/upstream to debian/upstream/metadata
- * debian/control:
- - add myself to Uploaders
- - cme fix dpkg-control
- - debhelper 9
- - remove unneeded Build-Depends
- * debian/README.source: removed in favour of DEP5 headers
- * Make sure dnal has a valid return value (this affects the test suite
- of python-biopython on some architectures - see #751277)
- * debian/rules:
- - drop useless xz compression
- - add dh_auto_test
- * debian/patches/10_fix_path_to_data_files.patch: Brute force patch to
- fix the PATH to the data files to make the tools finding the needed
- data for the test suite
-
- -- Andreas Tille <tille at debian.org> Mon, 04 Aug 2014 19:25:58 +0200
-
-wise (2.4.1-14) unstable; urgency=low
-
- * Fixed FTBFS bug (Closes: #716983).
-
- -- Philipp Benner <philipp at debian.org> Mon, 15 Jul 2013 18:22:15 +0200
-
-wise (2.4.1-13) unstable; urgency=low
-
- * Added mayhem bugfixes.
- * Moved examples/ from wise-doc to wise-data package.
- * Removed -O3 cflag from makefiles.
-
- -- Philipp Benner <philipp at debian.org> Sun, 07 Jul 2013 13:33:01 +0200
-
-wise (2.4.1-12) unstable; urgency=low
-
- * Added missing -D_FORTIFY_SOURCE=2 for hardening support
- * Standards version 3.9.4
-
- -- Philipp Benner <philipp at debian.org> Mon, 28 Jan 2013 20:33:16 +0100
-
-wise (2.4.1-11) unstable; urgency=low
-
- [ Andreas Tille ]
- * debian/upstream: Add publication data
-
- [ Philipp Benner ]
- * Added hardening flags
-
- -- Philipp Benner <philipp at debian.org> Sun, 27 Jan 2013 18:05:31 +0100
-
-wise (2.4.1-10) unstable; urgency=low
-
- * Convert debian/rules to dh, Closes: #666319, as it restores build flags.
- * Verbose debhelper in debian/rules.
- * Normalised and upgraded debian/copyright file with ‘cme fix’.
- * Pre-Depends on dpkg (>= 1.15.6~) (debian/control).
- * Conforms to Debian policy 3.9.3 (debian/control, no other changes needed).
- * Convert debian/rules to dh, Closes: #666319, as it restores build flags.
- * Documented metadata in debian/upstream.
-
- -- Charles Plessy <plessy at debian.org> Fri, 30 Mar 2012 19:25:53 +0900
-
-wise (2.4.1-9) unstable; urgency=low
-
- * Correct src/models/makefile to link --as-needed (Closes: #641333).
- * Conforms with Policy 3.9.2 (debian/control, no other changes needed).
- * Corrected VCS URLs (debian/control).
- * Use Debhelper 8 (debian/compat, debian/control).
- * Added build-arch and build-indep targets to debian/rules.
- * Machine-readable debian/copryight file conforms to DEP 5.
- * Compress binary package with xz (debian/rules).
-
- -- Charles Plessy <plessy at debian.org> Wed, 14 Sep 2011 17:52:32 +0900
-
-wise (2.4.1-8) unstable; urgency=low
-
- * Fixed conflicting definitions of getline(). (Closes: #552821)
- * Added README.source.
- * Standards version 3.8.3.
- * Fixed spelling error in package description.
-
- -- Philipp Benner <philipp at debian.org> Sat, 31 Oct 2009 21:25:52 +0000
-
-wise (2.4.1-7) unstable; urgency=low
-
- [ Steffen Moeller ]
- * Now builds with glib-2. (Closes: #523715). Special thank to Barry deFreese.
- * Updated policy to 3.8.1 (no changes required).
- * fixed api->API lintian warning.
-
- [ Charles Plessy ]
- * debian/control:
- - Added myself to the Uploaders.
- - Added ${misc:Depends} to the package dependencies.
- - Using Debhelper 7 (also debian/compat).
- - Eliminated redundancy between the long descriptions of wise and wise-doc.
- * Replaced ‘dh_clean -k’ by ‘dh_prep’ in debian/rules.
-
- -- Charles Plessy <plessy at debian.org> Mon, 15 Jun 2009 20:49:27 +0900
-
-wise (2.4.1-6) unstable; urgency=low
-
- * Updated policy to 3.8.0 (no changes required).
- * wise now suggests wise-doc (downgraded from 'recommends').
- [ Steffen Moeller ]
- * Using quilt instead of dpatch.
- [ Philipp Benner ]
-
- -- Philipp Benner <pbenner at uni-osnabrueck.de> Sun, 25 Jan 2009 22:57:27 +0000
-
-wise (2.4.1-5) unstable; urgency=low
-
- * Removed a bashism in debian/rules (Closes: #478639).
-
- -- Charles Plessy <plessy at debian.org> Sun, 04 May 2008 15:19:01 +0900
-
-wise (2.4.1-4) unstable; urgency=low
-
- * Changed the doc-base section according to the new policy
- [Charles Plessy].
-
- -- Philipp Benner <pbenner at uni-osnabrueck.de> Mon, 31 Mar 2008 10:07:35 +0200
-
-wise (2.4.1-3) unstable; urgency=low
-
- * New maintainer e-mail address.
- * debian/control: Added DM-Upload-Allowed: yes.
-
- -- Philipp Benner <pbenner at uni-osnabrueck.de> Mon, 14 Jan 2008 18:33:27 +0100
-
-wise (2.4.1-2) unstable; urgency=low
-
- * Using official Vcs-Browser and Vcs-Svn fields (debian/control).
- * Moved the Homepage: field out from the package's description
- + (Charles Plessy).
- * Converted copyright file to machine interpretable format.
- * Changed maintainer to Debian-Med Packaging Team.
-
- -- Philipp Benner <mail at philipp-benner.de> Sun, 02 Dec 2007 16:15:50 +0100
-
-wise (2.4.1-1) unstable; urgency=low
-
- * New upstream release.
-
- -- Philipp Benner <mail at philipp-benner.de> Sat, 15 Sep 2007 17:18:49 +0200
-
-wise (2.4.0-3) unstable; urgency=low
-
- * Removed debtags from debian/control.
- * Updated package description (Closes: #435904).
- * Excluded genewise21.eps and genewise6.eps from documentation
- + (workaround for a bug in gs-esp).
-
- -- Philipp Benner <mail at philipp-benner.de> Sun, 05 Aug 2007 20:21:35 +0200
-
-wise (2.4.0-2) unstable; urgency=low
-
- * Converted wise2.tex to a pdflatex compatible latex file
- + (workaround for a bug in dvips)
-
- -- Philipp Benner <mail at philipp-benner.de> Fri, 27 Jul 2007 18:46:33 +0200
-
-wise (2.4.0-1) unstable; urgency=low
-
- * New upstream release (Closes: #431392)
- * New dpatch (02_isnumber): src/models/phasemodel.c: replaces isnumber() by isdigit()
- * New dpatch (03_doc-nodycache): docs/wise2.tex: minor bugfix
-
- -- Philipp Benner <mail at philipp-benner.de> Tue, 24 Jul 2007 11:58:36 +0200
-
-wise (2.2.0-5) unstable; urgency=low
-
- * Removed obsolete dependencies (Closes: #422123)
-
- -- Philipp Benner <mail at philipp-benner.de> Sun, 6 May 2007 22:42:27 +0200
-
-wise (2.2.0-4) unstable; urgency=low
-
- * Adapted debian-med tags
- * Uscan support
- * Migrating to texlive
- * use /bin/sh instead of /bin/csh in src/welcome.csh
-
- -- Philipp Benner <mail at philipp-benner.de> Tue, 27 Mar 2007 19:29:08 +0200
-
-wise (2.2.0-3) unstable; urgency=low
-
- * package tags
- * fixed typos in package description
-
- -- Philipp Benner <mail at philipp-benner.de> Thu, 21 Sep 2006 14:22:39 +0200
-
-wise (2.2.0-2) unstable; urgency=low
-
- * removed \ref tags from package description
- * moved examples to package wise-doc
- * fixed typo in README.Debian
- * minor changes in debian/control
- * fixed typo in package description (Closes: #380451)
- * new html documentation
-
- -- Philipp Benner <mail at philipp-benner.de> Sun, 30 Jul 2006 14:08:20 +0200
-
-wise (2.2.0-1) unstable; urgency=low
-
- * Initial release (Closes: #379604)
-
- -- Philipp Benner <mail at philipp-benner.de> Sun, 23 Jul 2006 17:29:49 +0200
Copied: trunk/packages/wise/tags/2.4.1-17/debian/changelog (from rev 18104, trunk/packages/wise/trunk/debian/changelog)
===================================================================
--- trunk/packages/wise/tags/2.4.1-17/debian/changelog (rev 0)
+++ trunk/packages/wise/tags/2.4.1-17/debian/changelog 2014-09-23 12:54:00 UTC (rev 18105)
@@ -0,0 +1,227 @@
+wise (2.4.1-17) unstable; urgency=medium
+
+ * debian/tests/control: explicitly depend on wise. This avoids that
+ ‘sadt’ skips the test when wise-doc is not installed.
+ * debian/tests/run-unit-test: skip the first line of testman.pl, that
+ misses a proper shebang and trigger a failure.
+ * debian/control: shorten synopsis to less than 72 characters.
+ * Conforms with Policy 3.9.6.
+
+ -- Charles Plessy <plessy at debian.org> Tue, 23 Sep 2014 20:14:47 +0900
+
+wise (2.4.1-16) unstable; urgency=medium
+
+ * Make sure package builds also for arch only builds
+ Closes: #757275
+
+ -- Andreas Tille <tille at debian.org> Thu, 07 Aug 2014 09:49:11 +0200
+
+wise (2.4.1-15) unstable; urgency=medium
+
+ * Move debian/upstream to debian/upstream/metadata
+ * debian/control:
+ - add myself to Uploaders
+ - cme fix dpkg-control
+ - debhelper 9
+ - remove unneeded Build-Depends
+ * debian/README.source: removed in favour of DEP5 headers
+ * Make sure dnal has a valid return value (this affects the test suite
+ of python-biopython on some architectures - see #751277)
+ * debian/rules:
+ - drop useless xz compression
+ - add dh_auto_test
+ * debian/patches/10_fix_path_to_data_files.patch: Brute force patch to
+ fix the PATH to the data files to make the tools finding the needed
+ data for the test suite
+
+ -- Andreas Tille <tille at debian.org> Mon, 04 Aug 2014 19:25:58 +0200
+
+wise (2.4.1-14) unstable; urgency=low
+
+ * Fixed FTBFS bug (Closes: #716983).
+
+ -- Philipp Benner <philipp at debian.org> Mon, 15 Jul 2013 18:22:15 +0200
+
+wise (2.4.1-13) unstable; urgency=low
+
+ * Added mayhem bugfixes.
+ * Moved examples/ from wise-doc to wise-data package.
+ * Removed -O3 cflag from makefiles.
+
+ -- Philipp Benner <philipp at debian.org> Sun, 07 Jul 2013 13:33:01 +0200
+
+wise (2.4.1-12) unstable; urgency=low
+
+ * Added missing -D_FORTIFY_SOURCE=2 for hardening support
+ * Standards version 3.9.4
+
+ -- Philipp Benner <philipp at debian.org> Mon, 28 Jan 2013 20:33:16 +0100
+
+wise (2.4.1-11) unstable; urgency=low
+
+ [ Andreas Tille ]
+ * debian/upstream: Add publication data
+
+ [ Philipp Benner ]
+ * Added hardening flags
+
+ -- Philipp Benner <philipp at debian.org> Sun, 27 Jan 2013 18:05:31 +0100
+
+wise (2.4.1-10) unstable; urgency=low
+
+ * Convert debian/rules to dh, Closes: #666319, as it restores build flags.
+ * Verbose debhelper in debian/rules.
+ * Normalised and upgraded debian/copyright file with ‘cme fix’.
+ * Pre-Depends on dpkg (>= 1.15.6~) (debian/control).
+ * Conforms to Debian policy 3.9.3 (debian/control, no other changes needed).
+ * Convert debian/rules to dh, Closes: #666319, as it restores build flags.
+ * Documented metadata in debian/upstream.
+
+ -- Charles Plessy <plessy at debian.org> Fri, 30 Mar 2012 19:25:53 +0900
+
+wise (2.4.1-9) unstable; urgency=low
+
+ * Correct src/models/makefile to link --as-needed (Closes: #641333).
+ * Conforms with Policy 3.9.2 (debian/control, no other changes needed).
+ * Corrected VCS URLs (debian/control).
+ * Use Debhelper 8 (debian/compat, debian/control).
+ * Added build-arch and build-indep targets to debian/rules.
+ * Machine-readable debian/copryight file conforms to DEP 5.
+ * Compress binary package with xz (debian/rules).
+
+ -- Charles Plessy <plessy at debian.org> Wed, 14 Sep 2011 17:52:32 +0900
+
+wise (2.4.1-8) unstable; urgency=low
+
+ * Fixed conflicting definitions of getline(). (Closes: #552821)
+ * Added README.source.
+ * Standards version 3.8.3.
+ * Fixed spelling error in package description.
+
+ -- Philipp Benner <philipp at debian.org> Sat, 31 Oct 2009 21:25:52 +0000
+
+wise (2.4.1-7) unstable; urgency=low
+
+ [ Steffen Moeller ]
+ * Now builds with glib-2. (Closes: #523715). Special thank to Barry deFreese.
+ * Updated policy to 3.8.1 (no changes required).
+ * fixed api->API lintian warning.
+
+ [ Charles Plessy ]
+ * debian/control:
+ - Added myself to the Uploaders.
+ - Added ${misc:Depends} to the package dependencies.
+ - Using Debhelper 7 (also debian/compat).
+ - Eliminated redundancy between the long descriptions of wise and wise-doc.
+ * Replaced ‘dh_clean -k’ by ‘dh_prep’ in debian/rules.
+
+ -- Charles Plessy <plessy at debian.org> Mon, 15 Jun 2009 20:49:27 +0900
+
+wise (2.4.1-6) unstable; urgency=low
+
+ * Updated policy to 3.8.0 (no changes required).
+ * wise now suggests wise-doc (downgraded from 'recommends').
+ [ Steffen Moeller ]
+ * Using quilt instead of dpatch.
+ [ Philipp Benner ]
+
+ -- Philipp Benner <pbenner at uni-osnabrueck.de> Sun, 25 Jan 2009 22:57:27 +0000
+
+wise (2.4.1-5) unstable; urgency=low
+
+ * Removed a bashism in debian/rules (Closes: #478639).
+
+ -- Charles Plessy <plessy at debian.org> Sun, 04 May 2008 15:19:01 +0900
+
+wise (2.4.1-4) unstable; urgency=low
+
+ * Changed the doc-base section according to the new policy
+ [Charles Plessy].
+
+ -- Philipp Benner <pbenner at uni-osnabrueck.de> Mon, 31 Mar 2008 10:07:35 +0200
+
+wise (2.4.1-3) unstable; urgency=low
+
+ * New maintainer e-mail address.
+ * debian/control: Added DM-Upload-Allowed: yes.
+
+ -- Philipp Benner <pbenner at uni-osnabrueck.de> Mon, 14 Jan 2008 18:33:27 +0100
+
+wise (2.4.1-2) unstable; urgency=low
+
+ * Using official Vcs-Browser and Vcs-Svn fields (debian/control).
+ * Moved the Homepage: field out from the package's description
+ + (Charles Plessy).
+ * Converted copyright file to machine interpretable format.
+ * Changed maintainer to Debian-Med Packaging Team.
+
+ -- Philipp Benner <mail at philipp-benner.de> Sun, 02 Dec 2007 16:15:50 +0100
+
+wise (2.4.1-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Philipp Benner <mail at philipp-benner.de> Sat, 15 Sep 2007 17:18:49 +0200
+
+wise (2.4.0-3) unstable; urgency=low
+
+ * Removed debtags from debian/control.
+ * Updated package description (Closes: #435904).
+ * Excluded genewise21.eps and genewise6.eps from documentation
+ + (workaround for a bug in gs-esp).
+
+ -- Philipp Benner <mail at philipp-benner.de> Sun, 05 Aug 2007 20:21:35 +0200
+
+wise (2.4.0-2) unstable; urgency=low
+
+ * Converted wise2.tex to a pdflatex compatible latex file
+ + (workaround for a bug in dvips)
+
+ -- Philipp Benner <mail at philipp-benner.de> Fri, 27 Jul 2007 18:46:33 +0200
+
+wise (2.4.0-1) unstable; urgency=low
+
+ * New upstream release (Closes: #431392)
+ * New dpatch (02_isnumber): src/models/phasemodel.c: replaces isnumber() by isdigit()
+ * New dpatch (03_doc-nodycache): docs/wise2.tex: minor bugfix
+
+ -- Philipp Benner <mail at philipp-benner.de> Tue, 24 Jul 2007 11:58:36 +0200
+
+wise (2.2.0-5) unstable; urgency=low
+
+ * Removed obsolete dependencies (Closes: #422123)
+
+ -- Philipp Benner <mail at philipp-benner.de> Sun, 6 May 2007 22:42:27 +0200
+
+wise (2.2.0-4) unstable; urgency=low
+
+ * Adapted debian-med tags
+ * Uscan support
+ * Migrating to texlive
+ * use /bin/sh instead of /bin/csh in src/welcome.csh
+
+ -- Philipp Benner <mail at philipp-benner.de> Tue, 27 Mar 2007 19:29:08 +0200
+
+wise (2.2.0-3) unstable; urgency=low
+
+ * package tags
+ * fixed typos in package description
+
+ -- Philipp Benner <mail at philipp-benner.de> Thu, 21 Sep 2006 14:22:39 +0200
+
+wise (2.2.0-2) unstable; urgency=low
+
+ * removed \ref tags from package description
+ * moved examples to package wise-doc
+ * fixed typo in README.Debian
+ * minor changes in debian/control
+ * fixed typo in package description (Closes: #380451)
+ * new html documentation
+
+ -- Philipp Benner <mail at philipp-benner.de> Sun, 30 Jul 2006 14:08:20 +0200
+
+wise (2.2.0-1) unstable; urgency=low
+
+ * Initial release (Closes: #379604)
+
+ -- Philipp Benner <mail at philipp-benner.de> Sun, 23 Jul 2006 17:29:49 +0200
Deleted: trunk/packages/wise/tags/2.4.1-17/debian/control
===================================================================
--- trunk/packages/wise/trunk/debian/control 2014-09-23 10:38:00 UTC (rev 18098)
+++ trunk/packages/wise/tags/2.4.1-17/debian/control 2014-09-23 12:54:00 UTC (rev 18105)
@@ -1,68 +0,0 @@
-Source: wise
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Philipp Benner <philipp at debian.org>,
- Steffen Moeller <moeller at debian.org>,
- Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
-Section: science
-Priority: optional
-Testsuite: autopkgtest
-Build-Depends: debhelper (>= 9),
- texlive-latex-base,
- texlive-extra-utils,
- hevea,
- docbook-to-man,
- libglib2.0-dev
-Standards-Version: 3.9.5
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/wise/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/wise/trunk/
-Homepage: http://www.ebi.ac.uk/~birney/wise2/
-
-Package: wise
-Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- wise-data (= ${source:Version})
-Suggests: wise-doc (= ${source:Version})
-Description: comparison of biopolymers, commonly DNA and protein sequences
- Wise2 is a package focused on comparisons of biopolymers, commonly DNA
- and protein sequences. There are many other packages which do
- this, probably the best known being BLAST package (from NCBI) and the
- Fasta package (from Bill Pearson). There are other packages, such as
- the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
- on hidden Markov models (HMMs) of biopolymers.
- .
- Wise2's particular forte is the comparison of DNA sequence at the level
- of its protein translation. This comparison allows the simultaneous
- prediction of say gene structure with homology based alignment.
- .
- Wise2 also contains other algorithms, such as the venerable Smith-Waterman
- algorithm, or more modern ones such as Stephen Altschul's generalised
- gap penalties, or even experimental ones developed in house, such as
- dba. The development of these algorithms is due to the ease of developing
- such algorithms in the environment used by Wise2.
- .
- Wise2 has also been written with an eye for reuse and maintainability.
- Although it is a pure C package you can access its functionality
- directly in Perl. Parts of the package (or the entire package) can
- be used by other C or C++ programs without namespace clashes as all
- externally linked variables have the unique identifier Wise2 prepended.
-
-Package: wise-doc
-Architecture: all
-Section: doc
-Depends: ${misc:Depends}
-Recommends: wise (= ${source:Version}),
- xpdf-reader | pdf-viewer
-Description: documentation for the wise package
- This package contains the documentation for Wise2, a package focused on
- comparisons of biopolymers, commonly DNA and protein sequences.
-
-Package: wise-data
-Architecture: all
-Section: doc
-Depends: ${misc:Depends}
-Recommends: wise (= ${source:Version})
-Description: data files for the wise package
- This package contains data files for Wise2, a package focused on
- comparisons of biopolymers, commonly DNA and protein sequences.
Copied: trunk/packages/wise/tags/2.4.1-17/debian/control (from rev 18102, trunk/packages/wise/trunk/debian/control)
===================================================================
--- trunk/packages/wise/tags/2.4.1-17/debian/control (rev 0)
+++ trunk/packages/wise/tags/2.4.1-17/debian/control 2014-09-23 12:54:00 UTC (rev 18105)
@@ -0,0 +1,68 @@
+Source: wise
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Philipp Benner <philipp at debian.org>,
+ Steffen Moeller <moeller at debian.org>,
+ Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Testsuite: autopkgtest
+Build-Depends: debhelper (>= 9),
+ texlive-latex-base,
+ texlive-extra-utils,
+ hevea,
+ docbook-to-man,
+ libglib2.0-dev
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/wise/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/wise/trunk/
+Homepage: http://www.ebi.ac.uk/~birney/wise2/
+
+Package: wise
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ wise-data (= ${source:Version})
+Suggests: wise-doc (= ${source:Version})
+Description: comparison of biopolymers, like DNA and protein sequences
+ Wise2 is a package focused on comparisons of biopolymers, commonly DNA
+ and protein sequences. There are many other packages which do
+ this, probably the best known being BLAST package (from NCBI) and the
+ Fasta package (from Bill Pearson). There are other packages, such as
+ the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
+ on hidden Markov models (HMMs) of biopolymers.
+ .
+ Wise2's particular forte is the comparison of DNA sequence at the level
+ of its protein translation. This comparison allows the simultaneous
+ prediction of say gene structure with homology based alignment.
+ .
+ Wise2 also contains other algorithms, such as the venerable Smith-Waterman
+ algorithm, or more modern ones such as Stephen Altschul's generalised
+ gap penalties, or even experimental ones developed in house, such as
+ dba. The development of these algorithms is due to the ease of developing
+ such algorithms in the environment used by Wise2.
+ .
+ Wise2 has also been written with an eye for reuse and maintainability.
+ Although it is a pure C package you can access its functionality
+ directly in Perl. Parts of the package (or the entire package) can
+ be used by other C or C++ programs without namespace clashes as all
+ externally linked variables have the unique identifier Wise2 prepended.
+
+Package: wise-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}
+Recommends: wise (= ${source:Version}),
+ xpdf-reader | pdf-viewer
+Description: documentation for the wise package
+ This package contains the documentation for Wise2, a package focused on
+ comparisons of biopolymers, commonly DNA and protein sequences.
+
+Package: wise-data
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}
+Recommends: wise (= ${source:Version})
+Description: data files for the wise package
+ This package contains data files for Wise2, a package focused on
+ comparisons of biopolymers, commonly DNA and protein sequences.
Deleted: trunk/packages/wise/tags/2.4.1-17/debian/tests/control
===================================================================
--- trunk/packages/wise/trunk/debian/tests/control 2014-09-23 10:38:00 UTC (rev 18098)
+++ trunk/packages/wise/tags/2.4.1-17/debian/tests/control 2014-09-23 12:54:00 UTC (rev 18105)
@@ -1,3 +0,0 @@
-Tests: run-unit-test
-Depends: @, wise-data
-Restrictions: allow-stderr
Copied: trunk/packages/wise/tags/2.4.1-17/debian/tests/control (from rev 18099, trunk/packages/wise/trunk/debian/tests/control)
===================================================================
--- trunk/packages/wise/tags/2.4.1-17/debian/tests/control (rev 0)
+++ trunk/packages/wise/tags/2.4.1-17/debian/tests/control 2014-09-23 12:54:00 UTC (rev 18105)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: wise, wise-data
+Restrictions: allow-stderr
Deleted: trunk/packages/wise/tags/2.4.1-17/debian/tests/run-unit-test
===================================================================
--- trunk/packages/wise/trunk/debian/tests/run-unit-test 2014-09-23 10:38:00 UTC (rev 18098)
+++ trunk/packages/wise/tags/2.4.1-17/debian/tests/run-unit-test 2014-09-23 12:54:00 UTC (rev 18105)
@@ -1,11 +0,0 @@
-#!/bin/sh -e
-
-pkg=wise
-if [ "$ADTTMP" = "" ] ; then
- ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
-fi
-cd $ADTTMP
-cp /usr/share/doc/wise-data/examples/* $ADTTMP
-gunzip *.gz
-perl testman.pl < short.test
-# rm -f $ADTTMP/*
Copied: trunk/packages/wise/tags/2.4.1-17/debian/tests/run-unit-test (from rev 18100, trunk/packages/wise/trunk/debian/tests/run-unit-test)
===================================================================
--- trunk/packages/wise/tags/2.4.1-17/debian/tests/run-unit-test (rev 0)
+++ trunk/packages/wise/tags/2.4.1-17/debian/tests/run-unit-test 2014-09-23 12:54:00 UTC (rev 18105)
@@ -0,0 +1,11 @@
+#!/bin/bash -e
+
+pkg=wise
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp /usr/share/doc/wise-data/examples/* $ADTTMP
+gunzip *.gz
+perl <(sed 1d testman.pl) < short.test
+# rm -f $ADTTMP/*
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