Re: How to properly integrate cran2deb into Debian?
On 22/02/11 07:27, Andreas Tille wrote:
[...]
As far as I know the cran2deb packages will *not* automatically make it
into sid (be it from CRAN or BioConductor). That is actually the
problem I tried to discuss.
Hi, Andreas.
Sorry, I didn't realise that was the problem you are concerned about.
Having some packages hanging around does
not move them to ftpmaster. This is a manual step which needs actively
checking the copyright. We also can not start a Denial of Service
Attack on ftpmaster by pushing automatically 3000 packages in the
incoming queue.
I understand what you mean, but I've not suggested we do anything like
that. My first objective was to use cran2deb to create Bioconductor deb
packages for my own use under Ubuntu, as Steffen has done for Debian.
We've made our two repositories available for anyone who is interested.
How to submit the packages formally to Debian is a different topic.
So I repeat: If you want *any* BioConductor package
into sid you need to *name* them and let us work on the copyright file
and upload to new queue step by step. There is no automatic propagation
of these packages and there will never be. For a first shot onto this
you might just answer to this mail what BioConductor packages you used
the last two weeks. Lets start with these and add more later.
I only use Bioconductor via GenePattern but I'm helping my colleague
Philip de Groot at Wageningen University to package GenePattern. Many
Bioconductor R libraries are used in different GenePattern modules. At
present we install them from source using R. I could post Philip's R
Bioconductor install script, but it installs dozens of Bioconductor
libraries and their dependencies.
If you want me to name some important Bioconductor packages I use then I
suggest "simpleaffy" and its dependencies:
http://bioconductor.org/packages/2.6/bioc/html/simpleaffy.html
[...]
I perfectly understood this but besides of the purpose of a package
technically it does not matter from what archive you are building. It
just needs to be done. The Debian Med list tries to gather those
information which is connected to the purpose of application and will
adjust it to the general framework.
Debian-Med has already helped me achieve my first objective and I'm very
grateful for that. However, I must leave the task of deciding if
Bioconductor packages are of sufficient general interest to include them
in Debian Sid to other people. Many of us already install and use
Bioconductor packages directly from R, and we accept their licences.
Thanks for helping me to understand a little more what Debian-Med is
about but, as you said, the topic of submitting packages generated
automatically by cran2deb to Debian should be discussed elsewhere.
Bye,
Tony.
Reply to: