[Bioperl-l] ubuntu installation

Charles Plessy charles-listes+bioperl at plessy.org
Thu Jul 23 01:06:08 UTC 2009

Le Wed, Jul 22, 2009 at 05:41:15PM -0700, Robert Buels a écrit :
> According to `apt-cache show bioperl` on ubuntu, the Debian/Ubuntu  
> bioperl packages is maintained by the Debian-Med Packaging Team  
> <debian-med-packaging at lists.alioth.debian.org>, meaning they are the  
> ones who update and maintain it.  I wonder who 'they' are?  Are any of  
> you Debian Med packagers on this list?
> Looking at  
> http://packages.debian.org/search?suite=all&searchon=names&keywords=bioperl 
> it looks like 1.6 has made it into Debian testing and unstable, so I  
> would guess that it would probably be in the next ubuntu release, I  
> would think.
> However, looking at the ubuntu packages site,  
> http://packages.ubuntu.com/search?keywords=bioperl&searchon=names&suite=all&section=all 
> , it looks like karmic, the next release still has 1.5.2 in it.  This  
> could be a problem.  Perhaps we should email the Ubuntu MOTU Developers  
> <ubuntu-motu at lists.ubuntu.com> , who are maintaining the ubuntu version  
> of the package and ask them to make sure that 1.6 gets into Karmic?

Hello Robert,

there is a strange discrepancy between packages.ubuntu.com and launchpad.net,
and it seems that bioperl 1.6 is already in Karmic. Indeed, the source download
links in packages.ubuntu.com point to that version. I just notified the contact
person for packages.u.c of this problem.


The Ubuntu packages are directly synchronised from Debian and there is no
specific Ubuntu maintainer for them, but it seems that requests through
Launchpad bugs are answered, as in the case of the lastest request for
synchronisat (https://bugs.launchpad.net/ubuntu/+source/bioperl/+bug/324001).
I am not able to do tests on Ubuntu as I am only using Debian, so I recommend
to report problems to the distribution you use first. I monitor both and this
mailing list anyway.

By the way, feel free to make any proposition or comment on our mailing list
(debian-med at lists.debian.org) if you think that some key bioinformatics
programs are missing on your Debian or Ubuntu systems. Also, we welcome new
team members, so when you meet people who wonder how to contribute to open
source bioinformatics without writing software, do not hesitate to suggest them
to join our packaging team :)

Have a nice day,

Charles Plessy
Debian Med packaging team,
Tsurumi, Kanagawa, Japan

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