Bug 35727 – biopython-1.23.ebuild (update)

• Product: Gentoo Linux
• Status: RESOLVED TEST-REQUEST

[Description Peter Bienstman (RETIRED) 2003-12-13 07:41:42 UTC]

Ebuild for new version (also fixes a spelling error in the package description)

Reproducible: Always
Steps to Reproduce:
1.
2.
3.

[Comment 1 Peter Bienstman (RETIRED) 2003-12-13 07:42:23 UTC]

Created attachment 22138 [details]
new ebuild

[Comment 2 Alastair Tse (RETIRED) 2003-12-13 16:57:08 UTC]

throwing this to you george :)

[Comment 3 George Shapovalov (RETIRED) 2003-12-29 21:14:45 UTC]

Alastair: 
this should have gone to sci@... actually, now that we have a herd with working alias in place.

Peter:
First, no need to attach the ebuild when this is a trivial version bump. It is sufficient to rust drop a line that "I renamed the existing ebuild and it installed fine.." Or submit a patch of there were changes (in this case these were only decapitalisation of a few words in DESCRIPTION, so patch isn't even necessary). This makes it apparent what changes are necessary right away..


2nd: Looks like setup.py got updated for this version in a scewy way. During src_install I am getting this (last few lines):

byte-compiling /var/tmp/portage/biopython-1.23/image//usr/lib/python2.3/site-packages/Martel/RecordReader.py to RecordReader.pyc
running install_data
creating /usr/lib/python2.3/site-packages/Bio
error: could not create '/usr/lib/python2.3/site-packages/Bio': Permission denied

Note, I am running with userpriv usersandbox in FEATURES, so apparently this gets caught even before it gets to the "standard" sandbox. Could you please take a look at this?
Looks like setup.py does not honor DESTDIR setting (at least not everywhere). You may try searching for "install_data" goal and do some seding..

It might work without usersandbox and usepriv, but this wasn't the case in 1.21, so it is better to fix this.

George

[Comment 4 Peter Bienstman (RETIRED) 2003-12-30 02:07:54 UTC]

Sorry, I missed that because I had a /usr/lib/python2.2/site-packages/Bio directory around from a non-portage install of that package.

Meanwhile I've discovered that there's a distutils eclass, so I've converted the ebuild to use it, which fixes the problem.

[Comment 5 Peter Bienstman (RETIRED) 2003-12-30 02:08:49 UTC]

Created attachment 22838 [details]
biopython_1.21_1.23.diff

[Comment 6 George Shapovalov (RETIRED) 2003-12-30 18:47:51 UTC]

Ok, thats much better now :).

I committed the ebuild, please test.

George.