[med-svn] r9851 - in trunk/packages/t-coffee/tags: . 9.02.r1228-2/debian
Charles Plessy
plessy at alioth.debian.org
Fri Mar 2 05:25:33 UTC 2012
Author: plessy
Date: 2012-03-02 05:25:32 +0000 (Fri, 02 Mar 2012)
New Revision: 9851
Added:
trunk/packages/t-coffee/tags/9.02.r1228-2/
trunk/packages/t-coffee/tags/9.02.r1228-2/debian/changelog
trunk/packages/t-coffee/tags/9.02.r1228-2/debian/control
trunk/packages/t-coffee/tags/9.02.r1228-2/debian/t-coffee.install
Removed:
trunk/packages/t-coffee/tags/9.02.r1228-2/debian/changelog
trunk/packages/t-coffee/tags/9.02.r1228-2/debian/control
trunk/packages/t-coffee/tags/9.02.r1228-2/debian/t-coffee.install
Log:
[svn-buildpackage] Tagging t-coffee 9.02.r1228-2
Deleted: trunk/packages/t-coffee/tags/9.02.r1228-2/debian/changelog
===================================================================
--- trunk/packages/t-coffee/trunk/debian/changelog 2012-03-02 00:07:41 UTC (rev 9849)
+++ trunk/packages/t-coffee/tags/9.02.r1228-2/debian/changelog 2012-03-02 05:25:32 UTC (rev 9851)
@@ -1,152 +0,0 @@
-t-coffee (9.02.r1228-1) unstable; urgency=low
-
- * New upstream release (Closes: #649263).
- * Build new Fortran tool (debian/rules debian/contol debian/t-coffee.install)
- * Corrected debian/rules as upstream test suite was removed.
- * Complies with Policy 3.9.3 (debian/control, no other changes needed).
- * Removed doc-base registrations debian/t-coffee-doc.doc-base.technical and
- debian/t-coffee-doc.doc-base.tutorial, as the files disappeared upstream.
-
- -- Charles Plessy <plessy at debian.org> Mon, 27 Feb 2012 13:09:36 +0900
-
-t-coffee (8.99-1) unstable; urgency=low
-
- * New upstream release in Debian.
- * Converted and validated debian/copyright to DEP 5 machine-readable format.
- * Using debhelper 8 (debian/control, debian/compat).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.2.
- (debian/control, no change needed).
- * Corrected VCS URLs in debian/control.
- * Run upstream tests at build time (debian/rules, debian/README.test).
-
- -- Charles Plessy <plessy at debian.org> Tue, 21 Jun 2011 14:14:10 +0900
-
-t-coffee (8.99-0ubuntu1) lucid; urgency=low
-
- * Rebuild for new upstream release.
- * There is no changelog from upstream to read.
-
- -- Tim Booth <tbooth at ceh.ac.uk> Sat, 29 Jan 2011 15:18:01 +0000
-
-t-coffee (8.97-0ubuntu2) lucid; urgency=low
-
- * New upstream release, changed watch file and auto rebuild using uupdate
- * Cleared out old patch - apparently unneeded or else needs total re-write
-
- -- Tim Booth <tbooth at ceh.ac.uk> Tue, 23 Nov 2010 14:01:22 +0000
-
-t-coffee (8.95-1) lucid; urgency=low
-
- * New upstream version, rebuild by Tim for Bio-Linux/Lucid
-
- -- Tim Booth <tbooth at ceh.ac.uk> Mon, 01 Nov 2010 15:05:07 +0000
-
-t-coffee (8.84-1) unstable; urgency=low
-
- * New upstream version
-
- -- Andreas Tille <tille at debian.org> Thu, 24 Jun 2010 14:46:16 +0200
-
-t-coffee (8.47-1) unstable; urgency=low
-
- [ Charles Plessy ]
- * Collected Upstream information in debian/upstream-metadata.yaml.
-
- [ Andreas Tille ]
- * New upstream version
- * Source format 3.0 (quilt)
- * Standards-Version: 3.8.4 (no changes needed)
-
- -- Andreas Tille <tille at debian.org> Fri, 09 Apr 2010 21:08:32 +0200
-
-t-coffee (8.14-1) unstable; urgency=low
-
- * New upstream version
-
- -- Andreas Tille <tille at debian.org> Tue, 03 Nov 2009 13:56:33 +0100
-
-t-coffee (8.13-1) unstable; urgency=low
-
- * New upstream version
-
- -- Andreas Tille <tille at debian.org> Thu, 01 Oct 2009 22:13:34 +0200
-
-t-coffee (8.06-1) unstable; urgency=low
-
- [ Charles Plessy ]
- TODO:
- Identify differences and document relevant ones.
- Check that the patch can be dropped.
- Support PDB in getdata.
- Get the FORTRAN building right.
- NOTE
- The upstream install system was completely refactored, and T-Coffee
- includes new functionalities that require internet access. We have to
- understand them before updating our package.
-
- * New upstream release
- - say something about libsoap-lite-perl ?
- * debian/control:
- - t-coffee recommends libsoap-lite-perl.
- - Added missing comma in t-coffee Suggests field (Closes:#536956).
-
- [ Andreas Tille ]
- * debian/control:
- - Standards-Version: 3.8.3 (added README.source)
- - Added myself to uploaders
- - s/Debian-Med/Debian Med/
- - Bumped debhelper version to >= 7.1 to possibly enable short
- rules files.
- - Added "Depends: ${misc:Depends}" to all packages
-
- -- Andreas Tille <tille at debian.org> Fri, 25 Sep 2009 14:41:41 +0200
-
-t-coffee (5.72-1) unstable; urgency=low
-
- [ David Paleino ]
- * New upstream release
-
- [ Charles Plessy ]
- * Switched to CDBS.
- * debian/patches:
- - Upated the dm-coffee patch because dialign-t was renamed dialign-tx.
- - Dropped the unicode conversion patch.
- - Dropped the manpage patch (implements the clear rule through CDBS).
- * Updated my email address.
-
- -- Charles Plessy <plessy at debian.org> Mon, 30 Jun 2008 23:34:32 +0900
-
-t-coffee (5.31-1) unstable; urgency=low
-
- * New upstream version.
- * Debian menu transition: updated debian/t-coffee-doc.doc-base.
- * debian/patches/dmcoffee.patch: to make dmcoffee work
- out of the box.
- * debian/control:
- - Allowed Debian Maintainers to upload t-coffee.
- - Checked that the package conforms to Policy 3.7.3.
- - Using debhelper 5.
- - Updated homepage.
- - Moved t-coffee-doc to section doc.
- * debian/copyright: converted to machine-readable format.
- * debian/rules: builds only indep or only arch when called with
- binary-indep or binary-arch (Closes: #457921).
-
- -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 29 Dec 2007 18:54:09 +0100
-
-t-coffee (5.05-1) unstable; urgency=low
-
- * New upstream version.
- * Assigned maintainership to Debian-Med.
- * Moved boxshade from Recommended to Suggested.
- * Added use of quilt.
- * Homepage received its separate line.
-
- -- Steffen Moeller <moeller at debian.org> Mon, 24 Sep 2007 15:05:07 +0200
-
-t-coffee (2.50-1) unstable; urgency=low
-
- * Initial Release (Closes: Bug#205370).
-
- -- Steffen Moeller <moeller at pzr.uni-rostock.de> Fri, 13 May 2005 10:52:14 +0200
-
Copied: trunk/packages/t-coffee/tags/9.02.r1228-2/debian/changelog (from rev 9850, trunk/packages/t-coffee/trunk/debian/changelog)
===================================================================
--- trunk/packages/t-coffee/tags/9.02.r1228-2/debian/changelog (rev 0)
+++ trunk/packages/t-coffee/tags/9.02.r1228-2/debian/changelog 2012-03-02 05:25:32 UTC (rev 9851)
@@ -0,0 +1,159 @@
+t-coffee (9.02.r1228-2) unstable; urgency=low
+
+ * Recommend tm-align instead of distributing local copy
+ (debian/control, debian/t-coffee.install, Closes: #661516).
+
+ -- Charles Plessy <plessy at debian.org> Fri, 02 Mar 2012 14:04:20 +0900
+
+t-coffee (9.02.r1228-1) unstable; urgency=low
+
+ * New upstream release (Closes: #649263).
+ * Build new Fortran tool (debian/rules debian/contol debian/t-coffee.install)
+ * Corrected debian/rules as upstream test suite was removed.
+ * Complies with Policy 3.9.3 (debian/control, no other changes needed).
+ * Removed doc-base registrations debian/t-coffee-doc.doc-base.technical and
+ debian/t-coffee-doc.doc-base.tutorial, as the files disappeared upstream.
+
+ -- Charles Plessy <plessy at debian.org> Mon, 27 Feb 2012 13:09:36 +0900
+
+t-coffee (8.99-1) unstable; urgency=low
+
+ * New upstream release in Debian.
+ * Converted and validated debian/copyright to DEP 5 machine-readable format.
+ * Using debhelper 8 (debian/control, debian/compat).
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2.
+ (debian/control, no change needed).
+ * Corrected VCS URLs in debian/control.
+ * Run upstream tests at build time (debian/rules, debian/README.test).
+
+ -- Charles Plessy <plessy at debian.org> Tue, 21 Jun 2011 14:14:10 +0900
+
+t-coffee (8.99-0ubuntu1) lucid; urgency=low
+
+ * Rebuild for new upstream release.
+ * There is no changelog from upstream to read.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Sat, 29 Jan 2011 15:18:01 +0000
+
+t-coffee (8.97-0ubuntu2) lucid; urgency=low
+
+ * New upstream release, changed watch file and auto rebuild using uupdate
+ * Cleared out old patch - apparently unneeded or else needs total re-write
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 23 Nov 2010 14:01:22 +0000
+
+t-coffee (8.95-1) lucid; urgency=low
+
+ * New upstream version, rebuild by Tim for Bio-Linux/Lucid
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Mon, 01 Nov 2010 15:05:07 +0000
+
+t-coffee (8.84-1) unstable; urgency=low
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Thu, 24 Jun 2010 14:46:16 +0200
+
+t-coffee (8.47-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * Collected Upstream information in debian/upstream-metadata.yaml.
+
+ [ Andreas Tille ]
+ * New upstream version
+ * Source format 3.0 (quilt)
+ * Standards-Version: 3.8.4 (no changes needed)
+
+ -- Andreas Tille <tille at debian.org> Fri, 09 Apr 2010 21:08:32 +0200
+
+t-coffee (8.14-1) unstable; urgency=low
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Tue, 03 Nov 2009 13:56:33 +0100
+
+t-coffee (8.13-1) unstable; urgency=low
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Thu, 01 Oct 2009 22:13:34 +0200
+
+t-coffee (8.06-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ TODO:
+ Identify differences and document relevant ones.
+ Check that the patch can be dropped.
+ Support PDB in getdata.
+ Get the FORTRAN building right.
+ NOTE
+ The upstream install system was completely refactored, and T-Coffee
+ includes new functionalities that require internet access. We have to
+ understand them before updating our package.
+
+ * New upstream release
+ - say something about libsoap-lite-perl ?
+ * debian/control:
+ - t-coffee recommends libsoap-lite-perl.
+ - Added missing comma in t-coffee Suggests field (Closes:#536956).
+
+ [ Andreas Tille ]
+ * debian/control:
+ - Standards-Version: 3.8.3 (added README.source)
+ - Added myself to uploaders
+ - s/Debian-Med/Debian Med/
+ - Bumped debhelper version to >= 7.1 to possibly enable short
+ rules files.
+ - Added "Depends: ${misc:Depends}" to all packages
+
+ -- Andreas Tille <tille at debian.org> Fri, 25 Sep 2009 14:41:41 +0200
+
+t-coffee (5.72-1) unstable; urgency=low
+
+ [ David Paleino ]
+ * New upstream release
+
+ [ Charles Plessy ]
+ * Switched to CDBS.
+ * debian/patches:
+ - Upated the dm-coffee patch because dialign-t was renamed dialign-tx.
+ - Dropped the unicode conversion patch.
+ - Dropped the manpage patch (implements the clear rule through CDBS).
+ * Updated my email address.
+
+ -- Charles Plessy <plessy at debian.org> Mon, 30 Jun 2008 23:34:32 +0900
+
+t-coffee (5.31-1) unstable; urgency=low
+
+ * New upstream version.
+ * Debian menu transition: updated debian/t-coffee-doc.doc-base.
+ * debian/patches/dmcoffee.patch: to make dmcoffee work
+ out of the box.
+ * debian/control:
+ - Allowed Debian Maintainers to upload t-coffee.
+ - Checked that the package conforms to Policy 3.7.3.
+ - Using debhelper 5.
+ - Updated homepage.
+ - Moved t-coffee-doc to section doc.
+ * debian/copyright: converted to machine-readable format.
+ * debian/rules: builds only indep or only arch when called with
+ binary-indep or binary-arch (Closes: #457921).
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 29 Dec 2007 18:54:09 +0100
+
+t-coffee (5.05-1) unstable; urgency=low
+
+ * New upstream version.
+ * Assigned maintainership to Debian-Med.
+ * Moved boxshade from Recommended to Suggested.
+ * Added use of quilt.
+ * Homepage received its separate line.
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 24 Sep 2007 15:05:07 +0200
+
+t-coffee (2.50-1) unstable; urgency=low
+
+ * Initial Release (Closes: Bug#205370).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Fri, 13 May 2005 10:52:14 +0200
+
Deleted: trunk/packages/t-coffee/tags/9.02.r1228-2/debian/control
===================================================================
--- trunk/packages/t-coffee/trunk/debian/control 2012-03-02 00:07:41 UTC (rev 9849)
+++ trunk/packages/t-coffee/tags/9.02.r1228-2/debian/control 2012-03-02 05:25:32 UTC (rev 9851)
@@ -1,58 +0,0 @@
-Source: t-coffee
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Steffen Moeller <moeller at debian.org>,
- Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 8), cdbs, quilt, gfortran
-Standards-Version: 3.9.3
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/t-coffee/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/t-coffee/trunk/
-Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
-
-Package: t-coffee
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: libsoap-lite-perl, libxml-simple-perl
-Suggests: boxshade, seaview, t-coffee-doc, t-coffee-examples,
- dialign-tx, kalign, mafft, muscle, poa, probcons, clustalw,
- amap-align, proda
-Description: Multiple Sequence Alignment
- T-Coffee is a multiple sequence alignment package. Given a set of
- sequences (Proteins or DNA), T-Coffee generates a multiple sequence
- alignment. Version 2.00 and higher can mix sequences and structures.
- .
- T-Coffee allows the combination of a collection of multiple/pairwise,
- global or local alignments into a single model. It also allows to
- estimate the level of consistency of each position within the new
- alignment with the rest of the alignments. See the pre-print for more
- information
- .
- T-Coffee has a special called M-Coffee that makes it possible to combine the
- output of many multiple sequence alignment packages. In its published version,
- it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and
- T-Coffee. A special version has been made for Debian, DM-Coffee, that uses
- only free software by replacing Clustal W by Kalign. Using the 8 Methods of
- M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite
- methods if you prefer.
-
-Package: t-coffee-examples
-Architecture: all
-Recommends: t-coffee
-Depends: ${misc:Depends}
-Description: annotated examples for the use of T-Coffee
- To help increasing the proficiency in the use of T-Coffee, this
- package provides examples for input sequences and their proper
- alignment.
-
-Package: t-coffee-doc
-Architecture: all
-Section: doc
-Depends: ${misc:Depends}
-Recommends: t-coffee
-Suggests: t-coffee-examples
-Description: PDF and HTML accompaning documents to T-Coffee
- The tool for multiple sequence alignment, T-Coffee, is explained
- both from the users' perspective and for its technical background.
Copied: trunk/packages/t-coffee/tags/9.02.r1228-2/debian/control (from rev 9850, trunk/packages/t-coffee/trunk/debian/control)
===================================================================
--- trunk/packages/t-coffee/tags/9.02.r1228-2/debian/control (rev 0)
+++ trunk/packages/t-coffee/tags/9.02.r1228-2/debian/control 2012-03-02 05:25:32 UTC (rev 9851)
@@ -0,0 +1,58 @@
+Source: t-coffee
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 8), cdbs, quilt, gfortran
+Standards-Version: 3.9.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/t-coffee/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/t-coffee/trunk/
+Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
+
+Package: t-coffee
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: libsoap-lite-perl, libxml-simple-perl, tm-align
+Suggests: boxshade, seaview, t-coffee-doc, t-coffee-examples,
+ dialign-tx, kalign, mafft, muscle, poa, probcons, clustalw,
+ amap-align, proda
+Description: Multiple Sequence Alignment
+ T-Coffee is a multiple sequence alignment package. Given a set of
+ sequences (Proteins or DNA), T-Coffee generates a multiple sequence
+ alignment. Version 2.00 and higher can mix sequences and structures.
+ .
+ T-Coffee allows the combination of a collection of multiple/pairwise,
+ global or local alignments into a single model. It also allows to
+ estimate the level of consistency of each position within the new
+ alignment with the rest of the alignments. See the pre-print for more
+ information
+ .
+ T-Coffee has a special called M-Coffee that makes it possible to combine the
+ output of many multiple sequence alignment packages. In its published version,
+ it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and
+ T-Coffee. A special version has been made for Debian, DM-Coffee, that uses
+ only free software by replacing Clustal W by Kalign. Using the 8 Methods of
+ M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite
+ methods if you prefer.
+
+Package: t-coffee-examples
+Architecture: all
+Recommends: t-coffee
+Depends: ${misc:Depends}
+Description: annotated examples for the use of T-Coffee
+ To help increasing the proficiency in the use of T-Coffee, this
+ package provides examples for input sequences and their proper
+ alignment.
+
+Package: t-coffee-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}
+Recommends: t-coffee
+Suggests: t-coffee-examples
+Description: PDF and HTML accompaning documents to T-Coffee
+ The tool for multiple sequence alignment, T-Coffee, is explained
+ both from the users' perspective and for its technical background.
Deleted: trunk/packages/t-coffee/tags/9.02.r1228-2/debian/t-coffee.install
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee.install 2012-03-02 00:07:41 UTC (rev 9849)
+++ trunk/packages/t-coffee/tags/9.02.r1228-2/debian/t-coffee.install 2012-03-02 05:25:32 UTC (rev 9851)
@@ -1,2 +0,0 @@
-t_coffee_source/t_coffee /usr/bin
-t_coffee_source/TMalign /usr/bin
Copied: trunk/packages/t-coffee/tags/9.02.r1228-2/debian/t-coffee.install (from rev 9850, trunk/packages/t-coffee/trunk/debian/t-coffee.install)
===================================================================
--- trunk/packages/t-coffee/tags/9.02.r1228-2/debian/t-coffee.install (rev 0)
+++ trunk/packages/t-coffee/tags/9.02.r1228-2/debian/t-coffee.install 2012-03-02 05:25:32 UTC (rev 9851)
@@ -0,0 +1 @@
+t_coffee_source/t_coffee /usr/bin
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