New release of bioperl this december. Also, I've realized that there are a number of bioperl-* packages that would be nice to have as ebuilds (bioperl-run for example) and am suggesting a new name for the ebuild. I hope to submit a bioperl-run ebuild soon, along with it's corrolarry app-sci/ncbi-tools. There's an update to DEPEND and an uncommenting of the perl-module_src_test function. Finally, the install process has been cleaned up a bit, and the bioperl manpages are not created by default -- this some people may want to modify: allowing them to %man Bio::SomeModule instead of %perldoc Bio::SomeModule. If they desire that behaviour (and to waste diskspace :), they may uncomment the src_unpack function which contains a makefile patch as discussed on the bioperl-l list. Yours, Gontran
Created attachment 7251 [details] bioperl-live-1.2.ebuild
Created attachment 7252 [details, diff] bioperl-live-1.2-manpage.diff
Mind if I take this one, mcummings? sediener is planning to submit ebuilds that depend on it.
Unfortunately, portage doesn't currently have acceptable package move abilities, so I'm going to have to keep the name 'bioperl' for the central package for now, at least until move capability is improved. perl-module_src_test fails for me - two tests from t/RootIO.t fail. Can you reproduce that? It merges fine without perl-module_src_test.
Same thing here RootIO test 14 and 18 failed... I think that this is standard behavior for Bioperl.
Okay, I'm going to comment out the test part.
Committed. Sorry for the very long wait on it.
Erm... forgot to change the resolution.
Something else odd: even though I have DBD::mysql and GD emerged, bioperl says that they are not installed (at the beginning of the ebuild) When I re-emerged GD, DBI and DBD-mysql it worked properly. I think that we may need the r3 ebuild of DBD-mysql
