Author: osallou Date: 2014-05-20 13:14:45 +0000 (Tue, 20 May 2014) New Revision: 16967
Added: trunk/packages/biojava/tags/1:1.7.1-5/ trunk/packages/biojava/tags/1:1.7.1-5/debian/changelog trunk/packages/biojava/tags/1:1.7.1-5/debian/control Removed: trunk/packages/biojava/tags/1:1.7.1-5/debian/changelog trunk/packages/biojava/tags/1:1.7.1-5/debian/control Log: [svn-buildpackage] Tagging biojava-live 1:1.7.1-5 Deleted: trunk/packages/biojava/tags/1:1.7.1-5/debian/changelog =================================================================== --- trunk/packages/biojava/branches/1.7.1/debian/changelog 2014-05-20 12:21:32 UTC (rev 16964) +++ trunk/packages/biojava/tags/1:1.7.1-5/debian/changelog 2014-05-20 13:14:45 UTC (rev 16967) @@ -1,116 +0,0 @@ -biojava-live (1:1.7.1-4) unstable; urgency=low - - [ Andreas Tille ] - * debian/upstream: - - Author conform to BibTeX syntax - - Add eprint - - [ Olivier Sallou ] - * Fix watch file to follow biojava v1, not v3 - - -- Olivier Sallou <[email protected]> Fri, 31 Jan 2014 21:49:37 +0100 - -biojava-live (1:1.7.1-3) unstable; urgency=low - - * Use libcommons-collections3-java instead of libcommons-collections-java - - -- Olivier Sallou <[email protected]> Tue, 10 Sep 2013 09:39:36 +0200 - -biojava-live (1:1.7.1-2) unstable; urgency=low - - [ Jari Aalto ] - * Remove quilt and upgrade to packaging format "3.0 quilt" which - includes patch management built-in. - * Update buildxml.patch to DEP-3 and run "quilt refresh" to make it - apply cleanly. - * Update to Standards-Version to 3.9.3 (no changes needed) and debhelper 9. - * Update obsolete depends default-jdk-builddep to default-jdk. - Closes: #669122 - * Fix wrong-section-according-to-package-name (Lintian) by changing - section from science to java. - * Fix needless-dependency-on-jre (Lintian) by removing jre dependencies. - * Fix duplicate-short-description (Lintian). - * Fix extended-description-is-probably-too-short (Lintian). - - [ Andreas Tille ] - * debian/control: - - Short-Desc: Java 1.7 API is missleading regarding JDK version - rather - add the version at the end and declare the version-less metapackage as - default version - - Dropped default-jre-headless from Depends according to Java policy - - Fixed Vcs fields - * debian/watch: enable detecting new versions - * debian/{control,upstream}: Moved citations from long description to - upstream file - * libbiojava*.lintian: removed because now useless - * debian/compat: 9 - * debian/copyright: Rewritten to be compliant with DEP5 and verified - using `cme fix dpkg-copyright` - * debian/rules: s/dh_clean -k/dh_prep/ - - -- Andreas Tille <[email protected]> Wed, 18 Apr 2012 08:50:31 +0200 - -biojava-live (1:1.7.1-1) unstable; urgency=low - - * New upstream version. - * New epoch - - because of an unfortunate versioning of previous upload - - to indicate the now happening BioJava Hackathon in Cambridge, UK - - -- Steffen Moeller <[email protected]> Wed, 20 Jan 2010 02:08:17 +0100 - -biojava-live (1.7.svn.20090419-3) unstable; urgency=low - - * debian/control: - - Conflicts: libbiojava1.6-java - - Replaces: libbiojava1.6-java - - Enhanced long description of libbiojava-java-doc - Closes: #522269 - * debian/rules: set JAVA_HOME to enable proper clean target - - -- Andreas Tille <[email protected]> Fri, 26 Jun 2009 10:01:10 +0200 - -biojava-live (1.7.svn.20090419-2) unstable; urgency=low - - * Add Build Depends: ant-optional - Closes: #533896 - * Standards-Version: 3.8.2 (no changes needed) - - -- Andreas Tille <[email protected]> Mon, 22 Jun 2009 09:32:20 +0200 - -biojava-live (1.7.svn.20090419-1) unstable; urgency=low - - * New upstream version, addressing structures. - * Removed dependency on libjgrapht, so biojava can go to main. - * Conformance to 3.8.1 (no changes required). - - -- Steffen Moeller <[email protected]> Sun, 19 Apr 2009 18:30:54 +0200 - -biojava-live (1.6.1.svn.20090306-1) experimental; urgency=low - - [ Andreas Tille ] - * Initial release (Closes:#491025). - - [ Steffen Moeller ] - * Added dependency to quilt. - * Moved -doc to section doc. - * Added symlinks to jar file with pseudo-soname - * Need to be placed in contrib section as a start because of dependency - to libjgrapht that is still in contrib. - - -- Andreas Tille <[email protected]> Mon, 09 Mar 2009 13:50:45 +0100 - -biojava-live (1.6.0.svn.20080716-1) UNRELEASED; urgency=low - - * Renamed to biojava-live in analogy to upstream's name - and to keep the opportunity to add a biojava meta package - later on. - * License issue fixed that led to previous rejection of biojava. - - -- Steffen Moeller <[email protected]> Sun, 13 Jul 2008 15:56:27 +0200 - -biojava (1.5-1) UNRELEASED; urgency=low - - * New upstream release. - - -- Steffen Moeller <[email protected]> Tue, 03 Jul 2007 01:51:06 +0200 Copied: trunk/packages/biojava/tags/1:1.7.1-5/debian/changelog (from rev 16965, trunk/packages/biojava/branches/1.7.1/debian/changelog) =================================================================== --- trunk/packages/biojava/tags/1:1.7.1-5/debian/changelog (rev 0) +++ trunk/packages/biojava/tags/1:1.7.1-5/debian/changelog 2014-05-20 13:14:45 UTC (rev 16967) @@ -0,0 +1,123 @@ +biojava-live (1:1.7.1-5) unstable; urgency=medium + + * d/control: use libcommons-collections3 instead of + libcommons-collection in runtime deps (Closes: #748473). + + -- Olivier Sallou <[email protected]> Tue, 20 May 2014 15:03:23 +0200 + +biojava-live (1:1.7.1-4) unstable; urgency=low + + [ Andreas Tille ] + * debian/upstream: + - Author conform to BibTeX syntax + - Add eprint + + [ Olivier Sallou ] + * Fix watch file to follow biojava v1, not v3 + + -- Olivier Sallou <[email protected]> Fri, 31 Jan 2014 21:49:37 +0100 + +biojava-live (1:1.7.1-3) unstable; urgency=low + + * Use libcommons-collections3-java instead of libcommons-collections-java + + -- Olivier Sallou <[email protected]> Tue, 10 Sep 2013 09:39:36 +0200 + +biojava-live (1:1.7.1-2) unstable; urgency=low + + [ Jari Aalto ] + * Remove quilt and upgrade to packaging format "3.0 quilt" which + includes patch management built-in. + * Update buildxml.patch to DEP-3 and run "quilt refresh" to make it + apply cleanly. + * Update to Standards-Version to 3.9.3 (no changes needed) and debhelper 9. + * Update obsolete depends default-jdk-builddep to default-jdk. + Closes: #669122 + * Fix wrong-section-according-to-package-name (Lintian) by changing + section from science to java. + * Fix needless-dependency-on-jre (Lintian) by removing jre dependencies. + * Fix duplicate-short-description (Lintian). + * Fix extended-description-is-probably-too-short (Lintian). + + [ Andreas Tille ] + * debian/control: + - Short-Desc: Java 1.7 API is missleading regarding JDK version - rather + add the version at the end and declare the version-less metapackage as + default version + - Dropped default-jre-headless from Depends according to Java policy + - Fixed Vcs fields + * debian/watch: enable detecting new versions + * debian/{control,upstream}: Moved citations from long description to + upstream file + * libbiojava*.lintian: removed because now useless + * debian/compat: 9 + * debian/copyright: Rewritten to be compliant with DEP5 and verified + using `cme fix dpkg-copyright` + * debian/rules: s/dh_clean -k/dh_prep/ + + -- Andreas Tille <[email protected]> Wed, 18 Apr 2012 08:50:31 +0200 + +biojava-live (1:1.7.1-1) unstable; urgency=low + + * New upstream version. + * New epoch + - because of an unfortunate versioning of previous upload + - to indicate the now happening BioJava Hackathon in Cambridge, UK + + -- Steffen Moeller <[email protected]> Wed, 20 Jan 2010 02:08:17 +0100 + +biojava-live (1.7.svn.20090419-3) unstable; urgency=low + + * debian/control: + - Conflicts: libbiojava1.6-java + - Replaces: libbiojava1.6-java + - Enhanced long description of libbiojava-java-doc + Closes: #522269 + * debian/rules: set JAVA_HOME to enable proper clean target + + -- Andreas Tille <[email protected]> Fri, 26 Jun 2009 10:01:10 +0200 + +biojava-live (1.7.svn.20090419-2) unstable; urgency=low + + * Add Build Depends: ant-optional + Closes: #533896 + * Standards-Version: 3.8.2 (no changes needed) + + -- Andreas Tille <[email protected]> Mon, 22 Jun 2009 09:32:20 +0200 + +biojava-live (1.7.svn.20090419-1) unstable; urgency=low + + * New upstream version, addressing structures. + * Removed dependency on libjgrapht, so biojava can go to main. + * Conformance to 3.8.1 (no changes required). + + -- Steffen Moeller <[email protected]> Sun, 19 Apr 2009 18:30:54 +0200 + +biojava-live (1.6.1.svn.20090306-1) experimental; urgency=low + + [ Andreas Tille ] + * Initial release (Closes:#491025). + + [ Steffen Moeller ] + * Added dependency to quilt. + * Moved -doc to section doc. + * Added symlinks to jar file with pseudo-soname + * Need to be placed in contrib section as a start because of dependency + to libjgrapht that is still in contrib. + + -- Andreas Tille <[email protected]> Mon, 09 Mar 2009 13:50:45 +0100 + +biojava-live (1.6.0.svn.20080716-1) UNRELEASED; urgency=low + + * Renamed to biojava-live in analogy to upstream's name + and to keep the opportunity to add a biojava meta package + later on. + * License issue fixed that led to previous rejection of biojava. + + -- Steffen Moeller <[email protected]> Sun, 13 Jul 2008 15:56:27 +0200 + +biojava (1.5-1) UNRELEASED; urgency=low + + * New upstream release. + + -- Steffen Moeller <[email protected]> Tue, 03 Jul 2007 01:51:06 +0200 Deleted: trunk/packages/biojava/tags/1:1.7.1-5/debian/control =================================================================== --- trunk/packages/biojava/branches/1.7.1/debian/control 2014-05-20 12:21:32 UTC (rev 16964) +++ trunk/packages/biojava/tags/1:1.7.1-5/debian/control 2014-05-20 13:14:45 UTC (rev 16967) @@ -1,82 +0,0 @@ -Source: biojava-live -Section: java -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Steffen Moeller <[email protected]>, - Andreas Tille <[email protected]>, - Olivier Sallou <[email protected]> -Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java, - libcommons-collections3-java (>= 2.1), libcommons-pool-java (>= 1.1), - libbytecode-java (>= 0.92.cvs.20070925), - default-jdk, junit4, - ant-optional -Build-Depends: debhelper (>= 9), cdbs, ant -Standards-Version: 3.9.5 -Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava/trunk/ -Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biojava/trunk/ -Homepage: http://www.biojava.org - -Package: libbiojava1.7-java -Architecture: all -Depends: ${shlibs:Depends}, ${misc:Depends}, - libcommons-pool-java (>= 1.1), - libcommons-collections-java (>= 2.1), - libcommons-dbcp-java (>= 1.1), - libhsqldb-java, - libbytecode-java -Suggests: java-virtual-machine, libjgrapht-java, libbiojava-java, libbiojava-java-doc -Conflicts: libbiojava1.6-java -Replaces: libbiojava1.6-java -Description: Java API to biological data and applications (version 1.7) - This package presents the Open Source Java API to biological databases - and a series of mostly sequence-based algorithms. The APIs are not - compatible between versions. In analogy to the dealing with shared - libraries of the C language, the jar file of this package has the - API version in its name. It is symbolically linked to the expected - biojava.jar filename in the package libbiojava-java. This will help - keeping multiple versions of the biojava API in parallel. - -Package: libbiojava-java -Architecture: all -Depends: libbiojava1.7-java, ${misc:Depends} -Conflicts: libbiojava1.6-java -Replaces: libbiojava1.6-java -Description: Java API to biological data and applications (default version) - BioJava is an open-source project dedicated to providing a Java framework - for processing biological data. It includes objects for manipulating - sequences, file parsers, DAS client and server support, access to BioSQL - and Ensembl databases, and powerful analysis and statistical routines - including a dynamic programming toolkit. - . - BioJava is provided by a vibrant community which meets annually at - the Bioinformatics Open Source Conference (BOSC) that traditionally - accompanies the Intelligent Systems in Molecular Biology (ISMB) - meeting. Much like BioPerl, the employment of this library is valuable - for everybody active in the field because of the many tricks of the - trade one learns just by communicating on the mailing list. - . - This is a wrapper package which should enable smooth upgrades to new - versions. - -Package: libbiojava-java-demos -Architecture: all -Depends: ${misc:Depends} -Recommends: libbiojava-java -Description: Example programs for BioJava - The package comes with a wealth of use cases for BioJava. It is generated - together with the API documentation but because of its size of ~3.7MB it - was decided to distribute it separately. - - -Package: libbiojava-java-doc -Section: doc -Architecture: all -Depends: ${misc:Depends} -Recommends: konqueror|html-browser -Suggests: libbiojava-java-demos, libbiojava-java -Description: [Biology] Documentation for BioJava - BioJava is an open-source project dedicated to providing a Java framework - for processing biological data. - . - This package contains the HTML documentation describing the API of BioJava - which was generated automatically by JavaDoc. Copied: trunk/packages/biojava/tags/1:1.7.1-5/debian/control (from rev 16965, trunk/packages/biojava/branches/1.7.1/debian/control) =================================================================== --- trunk/packages/biojava/tags/1:1.7.1-5/debian/control (rev 0) +++ trunk/packages/biojava/tags/1:1.7.1-5/debian/control 2014-05-20 13:14:45 UTC (rev 16967) @@ -0,0 +1,82 @@ +Source: biojava-live +Section: java +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Steffen Moeller <[email protected]>, + Andreas Tille <[email protected]>, + Olivier Sallou <[email protected]> +Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java, + libcommons-collections3-java (>= 2.1), libcommons-pool-java (>= 1.1), + libbytecode-java (>= 0.92.cvs.20070925), + default-jdk, junit4, + ant-optional +Build-Depends: debhelper (>= 9), cdbs, ant +Standards-Version: 3.9.5 +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biojava/trunk/ +Homepage: http://www.biojava.org + +Package: libbiojava1.7-java +Architecture: all +Depends: ${shlibs:Depends}, ${misc:Depends}, + libcommons-pool-java (>= 1.1), + libcommons-collections3-java, + libcommons-dbcp-java (>= 1.1), + libhsqldb-java, + libbytecode-java +Suggests: java-virtual-machine, libjgrapht-java, libbiojava-java, libbiojava-java-doc +Conflicts: libbiojava1.6-java +Replaces: libbiojava1.6-java +Description: Java API to biological data and applications (version 1.7) + This package presents the Open Source Java API to biological databases + and a series of mostly sequence-based algorithms. The APIs are not + compatible between versions. In analogy to the dealing with shared + libraries of the C language, the jar file of this package has the + API version in its name. It is symbolically linked to the expected + biojava.jar filename in the package libbiojava-java. This will help + keeping multiple versions of the biojava API in parallel. + +Package: libbiojava-java +Architecture: all +Depends: libbiojava1.7-java, ${misc:Depends} +Conflicts: libbiojava1.6-java +Replaces: libbiojava1.6-java +Description: Java API to biological data and applications (default version) + BioJava is an open-source project dedicated to providing a Java framework + for processing biological data. It includes objects for manipulating + sequences, file parsers, DAS client and server support, access to BioSQL + and Ensembl databases, and powerful analysis and statistical routines + including a dynamic programming toolkit. + . + BioJava is provided by a vibrant community which meets annually at + the Bioinformatics Open Source Conference (BOSC) that traditionally + accompanies the Intelligent Systems in Molecular Biology (ISMB) + meeting. Much like BioPerl, the employment of this library is valuable + for everybody active in the field because of the many tricks of the + trade one learns just by communicating on the mailing list. + . + This is a wrapper package which should enable smooth upgrades to new + versions. + +Package: libbiojava-java-demos +Architecture: all +Depends: ${misc:Depends} +Recommends: libbiojava-java +Description: Example programs for BioJava + The package comes with a wealth of use cases for BioJava. It is generated + together with the API documentation but because of its size of ~3.7MB it + was decided to distribute it separately. + + +Package: libbiojava-java-doc +Section: doc +Architecture: all +Depends: ${misc:Depends} +Recommends: konqueror|html-browser +Suggests: libbiojava-java-demos, libbiojava-java +Description: [Biology] Documentation for BioJava + BioJava is an open-source project dedicated to providing a Java framework + for processing biological data. + . + This package contains the HTML documentation describing the API of BioJava + which was generated automatically by JavaDoc. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
