Re: How to properly integrate cran2deb into Debian?
On 21/02/11 17:38, Andreas Tille wrote:
[...]
If Bioconductor is no longer releavant to Debian-Med, what were our
discussions in Travemuende, and Steffen's work on cran2deb all about?
Huh - that seems to be a perfect missunderstanding to me! How in the
world came you to the conclusion Bioconductor would not be relevant to
Debian Med?
Hi, Andreas.
Our misunderstanding is not perfect, but at least it's symmetrical :-)
I think Bioconductor *is* relevant to Debian-Med, and I'm grateful to
the Debian-Med developers who I met in Travemuende for their help with
automatically packaging Bioconductor for Ubuntu using cran2deb.
Do you think so because I suggested to move the discussion
to Debian Science list?
Yes, I misunderstood why you wanted to move the discussion...
My reason to do so was because there are
several technicans involved in R packaging lurking at this list (most
specifically the main R packagers like Dirk) but not here on the Debian
Med list and we would hide competent eyes from our discussion here. The
question was a pure technical one and not about the content of handling
bio-medical problems.
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.
So my original offer stays valid: Just provide a list of those
BioConductor packages which have the highest relevance for you and we
will include them into official Debian (in addition to the BioConductor
cran2deb effort).
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.
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of outdated packages.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same time sovling the problem of outdated packages for cran2deb *and*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.
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.
Bye,
Tony.
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