Bug 35727 - biopython-1.23.ebuild (update)
Bug#: 35727 Product:  Gentoo Linux Version: unspecified Platform: All
OS/Version: Linux Status: RESOLVED Severity: enhancement Priority: P2
Resolution: TEST-REQUEST Assigned To: george@gentoo.org Reported By: pbienst@gentoo.org
Component: Ebuilds
URL: 
Summary: biopython-1.23.ebuild (update)
Keywords:  
Status Whiteboard: 
Opened: 2003-12-13 07:41 0000
Description:   Opened: 2003-12-13 07:41 0000 
Ebuild for new version (also fixes a spelling error in the package description)

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

------- Comment #1 From Peter Bienstman (RETIRED) 2003-12-13 07:42:23 0000 ------- 
Created an attachment (id=22138) [details]
new ebuild

------- Comment #2 From Alastair Tse (RETIRED) 2003-12-13 16:57:08 0000 ------- 
throwing this to you george :)

------- Comment #3 From George Shapovalov 2003-12-29 21:14:45 0000 ------- 
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 From Peter Bienstman (RETIRED) 2003-12-30 02:07:54 0000 ------- 
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 From Peter Bienstman (RETIRED) 2003-12-30 02:08:49 0000 ------- 
Created an attachment (id=22838) [details]
biopython_1.21_1.23.diff

------- Comment #6 From George Shapovalov 2003-12-30 18:47:51 0000 ------- 
Ok, thats much better now :).

I committed the ebuild, please test.

George.