Author: osallou-guest Date: 2013-08-30 10:11:47 +0000 (Fri, 30 Aug 2013) New Revision: 14551
Added: trunk/packages/biomaj/tags/1.2.2-1/ trunk/packages/biomaj/tags/1.2.2-1/debian/changelog trunk/packages/biomaj/tags/1.2.2-1/debian/control trunk/packages/biomaj/tags/1.2.2-1/debian/patches/series Removed: trunk/packages/biomaj/tags/1.2.2-1/debian/changelog trunk/packages/biomaj/tags/1.2.2-1/debian/control trunk/packages/biomaj/tags/1.2.2-1/debian/patches/fix_ant_propertie_format trunk/packages/biomaj/tags/1.2.2-1/debian/patches/series Log: [svn-buildpackage] Tagging biomaj 1.2.2-1 Deleted: trunk/packages/biomaj/tags/1.2.2-1/debian/changelog =================================================================== --- trunk/packages/biomaj/trunk/debian/changelog 2013-08-29 21:19:48 UTC (rev 14548) +++ trunk/packages/biomaj/tags/1.2.2-1/debian/changelog 2013-08-30 10:11:47 UTC (rev 14551) @@ -1,164 +0,0 @@ -biomaj (1.2.1-3) unstable; urgency=low - - * Add patch to manage ant properties api change (Closes: #712328). - - -- Olivier Sallou <[email protected]> Tue, 18 Jun 2013 11:39:36 +0200 - -biomaj (1.2.1-2) unstable; urgency=low - - * Add patch to match libjgoodies-form-java >1.3, - FormFactory replaced by FormSpecs (Closes: #708454) - d/control: Depends on libjgoodies-form-java > 1.3 - - -- Olivier Sallou <[email protected]> Sun, 19 May 2013 13:21:55 +0200 - -biomaj (1.2.1-1) unstable; urgency=low - - * New usptream release - * Add Japanase debconf translation (Closes: #690698) - Thanks to victory <[email protected]> - - -- Olivier Sallou <[email protected]> Fri, 19 Oct 2012 17:04:19 +0200 - -biomaj (1.2.0-10) unstable; urgency=low - - * debian/rules, debian/postinst: fix permissions on - properties file. - - -- Olivier Sallou <[email protected]> Thu, 04 Oct 2012 18:34:01 +0200 - -biomaj (1.2.0-9) unstable; urgency=low - - * debian/patches/set_env_file_for_debian: - Prevent env.sh file update by program at install - (Closes: #688433) - - -- Olivier Sallou <[email protected]> Wed, 03 Oct 2012 13:54:44 +0200 - -biomaj (1.2.0-8) unstable; urgency=low - - [ Olivier Sallou ] - * debian/copyright: Fix copyright URL - * debian/control: Switch to Standards 3.9.4 - * debian/rules, debian/postinst, debian/postrm: fix conffile update - conflicting with Debian Policy (Closes: #688433). - - -- Olivier Sallou <[email protected]> Wed, 01 Aug 2012 15:59:55 +0200 - -biomaj (1.2.0-7) unstable; urgency=low - - [ Olivier Sallou ] - Patch from James Page <[email protected]> (Closes: #683517) - * Transition package to use default java implementation: - - d/rules: Specify source/target = 1.5 to ensure bytecode is backwards - compatible. - - d/control: BD on default-jdk only. Switch runtime dependency to - default-jre | java6-runtime. - - -- Olivier Sallou <[email protected]> Wed, 01 Aug 2012 14:58:41 +0200 - -biomaj (1.2.0-6) unstable; urgency=low - - [ Olivier Sallou ] - * Clean files for purge (Closes: #678490). - - [ Andreas Tille ] - * debian/upstream: Enhance upstream information (authors format, missing - fields) - - [Debconf translation updates] - * French (Olivier Sallou, proofread by the French l10n team). - - -- Olivier Sallou <[email protected]> Tue, 08 May 2012 22:46:34 +0200 - -biomaj (1.2.0-5) unstable; urgency=low - - * Add missing file to package to get the console help (Closes: #658833) - - biomaj.install - - -- Olivier Sallou <[email protected]> Wed, 01 Feb 2012 10:00:03 +0100 - -biomaj (1.2.0-4) unstable; urgency=low - - * [Olivier Sallou] - * config: remove biomaj/jdk_home, not needed anymore - - * Debconf templates and debian/control reviewed by the debian-l10n- - english team as part of the Smith review project. Closes: #653408 - * [Debconf translation updates] - * Russian (Yuri Kozlov). Closes: #656111 - * Italian (Francesca Ciceri). Closes: #656254 - * French (Olivier Sallou). Closes: #656066 - * Czech (Michal Simunek). Closes: #656670 - * Dutch; (Jeroen Schot). Closes: #657009 - * German (Chris Leick). Closes: #657024 - * Danish (Joe Hansen). Closes: #657341 - * Indonesian (Mahyuddin Susanto). Closes: #657463 - * Spanish; (Camaleón). Closes: #657491 - * Polish (Michał Kułach). Closes: #657512 - * Swedish (Martin Bagge / brother). Closes: #657548 - * Portuguese (Miguel Figueiredo). Closes: #657664 - - - -- Olivier Sallou <[email protected]> Fri, 16 Dec 2011 15:53:10 +0100 - -biomaj (1.2.0-3) unstable; urgency=low - - * Add Portuguese translation for debconf (Closes: #651680) - - Thanks to Pedro Ribeiro <[email protected]> - - -- Olivier Sallou <[email protected]> Fri, 16 Dec 2011 09:25:22 +0100 - -biomaj (1.2.0-2) unstable; urgency=low - - * Fix Mysql dependency name. - - -- Olivier Sallou <[email protected]> Fri, 11 Nov 2011 10:25:39 +0100 - -biomaj (1.2.0-1) unstable; urgency=low - - * New upstream release with new features and bug fixes. - * Change in database model, migration script ran at install - * New post processes added in default install (emboss) - - -- Olivier Sallou <[email protected]> Thu, 18 Aug 2011 09:55:23 +0200 - -biomaj (1.1.0-3) unstable; urgency=low - - * Change priority in debconf message for jdk home - * Add spanish translation of debconf: - Thanks to Camaleón <[email protected]> - Closes: #632952 - * Add sweden translation of debconf: - Thanks to Martin Bagge <[email protected]> - Closes: #628927 - * Add german translation of debconf: - Thanks to Chris Leick <[email protected]> - Closes: #629455 - * Change openjdk dependency to add default-jdk and sun jdk possible depends - Closes: #633523 - - -- Olivier Sallou <[email protected]> Thu, 11 Jul 2011 09:55:23 +0200 - -biomaj (1.1.0-2) unstable; urgency=low - - * Add russian translation of debconf: - Thanks to Yuri Kozlov <[email protected]> - Closes: #623807 - * debian/patches/fix623558_remove_pid: - Remove unnecessary pid file creation - Closes: #623558 - * debian/postrm,debian/preinst: - Issue for smooth upgrade, require old package - removal then new package install - Closes: #624284 - - - -- Olivier Sallou <[email protected]> Fri, 22 Apr 2011 16:27:11 +0200 - -biomaj (1.1.0-1) unstable; urgency=low - - * Initial release (Closes: #609038) - First Debian package, fixed copyright file to list all licenses - - -- Olivier Sallou <[email protected]> Wed, 05 Jan 2011 10:39:00 +0100 Copied: trunk/packages/biomaj/tags/1.2.2-1/debian/changelog (from rev 14549, trunk/packages/biomaj/trunk/debian/changelog) =================================================================== --- trunk/packages/biomaj/tags/1.2.2-1/debian/changelog (rev 0) +++ trunk/packages/biomaj/tags/1.2.2-1/debian/changelog 2013-08-30 10:11:47 UTC (rev 14551) @@ -0,0 +1,171 @@ +biomaj (1.2.2-1) unstable; urgency=low + + * New upstream release with minor fixes + d/patches/series: upstream bug 15914 fixed. + + -- Olivier Sallou <[email protected]> Tue, 18 Jun 2013 14:30:28 +0200 + +biomaj (1.2.1-3) unstable; urgency=low + + * Add patch to manage ant properties api change (Closes: #712328). + + -- Olivier Sallou <[email protected]> Tue, 18 Jun 2013 11:39:36 +0200 + +biomaj (1.2.1-2) unstable; urgency=low + + * Add patch to match libjgoodies-form-java >1.3, + FormFactory replaced by FormSpecs (Closes: #708454) + d/control: Depends on libjgoodies-form-java > 1.3 + + -- Olivier Sallou <[email protected]> Sun, 19 May 2013 13:21:55 +0200 + +biomaj (1.2.1-1) unstable; urgency=low + + * New usptream release + * Add Japanase debconf translation (Closes: #690698) + Thanks to victory <[email protected]> + + -- Olivier Sallou <[email protected]> Fri, 19 Oct 2012 17:04:19 +0200 + +biomaj (1.2.0-10) unstable; urgency=low + + * debian/rules, debian/postinst: fix permissions on + properties file. + + -- Olivier Sallou <[email protected]> Thu, 04 Oct 2012 18:34:01 +0200 + +biomaj (1.2.0-9) unstable; urgency=low + + * debian/patches/set_env_file_for_debian: + Prevent env.sh file update by program at install + (Closes: #688433) + + -- Olivier Sallou <[email protected]> Wed, 03 Oct 2012 13:54:44 +0200 + +biomaj (1.2.0-8) unstable; urgency=low + + [ Olivier Sallou ] + * debian/copyright: Fix copyright URL + * debian/control: Switch to Standards 3.9.4 + * debian/rules, debian/postinst, debian/postrm: fix conffile update + conflicting with Debian Policy (Closes: #688433). + + -- Olivier Sallou <[email protected]> Wed, 01 Aug 2012 15:59:55 +0200 + +biomaj (1.2.0-7) unstable; urgency=low + + [ Olivier Sallou ] + Patch from James Page <[email protected]> (Closes: #683517) + * Transition package to use default java implementation: + - d/rules: Specify source/target = 1.5 to ensure bytecode is backwards + compatible. + - d/control: BD on default-jdk only. Switch runtime dependency to + default-jre | java6-runtime. + + -- Olivier Sallou <[email protected]> Wed, 01 Aug 2012 14:58:41 +0200 + +biomaj (1.2.0-6) unstable; urgency=low + + [ Olivier Sallou ] + * Clean files for purge (Closes: #678490). + + [ Andreas Tille ] + * debian/upstream: Enhance upstream information (authors format, missing + fields) + + [Debconf translation updates] + * French (Olivier Sallou, proofread by the French l10n team). + + -- Olivier Sallou <[email protected]> Tue, 08 May 2012 22:46:34 +0200 + +biomaj (1.2.0-5) unstable; urgency=low + + * Add missing file to package to get the console help (Closes: #658833) + - biomaj.install + + -- Olivier Sallou <[email protected]> Wed, 01 Feb 2012 10:00:03 +0100 + +biomaj (1.2.0-4) unstable; urgency=low + + * [Olivier Sallou] + * config: remove biomaj/jdk_home, not needed anymore + + * Debconf templates and debian/control reviewed by the debian-l10n- + english team as part of the Smith review project. Closes: #653408 + * [Debconf translation updates] + * Russian (Yuri Kozlov). Closes: #656111 + * Italian (Francesca Ciceri). Closes: #656254 + * French (Olivier Sallou). Closes: #656066 + * Czech (Michal Simunek). Closes: #656670 + * Dutch; (Jeroen Schot). Closes: #657009 + * German (Chris Leick). Closes: #657024 + * Danish (Joe Hansen). Closes: #657341 + * Indonesian (Mahyuddin Susanto). Closes: #657463 + * Spanish; (Camaleón). Closes: #657491 + * Polish (Michał Kułach). Closes: #657512 + * Swedish (Martin Bagge / brother). Closes: #657548 + * Portuguese (Miguel Figueiredo). Closes: #657664 + + + -- Olivier Sallou <[email protected]> Fri, 16 Dec 2011 15:53:10 +0100 + +biomaj (1.2.0-3) unstable; urgency=low + + * Add Portuguese translation for debconf (Closes: #651680) + - Thanks to Pedro Ribeiro <[email protected]> + + -- Olivier Sallou <[email protected]> Fri, 16 Dec 2011 09:25:22 +0100 + +biomaj (1.2.0-2) unstable; urgency=low + + * Fix Mysql dependency name. + + -- Olivier Sallou <[email protected]> Fri, 11 Nov 2011 10:25:39 +0100 + +biomaj (1.2.0-1) unstable; urgency=low + + * New upstream release with new features and bug fixes. + * Change in database model, migration script ran at install + * New post processes added in default install (emboss) + + -- Olivier Sallou <[email protected]> Thu, 18 Aug 2011 09:55:23 +0200 + +biomaj (1.1.0-3) unstable; urgency=low + + * Change priority in debconf message for jdk home + * Add spanish translation of debconf: + Thanks to Camaleón <[email protected]> + Closes: #632952 + * Add sweden translation of debconf: + Thanks to Martin Bagge <[email protected]> + Closes: #628927 + * Add german translation of debconf: + Thanks to Chris Leick <[email protected]> + Closes: #629455 + * Change openjdk dependency to add default-jdk and sun jdk possible depends + Closes: #633523 + + -- Olivier Sallou <[email protected]> Thu, 11 Jul 2011 09:55:23 +0200 + +biomaj (1.1.0-2) unstable; urgency=low + + * Add russian translation of debconf: + Thanks to Yuri Kozlov <[email protected]> + Closes: #623807 + * debian/patches/fix623558_remove_pid: + Remove unnecessary pid file creation + Closes: #623558 + * debian/postrm,debian/preinst: + Issue for smooth upgrade, require old package + removal then new package install + Closes: #624284 + + + -- Olivier Sallou <[email protected]> Fri, 22 Apr 2011 16:27:11 +0200 + +biomaj (1.1.0-1) unstable; urgency=low + + * Initial release (Closes: #609038) + First Debian package, fixed copyright file to list all licenses + + -- Olivier Sallou <[email protected]> Wed, 05 Jan 2011 10:39:00 +0100 Deleted: trunk/packages/biomaj/tags/1.2.2-1/debian/control =================================================================== --- trunk/packages/biomaj/trunk/debian/control 2013-08-29 21:19:48 UTC (rev 14548) +++ trunk/packages/biomaj/tags/1.2.2-1/debian/control 2013-08-30 10:11:47 UTC (rev 14551) @@ -1,43 +0,0 @@ -Source: biomaj -Section: science -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Olivier Sallou <[email protected]> -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/biomaj/trunk/ -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biomaj/trunk/ -Homepage: http://biomaj.genouest.org -Build-Depends: debhelper (>= 7.1) -Build-Depends-Indep: debconf, po-debconf, default-jdk, ant, libhsqldb-java, ant-contrib, - liblog4j1.2-java, libcommons-net2-java, libcommons-dbcp-java, libgnumail-java, libcommons-pool-java, - libgnujaf-java, libjgoodies-forms-java (>= 1.3), liboro-java, libregexp-java, - libjcommon-java, libjsch-java, libjdom1-java, junit4, libsaxonb-java, libjdepend-java, - javahelper (>=0.25), libcommons-cli-java, libcommons-codec-java, libcommons-httpclient-java, libcommons-logging-java, - libjets3t-java -Standards-Version: 3.9.4 - -Package: biomaj -Architecture: all -Depends: ${misc:Depends}, ${java:Depends}, - default-jre | java6-runtime, ant (>= 1.9.1), libmysql-java, debconf, - libhsqldb-java,ant-contrib,liblog4j1.2-java,libcommons-net2-java (>= 2.2),libcommons-dbcp-java (>= 1.2), - libgnumail-java, libcommons-pool-java (>= 1.5), libgnujaf-java, libjgoodies-forms-java (>= 1.3), - liboro-java (>= 2.0),libregexp-java (>= 1.4),libjcommon-java (>= 1.0),libjsch-java (>= 0.1.42), - libjdom1-java (>= 1.1),junit4,libsaxonb-java (>= 0.9), libcommons-cli-java, libcommons-codec-java, - libcommons-httpclient-java, libcommons-logging-java,libjets3t-java, perl, - mysql-server -Suggests: ncbi-tools-bin, blast2 -Description: biological data-bank updater - BioMAJ downloads remote data banks, checks their status and applies - transformation workflows, with consistent state, to provide ready-to-use - data for biologists and bioinformaticians. For example, it can transform - original FASTA files into BLAST indexes. It is very flexible and its - post-processing facilities can be extended very easily. - -Package: biomaj-properties -Architecture: all -Depends: ${misc:Depends} -Description: biological data-bank updater - example properties files - This package contains a set of data bank properties files that can be - used as examples for BioMAJ. It contains descriptions for many existing - data banks with or without workflows to transform data. Some files may - require additional programs (such as BLAST) for post-processing. Copied: trunk/packages/biomaj/tags/1.2.2-1/debian/control (from rev 14550, trunk/packages/biomaj/trunk/debian/control) =================================================================== --- trunk/packages/biomaj/tags/1.2.2-1/debian/control (rev 0) +++ trunk/packages/biomaj/tags/1.2.2-1/debian/control 2013-08-30 10:11:47 UTC (rev 14551) @@ -0,0 +1,43 @@ +Source: biomaj +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/biomaj/trunk/ +Vcs-Browser: http://anonsvn.debian.org/viewvc/debian-med/trunk/packages/biomaj/trunk/ +Homepage: http://biomaj.genouest.org +Build-Depends: debhelper (>= 7.1) +Build-Depends-Indep: debconf, po-debconf, default-jdk, ant, libhsqldb-java, ant-contrib, + liblog4j1.2-java, libcommons-net2-java, libcommons-dbcp-java, libgnumail-java, libcommons-pool-java, + libgnujaf-java, libjgoodies-forms-java (>= 1.3), liboro-java, libregexp-java, + libjcommon-java, libjsch-java, libjdom1-java, junit4, libsaxonb-java, libjdepend-java, + javahelper (>=0.25), libcommons-cli-java, libcommons-codec-java, libcommons-httpclient-java, libcommons-logging-java, + libjets3t-java +Standards-Version: 3.9.4 + +Package: biomaj +Architecture: all +Depends: ${misc:Depends}, ${java:Depends}, + default-jre | java6-runtime, ant (>= 1.9.1), libmysql-java, debconf, + libhsqldb-java,ant-contrib,liblog4j1.2-java,libcommons-net2-java (>= 2.2),libcommons-dbcp-java (>= 1.2), + libgnumail-java, libcommons-pool-java (>= 1.5), libgnujaf-java, libjgoodies-forms-java (>= 1.3), + liboro-java (>= 2.0),libregexp-java (>= 1.4),libjcommon-java (>= 1.0),libjsch-java (>= 0.1.42), + libjdom1-java (>= 1.1),junit4,libsaxonb-java (>= 0.9), libcommons-cli-java, libcommons-codec-java, + libcommons-httpclient-java, libcommons-logging-java,libjets3t-java, perl, + mysql-server +Suggests: ncbi-tools-bin, blast2 +Description: biological data-bank updater + BioMAJ downloads remote data banks, checks their status and applies + transformation workflows, with consistent state, to provide ready-to-use + data for biologists and bioinformaticians. For example, it can transform + original FASTA files into BLAST indexes. It is very flexible and its + post-processing facilities can be extended very easily. + +Package: biomaj-properties +Architecture: all +Depends: ${misc:Depends} +Description: biological data-bank updater - example properties files + This package contains a set of data bank properties files that can be + used as examples for BioMAJ. It contains descriptions for many existing + data banks with or without workflows to transform data. Some files may + require additional programs (such as BLAST) for post-processing. Deleted: trunk/packages/biomaj/tags/1.2.2-1/debian/patches/fix_ant_propertie_format =================================================================== --- trunk/packages/biomaj/trunk/debian/patches/fix_ant_propertie_format 2013-08-29 21:19:48 UTC (rev 14548) +++ trunk/packages/biomaj/tags/1.2.2-1/debian/patches/fix_ant_propertie_format 2013-08-30 10:11:47 UTC (rev 14551) @@ -1,32 +0,0 @@ -Subject: ant API change -Description: ant > 1.9 update the getProperties() method - to return a different type (Object instead of String). - this patch modifies the method to manage objects. -Author: Olivier Sallou <[email protected]> -Forwarded: yes -Bug: 15914 ---- a/usr/share/biomaj/src/org/inria/biomaj/exe/bank/BankFactory.java -+++ b/usr/share/biomaj/src/org/inria/biomaj/exe/bank/BankFactory.java -@@ -384,7 +384,7 @@ - return value; - } - -- public static String getRecursiveProperty(Hashtable<String, String> prop,String keyOrigine) throws BiomajException { -+ public static String getRecursiveProperty(Hashtable<String, Object> prop,String keyOrigine) throws BiomajException { - - if ((prop == null)||(keyOrigine == null)) - throw new BiomajException("error.dev","Properties data are not set."); -@@ -392,11 +392,11 @@ - if (!prop.containsKey(keyOrigine)) { - String name = ""; - if (prop.containsKey(BiomajConst.dbNameProperty)) -- name = prop.get(BiomajConst.dbNameProperty); -+ name = (String) prop.get(BiomajConst.dbNameProperty); - throw new BiomajException("biomaj.property.define.error",name,keyOrigine); - } - -- String value = prop.get(keyOrigine); -+ String value = (String) prop.get(keyOrigine); - - - if (value.startsWith("${")) Deleted: trunk/packages/biomaj/tags/1.2.2-1/debian/patches/series =================================================================== --- trunk/packages/biomaj/trunk/debian/patches/series 2013-08-29 21:19:48 UTC (rev 14548) +++ trunk/packages/biomaj/tags/1.2.2-1/debian/patches/series 2013-08-30 10:11:47 UTC (rev 14551) @@ -1,4 +0,0 @@ -removeSqlToolDependency -set_env_file_for_debian -useFormSpecs_from_jgoodies -fix_ant_propertie_format Copied: trunk/packages/biomaj/tags/1.2.2-1/debian/patches/series (from rev 14549, trunk/packages/biomaj/trunk/debian/patches/series) =================================================================== --- trunk/packages/biomaj/tags/1.2.2-1/debian/patches/series (rev 0) +++ trunk/packages/biomaj/tags/1.2.2-1/debian/patches/series 2013-08-30 10:11:47 UTC (rev 14551) @@ -0,0 +1,3 @@ +removeSqlToolDependency +set_env_file_for_debian +useFormSpecs_from_jgoodies _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
