htsjdk (3.0.2+dfsg-1~exp0) experimental; urgency=medium * New upstream version 3.0.2+dfsg * Refreshing patches * Raising Standards version to 4.6.1 (no change) * Updating d/watch after a change in Github layout * Updating the POM file and its signature * Depending on libmjson-java instead of libjson-simple-java * Installing the javadoc in /usr/share/doc/libhtsjdk-java/ * Updating the Lintian override related to embedded JS after a change in Lintian syntax * Passing long instead of int in HtsCRAMCodec30And21QueryTest * Excluding new tests requiring the network * Deactivating testFlushNotSpammed which seems to be GC-dependent * Using rhino instead of nashorn as JS engine, to build against openjdk-17 -- Pierre Gruet Tue, 01 Nov 2022 17:37:52 +0100 htsjdk (2.24.1+dfsg-3) unstable; urgency=medium * Restricting the architectures set to run pilon-related autopkgtest, based on the actual tests run in the pilon package -- Pierre Gruet Sat, 05 Mar 2022 07:33:09 +0100 htsjdk (2.24.1+dfsg-2) unstable; urgency=medium * Adding eight autopkgtests to test reverse-dependencies when upgrading htsjdk (Closes: #920588) -- Pierre Gruet Fri, 04 Mar 2022 22:53:22 +0100 htsjdk (2.24.1+dfsg-1) unstable; urgency=medium [ Olivier Sallou ] * lintian fixes in d/patches [ Pierre Gruet ] * New upstream version 2.24.1+dfsg * Setting Standards version to 4.6.0 (no change) * Refreshing d/copyright * Refreshing poms * Refreshing patches * Skipping more tests using http * Refreshing classpath of the build jar * Updating dependencies list * Using json-simple instead of unpackaged mjson * Adding myself as uploader * Removing default gbp.conf file * Adding a Lintian override for the embedded Javascript * Marking the -doc package as Multi-Arch: foreign * Trim trailing whitespace. * Use secure URI in Homepage field. * Forwarding patches * Adding description of patch 120-fix-build.patch * Refreshing libhtsjdk-java.README.Debian -- Pierre Gruet Tue, 23 Nov 2021 22:03:25 +0100 htsjdk (2.23.0+dfsg-2) unstable; urgency=medium * source-only upload -- Olivier Sallou Tue, 22 Sep 2020 13:14:11 +0000 htsjdk (2.23.0+dfsg-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Remove trailing whitespace in debian/changelog (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. -- Andreas Tille Thu, 10 Sep 2020 17:20:43 +0200 htsjdk (2.22.0+dfsg-1) unstable; urgency=medium * New upstream release -- Olivier Sallou Fri, 29 May 2020 11:08:17 +0000 htsjdk (2.18.2+dfsg-2) unstable; urgency=medium [ Matthias Klose ] * Disabled the java/htsjdk/samtools/util/HttpUtilsTest test, requires network access. Closes: #923539 -- Andreas Tille Fri, 01 Mar 2019 23:04:57 +0100 htsjdk (2.18.2+dfsg-1) unstable; urgency=medium * New upstream version * debhelper 12 * Standards-Version: 4.3.0 * Remove trailing whitespace in debian/changelog [ Olivier Sallou ] * d/p/110-debian-lib-version.patch: use scala-library 2.11, v2.12 not yet in Debian * fix some reflection tests issues with testng -- Andreas Tille Thu, 24 Jan 2019 17:31:54 +0100 htsjdk (2.16.1+dfsg-3) unstable; urgency=medium * Fix FTBS on debian test servers due to ip/name resolution Remove related test. Closes: #913839 -- Olivier Sallou Fri, 16 Nov 2018 11:06:41 +0000 htsjdk (2.16.1+dfsg-2) unstable; urgency=medium * Fix FTBS with OpenJDK 11 (Closes: #913566) -- Olivier Sallou Mon, 12 Nov 2018 15:38:32 +0000 htsjdk (2.16.1+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version * debhelper 11 * Standards-Version: 4.2.1 * Skip test requiring http connection * d/rules: Respect DEB_BUILD_OPTIONS in override_dh_auto_test [ Olivier Sallou ] * Skip test requiring ftp connection -- Andreas Tille Wed, 19 Sep 2018 08:11:13 +0200 htsjdk (2.14.3+dfsg-3) unstable; urgency=medium * Reintroduce unit tests after jcommander fix -- Olivier Sallou Mon, 06 Aug 2018 07:03:33 +0000 htsjdk (2.14.3+dfsg-2) unstable; urgency=medium * Upload to unstable * Bumped versioned Build-Depends on default-jdk -- Andreas Tille Thu, 24 May 2018 07:53:54 +0200 htsjdk (2.14.3+dfsg-1) experimental; urgency=medium [ Andreas Tille ] * New upstream version Closes: #894289 * cme fix dpkg-control * Standards-Version: 4.1.4 * Point Vcs-fields to salsa.d.o * Update d/copyright * d/rules: fix get-poms target * Use 2to3 to convert Python script to Python3 [ Olivier Sallou ] * d/patches/30-disable-scalatest.patch Disable scala testing as scalatest is not available in Debian yet * d/rules * Fix JDK9 with --add-modules java.xml.bind in javadoc generation * Fix javadoc generation [TODO - O. Sallou in progress] * Reintroduce unit tests now that gradle 3.4 is available in sid - [done] new patch added for latest upstream, referencing junit classes - [done] added testng() call in build.gradle with a patch and set test call in d/rules back - testng fails now with jcommander classnotfound exception, this is a testng bug (#895886: testng: jcommander classes not found), wait to be fixed to enable tests in d/rules -- Andreas Tille Tue, 17 Apr 2018 15:14:40 +0200 htsjdk (2.8.1+dfsg-2) unstable; urgency=medium * d/patches/50-fix-build.patch, d/rules: fix testng declaration and disable unit testing due to gradle bug that will be fixed by gradle 3.4 => lower severity of #877590 -- Olivier Sallou Wed, 01 Nov 2017 09:25:25 +0000 htsjdk (2.8.1+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version Closes: #847736 * debhelper 10 * d/watch: version=4 [ Vincent Danjean ] * Add junit4 to Build-Depends -- Andreas Tille Sun, 18 Dec 2016 12:40:37 +0100 htsjdk (2.7.0+dfsg-2) unstable; urgency=medium * Fix mess in this changelog (the previous upload is missing the 2.6.1+dfsg-1 entry) -- Vincent Danjean Sun, 27 Nov 2016 21:14:49 +0100 htsjdk (2.7.0+dfsg-1) unstable; urgency=medium * New upstream version -- Vincent Danjean Wed, 16 Nov 2016 21:16:10 +0100 htsjdk (2.6.1+dfsg-1) unstable; urgency=medium * New upstream version -- Andreas Tille Sat, 10 Sep 2016 08:10:12 +0200 htsjdk (2.5.0+dfsg.2-2) unstable; urgency=medium [ Vincent Danjean ] * Tweak build-dependencies [ Andreas Tille ] * Remove some more tests needing http or ftp connections Closes: #830298 -- Andreas Tille Sun, 10 Jul 2016 19:11:39 +0200 htsjdk (2.5.0+dfsg.2-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version * Take over change from debian/jessie-backports branch to successfully obtain JAVA_HOME * Bump Standards-Version to 3.9.8 * Simplified watch file [ Vincent Danjean ] * Skip tests checking the use of the local zip implementation * Adaptation to the new gradle build system * Rework debian/copyright (new source layout) * Add a maven2 pom file for htsjdk -- Vincent Danjean Thu, 07 Jul 2016 00:12:44 +0200 htsjdk (2.1.1+dfsg.1-1) unstable; urgency=medium [ Andreas Tille ] * Make sure repackaged tarball is compressed with xz [ Vincent Danjean ] * New upstream version * Bump Standard-Version to 3.9.7 * Switch back to default-jdk now that it is >= 1.8 -- Vincent Danjean Mon, 14 Mar 2016 22:13:50 +0100 htsjdk (2.0.1+dfsg.1-1) unstable; urgency=medium * New upstream version * remove network tests (Closes: #808593) -- Andreas Tille Mon, 15 Feb 2016 08:28:50 +0100 htsjdk (1.138+dfsg.1-4) unstable; urgency=medium * rename (again) the source package, as htsjdk (1.138+dfsg.1-2) passed the NEW queue. Both name (htsjdk and libhtsjdk-java) are acceptable, so continuing with the one accepted by the FTP team. -- Vincent Danjean Sat, 19 Dec 2015 21:30:58 +0100 libhtsjdk-java (1.138+dfsg.1-3) unstable; urgency=medium * Dump minor debian version part. Even if htsjdk source packages have been rejected from tyhe NEW queue as requested by ftpmaster, the binary packages have been registered and a conflict occured: "libhtsjdk-java_1.138+dfsg.1-1_all.deb: Does not match binary in database." * Really Closes: #798201 -- Vincent Danjean Mon, 07 Sep 2015 12:23:11 +0200 libhtsjdk-java (1.138+dfsg.1-1) unstable; urgency=medium * as Andreas Tille suggestions: + removed Shaun Jackman from Uploaders (can be added back if required) + rename source package from htsjdk to libhtsjdk-java (Closes: #798201) + fix a typo in README.Debian -- Vincent Danjean Mon, 07 Sep 2015 10:10:37 +0200 htsjdk (1.138+dfsg.1-2) unstable; urgency=medium * Fix version in MANIFEST -- Vincent Danjean Mon, 07 Sep 2015 01:31:14 +0200 htsjdk (1.138+dfsg.1-1) unstable; urgency=medium * Upstream split from picard-tools * Initial release. Closes: #798201. -- Vincent Danjean Sun, 06 Sep 2015 01:06:42 +0200