[med-svn] r15529 - in trunk/packages/altree/tags: . 1.3.1-1/debian

Vincent Danjean vdanjean at moszumanska.debian.org
Fri Dec 13 22:51:05 UTC 2013


Author: vdanjean
Date: 2013-12-13 22:51:05 +0000 (Fri, 13 Dec 2013)
New Revision: 15529

Added:
   trunk/packages/altree/tags/1.3.1-1/
   trunk/packages/altree/tags/1.3.1-1/debian/changelog
   trunk/packages/altree/tags/1.3.1-1/debian/control
Removed:
   trunk/packages/altree/tags/1.3.1-1/debian/changelog
   trunk/packages/altree/tags/1.3.1-1/debian/control
Log:
[svn-buildpackage] Tagging altree 1.3.1-1

Deleted: trunk/packages/altree/tags/1.3.1-1/debian/changelog
===================================================================
--- trunk/packages/altree/trunk/debian/changelog	2013-11-22 22:38:54 UTC (rev 15254)
+++ trunk/packages/altree/tags/1.3.1-1/debian/changelog	2013-12-13 22:51:05 UTC (rev 15529)
@@ -1,153 +0,0 @@
-altree (1.2.1-1) unstable; urgency=low
-
-  [ Andreas Tille ]
-  * debian/upstream: Add eprint
-  * debian/reference: Removed in favour of debian/upstream
-
-  [ Vincent Danjean ]
-  * New (stable) upstream release 1.2.1
-  * debian/{README.Debian,watch}: No need to skip old last version 1.1.1
-  * debian/patches/*: latex bug fixed upstream
-
- -- Vincent Danjean <vdanjean at debian.org>  Sat, 09 Jun 2012 22:45:06 +0200
-
-altree (1.0.1-7) unstable; urgency=low
-
-  [ Thorsten Alteholz ]
-  * debian/rules: target get-orig-source added
-
-  [ Charles Plessy ]
-  * Renamed debian/upstream-metadata.yaml to debian/upstream
-
-  [ Andreas Tille ]
-  * debian/upstream: Single Reference field instead of Reference-*
-  * debian/watch: Do not download version 1.1.1 as the author has
-    asked for in
-      http://lists.debian.org/debian-med/2009/08/msg00104.html
-  * debian/README.Debian: Document the "do not package new version"
-    issue
-  * debian/control: Standards-Version: 3.9.3 (no changes needed)
-  * debian/changelog: Verified DEP5 using
-      cme fix dpkg-copyright
-  * debian/patches/build-with-recent-tetex.patch: Drop dvips option
-    Closes: #669551
-  * debhelper 9 (control+compat)
-
- -- Andreas Tille <tille at debian.org>  Sun, 22 Apr 2012 08:40:48 +0200
-
-altree (1.0.1-5) unstable; urgency=low
-
-  * Upload source package without 3.0 (quilt) autopatch leftover.
-    Closes: #643045. 
-  * Corrected VCS URLs in debian/control.
-  * Use Debhelper 8 (debian/control, debian/compat). 
-  * Converted debian/copyright to machine-readable format 1.0 (DEP 5).
-  * Compress binary packages with xz (debian/rules).
-  * Conforms with Policy 3.9.2 (debian/control, no other changes needed).
-
- -- Charles Plessy <plessy at debian.org>  Tue, 27 Sep 2011 08:31:14 +0900
-
-altree (1.0.1-4) unstable; urgency=low
-
-  [ Charles Plessy ]
-  * Depends on libtamuanova-perl (debian/control).
-  * Added a BibTeX reference in debian/reference and install it through
-    debian/altree.docs.
-  * Refreshed debian/copyright.
-  * Using debhelper 7 (debian/compat, debian/control).
-  * Incremented Standards-Version to reflect conformance to Policy 3.8.1
-    (no changes needed).
-  * Bash completion:
-    - Build-depend on bash-completion >= 1:1 in debian/control.
-    - Install the altree completion file using dh_bash-completion.
-  * Added information about Upstream in debian/upstream-metadata.yaml.
-
-  [ David Paleino ]
-  * debian/control:
-    - removed unneeded Build-Dependencies
-    - added ${misc:Depends} dependency to altree-examples
-    - removed myself from Uploaders
-  * debian/rules:
-    - removing unneeded included Makefile
-
-  [Andreas Tille]
-  * use short debhelper instead of cdbs because the install target
-    did not worked properly any more
-  * debian/source/format: 3.0 (quilt)
-  * debian/control:
-    - Standards-Version: 3.9.1
-    - Added myself to Uploaders
-    - Added Build-Depends: ghostscript to avoid errors in LaTeX run
-      Closes: #614538
-    - Removed libtamuanova-perl from Depends again because it has no
-      installation candidate
-
- -- Andreas Tille <tille at debian.org>  Tue, 22 Feb 2011 14:37:21 +0100
-
-altree (1.0.1-3) unstable; urgency=low
-
-  [ Charles Plessy ]
-  * Initial release for Debian (Closes: #461506)
-  * debian/copyright: converted to machine-readable format.
-  * debian/control:
-    - Added texlive-lang-french, texlive-latex-base, texlive-latex-recommended
-      and texlive-latex-extra as build dependencies.
-    - Updated my email address.
-
-  [ David Paleino ]
-  * Added debian/watch
-  * debian/compat and debhelper dependency updated
-  * debian/control:
-    - added myself in Uploaders
-    - Standards-Version is now 3.7.3
-
-  [ Vincent Danjean ]
-  * remove unused debian/control.in file
-  * Fix copyright (and update email addresses)
-  * Fix build-depends:
-    + remove debian part of version (thanks lintian)
-    + change latex-utils to latex-make (always present with this name in
-      Debian)
-  * Fix depends: add ${perl:Depends}
-  * remove empty dir in package (/usr/sbin)
-  => package lintian clean now
-
- -- Vincent Danjean <vdanjean at debian.org>  Mon, 12 May 2008 08:19:31 +0200
-
-altree (1.0.1-1) unstable; urgency=low
-
-  * New upstream release
-
- -- Vincent Danjean <Vincent.Danjean at ens-lyon.org>  Fri, 13 Jan 2006 15:46:52 +0100
-
-altree (1.0.0-1) unstable; urgency=low
-
-  * New upstream release
-
- -- Vincent Danjean <Vincent.Danjean at ens-lyon.org>  Fri, 13 Jan 2006 09:40:02 +0100
-
-altree (0.9.2-2) unstable; urgency=low
-
-  * Update FSF address in copyright file
-
- -- Vincent Danjean <Vincent.Danjean at ens-lyon.org>  Sat, 10 Sep 2005 10:25:23 +0200
-
-altree (0.9.2-1) unstable; urgency=low
-
-  * New upstream release
-  * New upstream name
-
- -- Vincent Danjean <Vincent.Danjean at ens-lyon.org>  Tue,  2 Aug 2005 19:52:19 +0200
-
-alphy (0.9.1d-1) unstable; urgency=low
-
-  * New upstream release
-
- -- Vincent Danjean <Vincent.Danjean at ens-lyon.org>  Tue, 26 Jul 2005 00:08:40 +0200
-
-alphy (0.9.1c-1) unstable; urgency=low
-
-  * Initial release
-
- -- Vincent Danjean <Vincent.Danjean at ens-lyon.org>  Mon, 25 Jul 2005 22:22:50 +0200
-

Copied: trunk/packages/altree/tags/1.3.1-1/debian/changelog (from rev 15528, trunk/packages/altree/trunk/debian/changelog)
===================================================================
--- trunk/packages/altree/tags/1.3.1-1/debian/changelog	                        (rev 0)
+++ trunk/packages/altree/tags/1.3.1-1/debian/changelog	2013-12-13 22:51:05 UTC (rev 15529)
@@ -0,0 +1,178 @@
+altree (1.3.1-1) unstable; urgency=low
+
+  * New upstream release
+    + fix a SEGV when ALTREE_PARALLEL is used with more processors
+      than requested permutations (-r program parameter)
+    + Fix "FTBFS with perl 5.12.0-1: long doubles" (Closes: #578550)
+  * debian/control:
+    Add B-D on libtest-deep-perl (required when fixing 578550)
+
+ -- Vincent Danjean <vdanjean at debian.org>  Fri, 13 Dec 2013 23:27:04 +0100
+
+altree (1.3.0-1) unstable; urgency=low
+
+  * New upstream release
+    + Mostly performance improvment
+  * debian/control:
+    + bump Standard-Version (no change needed)
+    + put canonical vcs fields
+    + remove outdated DM-Upload-Allowed field
+    + improve altree-examples long description
+    + add libgsl0-dev and libatlas-base-dev as new build-dependency
+    + remove libpdl-stats-perl as (build-)dependency
+
+ -- Vincent Danjean <vdanjean at debian.org>  Fri, 22 Nov 2013 23:57:43 +0100
+
+altree (1.2.1-1) unstable; urgency=low
+
+  [ Andreas Tille ]
+  * debian/upstream: Add eprint
+  * debian/reference: Removed in favour of debian/upstream
+
+  [ Vincent Danjean ]
+  * New (stable) upstream release 1.2.1
+  * debian/{README.Debian,watch}: No need to skip old last version 1.1.1
+  * debian/patches/*: latex bug fixed upstream
+
+ -- Vincent Danjean <vdanjean at debian.org>  Sat, 09 Jun 2012 22:45:06 +0200
+
+altree (1.0.1-7) unstable; urgency=low
+
+  [ Thorsten Alteholz ]
+  * debian/rules: target get-orig-source added
+
+  [ Charles Plessy ]
+  * Renamed debian/upstream-metadata.yaml to debian/upstream
+
+  [ Andreas Tille ]
+  * debian/upstream: Single Reference field instead of Reference-*
+  * debian/watch: Do not download version 1.1.1 as the author has
+    asked for in
+      http://lists.debian.org/debian-med/2009/08/msg00104.html
+  * debian/README.Debian: Document the "do not package new version"
+    issue
+  * debian/control: Standards-Version: 3.9.3 (no changes needed)
+  * debian/changelog: Verified DEP5 using
+      cme fix dpkg-copyright
+  * debian/patches/build-with-recent-tetex.patch: Drop dvips option
+    Closes: #669551
+  * debhelper 9 (control+compat)
+
+ -- Andreas Tille <tille at debian.org>  Sun, 22 Apr 2012 08:40:48 +0200
+
+altree (1.0.1-5) unstable; urgency=low
+
+  * Upload source package without 3.0 (quilt) autopatch leftover.
+    Closes: #643045. 
+  * Corrected VCS URLs in debian/control.
+  * Use Debhelper 8 (debian/control, debian/compat). 
+  * Converted debian/copyright to machine-readable format 1.0 (DEP 5).
+  * Compress binary packages with xz (debian/rules).
+  * Conforms with Policy 3.9.2 (debian/control, no other changes needed).
+
+ -- Charles Plessy <plessy at debian.org>  Tue, 27 Sep 2011 08:31:14 +0900
+
+altree (1.0.1-4) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * Depends on libtamuanova-perl (debian/control).
+  * Added a BibTeX reference in debian/reference and install it through
+    debian/altree.docs.
+  * Refreshed debian/copyright.
+  * Using debhelper 7 (debian/compat, debian/control).
+  * Incremented Standards-Version to reflect conformance to Policy 3.8.1
+    (no changes needed).
+  * Bash completion:
+    - Build-depend on bash-completion >= 1:1 in debian/control.
+    - Install the altree completion file using dh_bash-completion.
+  * Added information about Upstream in debian/upstream-metadata.yaml.
+
+  [ David Paleino ]
+  * debian/control:
+    - removed unneeded Build-Dependencies
+    - added ${misc:Depends} dependency to altree-examples
+    - removed myself from Uploaders
+  * debian/rules:
+    - removing unneeded included Makefile
+
+  [Andreas Tille]
+  * use short debhelper instead of cdbs because the install target
+    did not worked properly any more
+  * debian/source/format: 3.0 (quilt)
+  * debian/control:
+    - Standards-Version: 3.9.1
+    - Added myself to Uploaders
+    - Added Build-Depends: ghostscript to avoid errors in LaTeX run
+      Closes: #614538
+    - Removed libtamuanova-perl from Depends again because it has no
+      installation candidate
+
+ -- Andreas Tille <tille at debian.org>  Tue, 22 Feb 2011 14:37:21 +0100
+
+altree (1.0.1-3) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * Initial release for Debian (Closes: #461506)
+  * debian/copyright: converted to machine-readable format.
+  * debian/control:
+    - Added texlive-lang-french, texlive-latex-base, texlive-latex-recommended
+      and texlive-latex-extra as build dependencies.
+    - Updated my email address.
+
+  [ David Paleino ]
+  * Added debian/watch
+  * debian/compat and debhelper dependency updated
+  * debian/control:
+    - added myself in Uploaders
+    - Standards-Version is now 3.7.3
+
+  [ Vincent Danjean ]
+  * remove unused debian/control.in file
+  * Fix copyright (and update email addresses)
+  * Fix build-depends:
+    + remove debian part of version (thanks lintian)
+    + change latex-utils to latex-make (always present with this name in
+      Debian)
+  * Fix depends: add ${perl:Depends}
+  * remove empty dir in package (/usr/sbin)
+  => package lintian clean now
+
+ -- Vincent Danjean <vdanjean at debian.org>  Mon, 12 May 2008 08:19:31 +0200
+
+altree (1.0.1-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Vincent Danjean <Vincent.Danjean at ens-lyon.org>  Fri, 13 Jan 2006 15:46:52 +0100
+
+altree (1.0.0-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Vincent Danjean <Vincent.Danjean at ens-lyon.org>  Fri, 13 Jan 2006 09:40:02 +0100
+
+altree (0.9.2-2) unstable; urgency=low
+
+  * Update FSF address in copyright file
+
+ -- Vincent Danjean <Vincent.Danjean at ens-lyon.org>  Sat, 10 Sep 2005 10:25:23 +0200
+
+altree (0.9.2-1) unstable; urgency=low
+
+  * New upstream release
+  * New upstream name
+
+ -- Vincent Danjean <Vincent.Danjean at ens-lyon.org>  Tue,  2 Aug 2005 19:52:19 +0200
+
+alphy (0.9.1d-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Vincent Danjean <Vincent.Danjean at ens-lyon.org>  Tue, 26 Jul 2005 00:08:40 +0200
+
+alphy (0.9.1c-1) unstable; urgency=low
+
+  * Initial release
+
+ -- Vincent Danjean <Vincent.Danjean at ens-lyon.org>  Mon, 25 Jul 2005 22:22:50 +0200
+

Deleted: trunk/packages/altree/tags/1.3.1-1/debian/control
===================================================================
--- trunk/packages/altree/trunk/debian/control	2013-11-22 22:38:54 UTC (rev 15254)
+++ trunk/packages/altree/tags/1.3.1-1/debian/control	2013-12-13 22:51:05 UTC (rev 15529)
@@ -1,38 +0,0 @@
-Source: altree
-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>,
- Vincent Danjean <vdanjean at debian.org>,
- Andreas Tille <tille at debian.org>
-Build-Depends: bash-completion, debhelper (>= 9), latex-make, ghostscript,
- texlive-lang-french, texlive-latex-extra, texlive-latex-recommended,
- texlive-fonts-recommended,
- libmath-tamuanova-perl, libpdl-stats-perl
-Standards-Version: 3.9.3
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/altree/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/altree/trunk/
-Homepage: http://claire.bardel.free.fr/software.html
-
-Package: altree
-Architecture: any
-Conflicts: libcutils-perl, alphy
-Replaces: libcutils-perl, alphy
-Provides: libcutils-perl, alphy
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends},
- libmath-tamuanova-perl, libpdl-stats-perl
-Suggests: altree-examples
-Description: program to perform phylogeny-based association and localization analysis
- ALTree was designed to perform association detection and localization of
- susceptibility sites using haplotype phylogenetic trees: first, it allows the
- detection of an association between a candidate gene and a disease, and second,
- it enables to make hypothesis about the susceptibility loci.
-
-Package: altree-examples
-Architecture: all
-Recommends: altree (= ${binary:Version})
-Depends: ${misc:Depends}
-Description: example files for ALTree
- This package contains the example files for the ALTree package discussed in
- its PDF manual.

Copied: trunk/packages/altree/tags/1.3.1-1/debian/control (from rev 15528, trunk/packages/altree/trunk/debian/control)
===================================================================
--- trunk/packages/altree/tags/1.3.1-1/debian/control	                        (rev 0)
+++ trunk/packages/altree/tags/1.3.1-1/debian/control	2013-12-13 22:51:05 UTC (rev 15529)
@@ -0,0 +1,43 @@
+Source: altree
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <plessy at debian.org>,
+ Vincent Danjean <vdanjean at debian.org>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: bash-completion, debhelper (>= 9), latex-make, ghostscript,
+ texlive-lang-french, texlive-latex-extra, texlive-latex-recommended,
+ texlive-fonts-recommended,
+ libmath-tamuanova-perl, libgsl0-dev, libatlas-base-dev,
+ libtest-deep-perl
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/altree/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/altree/trunk/
+Homepage: http://claire.bardel.free.fr/software.html
+
+Package: altree
+Architecture: any
+Conflicts: libcutils-perl, alphy
+Replaces: libcutils-perl, alphy
+Provides: libcutils-perl, alphy
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends},
+ libmath-tamuanova-perl
+Suggests: altree-examples
+Description: program to perform phylogeny-based association and localization analysis
+ ALTree was designed to perform association detection and localization of
+ susceptibility sites using haplotype phylogenetic trees: first, it allows the
+ detection of an association between a candidate gene and a disease, and second,
+ it enables to make hypothesis about the susceptibility loci.
+
+Package: altree-examples
+Architecture: all
+Recommends: altree (= ${binary:Version})
+Depends: ${misc:Depends}
+Description: example files for ALTree
+ ALTree was designed to perform association detection and localization of
+ susceptibility sites using haplotype phylogenetic trees: first, it allows the
+ detection of an association between a candidate gene and a disease, and second,
+ it enables to make hypothesis about the susceptibility loci.
+ .
+ This package contains the example files for the ALTree package discussed in
+ its PDF manual.




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