Bug 13826 – Updated Ebuild bioperl-live-1.2.ebuild

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Gontran Zepeda 2003-01-13 02:29:12 UTC]

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

[Comment 1 Gontran Zepeda 2003-01-13 02:30:09 UTC]

Created attachment 7251 [details]
bioperl-live-1.2.ebuild

[Comment 2 Gontran Zepeda 2003-01-13 02:31:43 UTC]

Created attachment 7252 [details, diff]
bioperl-live-1.2-manpage.diff

[Comment 3 Jon Portnoy (RETIRED) 2003-04-24 10:17:05 UTC]

Mind if I take this one, mcummings? sediener is planning to submit ebuilds that depend on it.

[Comment 4 Jon Portnoy (RETIRED) 2003-04-24 15:54:28 UTC]

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.

[Comment 5 Stephen Diener (RETIRED) 2003-04-25 19:14:22 UTC]

Same thing here  RootIO test 14 and 18 failed... I think that this is standard behavior for Bioperl.  

[Comment 6 Jon Portnoy (RETIRED) 2003-04-25 19:18:17 UTC]

Okay, I'm going to comment out the test part.

[Comment 7 Jon Portnoy (RETIRED) 2003-04-25 19:28:33 UTC]

Committed. Sorry for the very long wait on it.

[Comment 8 Jon Portnoy (RETIRED) 2003-04-25 19:29:07 UTC]

Erm... forgot to change the resolution.

[Comment 9 Stephen Diener (RETIRED) 2003-04-25 19:39:21 UTC]

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