ruby-bio (1.5.0-2) unstable; urgency=medium * restore fix_definition_CutSymbol_in_test_cut_symbol.patch to avoid transient FTBFS because of undefined CutSymbol class * Bump Standards-Version to 3.9.7 (no changes needed) * Use https in Vcs-* fields * Fix syntax of copyright file -- Cédric Boutillier Thu, 03 Mar 2016 21:32:25 +0100 ruby-bio (1.5.0-1) unstable; urgency=medium * Team upload. * New upstream version (Closes: #804068) * Remove upstream-applied patch fix_shebang_for_examples * Refresh Debian packaging using dh-make-ruby -w. Bumps Standard-Version to 3.9.6. -- Christian Hofstaedtler Sun, 08 Nov 2015 22:16:50 +0000 ruby-bio (1.4.3.0001-2) unstable; urgency=low * debian/ruby-tests.rb: choose to define external encoding if Encoding is defined instead of checking version of Ruby, which was too strict. (Closes: #720240) * Tighten dependency on ruby-libxml and gem2deb to ensure Ruby 2.0 support. (Closes: #730644) * Bump Standards-Version to 3.9.5 (no changes needed) -- Cédric Boutillier Tue, 24 Dec 2013 21:18:56 +0100 ruby-bio (1.4.3.0001-1) unstable; urgency=low * Imported Upstream version 1.4.3.0001 * debian/control: + remove obsolete DM-Upload-Allowed flag + use canonical URI in Vcs-* fields + build-depend on ruby-test-unit + bump Standards-Version to 3.9.4 (no changes needed) + update my email address + drop transitional packages * debian/patches: + drop disable-test-soap.patch, fixed upstream + drop fix_definition_CutSymbol_in_test_cut_symbol.patch, fixed upstream + drop do_not_rely_on_keys_order_for_hashes.patch, fixed upstream + omit chi2 tests instead of commenting them out + add remove_rubygems.patch: remove requirement on rubygems from bin/bioruby * debian/ruby-tests.rb: do not exclude manually tests requiring network in ruby-tests.rb, now moved to a dedicated directory by upstream * remove debian/source/lintian-overrides, related to transitional packages * install KNOWN_ISSUES.rdoc as documentation * provide more complete copyright information -- Cédric Boutillier Tue, 06 Aug 2013 23:19:36 +0200 ruby-bio (1.4.2-3) unstable; urgency=low [ Andreas Tille ] * debian/upstream: Add citation information according to https://wiki.debian.org/UpstreamMetadata (Closes: #675061) [ Cédric Boutillier ] * Add myself to Uploaders: * Bump Standards-Version: to 3.9.3 (no changes needed) * Update debian/copyright to cover also setup.rb, sample/* and test/data/uniprot/p53_human.uniprot * debian/patches: + add disable_tests_using_chi2.patch, disabling randomly failing tests + add do_not_rely_on_keys_order_for_hashes.patch, fixing FTBFS (Closes: #674337) + add fix_shebang_for_examples.patch, ensuring the shebang in sample/biofetch.rb is correct * Build-depend on gem2deb >= 0.3.0 * Register HTML tutorials in doc-base -- Cédric Boutillier Mon, 25 Jun 2012 11:34:26 +0200 ruby-bio (1.4.2-2) unstable; urgency=low * Remove some tests depending on a access to the Internet. Closes: #654985 * Add fix_definition_CutSymbol_in_test_cut_symbol.patch to ensure that Bio::RestrictionEnzyme::CutSymbol is defined * Set to extra the priority of transitional packages * Depends on ruby-libxml instead of libxml-ruby -- Cédric Boutillier Fri, 17 Feb 2012 15:22:29 +0100 ruby-bio (1.4.2-1) unstable; urgency=low * New upstream version. + Fixes build failure. Closes: #642035. * fix typos in debian/copyright. * document disable-test-soap.patch. -- Lucas Nussbaum Sun, 25 Sep 2011 11:01:38 +0200 ruby-bio (1.4.1-2) unstable; urgency=low * Switch to gem2deb packaging. Rename binary and source package, introduce transitional packages. -- Lucas Nussbaum Thu, 28 Jul 2011 17:25:55 +0200 bioruby (1.4.1-1) unstable; urgency=low * New upstream version * debian/control: - Standards-Version: 3.9.1 (no changes needed) - Added Recommends: hmmer, mafft, muscle, probcons, sim4, t-coffee which are called in lib/bio/appl - Added Suggests: clustalw (non-free), emboss (large and thus not always wanted on the system just for BioRuby development) * Source format 3.0 (quilt) -- Andreas Tille Thu, 25 Nov 2010 16:04:31 +0100 bioruby (1.4.0-2) unstable; urgency=low * Fixed long description Closes: #453022 * New upstream version from past upload just Closes: #524180 -- Andreas Tille Fri, 22 Jan 2010 16:26:50 +0100 bioruby (1.4.0-1) unstable; urgency=low * New upstream version -- Andreas Tille Thu, 21 Jan 2010 11:42:04 +0100 bioruby (1.3.1-1) unstable; urgency=low * debian/control: - Group maintenance in Debian Med team - Added myself as uploader - Standards-Version: 3.8.3 (no changes needed) - Debhelper >= 7.1 - Homepage and Vcs fileds -- Andreas Tille Sun, 04 Oct 2009 09:15:28 +0200 bioruby (1.1.0-1) unstable; urgency=low * New upstream version + Bioruby is now distributed under the same terms as ruby itself. This gives you the option of using the GPL or a similar copyleft license. See /usr/share/doc/libbio-ruby/copyright for details on the alternate license. + Lots of new and obsolete classes, see the upstream changelog for details + BioRuby shell rewritten to utilize the rails generators + Many bugfixes * Re-work build system to utilize install.rb instead of my custom rules file + Enable unit tests in the build + Don't hardcode the binary names when hacking off the .rb suffix. Use wildcards and a for loop to rename them + Remove the libbio-ruby1.8.dirs file. The directories get installed by the install.rb now + The docs are built by install.rb now, so don't do custom stuff for them in debian/rules + Move building the manpages to the build-stamp target, rather than the build target + Add ruby to build-depends -- David Nusinow Sun, 22 Jul 2007 18:42:39 -0400 bioruby (1.0.0-1) unstable; urgency=low * New upstream version * Add the bioruby shell program * Add the Changes-0.7.html doc describing updates since 0.6.x * Bump standards version to 3.7.2.0. No changes needed. * Bump debhelper compat to 5 * Move debhelper to build-depends from build-depends-indep -- David Nusinow Thu, 17 Aug 2006 00:28:21 +0000 bioruby (0.6.4-1) unstable; urgency=low * New upstream release + siRNA designer class is contributed by Itoshi Nikaido. (lib/bio/util/sirna.rb) + fastacmd wrapper is contributed by Shinji Shigenobu. (lib/bio/io/fastacmd.rb) + bl2seq parser is contributed by Tomoaki Nishiyama. (lib/bio/appl/bl2seq/report.rb) + new application execution factory is provided. (lib/bio/command.rb) + FlatFile class can accept Blast results, Spidey, Blat, Sim4 and some KEGG formats (KO, GLYCAN, REACTION) + some methods are added to SPTr class proposed by Luca Pireddu. (lib/bio/db/embl/sptr.rb) + external2go parser is added. (lib/bio/db/go.rb) + improved amino/nucleic data classes to have some handy methods. (lib/bio/data/) + fixed hmmer parser (by Masashi Fujita) and remote execution of blast and fasta using GenomeNet. + some English documentations are added. (doc/) * Re-organize debian/rules handling of docs + Ship new English tutorial and KEGG_API. These are turned to html with rd2 + Put document building commands in the build target instead of configure + Add commands to remove generated documents in the clean target + Put package building commands in binary-indep where they belong * Add build-dependency on rdtool to build html docs using rd2 * Minor debian/copyright cleanup to get rid of stupid lintian warning about boilerplate * Change Build-Depends to Build-Depends-Indep * Update standards version to 3.6.2. No changes needed. * Add ruby1.8 to recommends for libbio-ruby1.8 -- David Nusinow Thu, 1 Sep 2005 14:04:35 -0400 bioruby (0.6.2-3) unstable; urgency=low * Add watch file -- David Nusinow Thu, 7 Apr 2005 22:12:44 -0400 bioruby (0.6.2-2) unstable; urgency=low * Depend on libruby1.8 instead of ruby1.8 to bring in line with ruby policy * Add Recommends on blast2 for local blast * Depend on docbook-to-man; closes: #302360 -- David Nusinow Tue, 1 Feb 2005 00:25:45 -0500 bioruby (0.6.2-1) unstable; urgency=low * Initial Release. -- David Nusinow Mon, 31 Jan 2005 11:11:55 -0500