[med-svn] r15805 - in trunk/packages/logol/tags: . 1.6.9-3/debian 1.6.9-3/debian/patches
olivier sallou
osallou-guest at moszumanska.debian.org
Fri Jan 17 08:21:42 UTC 2014
Author: osallou-guest
Date: 2014-01-17 08:21:42 +0000 (Fri, 17 Jan 2014)
New Revision: 15805
Added:
trunk/packages/logol/tags/1.6.9-3/
trunk/packages/logol/tags/1.6.9-3/debian/changelog
trunk/packages/logol/tags/1.6.9-3/debian/control
trunk/packages/logol/tags/1.6.9-3/debian/patches/remove_rubygems_usage
trunk/packages/logol/tags/1.6.9-3/debian/patches/series
Removed:
trunk/packages/logol/tags/1.6.9-3/debian/changelog
trunk/packages/logol/tags/1.6.9-3/debian/control
trunk/packages/logol/tags/1.6.9-3/debian/patches/series
Log:
[svn-buildpackage] Tagging logol 1.6.9-3
Deleted: trunk/packages/logol/tags/1.6.9-3/debian/changelog
===================================================================
--- trunk/packages/logol/trunk/debian/changelog 2014-01-16 21:08:39 UTC (rev 15802)
+++ trunk/packages/logol/tags/1.6.9-3/debian/changelog 2014-01-17 08:21:42 UTC (rev 15805)
@@ -1,112 +0,0 @@
-logol (1.6.9-2) unstable; urgency=low
-
- * Fix prolog doc generation (Closes: #730916).
-
- -- Olivier Sallou <osallou at debian.org> Sun, 01 Dec 2013 11:55:42 +0100
-
-logol (1.6.9-1) unstable; urgency=low
-
- * New upstream release (bug fixes, add Windows support
- for Sicstus 4.2.x and Swi-prolog).
-
- -- Olivier Sallou <osallou at debian.org> Mon, 11 Nov 2013 10:11:17 +0100
-
-logol (1.6.6-1) unstable; urgency=low
-
- * New upstream releas (bug fixes on morphisms and doc).
-
- -- Olivier Sallou <osallou at debian.org> Wed, 30 Oct 2013 16:21:09 +0100
-
-logol (1.6.5-1) unstable; urgency=low
-
- * New upstream release (memory footprint optimisation in some cases).
-
- -- Olivier Sallou <osallou at debian.org> Fri, 25 Oct 2013 13:48:22 +0200
-
-logol (1.6.4-1) unstable; urgency=low
-
- * New upstream release fixing bugs
-
- -- Olivier Sallou <osallou at debian.org> Tue, 22 Oct 2013 08:35:45 +0200
-
-logol (1.6.3-1) unstable; urgency=low
-
- * New upstream release fixing important bugs on distance search
- * Remove patch for doc generation after swi-prolog fix
-
- -- Olivier Sallou <osallou at debian.org> Mon, 02 Sep 2013 08:54:46 +0200
-
-logol (1.6.2-3) unstable; urgency=low
-
- * Fix swi-prolog compilation (Closes: #719030).
-
- -- Olivier Sallou <osallou at debian.org> Thu, 08 Aug 2013 10:30:12 +0200
-
-logol (1.6.2-2) unstable; urgency=low
-
- [ Olivier Sallou ]
- * Remove deprecated DM-Upload field.
-
- [ Dmitrijs Ledkovs ]
- * Bump standards version to 3.9.4.
- * Remove empty postinst script.
- * Add dependancy on texlive-latex-extra, needed to fix documentation
- FTBFS with new TeX Live.
-
- -- Dmitrijs Ledkovs <dmitrij.ledkov at ubuntu.com> Mon, 03 Jun 2013 23:36:49 +0100
-
-logol (1.6.2-1) unstable; urgency=low
-
- * New upstream release (bug fixes)
-
- -- Olivier Sallou <osallou at debian.org> Fri, 24 May 2013 14:37:24 +0200
-
-logol (1.6.1-1) unstable; urgency=low
-
- * New upstream release (bug fixes)
-
- -- Olivier Sallou <osallou at debian.org> Tue, 09 Apr 2013 16:57:33 +0200
-
-logol (1.6.0-1) unstable; urgency=low
-
- * New upstream release with bug fixes
-
- -- Olivier Sallou <osallou at debian.org> Fri, 15 Feb 2013 10:05:50 +0100
-
-logol (1.5.0-6) unstable; urgency=low
-
- [ Olivier Sallou ]
- * debian/control: Fix typo in description (Closes: #685079).
- Thanks to Erik Esterer <erik.esterer at gmail.com>
-
- -- Olivier Sallou <osallou at debian.org> Fri, 17 Aug 2012 08:00:58 +0200
-
-logol (1.5.0-5) unstable; urgency=low
-
- [ Olivier Sallou]
- * Transition package to use default java implementation:
- From james.page at ubuntu.com (Closes: #684158)
- - d/control: BD on default-jdk (>= 1:1.6), switch runtime dependency
- to default-jre | java6-runtime.
- - d/rules: Specify source/target = 1.5 to ensure backwards compatible
- bytecode is built.
-
- -- Olivier Sallou <osallou at debian.org> Tue, 07 Aug 2012 15:18:43 +0200
-
-logol (1.5.0-4) unstable; urgency=low
-
- * debian/postinst: remove directory permissions (Closes: #683647).
-
- -- Olivier Sallou <osallou at debian.org> Thu, 02 Aug 2012 17:09:31 +0200
-
-logol (1.5.0-2) unstable; urgency=low
-
- * Support Arch dependent and arch independent separate builds.
-
- -- Olivier Sallou <osallou at debian.org> Sun, 01 Jul 2012 23:49:16 +0200
-
-logol (1.5.0-1) unstable; urgency=low
-
- * Initial release (Closes: #678373).
-
- -- Olivier Sallou <osallou at debian.org> Thu, 21 Jun 2012 12:50:22 +0200
Copied: trunk/packages/logol/tags/1.6.9-3/debian/changelog (from rev 15803, trunk/packages/logol/trunk/debian/changelog)
===================================================================
--- trunk/packages/logol/tags/1.6.9-3/debian/changelog (rev 0)
+++ trunk/packages/logol/tags/1.6.9-3/debian/changelog 2014-01-17 08:21:42 UTC (rev 15805)
@@ -0,0 +1,120 @@
+logol (1.6.9-3) unstable; urgency=low
+
+ * d/control,d/patches: Remove rubygems dependency, thanks to
+ Cédric Boutillier <boutil at debian.org> (Closes: #735579).
+ * Upgrade to Standards 3.9.5.
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 17 Jan 2014 09:07:38 +0100
+
+logol (1.6.9-2) unstable; urgency=low
+
+ * Fix prolog doc generation (Closes: #730916).
+
+ -- Olivier Sallou <osallou at debian.org> Sun, 01 Dec 2013 11:55:42 +0100
+
+logol (1.6.9-1) unstable; urgency=low
+
+ * New upstream release (bug fixes, add Windows support
+ for Sicstus 4.2.x and Swi-prolog).
+
+ -- Olivier Sallou <osallou at debian.org> Mon, 11 Nov 2013 10:11:17 +0100
+
+logol (1.6.6-1) unstable; urgency=low
+
+ * New upstream releas (bug fixes on morphisms and doc).
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 30 Oct 2013 16:21:09 +0100
+
+logol (1.6.5-1) unstable; urgency=low
+
+ * New upstream release (memory footprint optimisation in some cases).
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 25 Oct 2013 13:48:22 +0200
+
+logol (1.6.4-1) unstable; urgency=low
+
+ * New upstream release fixing bugs
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 22 Oct 2013 08:35:45 +0200
+
+logol (1.6.3-1) unstable; urgency=low
+
+ * New upstream release fixing important bugs on distance search
+ * Remove patch for doc generation after swi-prolog fix
+
+ -- Olivier Sallou <osallou at debian.org> Mon, 02 Sep 2013 08:54:46 +0200
+
+logol (1.6.2-3) unstable; urgency=low
+
+ * Fix swi-prolog compilation (Closes: #719030).
+
+ -- Olivier Sallou <osallou at debian.org> Thu, 08 Aug 2013 10:30:12 +0200
+
+logol (1.6.2-2) unstable; urgency=low
+
+ [ Olivier Sallou ]
+ * Remove deprecated DM-Upload field.
+
+ [ Dmitrijs Ledkovs ]
+ * Bump standards version to 3.9.4.
+ * Remove empty postinst script.
+ * Add dependancy on texlive-latex-extra, needed to fix documentation
+ FTBFS with new TeX Live.
+
+ -- Dmitrijs Ledkovs <dmitrij.ledkov at ubuntu.com> Mon, 03 Jun 2013 23:36:49 +0100
+
+logol (1.6.2-1) unstable; urgency=low
+
+ * New upstream release (bug fixes)
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 24 May 2013 14:37:24 +0200
+
+logol (1.6.1-1) unstable; urgency=low
+
+ * New upstream release (bug fixes)
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 09 Apr 2013 16:57:33 +0200
+
+logol (1.6.0-1) unstable; urgency=low
+
+ * New upstream release with bug fixes
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 15 Feb 2013 10:05:50 +0100
+
+logol (1.5.0-6) unstable; urgency=low
+
+ [ Olivier Sallou ]
+ * debian/control: Fix typo in description (Closes: #685079).
+ Thanks to Erik Esterer <erik.esterer at gmail.com>
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 17 Aug 2012 08:00:58 +0200
+
+logol (1.5.0-5) unstable; urgency=low
+
+ [ Olivier Sallou]
+ * Transition package to use default java implementation:
+ From james.page at ubuntu.com (Closes: #684158)
+ - d/control: BD on default-jdk (>= 1:1.6), switch runtime dependency
+ to default-jre | java6-runtime.
+ - d/rules: Specify source/target = 1.5 to ensure backwards compatible
+ bytecode is built.
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 07 Aug 2012 15:18:43 +0200
+
+logol (1.5.0-4) unstable; urgency=low
+
+ * debian/postinst: remove directory permissions (Closes: #683647).
+
+ -- Olivier Sallou <osallou at debian.org> Thu, 02 Aug 2012 17:09:31 +0200
+
+logol (1.5.0-2) unstable; urgency=low
+
+ * Support Arch dependent and arch independent separate builds.
+
+ -- Olivier Sallou <osallou at debian.org> Sun, 01 Jul 2012 23:49:16 +0200
+
+logol (1.5.0-1) unstable; urgency=low
+
+ * Initial release (Closes: #678373).
+
+ -- Olivier Sallou <osallou at debian.org> Thu, 21 Jun 2012 12:50:22 +0200
Deleted: trunk/packages/logol/tags/1.6.9-3/debian/control
===================================================================
--- trunk/packages/logol/trunk/debian/control 2014-01-16 21:08:39 UTC (rev 15802)
+++ trunk/packages/logol/tags/1.6.9-3/debian/control 2014-01-17 08:21:42 UTC (rev 15805)
@@ -1,37 +0,0 @@
-Source: logol
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Olivier Sallou <osallou at debian.org>
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/logol/trunk/
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/logol/
-Build-Depends: debhelper (>= 8.0.0),default-jdk (>= 1:1.6),ant,ruby (>=1.8),rubygems, gawk, swi-prolog (>=6.4.1-3),
- libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java, libcommons-collections3-java, libcommons-configuration-java,
- libcommons-lang-java, libcommons-logging-java, libxalan2-java, libxerces2-java, junit4, libgnumail-java,
- liblog4j1.2-java,texlive, texlive-latex-extra, tex4ht, libncursesw5-dev, ruby-cassiopee (>=0.1.12), ant-optional
-Standards-Version: 3.9.4
-Homepage: http://logol.genouest.org
-
-Package: logol
-Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}, default-jre | java6-runtime, ruby (>=1.8),rubygems, gawk,
- libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java, libcommons-collections3-java, libcommons-configuration-java,
- libcommons-lang-java, libcommons-logging-java, libxalan2-java, libxerces2-java, libgnumail-java, liblog4j1.2-java,
- ruby-cassiopee (>=0.1.12), logol-bin
-Description: Pattern matching tool using Logol language
- Logol is a pattern matching tool using the Logol language.
- It searches with a specific grammar a pattern in small
- or large sequence (dna, rna, protein). It provides complete
- result matching with the original grammar in the results.
-
-Package: logol-bin
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, swi-prolog(>=6.4.1-3), libncursesw5
-Description: Pattern matching tool using Logol language
- This package contains the Prolog binaries used by Logol to parse
- the sequence and match the grammar.
- .
- Logol is a pattern matching tool using the Logol language.
- It searches with a specific grammar a pattern in small
- or large sequence (dna, rna, protein). It provides complete
- result matching with the original grammar in the results.
Copied: trunk/packages/logol/tags/1.6.9-3/debian/control (from rev 15803, trunk/packages/logol/trunk/debian/control)
===================================================================
--- trunk/packages/logol/tags/1.6.9-3/debian/control (rev 0)
+++ trunk/packages/logol/tags/1.6.9-3/debian/control 2014-01-17 08:21:42 UTC (rev 15805)
@@ -0,0 +1,44 @@
+Source: logol
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/logol/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/logol/
+Build-Depends: debhelper (>= 8.0.0),default-jdk (>= 1:1.6),ant,ruby,
+ gawk, swi-prolog (>=6.4.1-3),
+ libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java,
+ libcommons-collections3-java, libcommons-configuration-java,
+ libcommons-lang-java, libcommons-logging-java, libxalan2-java,
+ libxerces2-java, junit4, libgnumail-java,
+ liblog4j1.2-java,texlive, texlive-latex-extra, tex4ht,
+ libncursesw5-dev, ruby-cassiopee (>=0.1.12), ant-optional
+Standards-Version: 3.9.5
+Homepage: http://logol.genouest.org
+
+Package: logol
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, default-jre | java6-runtime,
+ ruby, gawk,
+ libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java,
+ libcommons-collections3-java, libcommons-configuration-java,
+ libcommons-lang-java, libcommons-logging-java, libxalan2-java,
+ libxerces2-java, libgnumail-java, liblog4j1.2-java,
+ ruby-cassiopee (>=0.1.12), logol-bin
+Description: Pattern matching tool using Logol language
+ Logol is a pattern matching tool using the Logol language.
+ It searches with a specific grammar a pattern in small
+ or large sequence (dna, rna, protein). It provides complete
+ result matching with the original grammar in the results.
+
+Package: logol-bin
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, swi-prolog(>=6.4.1-3), libncursesw5
+Description: Pattern matching tool using Logol language
+ This package contains the Prolog binaries used by Logol to parse
+ the sequence and match the grammar.
+ .
+ Logol is a pattern matching tool using the Logol language.
+ It searches with a specific grammar a pattern in small
+ or large sequence (dna, rna, protein). It provides complete
+ result matching with the original grammar in the results.
Copied: trunk/packages/logol/tags/1.6.9-3/debian/patches/remove_rubygems_usage (from rev 15804, trunk/packages/logol/trunk/debian/patches/remove_rubygems_usage)
===================================================================
--- trunk/packages/logol/tags/1.6.9-3/debian/patches/remove_rubygems_usage (rev 0)
+++ trunk/packages/logol/tags/1.6.9-3/debian/patches/remove_rubygems_usage 2014-01-17 08:21:42 UTC (rev 15805)
@@ -0,0 +1,28 @@
+Subject: Remove explicit use of rubygems
+Description: Supported version of Ruby in Jessie+ are higher that 1.9
+ and they all automatically load rubygems
+Author: Cédric Boutillier <boutil at debian.org>
+Last-Update: 2014-01-16
+
+--- a/tools/logolIndex.rb
++++ b/tools/logolIndex.rb
+@@ -1,5 +1,4 @@
+ #!/usr/bin/env ruby
+-require 'rubygems'
+ require 'optparse'
+ require 'logger'
+ require 'cassiopee-mt'
+--- a/tools/logolSearch.rb
++++ b/tools/logolSearch.rb
+@@ -22,9 +22,9 @@
+ DIR=File.expand_path(File.dirname(__FILE__))
+
+ if muteOnly == 1
+- cmd = "ruby -rubygems "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError+" --hamming"
++ cmd = "ruby "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError+" --hamming"
+ else
+- cmd = "ruby -rubygems "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError
++ cmd = "ruby "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError
+ end
+
+ Open3.popen3(cmd) do |stdin,stdout,stderr, wait_thr|
Deleted: trunk/packages/logol/tags/1.6.9-3/debian/patches/series
===================================================================
--- trunk/packages/logol/trunk/debian/patches/series 2014-01-16 21:08:39 UTC (rev 15802)
+++ trunk/packages/logol/tags/1.6.9-3/debian/patches/series 2014-01-17 08:21:42 UTC (rev 15805)
@@ -1,5 +0,0 @@
-fixLibPath
-fixDrmmato6.2
-setDebianDirs
-fix_doc_generation
-fix_pldoc
Copied: trunk/packages/logol/tags/1.6.9-3/debian/patches/series (from rev 15803, trunk/packages/logol/trunk/debian/patches/series)
===================================================================
--- trunk/packages/logol/tags/1.6.9-3/debian/patches/series (rev 0)
+++ trunk/packages/logol/tags/1.6.9-3/debian/patches/series 2014-01-17 08:21:42 UTC (rev 15805)
@@ -0,0 +1,6 @@
+fixLibPath
+fixDrmmato6.2
+setDebianDirs
+fix_doc_generation
+fix_pldoc
+remove_rubygems_usage
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