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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Fri, 25 Oct 2013 13:48:22 +0200 - -logol (1.6.4-1) unstable; urgency=low - - * New upstream release fixing bugs - - -- Olivier Sallou <[email protected]> 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 <[email protected]> Mon, 02 Sep 2013 08:54:46 +0200 - -logol (1.6.2-3) unstable; urgency=low - - * Fix swi-prolog compilation (Closes: #719030). - - -- Olivier Sallou <[email protected]> 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 <[email protected]> Mon, 03 Jun 2013 23:36:49 +0100 - -logol (1.6.2-1) unstable; urgency=low - - * New upstream release (bug fixes) - - -- Olivier Sallou <[email protected]> Fri, 24 May 2013 14:37:24 +0200 - -logol (1.6.1-1) unstable; urgency=low - - * New upstream release (bug fixes) - - -- Olivier Sallou <[email protected]> Tue, 09 Apr 2013 16:57:33 +0200 - -logol (1.6.0-1) unstable; urgency=low - - * New upstream release with bug fixes - - -- Olivier Sallou <[email protected]> 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 <[email protected]> - - -- Olivier Sallou <[email protected]> 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 [email protected] (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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Sun, 01 Jul 2012 23:49:16 +0200 - -logol (1.5.0-1) unstable; urgency=low - - * Initial release (Closes: #678373). - - -- Olivier Sallou <[email protected]> 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 <[email protected]> (Closes: #735579). + * Upgrade to Standards 3.9.5. + + -- Olivier Sallou <[email protected]> Fri, 17 Jan 2014 09:07:38 +0100 + +logol (1.6.9-2) unstable; urgency=low + + * Fix prolog doc generation (Closes: #730916). + + -- Olivier Sallou <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Fri, 25 Oct 2013 13:48:22 +0200 + +logol (1.6.4-1) unstable; urgency=low + + * New upstream release fixing bugs + + -- Olivier Sallou <[email protected]> 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 <[email protected]> Mon, 02 Sep 2013 08:54:46 +0200 + +logol (1.6.2-3) unstable; urgency=low + + * Fix swi-prolog compilation (Closes: #719030). + + -- Olivier Sallou <[email protected]> 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 <[email protected]> Mon, 03 Jun 2013 23:36:49 +0100 + +logol (1.6.2-1) unstable; urgency=low + + * New upstream release (bug fixes) + + -- Olivier Sallou <[email protected]> Fri, 24 May 2013 14:37:24 +0200 + +logol (1.6.1-1) unstable; urgency=low + + * New upstream release (bug fixes) + + -- Olivier Sallou <[email protected]> Tue, 09 Apr 2013 16:57:33 +0200 + +logol (1.6.0-1) unstable; urgency=low + + * New upstream release with bug fixes + + -- Olivier Sallou <[email protected]> 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 <[email protected]> + + -- Olivier Sallou <[email protected]> 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 [email protected] (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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Sun, 01 Jul 2012 23:49:16 +0200 + +logol (1.5.0-1) unstable; urgency=low + + * Initial release (Closes: #678373). + + -- Olivier Sallou <[email protected]> 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 <[email protected]> -Uploaders: Olivier Sallou <[email protected]> -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 <[email protected]> +Uploaders: Olivier Sallou <[email protected]> +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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
