Changelog
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.
ruby-bio (1.4.1-2) unstable; urgency=low
* Switch to gem2deb packaging. Rename binary and source package, introduce
transitional packages.
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)
bioruby (1.4.0-2) unstable; urgency=low
* Fixed long description
Closes: #453022
* New upstream version from past upload just
Closes: #524180
bioruby (1.4.0-1) unstable; urgency=low
* New upstream version
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
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
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
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
bioruby (0.6.2-3) unstable; urgency=low
* Add watch file
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
bioruby (0.6.2-1) unstable; urgency=low
* Initial Release.
-- Ubuntu Archive Auto-Sync <email address hidden> Mon, 17 Oct 2011 13:14:47 +0000
