Author: vdanjean Date: 2015-12-08 20:11:18 +0000 (Tue, 08 Dec 2015) New Revision: 20685
Added: trunk/packages/altree/tags/1.3.1-3/ trunk/packages/altree/tags/1.3.1-3/debian/changelog trunk/packages/altree/tags/1.3.1-3/debian/control trunk/packages/altree/tags/1.3.1-3/debian/rules Removed: trunk/packages/altree/tags/1.3.1-3/debian/changelog trunk/packages/altree/tags/1.3.1-3/debian/control trunk/packages/altree/tags/1.3.1-3/debian/rules Log: [svn-buildpackage] Tagging altree 1.3.1-3 Deleted: trunk/packages/altree/tags/1.3.1-3/debian/changelog =================================================================== --- trunk/packages/altree/trunk/debian/changelog 2015-12-08 18:12:41 UTC (rev 20681) +++ trunk/packages/altree/tags/1.3.1-3/debian/changelog 2015-12-08 20:11:18 UTC (rev 20685) @@ -1,196 +0,0 @@ -altree (1.3.1-3) UNRELEASED; urgency=medium - - * [debian/control] Update build dependencies for GSL 2, change libgsl0-dev to - libgsl-dev. Thanks Bas Couwenberg <[email protected]> (Closes: #807173) - - -- Vincent Danjean <[email protected]> Sun, 06 Dec 2015 15:22:44 +0100 - -altree (1.3.1-2) unstable; urgency=medium - - * Fix "FTBFS with clang instead of gcc" - clang does not support nested functions so removing them. - Instead of inlining the nested function as proposed in the submitted - patch (thanks Arthur <[email protected]>), use a external function - with an explicit context (Closes: #742843) - * bump standard-version (no change needed) - - -- Vincent Danjean <[email protected]> Sun, 30 Mar 2014 23:43:51 +0200 - -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 <[email protected]> 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improvment - * debian/control: - + bump Standard-Version (no change needed) - + put canonical vcs fields - + remove outdated DM-Upload-Allowed field - + improve altree-examples long description - + add libgsl0-dev and libatlas-base-dev as new build-dependency - + remove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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Mon, 12 May 2008 08:19:31 +0200 - -altree (1.0.1-1) unstable; urgency=low - - * New upstream release - - -- Vincent Danjean <[email protected]> Fri, 13 Jan 2006 15:46:52 +0100 - -altree (1.0.0-1) unstable; urgency=low - - * New upstream release - - -- Vincent Danjean <[email protected]> Fri, 13 Jan 2006 09:40:02 +0100 - -altree (0.9.2-2) unstable; urgency=low - - * Update FSF address in copyright file - - -- Vincent Danjean <[email protected]> Sat, 10 Sep 2005 10:25:23 +0200 - -altree (0.9.2-1) unstable; urgency=low - - * New upstream release - * New upstream name - - -- Vincent Danjean <[email protected]> Tue, 2 Aug 2005 19:52:19 +0200 - -alphy (0.9.1d-1) unstable; urgency=low - - * New upstream release - - -- Vincent Danjean <[email protected]> Tue, 26 Jul 2005 00:08:40 +0200 - -alphy (0.9.1c-1) unstable; urgency=low - - * Initial release - - -- Vincent Danjean <[email protected]> Mon, 25 Jul 2005 22:22:50 +0200 - Copied: trunk/packages/altree/tags/1.3.1-3/debian/changelog (from rev 20684, trunk/packages/altree/trunk/debian/changelog) =================================================================== --- trunk/packages/altree/tags/1.3.1-3/debian/changelog (rev 0) +++ trunk/packages/altree/tags/1.3.1-3/debian/changelog 2015-12-08 20:11:18 UTC (rev 20685) @@ -0,0 +1,199 @@ +altree (1.3.1-3) unstable; urgency=medium + + * [debian/control] Update build dependencies for GSL 2, change libgsl0-dev to + libgsl-dev. Thanks Bas Couwenberg <[email protected]> (Closes: #807173) + * Fix "FTBFS with perl 5.22 in experimental (MakeMaker changes)" by removing + manual (wrong) call to "make install PREFIX=..." (Closes: #807423) + * [debian/control] Bump Standards-Version (no changes needed) + + -- Vincent Danjean <[email protected]> Tue, 08 Dec 2015 20:47:26 +0100 + +altree (1.3.1-2) unstable; urgency=medium + + * Fix "FTBFS with clang instead of gcc" + clang does not support nested functions so removing them. + Instead of inlining the nested function as proposed in the submitted + patch (thanks Arthur <[email protected]>), use a external function + with an explicit context (Closes: #742843) + * bump standard-version (no change needed) + + -- Vincent Danjean <[email protected]> Sun, 30 Mar 2014 23:43:51 +0200 + +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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Mon, 12 May 2008 08:19:31 +0200 + +altree (1.0.1-1) unstable; urgency=low + + * New upstream release + + -- Vincent Danjean <[email protected]> Fri, 13 Jan 2006 15:46:52 +0100 + +altree (1.0.0-1) unstable; urgency=low + + * New upstream release + + -- Vincent Danjean <[email protected]> Fri, 13 Jan 2006 09:40:02 +0100 + +altree (0.9.2-2) unstable; urgency=low + + * Update FSF address in copyright file + + -- Vincent Danjean <[email protected]> Sat, 10 Sep 2005 10:25:23 +0200 + +altree (0.9.2-1) unstable; urgency=low + + * New upstream release + * New upstream name + + -- Vincent Danjean <[email protected]> Tue, 2 Aug 2005 19:52:19 +0200 + +alphy (0.9.1d-1) unstable; urgency=low + + * New upstream release + + -- Vincent Danjean <[email protected]> Tue, 26 Jul 2005 00:08:40 +0200 + +alphy (0.9.1c-1) unstable; urgency=low + + * Initial release + + -- Vincent Danjean <[email protected]> Mon, 25 Jul 2005 22:22:50 +0200 + Deleted: trunk/packages/altree/tags/1.3.1-3/debian/control =================================================================== --- trunk/packages/altree/trunk/debian/control 2015-12-08 18:12:41 UTC (rev 20681) +++ trunk/packages/altree/tags/1.3.1-3/debian/control 2015-12-08 20:11:18 UTC (rev 20685) @@ -1,43 +0,0 @@ -Source: altree -Section: science -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Charles Plessy <[email protected]>, - Vincent Danjean <[email protected]>, - Andreas Tille <[email protected]> -Build-Depends: bash-completion, debhelper (>= 9), latex-make, ghostscript, - texlive-lang-french, texlive-latex-extra, texlive-latex-recommended, - texlive-fonts-recommended, - libmath-tamuanova-perl, libgsl-dev, libatlas-base-dev, - libtest-deep-perl -Standards-Version: 3.9.5 -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. Copied: trunk/packages/altree/tags/1.3.1-3/debian/control (from rev 20683, trunk/packages/altree/trunk/debian/control) =================================================================== --- trunk/packages/altree/tags/1.3.1-3/debian/control (rev 0) +++ trunk/packages/altree/tags/1.3.1-3/debian/control 2015-12-08 20:11:18 UTC (rev 20685) @@ -0,0 +1,43 @@ +Source: altree +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Charles Plessy <[email protected]>, + Vincent Danjean <[email protected]>, + Andreas Tille <[email protected]> +Build-Depends: bash-completion, debhelper (>= 9), latex-make, ghostscript, + texlive-lang-french, texlive-latex-extra, texlive-latex-recommended, + texlive-fonts-recommended, + libmath-tamuanova-perl, libgsl-dev, libatlas-base-dev, + libtest-deep-perl +Standards-Version: 3.9.6 +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. Deleted: trunk/packages/altree/tags/1.3.1-3/debian/rules =================================================================== --- trunk/packages/altree/trunk/debian/rules 2015-12-08 18:12:41 UTC (rev 20681) +++ trunk/packages/altree/tags/1.3.1-3/debian/rules 2015-12-08 20:11:18 UTC (rev 20685) @@ -1,30 +0,0 @@ -#!/usr/bin/make -f -# -*- makefile -*- -# debian/rules file for altree -# Andreas Tille <[email protected]> -# GPL - -%: - dh $@ - -override_dh_auto_clean: - $(MAKE) -C Documentation distclean - dh_auto_clean - -override_dh_auto_build: - $(MAKE) -C Documentation pdf - dh_auto_build - -override_dh_auto_install: - $(MAKE) PREFIX=debian/altree/usr install - -override_dh_compress: - dh_compress --exclude=.pdf - -override_dh_builddeb: - dh_builddeb -- -Z xz - -get-orig-source: - mkdir -p ../tarballs - uscan --verbose --force-download --destdir=../tarballs - Copied: trunk/packages/altree/tags/1.3.1-3/debian/rules (from rev 20682, trunk/packages/altree/trunk/debian/rules) =================================================================== --- trunk/packages/altree/tags/1.3.1-3/debian/rules (rev 0) +++ trunk/packages/altree/tags/1.3.1-3/debian/rules 2015-12-08 20:11:18 UTC (rev 20685) @@ -0,0 +1,27 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# debian/rules file for altree +# Andreas Tille <[email protected]> +# GPL + +%: + dh $@ + +override_dh_auto_clean: + $(MAKE) -C Documentation distclean + dh_auto_clean + +override_dh_auto_build: + $(MAKE) -C Documentation pdf + dh_auto_build + +override_dh_compress: + dh_compress --exclude=.pdf + +override_dh_builddeb: + dh_builddeb -- -Z xz + +get-orig-source: + mkdir -p ../tarballs + uscan --verbose --force-download --destdir=../tarballs + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
