[med-svn] r18328 - in trunk/packages/biomaj/tags: . 1.2.3-4/debian 1.2.3-4/debian/patches
Emmanuel Bourg
ebourg-guest at moszumanska.debian.org
Fri Oct 17 11:16:17 UTC 2014
Author: ebourg-guest
Date: 2014-10-17 11:16:17 +0000 (Fri, 17 Oct 2014)
New Revision: 18328
Added:
trunk/packages/biomaj/tags/1.2.3-4/
trunk/packages/biomaj/tags/1.2.3-4/debian/changelog
trunk/packages/biomaj/tags/1.2.3-4/debian/compat
trunk/packages/biomaj/tags/1.2.3-4/debian/control
trunk/packages/biomaj/tags/1.2.3-4/debian/copyright
trunk/packages/biomaj/tags/1.2.3-4/debian/patches/javamail.patch
trunk/packages/biomaj/tags/1.2.3-4/debian/patches/series
Removed:
trunk/packages/biomaj/tags/1.2.3-4/debian/changelog
trunk/packages/biomaj/tags/1.2.3-4/debian/compat
trunk/packages/biomaj/tags/1.2.3-4/debian/control
trunk/packages/biomaj/tags/1.2.3-4/debian/copyright
trunk/packages/biomaj/tags/1.2.3-4/debian/patches/series
Log:
[svn-buildpackage] Tagging biomaj 1.2.3-4
Deleted: trunk/packages/biomaj/tags/1.2.3-4/debian/changelog
===================================================================
--- trunk/packages/biomaj/trunk/debian/changelog 2014-10-16 20:31:48 UTC (rev 18323)
+++ trunk/packages/biomaj/tags/1.2.3-4/debian/changelog 2014-10-17 11:16:17 UTC (rev 18328)
@@ -1,197 +0,0 @@
-biomaj (1.2.3-3) unstable; urgency=low
-
- * d/control: remove dependency on mysql-server but rather set it
- to mysql-client as server can be remote.
-
- -- Olivier Sallou <osallou at debian.org> Sun, 10 Nov 2013 09:00:17 +0100
-
-biomaj (1.2.3-2) unstable; urgency=low
-
- * d/control: Fix browse url for svn
- d/config: Fix test for non-interactive mode
-
- -- Olivier Sallou <osallou at debian.org> Wed, 06 Nov 2013 09:51:55 +0100
-
-biomaj (1.2.3-1) unstable; urgency=low
-
- * New upstream release (fixes on local storage and stage option).
-
- -- Olivier Sallou <osallou at debian.org> Wed, 30 Oct 2013 15:34:34 +0100
-
-biomaj (1.2.2-2) unstable; urgency=low
-
- * d/postinst: Fix install in noninteractive mode (Closes: #721773).
-
- -- Olivier Sallou <osallou at debian.org> Fri, 30 Aug 2013 12:11:50 +0200
-
-biomaj (1.2.2-1) unstable; urgency=low
-
- * New upstream release with minor fixes
- d/patches/series: upstream bug 15914 fixed.
-
- -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> 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 <victory.deb at gmail.com>
-
- -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> Wed, 01 Aug 2012 15:59:55 +0200
-
-biomaj (1.2.0-7) unstable; urgency=low
-
- [ Olivier Sallou ]
- Patch from James Page <james.page at ubuntu.com> (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 <osallou at debian.org> 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 <osallou at debian.org> 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 <olivier.sallou at irisa.fr> 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 <olivier.sallou at irisa.fr> 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 <p.m42.ribeiro at gmail.com>
-
- -- Olivier Sallou <olivier.sallou at irisa.fr> Fri, 16 Dec 2011 09:25:22 +0100
-
-biomaj (1.2.0-2) unstable; urgency=low
-
- * Fix Mysql dependency name.
-
- -- Olivier Sallou <olivier.sallou at irisa.fr> 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 <olivier.sallou at irisa.fr> 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 <noelamac at gmail.com>
- Closes: #632952
- * Add sweden translation of debconf:
- Thanks to Martin Bagge <brother at bsnet.se>
- Closes: #628927
- * Add german translation of debconf:
- Thanks to Chris Leick <c.leick at vollbio.de>
- Closes: #629455
- * Change openjdk dependency to add default-jdk and sun jdk possible depends
- Closes: #633523
-
- -- Olivier Sallou <olivier.sallou at irisa.fr> 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 <yuray at komyakino.ru>
- 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 <olivier.sallou at irisa.fr> 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 <olivier.sallou at irisa.fr> Wed, 05 Jan 2011 10:39:00 +0100
Copied: trunk/packages/biomaj/tags/1.2.3-4/debian/changelog (from rev 18327, trunk/packages/biomaj/trunk/debian/changelog)
===================================================================
--- trunk/packages/biomaj/tags/1.2.3-4/debian/changelog (rev 0)
+++ trunk/packages/biomaj/tags/1.2.3-4/debian/changelog 2014-10-17 11:16:17 UTC (rev 18328)
@@ -0,0 +1,209 @@
+biomaj (1.2.3-4) unstable; urgency=medium
+
+ * Team upload.
+ * Replaced the dependency on libgnumail-java with libmail-java
+ * Standards-Version updated to 3.9.6 (no changes)
+ * Switch to debhelper level 9
+ * debian/copyright:
+ - Fixed the short name for the BSD license
+ - Reordered the paragraphs to avoid a Lintian warning about unsued files
+
+ -- Emmanuel Bourg <ebourg at apache.org> Fri, 17 Oct 2014 11:52:38 +0200
+
+biomaj (1.2.3-3) unstable; urgency=low
+
+ * d/control: remove dependency on mysql-server but rather set it
+ to mysql-client as server can be remote.
+
+ -- Olivier Sallou <osallou at debian.org> Sun, 10 Nov 2013 09:00:17 +0100
+
+biomaj (1.2.3-2) unstable; urgency=low
+
+ * d/control: Fix browse url for svn
+ d/config: Fix test for non-interactive mode
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 06 Nov 2013 09:51:55 +0100
+
+biomaj (1.2.3-1) unstable; urgency=low
+
+ * New upstream release (fixes on local storage and stage option).
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 30 Oct 2013 15:34:34 +0100
+
+biomaj (1.2.2-2) unstable; urgency=low
+
+ * d/postinst: Fix install in noninteractive mode (Closes: #721773).
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 30 Aug 2013 12:11:50 +0200
+
+biomaj (1.2.2-1) unstable; urgency=low
+
+ * New upstream release with minor fixes
+ d/patches/series: upstream bug 15914 fixed.
+
+ -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> 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 <victory.deb at gmail.com>
+
+ -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> Wed, 01 Aug 2012 15:59:55 +0200
+
+biomaj (1.2.0-7) unstable; urgency=low
+
+ [ Olivier Sallou ]
+ Patch from James Page <james.page at ubuntu.com> (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 <osallou at debian.org> 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 <osallou at debian.org> 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 <olivier.sallou at irisa.fr> 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 <olivier.sallou at irisa.fr> 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 <p.m42.ribeiro at gmail.com>
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Fri, 16 Dec 2011 09:25:22 +0100
+
+biomaj (1.2.0-2) unstable; urgency=low
+
+ * Fix Mysql dependency name.
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> 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 <olivier.sallou at irisa.fr> 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 <noelamac at gmail.com>
+ Closes: #632952
+ * Add sweden translation of debconf:
+ Thanks to Martin Bagge <brother at bsnet.se>
+ Closes: #628927
+ * Add german translation of debconf:
+ Thanks to Chris Leick <c.leick at vollbio.de>
+ Closes: #629455
+ * Change openjdk dependency to add default-jdk and sun jdk possible depends
+ Closes: #633523
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> 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 <yuray at komyakino.ru>
+ 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 <olivier.sallou at irisa.fr> 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 <olivier.sallou at irisa.fr> Wed, 05 Jan 2011 10:39:00 +0100
Deleted: trunk/packages/biomaj/tags/1.2.3-4/debian/compat
===================================================================
--- trunk/packages/biomaj/trunk/debian/compat 2014-10-16 20:31:48 UTC (rev 18323)
+++ trunk/packages/biomaj/tags/1.2.3-4/debian/compat 2014-10-17 11:16:17 UTC (rev 18328)
@@ -1 +0,0 @@
-7
Copied: trunk/packages/biomaj/tags/1.2.3-4/debian/compat (from rev 18324, trunk/packages/biomaj/trunk/debian/compat)
===================================================================
--- trunk/packages/biomaj/tags/1.2.3-4/debian/compat (rev 0)
+++ trunk/packages/biomaj/tags/1.2.3-4/debian/compat 2014-10-17 11:16:17 UTC (rev 18328)
@@ -0,0 +1 @@
+9
Deleted: trunk/packages/biomaj/tags/1.2.3-4/debian/control
===================================================================
--- trunk/packages/biomaj/trunk/debian/control 2014-10-16 20:31:48 UTC (rev 18323)
+++ trunk/packages/biomaj/tags/1.2.3-4/debian/control 2014-10-17 11:16:17 UTC (rev 18328)
@@ -1,43 +0,0 @@
-Source: biomaj
-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/biomaj/trunk/
-Vcs-Browser: http://anonscm.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-client
-Suggests: ncbi-tools-bin, blast2, mysql-server
-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/1.2.3-4/debian/control (from rev 18326, trunk/packages/biomaj/trunk/debian/control)
===================================================================
--- trunk/packages/biomaj/tags/1.2.3-4/debian/control (rev 0)
+++ trunk/packages/biomaj/tags/1.2.3-4/debian/control 2014-10-17 11:16:17 UTC (rev 18328)
@@ -0,0 +1,83 @@
+Source: biomaj
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Build-Depends: debhelper (>= 9)
+Build-Depends-Indep: ant,
+ ant-contrib,
+ debconf,
+ default-jdk,
+ javahelper (>=0.25),
+ junit4,
+ libcommons-cli-java,
+ libcommons-codec-java,
+ libcommons-dbcp-java,
+ libcommons-httpclient-java,
+ libcommons-logging-java,
+ libcommons-net2-java,
+ libcommons-pool-java,
+ libmail-java,
+ libhsqldb-java,
+ libjcommon-java,
+ libjdepend-java,
+ libjdom1-java,
+ libjets3t-java,
+ libjgoodies-forms-java (>= 1.3),
+ libjsch-java,
+ liblog4j1.2-java,
+ liboro-java,
+ libregexp-java,
+ libsaxonb-java,
+ po-debconf
+Standards-Version: 3.9.6
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biomaj/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biomaj/trunk/
+Homepage: http://biomaj.genouest.org
+
+Package: biomaj
+Architecture: all
+Depends: ant (>= 1.9.1),
+ ant-contrib,
+ debconf,
+ default-jre | java6-runtime,
+ junit4,
+ libcommons-cli-java,
+ libcommons-codec-java,
+ libcommons-dbcp-java (>= 1.2),
+ libcommons-httpclient-java,
+ libcommons-logging-java,
+ libcommons-net2-java (>= 2.2),
+ libcommons-pool-java (>= 1.5),
+ libmail-java,
+ libhsqldb-java,
+ libjcommon-java (>= 1.0),
+ libjdom1-java (>= 1.1),
+ libjets3t-java,
+ libjgoodies-forms-java (>= 1.3),
+ libjsch-java (>= 0.1.42),
+ liblog4j1.2-java,
+ libmysql-java,
+ liboro-java (>= 2.0),
+ libregexp-java (>= 1.4),
+ libsaxonb-java (>= 0.9),
+ mysql-client,
+ perl,
+ ${java:Depends},
+ ${misc:Depends}
+Suggests: blast2, mysql-server, ncbi-tools-bin
+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/1.2.3-4/debian/copyright
===================================================================
--- trunk/packages/biomaj/trunk/debian/copyright 2014-10-16 20:31:48 UTC (rev 18323)
+++ trunk/packages/biomaj/tags/1.2.3-4/debian/copyright 2014-10-17 11:16:17 UTC (rev 18328)
@@ -1,1058 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: BioMAJ
-Source: svn://scm.gforge.inria.fr/svn/biomaj/
-
-Files: debian/*
-Copyright: 2011 Olivier Sallou <olivier.sallou at irisa.fr>
-License: GPL-3
- On Debian systems, the full text of the GNU General Public
- License version 3 can be found in the file
- `/usr/share/common-licenses/GPL-3'.
-
-Files: usr/share/biomaj/workflows/mirror.xml usr/share/biomaj/src/org/gmod/biomaj/ant/conditions/DirectoryHasFilesCondition.java usr/share/biomaj/src/org/gmod/biomaj/ant/task/SymlinkList.java usr/share/biomaj/src/org/gmod/biomaj/ant/task/net/FileCheck.java usr/share/biomaj/src/org/gmod/biomaj/ant/task/net/FtpListingParser.java usr/share/biomaj/src/org/gmod/ant/selectors/FilenamePatternSelector.java usr/share/biomaj/build.xml
-Copyright: 2004 Indiana University
-License: BSD
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- 1. Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- 2. Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
- 3. Neither the name of the University nor the names of its contributors
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- .
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- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
- OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
- OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- SUCH DAMAGE.
-
-Files: *
-Copyright: 2011 GenOuest Platform <support at genouest.org>
-License: CeCILL
- Notice
- .
- This Agreement is a Free Software license agreement that is the result
- of discussions between its authors in order to ensure compliance with
- the two main principles guiding its drafting:
- .
- * firstly, compliance with the principles governing the distribution
- of Free Software: access to source code, broad rights granted to
- users,
- * secondly, the election of a governing law, French law, with which
- it is conformant, both as regards the law of torts and
- intellectual property law, and the protection that it offers to
- both authors and holders of the economic rights over software.
- .
- The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
- license are:
- .
- Commissariat à l'Energie Atomique - CEA, a public scientific, technical
- and industrial research establishment, having its principal place of
- business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
- .
- Centre National de la Recherche Scientifique - CNRS, a public scientific
- and technological establishment, having its principal place of business
- at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
- .
- Institut National de Recherche en Informatique et en Automatique -
- INRIA, a public scientific and technological establishment, having its
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- and/or developing or reproducing the software by the user are brought to
- the user's attention, given its Free Software status, which may make it
- complicated to use, with the result that its use is reserved for
- developers and experienced professionals having in-depth computer
- knowledge. Users are therefore encouraged to load and test the
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- enabling the security of their systems and/or data to be ensured and,
- more generally, to use and operate it in the same conditions of
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- removed herefrom.
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- This Agreement may apply to any or all software for which the holder of
- the economic rights decides to submit the use thereof to its provisions.
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- and that, in the event that only the object code of the Modified
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- 5.3.3 DISTRIBUTION OF EXTERNAL MODULES
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- 5.3.4 COMPATIBILITY WITH THE GNU GPL
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- The Licensee can include a code that is subject to the provisions of one
- of the versions of the GNU GPL in the Modified or unmodified Software,
- and distribute that entire code under the terms of the same version of
- the GNU GPL.
- .
- The Licensee can include the Modified or unmodified Software in a code
- that is subject to the provisions of one of the versions of the GNU GPL,
- and distribute that entire code under the terms of the same version of
- the GNU GPL.
- .
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- Article 6 - INTELLECTUAL PROPERTY
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- .
- 6.1 OVER THE INITIAL SOFTWARE
- .
- The Holder owns the economic rights over the Initial Software. Any or
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- govern its distribution.
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- Article 7 - RELATED SERVICES
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- .
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- Article 9 - WARRANTY
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- state-of-the-art when the Software was distributed did not enable all
- possible uses to be tested and verified, nor for the presence of
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- are deemed authentic.
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- Article 12 - NEW VERSIONS OF THE AGREEMENT
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- Agreement.
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- .
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- Article 13 - GOVERNING LAW AND JURISDICTION
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- jurisdiction, by the more diligent Party.
- .
- .
- Version 2.0 dated 2006-09-05.
-
-Files: usr/share/biomaj/workflows/*
-Copyright: 2011 INRIA/INRA
-License: CeCILL-B
- Notice
- .
- This Agreement is a Free Software license agreement that is the result
- of discussions between its authors in order to ensure compliance with
- the two main principles guiding its drafting:
- .
- * firstly, compliance with the principles governing the distribution
- of Free Software: access to source code, broad rights granted to
- users,
- * secondly, the election of a governing law, French law, with which
- it is conformant, both as regards the law of torts and
- intellectual property law, and the protection that it offers to
- both authors and holders of the economic rights over software.
- .
- The authors of the CeCILL-B (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
- license are:
- .
- Commissariat à l'Energie Atomique - CEA, a public scientific, technical
- and industrial research establishment, having its principal place of
- business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
- .
- Centre National de la Recherche Scientifique - CNRS, a public scientific
- and technological establishment, having its principal place of business
- at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
- .
- Institut National de Recherche en Informatique et en Automatique -
- INRIA, a public scientific and technological establishment, having its
- principal place of business at Domaine de Voluceau, Rocquencourt, BP
- 105, 78153 Le Chesnay cedex, France.
- .
- .
- Preamble
- .
- This Agreement is an open source software license intended to give users
- significant freedom to modify and redistribute the software licensed
- hereunder.
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- of giving credits for everybody that distributes a software
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- contributions to be properly identified and acknowledged.
- .
- In consideration of access to the source code and the rights to copy,
- modify and redistribute granted by the license, users are provided only
- with a limited warranty and the software's author, the holder of the
- economic rights, and the successive licensors only have limited liability.
- .
- In this respect, the risks associated with loading, using, modifying
- and/or developing or reproducing the software by the user are brought to
- the user's attention, given its Free Software status, which may make it
- complicated to use, with the result that its use is reserved for
- developers and experienced professionals having in-depth computer
- knowledge. Users are therefore encouraged to load and test the
- suitability of the software as regards their requirements in conditions
- enabling the security of their systems and/or data to be ensured and,
- more generally, to use and operate it in the same conditions of
- security. This Agreement may be freely reproduced and published,
- provided it is not altered, and that no provisions are either added or
- removed herefrom.
- .
- This Agreement may apply to any or all software for which the holder of
- the economic rights decides to submit the use thereof to its provisions.
- .
- .
- Article 1 - DEFINITIONS
- .
- For the purpose of this Agreement, when the following expressions
- commence with a capital letter, they shall have the following meaning:
- .
- Agreement: means this license agreement, and its possible subsequent
- versions and annexes.
- .
- Software: means the software in its Object Code and/or Source Code form
- and, where applicable, its documentation, "as is" when the Licensee
- accepts the Agreement.
- .
- Initial Software: means the Software in its Source Code and possibly its
- Object Code form and, where applicable, its documentation, "as is" when
- it is first distributed under the terms and conditions of the Agreement.
- .
- Modified Software: means the Software modified by at least one
- Contribution.
- .
- Source Code: means all the Software's instructions and program lines to
- which access is required so as to modify the Software.
- .
- Object Code: means the binary files originating from the compilation of
- the Source Code.
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- Holder: means the holder(s) of the economic rights over the Initial
- Software.
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- adaptations and/or new functions integrated into the Software by any or
- all Contributors, as well as any or all Internal Modules.
- .
- Module: means a set of sources files including their documentation that
- enables supplementary functions or services in addition to those offered
- by the Software.
- .
- External Module: means any or all Modules, not derived from the
- Software, so that this Module and the Software run in separate address
- spaces, with one calling the other when they are run.
- .
- Internal Module: means any or all Module, connected to the Software so
- that they both execute in the same address space.
- .
- Parties: mean both the Licensee and the Licensor.
- .
- These expressions may be used both in singular and plural form.
- .
- .
- Article 2 - PURPOSE
- .
- The purpose of the Agreement is the grant by the Licensor to the
- Licensee of a non-exclusive, transferable and worldwide license for the
- Software as set forth in Article 5 hereinafter for the whole term of the
- protection granted by the rights over said Software.
- .
- .
- Article 3 - ACCEPTANCE
- .
- 3.1 The Licensee shall be deemed as having accepted the terms and
- conditions of this Agreement upon the occurrence of the first of the
- following events:
- .
- * (i) loading the Software by any or all means, notably, by
- downloading from a remote server, or by loading from a physical
- medium;
- * (ii) the first time the Licensee exercises any of the rights
- granted hereunder.
- .
- 3.2 One copy of the Agreement, containing a notice relating to the
- characteristics of the Software, to the limited warranty, and to the
- fact that its use is restricted to experienced users has been provided
- to the Licensee prior to its acceptance as set forth in Article 3.1
- hereinabove, and the Licensee hereby acknowledges that it has read and
- understood it.
- .
- .
- Article 4 - EFFECTIVE DATE AND TERM
- .
- .
- 4.1 EFFECTIVE DATE
- .
- The Agreement shall become effective on the date when it is accepted by
- the Licensee as set forth in Article 3.1.
- .
- .
- 4.2 TERM
- .
- The Agreement shall remain in force for the entire legal term of
- protection of the economic rights over the Software.
- .
- .
- Article 5 - SCOPE OF RIGHTS GRANTED
- .
- The Licensor hereby grants to the Licensee, who accepts, the following
- rights over the Software for any or all use, and for the term of the
- Agreement, on the basis of the terms and conditions set forth hereinafter.
- .
- Besides, if the Licensor owns or comes to own one or more patents
- protecting all or part of the functions of the Software or of its
- components, the Licensor undertakes not to enforce the rights granted by
- these patents against successive Licensees using, exploiting or
- modifying the Software. If these patents are transferred, the Licensor
- undertakes to have the transferees subscribe to the obligations set
- forth in this paragraph.
- .
- .
- 5.1 RIGHT OF USE
- .
- The Licensee is authorized to use the Software, without any limitation
- as to its fields of application, with it being hereinafter specified
- that this comprises:
- .
- 1. permanent or temporary reproduction of all or part of the Software
- by any or all means and in any or all form.
- .
- 2. loading, displaying, running, or storing the Software on any or
- all medium.
- .
- 3. entitlement to observe, study or test its operation so as to
- determine the ideas and principles behind any or all constituent
- elements of said Software. This shall apply when the Licensee
- carries out any or all loading, displaying, running, transmission
- or storage operation as regards the Software, that it is entitled
- to carry out hereunder.
- .
- .
- 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
- .
- The right to make Contributions includes the right to translate, adapt,
- arrange, or make any or all modifications to the Software, and the right
- to reproduce the resulting software.
- .
- The Licensee is authorized to make any or all Contributions to the
- Software provided that it includes an explicit notice that it is the
- author of said Contribution and indicates the date of the creation thereof.
- .
- .
- 5.3 RIGHT OF DISTRIBUTION
- .
- In particular, the right of distribution includes the right to publish,
- transmit and communicate the Software to the general public on any or
- all medium, and by any or all means, and the right to market, either in
- consideration of a fee, or free of charge, one or more copies of the
- Software by any means.
- .
- The Licensee is further authorized to distribute copies of the modified
- or unmodified Software to third parties according to the terms and
- conditions set forth hereinafter.
- .
- .
- 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
- .
- The Licensee is authorized to distribute true copies of the Software in
- Source Code or Object Code form, provided that said distribution
- complies with all the provisions of the Agreement and is accompanied by:
- .
- 1. a copy of the Agreement,
- .
- 2. a notice relating to the limitation of both the Licensor's
- warranty and liability as set forth in Articles 8 and 9,
- .
- and that, in the event that only the Object Code of the Software is
- redistributed, the Licensee allows effective access to the full Source
- Code of the Software at a minimum during the entire period of its
- distribution of the Software, it being understood that the additional
- cost of acquiring the Source Code shall not exceed the cost of
- transferring the data.
- .
- .
- 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
- .
- If the Licensee makes any Contribution to the Software, the resulting
- Modified Software may be distributed under a license agreement other
- than this Agreement subject to compliance with the provisions of Article
- 5.3.4.
- .
- .
- 5.3.3 DISTRIBUTION OF EXTERNAL MODULES
- .
- When the Licensee has developed an External Module, the terms and
- conditions of this Agreement do not apply to said External Module, that
- may be distributed under a separate license agreement.
- .
- .
- 5.3.4 CREDITS
- .
- Any Licensee who may distribute a Modified Software hereby expressly
- agrees to:
- .
- 1. indicate in the related documentation that it is based on the
- Software licensed hereunder, and reproduce the intellectual
- property notice for the Software,
- .
- 2. ensure that written indications of the Software intended use,
- intellectual property notice and license hereunder are included in
- easily accessible format from the Modified Software interface,
- .
- 3. mention, on a freely accessible website describing the Modified
- Software, at least throughout the distribution term thereof, that
- it is based on the Software licensed hereunder, and reproduce the
- Software intellectual property notice,
- .
- 4. where it is distributed to a third party that may distribute a
- Modified Software without having to make its source code
- available, make its best efforts to ensure that said third party
- agrees to comply with the obligations set forth in this Article .
- .
- If the Software, whether or not modified, is distributed with an
- External Module designed for use in connection with the Software, the
- Licensee shall submit said External Module to the foregoing obligations.
- .
- .
- 5.3.5 COMPATIBILITY WITH THE CeCILL AND CeCILL-C LICENSES
- .
- Where a Modified Software contains a Contribution subject to the CeCILL
- license, the provisions set forth in Article 5.3.4 shall be optional.
- .
- A Modified Software may be distributed under the CeCILL-C license. In
- such a case the provisions set forth in Article 5.3.4 shall be optional.
- .
- .
- Article 6 - INTELLECTUAL PROPERTY
- .
- .
- 6.1 OVER THE INITIAL SOFTWARE
- .
- The Holder owns the economic rights over the Initial Software. Any or
- all use of the Initial Software is subject to compliance with the terms
- and conditions under which the Holder has elected to distribute its work
- and no one shall be entitled to modify the terms and conditions for the
- distribution of said Initial Software.
- .
- The Holder undertakes that the Initial Software will remain ruled at
- least by this Agreement, for the duration set forth in Article 4.2.
- .
- .
- 6.2 OVER THE CONTRIBUTIONS
- .
- The Licensee who develops a Contribution is the owner of the
- intellectual property rights over this Contribution as defined by
- applicable law.
- .
- .
- 6.3 OVER THE EXTERNAL MODULES
- .
- The Licensee who develops an External Module is the owner of the
- intellectual property rights over this External Module as defined by
- applicable law and is free to choose the type of agreement that shall
- govern its distribution.
- .
- .
- 6.4 JOINT PROVISIONS
- .
- The Licensee expressly undertakes:
- .
- 1. not to remove, or modify, in any manner, the intellectual property
- notices attached to the Software;
- .
- 2. to reproduce said notices, in an identical manner, in the copies
- of the Software modified or not.
- .
- The Licensee undertakes not to directly or indirectly infringe the
- intellectual property rights of the Holder and/or Contributors on the
- Software and to take, where applicable, vis-à-vis its staff, any and all
- measures required to ensure respect of said intellectual property rights
- of the Holder and/or Contributors.
- .
- .
- Article 7 - RELATED SERVICES
- .
- 7.1 Under no circumstances shall the Agreement oblige the Licensor to
- provide technical assistance or maintenance services for the Software.
- .
- However, the Licensor is entitled to offer this type of services. The
- terms and conditions of such technical assistance, and/or such
- maintenance, shall be set forth in a separate instrument. Only the
- Licensor offering said maintenance and/or technical assistance services
- shall incur liability therefor.
- .
- 7.2 Similarly, any Licensor is entitled to offer to its licensees, under
- its sole responsibility, a warranty, that shall only be binding upon
- itself, for the redistribution of the Software and/or the Modified
- Software, under terms and conditions that it is free to decide. Said
- warranty, and the financial terms and conditions of its application,
- shall be subject of a separate instrument executed between the Licensor
- and the Licensee.
- .
- .
- Article 8 - LIABILITY
- .
- 8.1 Subject to the provisions of Article 8.2, the Licensee shall be
- entitled to claim compensation for any direct loss it may have suffered
- from the Software as a result of a fault on the part of the relevant
- Licensor, subject to providing evidence thereof.
- .
- 8.2 The Licensor's liability is limited to the commitments made under
- this Agreement and shall not be incurred as a result of in particular:
- (i) loss due the Licensee's total or partial failure to fulfill its
- obligations, (ii) direct or consequential loss that is suffered by the
- Licensee due to the use or performance of the Software, and (iii) more
- generally, any consequential loss. In particular the Parties expressly
- agree that any or all pecuniary or business loss (i.e. loss of data,
- loss of profits, operating loss, loss of customers or orders,
- opportunity cost, any disturbance to business activities) or any or all
- legal proceedings instituted against the Licensee by a third party,
- shall constitute consequential loss and shall not provide entitlement to
- any or all compensation from the Licensor.
- .
- .
- Article 9 - WARRANTY
- .
- 9.1 The Licensee acknowledges that the scientific and technical
- state-of-the-art when the Software was distributed did not enable all
- possible uses to be tested and verified, nor for the presence of
- possible defects to be detected. In this respect, the Licensee's
- attention has been drawn to the risks associated with loading, using,
- modifying and/or developing and reproducing the Software which are
- reserved for experienced users.
- .
- The Licensee shall be responsible for verifying, by any or all means,
- the suitability of the product for its requirements, its good working
- order, and for ensuring that it shall not cause damage to either persons
- or properties.
- .
- 9.2 The Licensor hereby represents, in good faith, that it is entitled
- to grant all the rights over the Software (including in particular the
- rights set forth in Article 5).
- .
- 9.3 The Licensee acknowledges that the Software is supplied "as is" by
- the Licensor without any other express or tacit warranty, other than
- that provided for in Article 9.2 and, in particular, without any warranty
- as to its commercial value, its secured, safe, innovative or relevant
- nature.
- .
- Specifically, the Licensor does not warrant that the Software is free
- from any error, that it will operate without interruption, that it will
- be compatible with the Licensee's own equipment and software
- configuration, nor that it will meet the Licensee's requirements.
- .
- 9.4 The Licensor does not either expressly or tacitly warrant that the
- Software does not infringe any third party intellectual property right
- relating to a patent, software or any other property right. Therefore,
- the Licensor disclaims any and all liability towards the Licensee
- arising out of any or all proceedings for infringement that may be
- instituted in respect of the use, modification and redistribution of the
- Software. Nevertheless, should such proceedings be instituted against
- the Licensee, the Licensor shall provide it with technical and legal
- assistance for its defense. Such technical and legal assistance shall be
- decided on a case-by-case basis between the relevant Licensor and the
- Licensee pursuant to a memorandum of understanding. The Licensor
- disclaims any and all liability as regards the Licensee's use of the
- name of the Software. No warranty is given as regards the existence of
- prior rights over the name of the Software or as regards the existence
- of a trademark.
- .
- .
- Article 10 - TERMINATION
- .
- 10.1 In the event of a breach by the Licensee of its obligations
- hereunder, the Licensor may automatically terminate this Agreement
- thirty (30) days after notice has been sent to the Licensee and has
- remained ineffective.
- .
- 10.2 A Licensee whose Agreement is terminated shall no longer be
- authorized to use, modify or distribute the Software. However, any
- licenses that it may have granted prior to termination of the Agreement
- shall remain valid subject to their having been granted in compliance
- with the terms and conditions hereof.
- .
- .
- Article 11 - MISCELLANEOUS
- .
- .
- 11.1 EXCUSABLE EVENTS
- .
- Neither Party shall be liable for any or all delay, or failure to
- perform the Agreement, that may be attributable to an event of force
- majeure, an act of God or an outside cause, such as defective
- functioning or interruptions of the electricity or telecommunications
- networks, network paralysis following a virus attack, intervention by
- government authorities, natural disasters, water damage, earthquakes,
- fire, explosions, strikes and labor unrest, war, etc.
- .
- 11.2 Any failure by either Party, on one or more occasions, to invoke
- one or more of the provisions hereof, shall under no circumstances be
- interpreted as being a waiver by the interested Party of its right to
- invoke said provision(s) subsequently.
- .
- 11.3 The Agreement cancels and replaces any or all previous agreements,
- whether written or oral, between the Parties and having the same
- purpose, and constitutes the entirety of the agreement between said
- Parties concerning said purpose. No supplement or modification to the
- terms and conditions hereof shall be effective as between the Parties
- unless it is made in writing and signed by their duly authorized
- representatives.
- .
- 11.4 In the event that one or more of the provisions hereof were to
- conflict with a current or future applicable act or legislative text,
- said act or legislative text shall prevail, and the Parties shall make
- the necessary amendments so as to comply with said act or legislative
- text. All other provisions shall remain effective. Similarly, invalidity
- of a provision of the Agreement, for any reason whatsoever, shall not
- cause the Agreement as a whole to be invalid.
- .
- .
- 11.5 LANGUAGE
- .
- The Agreement is drafted in both French and English and both versions
- are deemed authentic.
- .
- .
- Article 12 - NEW VERSIONS OF THE AGREEMENT
- .
- 12.1 Any person is authorized to duplicate and distribute copies of this
- Agreement.
- .
- 12.2 So as to ensure coherence, the wording of this Agreement is
- protected and may only be modified by the authors of the License, who
- reserve the right to periodically publish updates or new versions of the
- Agreement, each with a separate number. These subsequent versions may
- address new issues encountered by Free Software.
- .
- 12.3 Any Software distributed under a given version of the Agreement may
- only be subsequently distributed under the same version of the Agreement
- or a subsequent version.
- .
- .
- Article 13 - GOVERNING LAW AND JURISDICTION
- .
- 13.1 The Agreement is governed by French law. The Parties agree to
- endeavor to seek an amicable solution to any disagreements or disputes
- that may arise during the performance of the Agreement.
- .
- 13.2 Failing an amicable solution within two (2) months as from their
- occurrence, and unless emergency proceedings are necessary, the
- disagreements or disputes shall be referred to the Paris Courts having
- jurisdiction, by the more diligent Party.
- .
- .
- Version 1.0 dated 2006-09-05.
Copied: trunk/packages/biomaj/tags/1.2.3-4/debian/copyright (from rev 18324, trunk/packages/biomaj/trunk/debian/copyright)
===================================================================
--- trunk/packages/biomaj/tags/1.2.3-4/debian/copyright (rev 0)
+++ trunk/packages/biomaj/tags/1.2.3-4/debian/copyright 2014-10-17 11:16:17 UTC (rev 18328)
@@ -0,0 +1,1065 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: BioMAJ
+Source: svn://scm.gforge.inria.fr/svn/biomaj/
+
+Files: *
+Copyright: 2011, GenOuest Platform <support at genouest.org>
+License: CeCILL
+
+Files: debian/*
+Copyright: 2011 Olivier Sallou <olivier.sallou at irisa.fr>
+License: GPL-3
+ On Debian systems, the full text of the GNU General Public
+ License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'.
+
+Files: usr/share/biomaj/workflows/mirror.xml
+ usr/share/biomaj/src/org/gmod/biomaj/ant/conditions/DirectoryHasFilesCondition.java
+ usr/share/biomaj/src/org/gmod/biomaj/ant/task/SymlinkList.java
+ usr/share/biomaj/src/org/gmod/biomaj/ant/task/net/FileCheck.java
+ usr/share/biomaj/src/org/gmod/biomaj/ant/task/net/FtpListingParser.java
+ usr/share/biomaj/src/org/gmod/ant/selectors/FilenamePatternSelector.java
+ usr/share/biomaj/build.xml
+Copyright: 2004 Indiana University
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ 3. Neither the name of the University nor the names of its contributors
+ may be used to endorse or promote products derived from this software
+ without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+License: CeCILL
+ Notice
+ .
+ This Agreement is a Free Software license agreement that is the result
+ of discussions between its authors in order to ensure compliance with
+ the two main principles guiding its drafting:
+ .
+ * firstly, compliance with the principles governing the distribution
+ of Free Software: access to source code, broad rights granted to
+ users,
+ * secondly, the election of a governing law, French law, with which
+ it is conformant, both as regards the law of torts and
+ intellectual property law, and the protection that it offers to
+ both authors and holders of the economic rights over software.
+ .
+ The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+ license are:
+ .
+ Commissariat à l'Energie Atomique - CEA, a public scientific, technical
+ and industrial research establishment, having its principal place of
+ business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
+ .
+ Centre National de la Recherche Scientifique - CNRS, a public scientific
+ and technological establishment, having its principal place of business
+ at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
+ .
+ Institut National de Recherche en Informatique et en Automatique -
+ INRIA, a public scientific and technological establishment, having its
+ principal place of business at Domaine de Voluceau, Rocquencourt, BP
+ 105, 78153 Le Chesnay cedex, France.
+ .
+ .
+ Preamble
+ .
+ The purpose of this Free Software license agreement is to grant users
+ the right to modify and redistribute the software governed by this
+ license within the framework of an open source distribution model.
+ .
+ The exercising of these rights is conditional upon certain obligations
+ for users so as to preserve this status for all subsequent redistributions.
+ .
+ In consideration of access to the source code and the rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors only have limited liability.
+ .
+ In this respect, the risks associated with loading, using, modifying
+ and/or developing or reproducing the software by the user are brought to
+ the user's attention, given its Free Software status, which may make it
+ complicated to use, with the result that its use is reserved for
+ developers and experienced professionals having in-depth computer
+ knowledge. Users are therefore encouraged to load and test the
+ suitability of the software as regards their requirements in conditions
+ enabling the security of their systems and/or data to be ensured and,
+ more generally, to use and operate it in the same conditions of
+ security. This Agreement may be freely reproduced and published,
+ provided it is not altered, and that no provisions are either added or
+ removed herefrom.
+ .
+ This Agreement may apply to any or all software for which the holder of
+ the economic rights decides to submit the use thereof to its provisions.
+ .
+ .
+ Article 1 - DEFINITIONS
+ .
+ For the purpose of this Agreement, when the following expressions
+ commence with a capital letter, they shall have the following meaning:
+ .
+ Agreement: means this license agreement, and its possible subsequent
+ versions and annexes.
+ .
+ Software: means the software in its Object Code and/or Source Code form
+ and, where applicable, its documentation, "as is" when the Licensee
+ accepts the Agreement.
+ .
+ Initial Software: means the Software in its Source Code and possibly its
+ Object Code form and, where applicable, its documentation, "as is" when
+ it is first distributed under the terms and conditions of the Agreement.
+ .
+ Modified Software: means the Software modified by at least one
+ Contribution.
+ .
+ Source Code: means all the Software's instructions and program lines to
+ which access is required so as to modify the Software.
+ .
+ Object Code: means the binary files originating from the compilation of
+ the Source Code.
+ .
+ Holder: means the holder(s) of the economic rights over the Initial
+ Software.
+ .
+ Licensee: means the Software user(s) having accepted the Agreement.
+ .
+ Contributor: means a Licensee having made at least one Contribution.
+ .
+ Licensor: means the Holder, or any other individual or legal entity, who
+ distributes the Software under the Agreement.
+ .
+ Contribution: means any or all modifications, corrections, translations,
+ adaptations and/or new functions integrated into the Software by any or
+ all Contributors, as well as any or all Internal Modules.
+ .
+ Module: means a set of sources files including their documentation that
+ enables supplementary functions or services in addition to those offered
+ by the Software.
+ .
+ External Module: means any or all Modules, not derived from the
+ Software, so that this Module and the Software run in separate address
+ spaces, with one calling the other when they are run.
+ .
+ Internal Module: means any or all Module, connected to the Software so
+ that they both execute in the same address space.
+ .
+ GNU GPL: means the GNU General Public License version 2 or any
+ subsequent version, as published by the Free Software Foundation Inc.
+ .
+ Parties: mean both the Licensee and the Licensor.
+ .
+ These expressions may be used both in singular and plural form.
+ .
+ .
+ Article 2 - PURPOSE
+ .
+ The purpose of the Agreement is the grant by the Licensor to the
+ Licensee of a non-exclusive, transferable and worldwide license for the
+ Software as set forth in Article 5 hereinafter for the whole term of the
+ protection granted by the rights over said Software.
+ .
+ .
+ Article 3 - ACCEPTANCE
+ .
+ 3.1 The Licensee shall be deemed as having accepted the terms and
+ conditions of this Agreement upon the occurrence of the first of the
+ following events:
+ .
+ * (i) loading the Software by any or all means, notably, by
+ downloading from a remote server, or by loading from a physical
+ medium;
+ * (ii) the first time the Licensee exercises any of the rights
+ granted hereunder.
+ .
+ 3.2 One copy of the Agreement, containing a notice relating to the
+ characteristics of the Software, to the limited warranty, and to the
+ fact that its use is restricted to experienced users has been provided
+ to the Licensee prior to its acceptance as set forth in Article 3.1
+ hereinabove, and the Licensee hereby acknowledges that it has read and
+ understood it.
+ .
+ .
+ Article 4 - EFFECTIVE DATE AND TERM
+ .
+ .
+ 4.1 EFFECTIVE DATE
+ .
+ The Agreement shall become effective on the date when it is accepted by
+ the Licensee as set forth in Article 3.1.
+ .
+ .
+ 4.2 TERM
+ .
+ The Agreement shall remain in force for the entire legal term of
+ protection of the economic rights over the Software.
+ .
+ .
+ Article 5 - SCOPE OF RIGHTS GRANTED
+ .
+ The Licensor hereby grants to the Licensee, who accepts, the following
+ rights over the Software for any or all use, and for the term of the
+ Agreement, on the basis of the terms and conditions set forth hereinafter.
+ .
+ Besides, if the Licensor owns or comes to own one or more patents
+ protecting all or part of the functions of the Software or of its
+ components, the Licensor undertakes not to enforce the rights granted by
+ these patents against successive Licensees using, exploiting or
+ modifying the Software. If these patents are transferred, the Licensor
+ undertakes to have the transferees subscribe to the obligations set
+ forth in this paragraph.
+ .
+ .
+ 5.1 RIGHT OF USE
+ .
+ The Licensee is authorized to use the Software, without any limitation
+ as to its fields of application, with it being hereinafter specified
+ that this comprises:
+ .
+ 1. permanent or temporary reproduction of all or part of the Software
+ by any or all means and in any or all form.
+ .
+ 2. loading, displaying, running, or storing the Software on any or
+ all medium.
+ .
+ 3. entitlement to observe, study or test its operation so as to
+ determine the ideas and principles behind any or all constituent
+ elements of said Software. This shall apply when the Licensee
+ carries out any or all loading, displaying, running, transmission
+ or storage operation as regards the Software, that it is entitled
+ to carry out hereunder.
+ .
+ .
+ 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+ .
+ The right to make Contributions includes the right to translate, adapt,
+ arrange, or make any or all modifications to the Software, and the right
+ to reproduce the resulting software.
+ .
+ The Licensee is authorized to make any or all Contributions to the
+ Software provided that it includes an explicit notice that it is the
+ author of said Contribution and indicates the date of the creation thereof.
+ .
+ .
+ 5.3 RIGHT OF DISTRIBUTION
+ .
+ In particular, the right of distribution includes the right to publish,
+ transmit and communicate the Software to the general public on any or
+ all medium, and by any or all means, and the right to market, either in
+ consideration of a fee, or free of charge, one or more copies of the
+ Software by any means.
+ .
+ The Licensee is further authorized to distribute copies of the modified
+ or unmodified Software to third parties according to the terms and
+ conditions set forth hereinafter.
+ .
+ .
+ 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+ .
+ The Licensee is authorized to distribute true copies of the Software in
+ Source Code or Object Code form, provided that said distribution
+ complies with all the provisions of the Agreement and is accompanied by:
+ .
+ 1. a copy of the Agreement,
+ .
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+ .
+ and that, in the event that only the Object Code of the Software is
+ redistributed, the Licensee allows future Licensees unhindered access to
+ the full Source Code of the Software by indicating how to access it, it
+ being understood that the additional cost of acquiring the Source Code
+ shall not exceed the cost of transferring the data.
+ .
+ .
+ 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+ .
+ When the Licensee makes a Contribution to the Software, the terms and
+ conditions for the distribution of the resulting Modified Software
+ become subject to all the provisions of this Agreement.
+ .
+ The Licensee is authorized to distribute the Modified Software, in
+ source code or object code form, provided that said distribution
+ complies with all the provisions of the Agreement and is accompanied by:
+ .
+ 1. a copy of the Agreement,
+ .
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+ .
+ and that, in the event that only the object code of the Modified
+ Software is redistributed, the Licensee allows future Licensees
+ unhindered access to the full source code of the Modified Software by
+ indicating how to access it, it being understood that the additional
+ cost of acquiring the source code shall not exceed the cost of
+ transferring the data.
+ .
+ .
+ 5.3.3 DISTRIBUTION OF EXTERNAL MODULES
+ .
+ When the Licensee has developed an External Module, the terms and
+ conditions of this Agreement do not apply to said External Module, that
+ may be distributed under a separate license agreement.
+ .
+ .
+ 5.3.4 COMPATIBILITY WITH THE GNU GPL
+ .
+ The Licensee can include a code that is subject to the provisions of one
+ of the versions of the GNU GPL in the Modified or unmodified Software,
+ and distribute that entire code under the terms of the same version of
+ the GNU GPL.
+ .
+ The Licensee can include the Modified or unmodified Software in a code
+ that is subject to the provisions of one of the versions of the GNU GPL,
+ and distribute that entire code under the terms of the same version of
+ the GNU GPL.
+ .
+ .
+ Article 6 - INTELLECTUAL PROPERTY
+ .
+ .
+ 6.1 OVER THE INITIAL SOFTWARE
+ .
+ The Holder owns the economic rights over the Initial Software. Any or
+ all use of the Initial Software is subject to compliance with the terms
+ and conditions under which the Holder has elected to distribute its work
+ and no one shall be entitled to modify the terms and conditions for the
+ distribution of said Initial Software.
+ .
+ The Holder undertakes that the Initial Software will remain ruled at
+ least by this Agreement, for the duration set forth in Article 4.2.
+ .
+ .
+ 6.2 OVER THE CONTRIBUTIONS
+ .
+ The Licensee who develops a Contribution is the owner of the
+ intellectual property rights over this Contribution as defined by
+ applicable law.
+ .
+ .
+ 6.3 OVER THE EXTERNAL MODULES
+ .
+ The Licensee who develops an External Module is the owner of the
+ intellectual property rights over this External Module as defined by
+ applicable law and is free to choose the type of agreement that shall
+ govern its distribution.
+ .
+ .
+ 6.4 JOINT PROVISIONS
+ .
+ The Licensee expressly undertakes:
+ .
+ 1. not to remove, or modify, in any manner, the intellectual property
+ notices attached to the Software;
+ .
+ 2. to reproduce said notices, in an identical manner, in the copies
+ of the Software modified or not.
+ .
+ The Licensee undertakes not to directly or indirectly infringe the
+ intellectual property rights of the Holder and/or Contributors on the
+ Software and to take, where applicable, vis-à-vis its staff, any and all
+ measures required to ensure respect of said intellectual property rights
+ of the Holder and/or Contributors.
+ .
+ .
+ Article 7 - RELATED SERVICES
+ .
+ 7.1 Under no circumstances shall the Agreement oblige the Licensor to
+ provide technical assistance or maintenance services for the Software.
+ .
+ However, the Licensor is entitled to offer this type of services. The
+ terms and conditions of such technical assistance, and/or such
+ maintenance, shall be set forth in a separate instrument. Only the
+ Licensor offering said maintenance and/or technical assistance services
+ shall incur liability therefor.
+ .
+ 7.2 Similarly, any Licensor is entitled to offer to its licensees, under
+ its sole responsibility, a warranty, that shall only be binding upon
+ itself, for the redistribution of the Software and/or the Modified
+ Software, under terms and conditions that it is free to decide. Said
+ warranty, and the financial terms and conditions of its application,
+ shall be subject of a separate instrument executed between the Licensor
+ and the Licensee.
+ .
+ .
+ Article 8 - LIABILITY
+ .
+ 8.1 Subject to the provisions of Article 8.2, the Licensee shall be
+ entitled to claim compensation for any direct loss it may have suffered
+ from the Software as a result of a fault on the part of the relevant
+ Licensor, subject to providing evidence thereof.
+ .
+ 8.2 The Licensor's liability is limited to the commitments made under
+ this Agreement and shall not be incurred as a result of in particular:
+ (i) loss due the Licensee's total or partial failure to fulfill its
+ obligations, (ii) direct or consequential loss that is suffered by the
+ Licensee due to the use or performance of the Software, and (iii) more
+ generally, any consequential loss. In particular the Parties expressly
+ agree that any or all pecuniary or business loss (i.e. loss of data,
+ loss of profits, operating loss, loss of customers or orders,
+ opportunity cost, any disturbance to business activities) or any or all
+ legal proceedings instituted against the Licensee by a third party,
+ shall constitute consequential loss and shall not provide entitlement to
+ any or all compensation from the Licensor.
+ .
+ .
+ Article 9 - WARRANTY
+ .
+ 9.1 The Licensee acknowledges that the scientific and technical
+ state-of-the-art when the Software was distributed did not enable all
+ possible uses to be tested and verified, nor for the presence of
+ possible defects to be detected. In this respect, the Licensee's
+ attention has been drawn to the risks associated with loading, using,
+ modifying and/or developing and reproducing the Software which are
+ reserved for experienced users.
+ .
+ The Licensee shall be responsible for verifying, by any or all means,
+ the suitability of the product for its requirements, its good working
+ order, and for ensuring that it shall not cause damage to either persons
+ or properties.
+ .
+ 9.2 The Licensor hereby represents, in good faith, that it is entitled
+ to grant all the rights over the Software (including in particular the
+ rights set forth in Article 5).
+ .
+ 9.3 The Licensee acknowledges that the Software is supplied "as is" by
+ the Licensor without any other express or tacit warranty, other than
+ that provided for in Article 9.2 and, in particular, without any warranty
+ as to its commercial value, its secured, safe, innovative or relevant
+ nature.
+ .
+ Specifically, the Licensor does not warrant that the Software is free
+ from any error, that it will operate without interruption, that it will
+ be compatible with the Licensee's own equipment and software
+ configuration, nor that it will meet the Licensee's requirements.
+ .
+ 9.4 The Licensor does not either expressly or tacitly warrant that the
+ Software does not infringe any third party intellectual property right
+ relating to a patent, software or any other property right. Therefore,
+ the Licensor disclaims any and all liability towards the Licensee
+ arising out of any or all proceedings for infringement that may be
+ instituted in respect of the use, modification and redistribution of the
+ Software. Nevertheless, should such proceedings be instituted against
+ the Licensee, the Licensor shall provide it with technical and legal
+ assistance for its defense. Such technical and legal assistance shall be
+ decided on a case-by-case basis between the relevant Licensor and the
+ Licensee pursuant to a memorandum of understanding. The Licensor
+ disclaims any and all liability as regards the Licensee's use of the
+ name of the Software. No warranty is given as regards the existence of
+ prior rights over the name of the Software or as regards the existence
+ of a trademark.
+ .
+ .
+ Article 10 - TERMINATION
+ .
+ 10.1 In the event of a breach by the Licensee of its obligations
+ hereunder, the Licensor may automatically terminate this Agreement
+ thirty (30) days after notice has been sent to the Licensee and has
+ remained ineffective.
+ .
+ 10.2 A Licensee whose Agreement is terminated shall no longer be
+ authorized to use, modify or distribute the Software. However, any
+ licenses that it may have granted prior to termination of the Agreement
+ shall remain valid subject to their having been granted in compliance
+ with the terms and conditions hereof.
+ .
+ .
+ Article 11 - MISCELLANEOUS
+ .
+ .
+ 11.1 EXCUSABLE EVENTS
+ .
+ Neither Party shall be liable for any or all delay, or failure to
+ perform the Agreement, that may be attributable to an event of force
+ majeure, an act of God or an outside cause, such as defective
+ functioning or interruptions of the electricity or telecommunications
+ networks, network paralysis following a virus attack, intervention by
+ government authorities, natural disasters, water damage, earthquakes,
+ fire, explosions, strikes and labor unrest, war, etc.
+ .
+ 11.2 Any failure by either Party, on one or more occasions, to invoke
+ one or more of the provisions hereof, shall under no circumstances be
+ interpreted as being a waiver by the interested Party of its right to
+ invoke said provision(s) subsequently.
+ .
+ 11.3 The Agreement cancels and replaces any or all previous agreements,
+ whether written or oral, between the Parties and having the same
+ purpose, and constitutes the entirety of the agreement between said
+ Parties concerning said purpose. No supplement or modification to the
+ terms and conditions hereof shall be effective as between the Parties
+ unless it is made in writing and signed by their duly authorized
+ representatives.
+ .
+ 11.4 In the event that one or more of the provisions hereof were to
+ conflict with a current or future applicable act or legislative text,
+ said act or legislative text shall prevail, and the Parties shall make
+ the necessary amendments so as to comply with said act or legislative
+ text. All other provisions shall remain effective. Similarly, invalidity
+ of a provision of the Agreement, for any reason whatsoever, shall not
+ cause the Agreement as a whole to be invalid.
+ .
+ .
+ 11.5 LANGUAGE
+ .
+ The Agreement is drafted in both French and English and both versions
+ are deemed authentic.
+ .
+ .
+ Article 12 - NEW VERSIONS OF THE AGREEMENT
+ .
+ 12.1 Any person is authorized to duplicate and distribute copies of this
+ Agreement.
+ .
+ 12.2 So as to ensure coherence, the wording of this Agreement is
+ protected and may only be modified by the authors of the License, who
+ reserve the right to periodically publish updates or new versions of the
+ Agreement, each with a separate number. These subsequent versions may
+ address new issues encountered by Free Software.
+ .
+ 12.3 Any Software distributed under a given version of the Agreement may
+ only be subsequently distributed under the same version of the Agreement
+ or a subsequent version, subject to the provisions of Article 5.3.4.
+ .
+ .
+ Article 13 - GOVERNING LAW AND JURISDICTION
+ .
+ 13.1 The Agreement is governed by French law. The Parties agree to
+ endeavor to seek an amicable solution to any disagreements or disputes
+ that may arise during the performance of the Agreement.
+ .
+ 13.2 Failing an amicable solution within two (2) months as from their
+ occurrence, and unless emergency proceedings are necessary, the
+ disagreements or disputes shall be referred to the Paris Courts having
+ jurisdiction, by the more diligent Party.
+ .
+ .
+ Version 2.0 dated 2006-09-05.
+
+Files: usr/share/biomaj/workflows/*
+Copyright: 2011 INRIA/INRA
+License: CeCILL-B
+ Notice
+ .
+ This Agreement is a Free Software license agreement that is the result
+ of discussions between its authors in order to ensure compliance with
+ the two main principles guiding its drafting:
+ .
+ * firstly, compliance with the principles governing the distribution
+ of Free Software: access to source code, broad rights granted to
+ users,
+ * secondly, the election of a governing law, French law, with which
+ it is conformant, both as regards the law of torts and
+ intellectual property law, and the protection that it offers to
+ both authors and holders of the economic rights over software.
+ .
+ The authors of the CeCILL-B (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+ license are:
+ .
+ Commissariat à l'Energie Atomique - CEA, a public scientific, technical
+ and industrial research establishment, having its principal place of
+ business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
+ .
+ Centre National de la Recherche Scientifique - CNRS, a public scientific
+ and technological establishment, having its principal place of business
+ at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
+ .
+ Institut National de Recherche en Informatique et en Automatique -
+ INRIA, a public scientific and technological establishment, having its
+ principal place of business at Domaine de Voluceau, Rocquencourt, BP
+ 105, 78153 Le Chesnay cedex, France.
+ .
+ .
+ Preamble
+ .
+ This Agreement is an open source software license intended to give users
+ significant freedom to modify and redistribute the software licensed
+ hereunder.
+ .
+ The exercising of this freedom is conditional upon a strong obligation
+ of giving credits for everybody that distributes a software
+ incorporating a software ruled by the current license so as all
+ contributions to be properly identified and acknowledged.
+ .
+ In consideration of access to the source code and the rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors only have limited liability.
+ .
+ In this respect, the risks associated with loading, using, modifying
+ and/or developing or reproducing the software by the user are brought to
+ the user's attention, given its Free Software status, which may make it
+ complicated to use, with the result that its use is reserved for
+ developers and experienced professionals having in-depth computer
+ knowledge. Users are therefore encouraged to load and test the
+ suitability of the software as regards their requirements in conditions
+ enabling the security of their systems and/or data to be ensured and,
+ more generally, to use and operate it in the same conditions of
+ security. This Agreement may be freely reproduced and published,
+ provided it is not altered, and that no provisions are either added or
+ removed herefrom.
+ .
+ This Agreement may apply to any or all software for which the holder of
+ the economic rights decides to submit the use thereof to its provisions.
+ .
+ .
+ Article 1 - DEFINITIONS
+ .
+ For the purpose of this Agreement, when the following expressions
+ commence with a capital letter, they shall have the following meaning:
+ .
+ Agreement: means this license agreement, and its possible subsequent
+ versions and annexes.
+ .
+ Software: means the software in its Object Code and/or Source Code form
+ and, where applicable, its documentation, "as is" when the Licensee
+ accepts the Agreement.
+ .
+ Initial Software: means the Software in its Source Code and possibly its
+ Object Code form and, where applicable, its documentation, "as is" when
+ it is first distributed under the terms and conditions of the Agreement.
+ .
+ Modified Software: means the Software modified by at least one
+ Contribution.
+ .
+ Source Code: means all the Software's instructions and program lines to
+ which access is required so as to modify the Software.
+ .
+ Object Code: means the binary files originating from the compilation of
+ the Source Code.
+ .
+ Holder: means the holder(s) of the economic rights over the Initial
+ Software.
+ .
+ Licensee: means the Software user(s) having accepted the Agreement.
+ .
+ Contributor: means a Licensee having made at least one Contribution.
+ .
+ Licensor: means the Holder, or any other individual or legal entity, who
+ distributes the Software under the Agreement.
+ .
+ Contribution: means any or all modifications, corrections, translations,
+ adaptations and/or new functions integrated into the Software by any or
+ all Contributors, as well as any or all Internal Modules.
+ .
+ Module: means a set of sources files including their documentation that
+ enables supplementary functions or services in addition to those offered
+ by the Software.
+ .
+ External Module: means any or all Modules, not derived from the
+ Software, so that this Module and the Software run in separate address
+ spaces, with one calling the other when they are run.
+ .
+ Internal Module: means any or all Module, connected to the Software so
+ that they both execute in the same address space.
+ .
+ Parties: mean both the Licensee and the Licensor.
+ .
+ These expressions may be used both in singular and plural form.
+ .
+ .
+ Article 2 - PURPOSE
+ .
+ The purpose of the Agreement is the grant by the Licensor to the
+ Licensee of a non-exclusive, transferable and worldwide license for the
+ Software as set forth in Article 5 hereinafter for the whole term of the
+ protection granted by the rights over said Software.
+ .
+ .
+ Article 3 - ACCEPTANCE
+ .
+ 3.1 The Licensee shall be deemed as having accepted the terms and
+ conditions of this Agreement upon the occurrence of the first of the
+ following events:
+ .
+ * (i) loading the Software by any or all means, notably, by
+ downloading from a remote server, or by loading from a physical
+ medium;
+ * (ii) the first time the Licensee exercises any of the rights
+ granted hereunder.
+ .
+ 3.2 One copy of the Agreement, containing a notice relating to the
+ characteristics of the Software, to the limited warranty, and to the
+ fact that its use is restricted to experienced users has been provided
+ to the Licensee prior to its acceptance as set forth in Article 3.1
+ hereinabove, and the Licensee hereby acknowledges that it has read and
+ understood it.
+ .
+ .
+ Article 4 - EFFECTIVE DATE AND TERM
+ .
+ .
+ 4.1 EFFECTIVE DATE
+ .
+ The Agreement shall become effective on the date when it is accepted by
+ the Licensee as set forth in Article 3.1.
+ .
+ .
+ 4.2 TERM
+ .
+ The Agreement shall remain in force for the entire legal term of
+ protection of the economic rights over the Software.
+ .
+ .
+ Article 5 - SCOPE OF RIGHTS GRANTED
+ .
+ The Licensor hereby grants to the Licensee, who accepts, the following
+ rights over the Software for any or all use, and for the term of the
+ Agreement, on the basis of the terms and conditions set forth hereinafter.
+ .
+ Besides, if the Licensor owns or comes to own one or more patents
+ protecting all or part of the functions of the Software or of its
+ components, the Licensor undertakes not to enforce the rights granted by
+ these patents against successive Licensees using, exploiting or
+ modifying the Software. If these patents are transferred, the Licensor
+ undertakes to have the transferees subscribe to the obligations set
+ forth in this paragraph.
+ .
+ .
+ 5.1 RIGHT OF USE
+ .
+ The Licensee is authorized to use the Software, without any limitation
+ as to its fields of application, with it being hereinafter specified
+ that this comprises:
+ .
+ 1. permanent or temporary reproduction of all or part of the Software
+ by any or all means and in any or all form.
+ .
+ 2. loading, displaying, running, or storing the Software on any or
+ all medium.
+ .
+ 3. entitlement to observe, study or test its operation so as to
+ determine the ideas and principles behind any or all constituent
+ elements of said Software. This shall apply when the Licensee
+ carries out any or all loading, displaying, running, transmission
+ or storage operation as regards the Software, that it is entitled
+ to carry out hereunder.
+ .
+ .
+ 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+ .
+ The right to make Contributions includes the right to translate, adapt,
+ arrange, or make any or all modifications to the Software, and the right
+ to reproduce the resulting software.
+ .
+ The Licensee is authorized to make any or all Contributions to the
+ Software provided that it includes an explicit notice that it is the
+ author of said Contribution and indicates the date of the creation thereof.
+ .
+ .
+ 5.3 RIGHT OF DISTRIBUTION
+ .
+ In particular, the right of distribution includes the right to publish,
+ transmit and communicate the Software to the general public on any or
+ all medium, and by any or all means, and the right to market, either in
+ consideration of a fee, or free of charge, one or more copies of the
+ Software by any means.
+ .
+ The Licensee is further authorized to distribute copies of the modified
+ or unmodified Software to third parties according to the terms and
+ conditions set forth hereinafter.
+ .
+ .
+ 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+ .
+ The Licensee is authorized to distribute true copies of the Software in
+ Source Code or Object Code form, provided that said distribution
+ complies with all the provisions of the Agreement and is accompanied by:
+ .
+ 1. a copy of the Agreement,
+ .
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+ .
+ and that, in the event that only the Object Code of the Software is
+ redistributed, the Licensee allows effective access to the full Source
+ Code of the Software at a minimum during the entire period of its
+ distribution of the Software, it being understood that the additional
+ cost of acquiring the Source Code shall not exceed the cost of
+ transferring the data.
+ .
+ .
+ 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+ .
+ If the Licensee makes any Contribution to the Software, the resulting
+ Modified Software may be distributed under a license agreement other
+ than this Agreement subject to compliance with the provisions of Article
+ 5.3.4.
+ .
+ .
+ 5.3.3 DISTRIBUTION OF EXTERNAL MODULES
+ .
+ When the Licensee has developed an External Module, the terms and
+ conditions of this Agreement do not apply to said External Module, that
+ may be distributed under a separate license agreement.
+ .
+ .
+ 5.3.4 CREDITS
+ .
+ Any Licensee who may distribute a Modified Software hereby expressly
+ agrees to:
+ .
+ 1. indicate in the related documentation that it is based on the
+ Software licensed hereunder, and reproduce the intellectual
+ property notice for the Software,
+ .
+ 2. ensure that written indications of the Software intended use,
+ intellectual property notice and license hereunder are included in
+ easily accessible format from the Modified Software interface,
+ .
+ 3. mention, on a freely accessible website describing the Modified
+ Software, at least throughout the distribution term thereof, that
+ it is based on the Software licensed hereunder, and reproduce the
+ Software intellectual property notice,
+ .
+ 4. where it is distributed to a third party that may distribute a
+ Modified Software without having to make its source code
+ available, make its best efforts to ensure that said third party
+ agrees to comply with the obligations set forth in this Article .
+ .
+ If the Software, whether or not modified, is distributed with an
+ External Module designed for use in connection with the Software, the
+ Licensee shall submit said External Module to the foregoing obligations.
+ .
+ .
+ 5.3.5 COMPATIBILITY WITH THE CeCILL AND CeCILL-C LICENSES
+ .
+ Where a Modified Software contains a Contribution subject to the CeCILL
+ license, the provisions set forth in Article 5.3.4 shall be optional.
+ .
+ A Modified Software may be distributed under the CeCILL-C license. In
+ such a case the provisions set forth in Article 5.3.4 shall be optional.
+ .
+ .
+ Article 6 - INTELLECTUAL PROPERTY
+ .
+ .
+ 6.1 OVER THE INITIAL SOFTWARE
+ .
+ The Holder owns the economic rights over the Initial Software. Any or
+ all use of the Initial Software is subject to compliance with the terms
+ and conditions under which the Holder has elected to distribute its work
+ and no one shall be entitled to modify the terms and conditions for the
+ distribution of said Initial Software.
+ .
+ The Holder undertakes that the Initial Software will remain ruled at
+ least by this Agreement, for the duration set forth in Article 4.2.
+ .
+ .
+ 6.2 OVER THE CONTRIBUTIONS
+ .
+ The Licensee who develops a Contribution is the owner of the
+ intellectual property rights over this Contribution as defined by
+ applicable law.
+ .
+ .
+ 6.3 OVER THE EXTERNAL MODULES
+ .
+ The Licensee who develops an External Module is the owner of the
+ intellectual property rights over this External Module as defined by
+ applicable law and is free to choose the type of agreement that shall
+ govern its distribution.
+ .
+ .
+ 6.4 JOINT PROVISIONS
+ .
+ The Licensee expressly undertakes:
+ .
+ 1. not to remove, or modify, in any manner, the intellectual property
+ notices attached to the Software;
+ .
+ 2. to reproduce said notices, in an identical manner, in the copies
+ of the Software modified or not.
+ .
+ The Licensee undertakes not to directly or indirectly infringe the
+ intellectual property rights of the Holder and/or Contributors on the
+ Software and to take, where applicable, vis-à-vis its staff, any and all
+ measures required to ensure respect of said intellectual property rights
+ of the Holder and/or Contributors.
+ .
+ .
+ Article 7 - RELATED SERVICES
+ .
+ 7.1 Under no circumstances shall the Agreement oblige the Licensor to
+ provide technical assistance or maintenance services for the Software.
+ .
+ However, the Licensor is entitled to offer this type of services. The
+ terms and conditions of such technical assistance, and/or such
+ maintenance, shall be set forth in a separate instrument. Only the
+ Licensor offering said maintenance and/or technical assistance services
+ shall incur liability therefor.
+ .
+ 7.2 Similarly, any Licensor is entitled to offer to its licensees, under
+ its sole responsibility, a warranty, that shall only be binding upon
+ itself, for the redistribution of the Software and/or the Modified
+ Software, under terms and conditions that it is free to decide. Said
+ warranty, and the financial terms and conditions of its application,
+ shall be subject of a separate instrument executed between the Licensor
+ and the Licensee.
+ .
+ .
+ Article 8 - LIABILITY
+ .
+ 8.1 Subject to the provisions of Article 8.2, the Licensee shall be
+ entitled to claim compensation for any direct loss it may have suffered
+ from the Software as a result of a fault on the part of the relevant
+ Licensor, subject to providing evidence thereof.
+ .
+ 8.2 The Licensor's liability is limited to the commitments made under
+ this Agreement and shall not be incurred as a result of in particular:
+ (i) loss due the Licensee's total or partial failure to fulfill its
+ obligations, (ii) direct or consequential loss that is suffered by the
+ Licensee due to the use or performance of the Software, and (iii) more
+ generally, any consequential loss. In particular the Parties expressly
+ agree that any or all pecuniary or business loss (i.e. loss of data,
+ loss of profits, operating loss, loss of customers or orders,
+ opportunity cost, any disturbance to business activities) or any or all
+ legal proceedings instituted against the Licensee by a third party,
+ shall constitute consequential loss and shall not provide entitlement to
+ any or all compensation from the Licensor.
+ .
+ .
+ Article 9 - WARRANTY
+ .
+ 9.1 The Licensee acknowledges that the scientific and technical
+ state-of-the-art when the Software was distributed did not enable all
+ possible uses to be tested and verified, nor for the presence of
+ possible defects to be detected. In this respect, the Licensee's
+ attention has been drawn to the risks associated with loading, using,
+ modifying and/or developing and reproducing the Software which are
+ reserved for experienced users.
+ .
+ The Licensee shall be responsible for verifying, by any or all means,
+ the suitability of the product for its requirements, its good working
+ order, and for ensuring that it shall not cause damage to either persons
+ or properties.
+ .
+ 9.2 The Licensor hereby represents, in good faith, that it is entitled
+ to grant all the rights over the Software (including in particular the
+ rights set forth in Article 5).
+ .
+ 9.3 The Licensee acknowledges that the Software is supplied "as is" by
+ the Licensor without any other express or tacit warranty, other than
+ that provided for in Article 9.2 and, in particular, without any warranty
+ as to its commercial value, its secured, safe, innovative or relevant
+ nature.
+ .
+ Specifically, the Licensor does not warrant that the Software is free
+ from any error, that it will operate without interruption, that it will
+ be compatible with the Licensee's own equipment and software
+ configuration, nor that it will meet the Licensee's requirements.
+ .
+ 9.4 The Licensor does not either expressly or tacitly warrant that the
+ Software does not infringe any third party intellectual property right
+ relating to a patent, software or any other property right. Therefore,
+ the Licensor disclaims any and all liability towards the Licensee
+ arising out of any or all proceedings for infringement that may be
+ instituted in respect of the use, modification and redistribution of the
+ Software. Nevertheless, should such proceedings be instituted against
+ the Licensee, the Licensor shall provide it with technical and legal
+ assistance for its defense. Such technical and legal assistance shall be
+ decided on a case-by-case basis between the relevant Licensor and the
+ Licensee pursuant to a memorandum of understanding. The Licensor
+ disclaims any and all liability as regards the Licensee's use of the
+ name of the Software. No warranty is given as regards the existence of
+ prior rights over the name of the Software or as regards the existence
+ of a trademark.
+ .
+ .
+ Article 10 - TERMINATION
+ .
+ 10.1 In the event of a breach by the Licensee of its obligations
+ hereunder, the Licensor may automatically terminate this Agreement
+ thirty (30) days after notice has been sent to the Licensee and has
+ remained ineffective.
+ .
+ 10.2 A Licensee whose Agreement is terminated shall no longer be
+ authorized to use, modify or distribute the Software. However, any
+ licenses that it may have granted prior to termination of the Agreement
+ shall remain valid subject to their having been granted in compliance
+ with the terms and conditions hereof.
+ .
+ .
+ Article 11 - MISCELLANEOUS
+ .
+ .
+ 11.1 EXCUSABLE EVENTS
+ .
+ Neither Party shall be liable for any or all delay, or failure to
+ perform the Agreement, that may be attributable to an event of force
+ majeure, an act of God or an outside cause, such as defective
+ functioning or interruptions of the electricity or telecommunications
+ networks, network paralysis following a virus attack, intervention by
+ government authorities, natural disasters, water damage, earthquakes,
+ fire, explosions, strikes and labor unrest, war, etc.
+ .
+ 11.2 Any failure by either Party, on one or more occasions, to invoke
+ one or more of the provisions hereof, shall under no circumstances be
+ interpreted as being a waiver by the interested Party of its right to
+ invoke said provision(s) subsequently.
+ .
+ 11.3 The Agreement cancels and replaces any or all previous agreements,
+ whether written or oral, between the Parties and having the same
+ purpose, and constitutes the entirety of the agreement between said
+ Parties concerning said purpose. No supplement or modification to the
+ terms and conditions hereof shall be effective as between the Parties
+ unless it is made in writing and signed by their duly authorized
+ representatives.
+ .
+ 11.4 In the event that one or more of the provisions hereof were to
+ conflict with a current or future applicable act or legislative text,
+ said act or legislative text shall prevail, and the Parties shall make
+ the necessary amendments so as to comply with said act or legislative
+ text. All other provisions shall remain effective. Similarly, invalidity
+ of a provision of the Agreement, for any reason whatsoever, shall not
+ cause the Agreement as a whole to be invalid.
+ .
+ .
+ 11.5 LANGUAGE
+ .
+ The Agreement is drafted in both French and English and both versions
+ are deemed authentic.
+ .
+ .
+ Article 12 - NEW VERSIONS OF THE AGREEMENT
+ .
+ 12.1 Any person is authorized to duplicate and distribute copies of this
+ Agreement.
+ .
+ 12.2 So as to ensure coherence, the wording of this Agreement is
+ protected and may only be modified by the authors of the License, who
+ reserve the right to periodically publish updates or new versions of the
+ Agreement, each with a separate number. These subsequent versions may
+ address new issues encountered by Free Software.
+ .
+ 12.3 Any Software distributed under a given version of the Agreement may
+ only be subsequently distributed under the same version of the Agreement
+ or a subsequent version.
+ .
+ .
+ Article 13 - GOVERNING LAW AND JURISDICTION
+ .
+ 13.1 The Agreement is governed by French law. The Parties agree to
+ endeavor to seek an amicable solution to any disagreements or disputes
+ that may arise during the performance of the Agreement.
+ .
+ 13.2 Failing an amicable solution within two (2) months as from their
+ occurrence, and unless emergency proceedings are necessary, the
+ disagreements or disputes shall be referred to the Paris Courts having
+ jurisdiction, by the more diligent Party.
+ .
+ .
+ Version 1.0 dated 2006-09-05.
Copied: trunk/packages/biomaj/tags/1.2.3-4/debian/patches/javamail.patch (from rev 18326, trunk/packages/biomaj/trunk/debian/patches/javamail.patch)
===================================================================
--- trunk/packages/biomaj/tags/1.2.3-4/debian/patches/javamail.patch (rev 0)
+++ trunk/packages/biomaj/tags/1.2.3-4/debian/patches/javamail.patch 2014-10-17 11:16:17 UTC (rev 18328)
@@ -0,0 +1,14 @@
+Description: Replaced the dependency on gnumail with the reference implementation
+Author: Emmanuel Bourg <ebourg at apache.org>
+Forwarded: no
+--- a/usr/share/biomaj/build.xml
++++ b/usr/share/biomaj/build.xml
+@@ -55,7 +55,7 @@
+ <property name="class1.path" value="${env.ANT_HOME}/lib/ant.jar ${env.ANT_HOME}/lib/ant-nodeps.jar ${env.ANT_HOME}/lib/ant-launcher.jar ${env.ANT_HOME}/lib/ant-apache-oro.jar"/>
+ <property name="class2.path" value="${lib.dir}/oro.jar ${lib.dir}/commons-net2.jar ${lib.dir}/ant-contrib.jar ${lib.dir}/junit4.jar"/>
+ <property name="class3.path" value="${lib.dir}/forms.jar ${lib.dir}/jakarta-regexp.jar ${lib.dir}/jdom.jar ${lib.dir}/log4j-1.2.jar ${lib.dir}/mysql-connector-java.jar"/>
+- <property name="class4.path" value="${lib.dir}/jcommon.jar ${lib.dir}/gnumail.jar ${lib.dir}/activation.jar ${lib.dir}/commons-cli.jar ${lib.dir}/jets3t.jar ${lib.dir}/sqltool.jar ${lib.dir}/commons-logging.jar ${lib.dir}/commons-codec.jar ${lib.dir}/commons-httpclient.jar"/>
++ <property name="class4.path" value="${lib.dir}/jcommon.jar ${lib.dir}/javax.mail.jar ${lib.dir}/commons-cli.jar ${lib.dir}/jets3t.jar ${lib.dir}/sqltool.jar ${lib.dir}/commons-logging.jar ${lib.dir}/commons-codec.jar ${lib.dir}/commons-httpclient.jar"/>
+ <property name="class5.path" value="${lib.dir}/hsqldb.jar ${lib.dir}/hsqldbutil.jar ${lib.dir}/commons-pool.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/jsch.jar" />
+
+ <path id="compile.classpath">
Deleted: trunk/packages/biomaj/tags/1.2.3-4/debian/patches/series
===================================================================
--- trunk/packages/biomaj/trunk/debian/patches/series 2014-10-16 20:31:48 UTC (rev 18323)
+++ trunk/packages/biomaj/tags/1.2.3-4/debian/patches/series 2014-10-17 11:16:17 UTC (rev 18328)
@@ -1,3 +0,0 @@
-removeSqlToolDependency
-set_env_file_for_debian
-useFormSpecs_from_jgoodies
Copied: trunk/packages/biomaj/tags/1.2.3-4/debian/patches/series (from rev 18326, trunk/packages/biomaj/trunk/debian/patches/series)
===================================================================
--- trunk/packages/biomaj/tags/1.2.3-4/debian/patches/series (rev 0)
+++ trunk/packages/biomaj/tags/1.2.3-4/debian/patches/series 2014-10-17 11:16:17 UTC (rev 18328)
@@ -0,0 +1,4 @@
+removeSqlToolDependency
+set_env_file_for_debian
+useFormSpecs_from_jgoodies
+javamail.patch
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