[Bio-Linux] Upgrading to Bio-Linux 7 from 6

[GOSSNER Anton]

Hi Tim,

gossnera at gossnera-desktop[gossnera] dpkg -s python-biopython          [ 9:25AM]
Package: python-biopython
Status: install ok installed
Priority: optional
Section: python
Installed-Size: 5835
Maintainer: Ubuntu Developers <ubuntu-devel-discuss at lists.ubuntu.com>
Architecture: amd64
Version: 1.58-1
Replaces: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1)
Provides: python2.7-biopython
Depends: python (<< 2.8), python (>= 2.7), python-support (>= 0.90.0), libc6 (>= 2.4), python-numpy, python-reportlab
Recommends: python-biopython-doc (= 1.58-1)
Suggests: python-tk, wise, muscle, clustalw, mafft, emboss, blast2
Conflicts: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1)
Description: Python library for bioinformatics
 The Biopython Project is an international association
 of developers of freely available Python tools for
 computational molecular biology.
 .
 It is a distributed collaborative effort to develop Python
 libraries and applications which address the needs of
 current and future work in bioinformatics. The source code
 is made available under the Biopython License, which is
 extremely liberal and compatible with almost every license
 in the world. We work along with the Open Bioinformatics
 Foundation, who generously provide web and CVS space for
 the project.
Original-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Homepage: http://biopython.org
Python-Version: 2.7
gossnera at gossnera-desktop[gossnera]                                                                                     [ 9:25AM]

















________________________________________
From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth [tbooth at ceh.ac.uk]
Sent: 30 November 2012 17:13
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] Upgrading to Bio-Linux 7 from 6

Hi Anton,

This is more likely a problem with my script than with your system, or
rather there is some minor issue and my script is making a meal of it.

What do you get when you ask dpkg specifically about biopython? - ie:

dpkg -s python-biopython

Also the thing with removing and reinstalling t-coffee is expected -
it's a crude workaround to a problem someone spotted during beta
testing.

Cheers,

TIM

On Fri, 2012-11-30 at 10:40 +0000, GOSSNER Anton wrote:
> Hi,
>
> Just wondered if anybody is having the same problem and has solved it or if need to do a full install.
>
> Following Tims instructions for upgrading, all gone well with initial upgrade of Ubuntu and start of Bio-Linux packages but always stops and exits with;
>
> Verifying that everything installed...
> python-biopython  failed to install
> python-biopython-doc  failed to install
> Not all packages installed properly - exiting.
>
> despite the fact python is installed;
>
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> python-software-properties is already the newest version.
>
>
> Have removed and reinstalled via Synaptic Package Manager, restarted and rerun the script numerous times and various different combinations of installing and uninstalling  python but to no avail also run "apt-get autoremove"
>
> No joy, any ideas?, also seems to uninstall Coffee and reinstall in every time I run the script.
>
> Anton

--
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB

http://nebc.nerc.ac.uk
+44 1491 69 2705
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