Ubuntu
python-biopython package

Please sync python-biopython (1.44-2) from sid to gutsy

Hardy (8.04)
Bug #156047

Bug #156047 reported by sundol on 2007-10-23

	Status	Importance	Assigned to
python-biopython (Debian)	Fix Released	Unknown	debbugs #452379
python-biopython (Ubuntu)	Fix Released	Undecided	Unassigned
Gutsy	Won't Fix	Undecided	Unassigned
Hardy	Fix Released	Undecided	Unassigned

Bug Description

Binary package hint: python-biopython

from Bio.PDB import *
works well at Feisty but not at Gutsy

How to reproduce ..
*************************
myid@mypc:~/$python
Python 2.5.1 (r251:54863, Oct 5 2007, 13:36:32)
[GCC 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)] on linux2
Type "help", "copyright", "credits" or "license" for more information.

>>> import Bio.PDB
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/var/lib/python-support/python2.5/Bio/PDB/__init__.py", line 15, in <module>
    from PDBParser import PDBParser
  File "/var/lib/python-support/python2.5/Bio/PDB/PDBParser.py", line 12, in <module>
    from StructureBuilder import StructureBuilder
  File "/var/lib/python-support/python2.5/Bio/PDB/StructureBuilder.py", line 21, in <module>
    from Atom import Atom, DisorderedAtom
  File "/var/lib/python-support/python2.5/Bio/PDB/Atom.py", line 11, in <module>
    from Vector import Vector
  File "/var/lib/python-support/python2.5/Bio/PDB/Vector.py", line 9, in <module>
    from LinearAlgebra import determinant, eigenvectors
ImportError: No module named LinearAlgebra

Tags:

Revision history for this message

sundol (hyunchul-love-me-deactivatedaccount-deactivatedaccount-deactivatedaccount) wrote on 2007-10-23:

My system has been upgraded to gutsy from feisty by synaptic package manager.
When it was feisty, this worked well.

Revision history for this message

sundol (hyunchul-love-me-deactivatedaccount-deactivatedaccount-deactivatedaccount) wrote on 2007-10-23: This is a dependency error

Sorry. Above conment was done by mistake.
Actually, it was a dependency error.

apt-get install python-numeric-ext solve this problem.

Revision history for this message

Tristan Leo (tleo) wrote on 2007-10-26: Re: import Bio.PDB of python-biopython at gutsy

Thank you for your bug report. I can confirm this bug in Gutsy.

Changed in python-biopython:
status:	New → Confirmed

Revision history for this message

Tristan Leo (tleo) wrote on 2007-10-26:

python-biopython_1.43-2ubuntu1.debdiff Edit (1.8 KiB, text/plain)

I hope this fix the bug and all is correct, it is my first debdiff.

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Ming Hua (minghua) wrote on 2007-10-26:

To be honest, I am not sure plainly adding python-numeric-ext as dependency is the best solution. Maybe the import error can be handled more gracefully and make python-numeric-ext just a Recommends.

I also think the Debian maintainer should be consulted before we try fix this bug with out own patch.

Tristan's patch looks mostly correct, except that the distribution in the changelog should be hardy, not gutsy.

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Johan Euphrosine (proppy) wrote on 2007-11-22:

I've reported the problem to debian BTS.

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Johan Euphrosine (proppy) wrote on 2007-11-22:

From the Debian maintainer:

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

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

Thanks

--
Philipp Benner

Changed in python-biopython:
assignee:	nobody → proppy
status:	Confirmed → In Progress

Revision history for this message

Johan Euphrosine (proppy) wrote on 2007-11-22:

python-biopython-recommends-python-numeric-ext-hardy.debdiff Edit (2.0 KiB, text/plain)

The following debdiff mirrors the changes from debian.
Please review.

Revision history for this message

Johan Euphrosine (proppy) wrote on 2007-11-22:

python-biopython-recommends-python-numeric-ext-hardy-2.debdiff Edit (2.0 KiB, text/plain)

Added change of maintainer in the changelog

Johan Euphrosine (proppy) on 2007-11-22

Changed in python-biopython:
assignee:	nobody → proppy
status:	New → In Progress
assignee:	proppy → nobody
status:	In Progress → Confirmed

Revision history for this message

Scott Kitterman (kitterman) wrote on 2007-11-23:

#10

Given that the Debian maintainer has said he'd fix this and there is not currently an Ubuntu diff, I'd wait for Debian to fix it rather than do an Ubuntu upload now that would require a manual merge (or at least manual sync request) when the fixed Debian is uploaded. Then I'd revist after Debian import freeze if needed.

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Luca Falavigna (dktrkranz) wrote on 2007-11-23:

#11

Additionally, this fix is valid only in Debian ATM. Debian's APT Development Team turned on installation of recommended packages since 0.7.7 (see http://lists.debian.org/debian-devel-announce/2007/08/msg00000.html, thanks norsetto for the link), while Hardy still has 0.7.6*.

Revision history for this message

Scott Kitterman (kitterman) wrote on 2007-11-23: Re: [Bug 156047] Re: import Bio.PDB of python-biopython at gutsy

#12

If it's required to make the package work Recommends is wrong whether or
not it's automatically installed.

Revision history for this message

Johan Euphrosine (proppy) wrote on 2007-11-23: Re: import Bio.PDB of python-biopython at gutsy

#13

The DD told me that this package should be uploaded before 13th, so I guess we can wait for it, as Scott Kitterman suggested, and then request for a Sync.

Revision history for this message

Andrea Veri (av) wrote on 2007-11-23:

#14

Un-subscribing u-u-s as far as nothing needs sponsorship here. Feel free to re-subscribe when Debian will upload a new revision, updating the Bug Title to a sync request. Thanks.

Revision history for this message

Nicolas Valcarcel (nvalcarcel) wrote on 2007-11-30:

#15

python-biopython_1.44-1ubuntu1.debdiff Edit (1.9 KiB, text/plain)

Here is a patch resolving this problem

Bug Watch Updater (bug-watch-updater) on 2007-12-04

Changed in python-biopython:
status:	Unknown → New

Revision history for this message

Johan Euphrosine (proppy) wrote on 2007-12-04:

#16

python-biopython (1.44-2) unstable; urgency=low

* Moved suggested package python-numeric-ext to recommends field
(Closes: #452379).

Revision history for this message

Cesare Tirabassi (norsetto) wrote on 2007-12-04:

#17

Published:

https://launchpad.net/ubuntu/+source/python-biopython/1.44-2

Please set it to fix released once all binaries are built.

Changed in python-biopython:
status:	Confirmed → Fix Committed

Revision history for this message

Cesare Tirabassi (norsetto) wrote on 2007-12-04:

#18

@Johan,

any reasons why the gutsy one is still in progress?
I thought we'd agreed that we won't fix it for gutsy, or am I mistaken?
Unsubscribing u-u-s.

Revision history for this message

Johan Euphrosine (proppy) wrote on 2007-12-04:

#19

IIRC

It has been said that moving python-numeric-ext to Recommends is not the correct fix for gutsy,
since gutsy's apt does not install Recommends by default.

Is moving the python-numeric-ext to Depends for gutsy the correct way to go ?
And then ask for an SRU ?

Or shall we ask apt and python-biopython to be updated in gutsy-backports ?

Revision history for this message

Cesare Tirabassi (norsetto) wrote on 2007-12-04:

#20

The way I understood it is that this was not material for an SRU. The fact that we can't apply the fix made in the development version is also against us.
Unless you receive opinions to the contrary, I would just mark it as won't fix.
The work-around solution is well documented in this bug report for other users with the same problem.

Revision history for this message

Johan Euphrosine (proppy) wrote on 2007-12-04:

#21

Sorry, I don't see "Won't Fix" in available BugStatutes

https://help.launchpad.net/BugStatuses states that:
Triaged and Won't Fix - are available only to members of your project's Bug Contact team and the project's owners.

Could someone for whom this option is available set the bug to "Won't Fix".

Thanks in advance.

Scott Kitterman (kitterman) on 2007-12-04

Changed in python-biopython:
assignee:	proppy → nobody
status:	In Progress → Won't Fix

Bug Watch Updater (bug-watch-updater) on 2007-12-05

Changed in python-biopython:
status:	New → Fix Released

Revision history for this message

Cesare Tirabassi (norsetto) wrote on 2007-12-05:

#22

python-biopython (1.44-2) unstable; urgency=low

  * Moved suggested package python-numeric-ext to recommends field
    (Closes: #452379).
  * Moved wise from recommends to suggests field.
  * Removed package tags from debian/control.
  * Added homepage field to debian/control.
  * Changed maintainer to Debian-Med Packaging Team.
  * Removed .DS_Store.gz file from doc package.

-- Ubuntu Archive Auto-Sync < <email address hidden>> Tue, 04 Dec 2007 11:55:42 +0000