Debian Bug report logs - #452379
python-biopython: import Bio.PDB failed on sid

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Johan Euphrosine <proppy@aminche.com>

To: submit@bugs.debian.org

Subject: python-biopython: import Bio.PDB failed on sid

Date: Thu, 22 Nov 2007 13:31:46 +0100

Package: python-biopython
Version: 1.43-2

Importing Bio.PDB in python/sid results in the following traceback:
>>> import Bio.PDB
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/var/lib/python-support/python2.4/Bio/PDB/__init__.py", line 15, in ?
    from PDBParser import PDBParser
  File "/var/lib/python-support/python2.4/Bio/PDB/PDBParser.py", line 12, in ?
    from StructureBuilder import StructureBuilder
  File "/var/lib/python-support/python2.4/Bio/PDB/StructureBuilder.py", line 21, in ?
    from Atom import Atom, DisorderedAtom 
  File "/var/lib/python-support/python2.4/Bio/PDB/Atom.py", line 11, in ?
    from Vector import Vector
  File "/var/lib/python-support/python2.4/Bio/PDB/Vector.py", line 9, in ?
    from LinearAlgebra import determinant, eigenvectors
ImportError: No module named LinearAlgebra

This problem is solved by:
apt-get install python-numeric-ext

I see python-numeric-ext is currently in python-biopython's Suggested packages:

# cat control | grep python-numeric-ext
Suggests: python-numeric-ext, python-tk

Should it be moved into Recommends to solve this issue ?

Thanks in advance.
-- 
bou ^

Message #10 received at 452379@bugs.debian.org (full text, mbox, reply):

From: Philipp Benner <pbenner@uos.de>

To: Johan Euphrosine <proppy@aminche.com>, 452379@bugs.debian.org

Subject: Re: Bug#452379: python-biopython: import Bio.PDB failed on sid

Date: Thu, 22 Nov 2007 13:25:19 +0100

> Should it be moved into Recommends to solve this issue ?

Right, I'll fix that with the next upload.

Thanks

-- 
Philipp Benner

Message #15 received at 452379@bugs.debian.org (full text, mbox, reply):

From: Johan Euphrosine <proppy@aminche.com>

To: 452379@bugs.debian.org

Subject: python-numeric-ext-recommends.debdiff

Date: Thu, 22 Nov 2007 13:50:40 +0100

[Message part 1 (text/plain, inline)]

If yes, please review that the following debdiff corrects the issue.
Thanks.

[python-numeric-ext-recommends.debdiff (application/octet-stream, attachment)]

[Message part 3 (text/plain, inline)]

-- 
bou ^

Message #20 received at 452379@bugs.debian.org (full text, mbox, reply):

From: Philipp Benner <pbenner@uos.de>

To: Johan Euphrosine <proppy@aminche.com>, 452379@bugs.debian.org

Subject: Re: Bug#452379: python-numeric-ext-recommends.debdiff

Date: Thu, 22 Nov 2007 13:51:04 +0100

On Thu, Nov 22, 2007 at 01:50:40PM +0100, Johan Euphrosine wrote:
> If yes, please review that the following debdiff corrects the issue.
> Thanks.

Looks good, is almost identical to my changes. Just have a look at
svn://svn.debian.org/debian-med/trunk/packages/python-biopython/

Regards

-- 
Philipp Benner

Message #25 received at 452379-done@bugs.debian.org (full text, mbox, reply):

From: Philipp Benner <pbenner@uos.de>

To: 452379-done@bugs.debian.org

Subject: manually closing this bug

Date: Tue, 4 Dec 2007 14:24:07 +0100

-- 
Philipp Benner

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