[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Re: How to properly integrate cran2deb into Debian?

On Mon, Feb 21, 2011 at 10:38:43PM +0000, Tony Travis wrote:
> Both me and Steffen have signed up to the cran2deb project, but you are  
> right that many others are working on CRAN. What surprised me is that  
> few people seem to be interested in packaging Bioconductor, which is not  
> part of CRAN. One reason, as we've discussed, is that Bioconductor is  
> not 'core' R. However, because the Bioconductor source archive is the  
> same format as CRAN it means we can, and did, use cran2deb on it.

... and because cran2deb is used I wanted to discuss with as many as
possible cran2deb people.

> In the short-term, I'll use the Ubuntu repository that Steffen helped me  
> to create on our bioinformatics server in Aberdeen. If and when the  
> cran2deb Bioconductor packages for Debian that Steffen has built make it  
> into Sid, and then into Ubuntu I'll look at them again.

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.  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.  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.

>>  This has several advantages but also the drawback
>> of outdated packages.  My concern was to keep the advantages by at the
>> same time sovling the problem of outdated packages for cran2deb *and*
>> BioConductor - but that's simply a non-biological question and does
>> not need to be discussed primarily here on this list.
> I think we need to be clear that we are not attempting to package CRAN,  
> rather we are using the same cran2deb software to package Bioconductor.

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.

>> Sorry if I have uses a misunderstandable wording
> No problem, and I hope I've explained clearly that my interest is in  
> Bioconductor not CRAN. I already use the official CRAN Ubuntu deb's.

Yes, you did, but you did not yet provided a list of your most favourite
BioConductor packages.

Kind regards



Reply to: