[EMBOSS] emboss update on ubuntu fails

Tiwari, Bela btiwari at ceh.ac.uk
Thu Aug 12 09:06:40 UTC 2010


This  is an issue specifically about the bio-linux-emboss package (which then calls on debian-med emboss package and the associated emboss-derivative packages).  Ie. nothing to do with the EMBOSS code itself. 

The central issue would appear to be the requirements of the emboss-related packages we supply,  which are appropriate for Ubuntu 10.04. In particular, the emboss-lib package depends on versions of packages that perhaps are not available for 8.04? (Without looking at this more closely, I couldn't say for sure).

However, as this issue is not an Emboss bug, it's probably best for me to get in touch with  Jörg directly rather than go into it in detail on this list.



Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental
Bioinformatics Centre
tel: 01491 69 2705

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
From: emboss-bounces at lists.open-bio.org [emboss-bounces at lists.open-bio.org] On Behalf Of Jörg Mühlisch [jmuehlis at uni-muenster.de]
Sent: 12 August 2010 09:00
To: emboss at lists.open-bio.org
Subject: [EMBOSS] emboss update on ubuntu fails

Hi All,

while updating emboss using synaptic I ran into a problem. I use

http://envgen.nox.ac.uk/bio-linux unstable bio-linux as package source.

On ubuntu 8.04 emboss-data and emboss-doc were upgraded to 6.3.1-3, but
emboss-lib was not updated from 6.0.1-11 and emboss was deinstalled, but
not replaced by 6.3.1-3. The column newest Version remains at 6.0.1-3
for both.
If I try to install the dependencies are not fullfilled:
  Hängt ab: »emboss-data (=6.0.1-11)«, aber es wird »6.3.1-3«
(Depends on: »emboss-data (=6.0.1-11)«, but »6.3.1-3« will be

On another 8.04 system the situation is the same, although emboss was
not deinstalled. If I update the packages I can not update emboss-data
(already installed), because the authenticity of the package can not be

Hope this will help to solve the problem.

For my situation the only solution I found would be to force
installation of 6.0.1-3 for all packages to fulfill the dependencies or
to deinstall and reinstall all packages, but I m afraid this will not
work, because the packages were not found.

I would appreciate any help to solve this problem.



Dr. Jörg Mühlisch

Klinik- und Poliklinik für Kinder und Jugendmedizin
Pädiatrische Hämatologie und Onkologie

Albert-Schweitzer-Str. 33
48129 Münster

Tel.: +49-251/83-52491
Fax.: +49-251/83-55740

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