Re: Packaging r-bioc-simpleaffy
Hello,
On 02/26/2011 02:48 PM, Tony Travis wrote:
> On 26/02/11 12:59, Karsten Hilbert wrote:
>>> We could overrule this, certainly, as Dirk keeps reminding us, this
>>> is our repository. But we certainly need to think twice about if those
>>> packages are not possibly too much evolving to be of any use in the
>>> main distribution in the first place. For BioConductor's Debian packages
>>> I would tend to think that a separate repository may be preferable.
>>
>> Does this not mean that there ought to be a more convenient way for
>> users to discover that they need to activate an additional repository
>> (say, by somehow providing "pointers" from dummy meta "packages" within
>> the main archive towards other repos, or else via some tasks-like
>> mechanism or some such) and a user-friendly way of enabling such
>> repos ?
>>
>> To provide this infrastructure is surely out of scope for Debian Med
>> proper but seems to be a useful target for Blends as such but needs
>> to be implemented in core Debian.
>
[Tony to Karsten:]
> I think you're right - In Bio-Linux, we already use a mirror of Dirk +
> Charles's CRAN-R package repository. We don't use the core Debian CRAN
> packages:
>
> # apt-cache policy r-base
> r-base:
> Installed: (none)
> Candidate: 2.12.1-1lucid0
> Version table:
> 2.12.1-1lucid0 0
> 500 http://www.stats.bris.ac.uk/R/bin/linux/ubuntu/ lucid/ Packages
> 2.10.1-2 0
> 500 http://gb.archive.ubuntu.com/ubuntu/ lucid/universe Packages
>
> I'm new to Debian-Med and I must admit that although I've found the
> people here to be very helpful indeed, I now realise that as Andreas
> said submitting all of Bioconductor as separate packages for inclusion
> in Debian "will never happen". In some respects, this underlies mine and
> Steffen's decision to create our own Debian/Ubuntu Bioconductor package
> repositories using cran2deb. As you've pointed out, this topic is
> outside the scope of Debian-Med, so we should probably take our
> discussion of packaging Bioconductor for Debian/Ubuntu elsewhere.
I may have some advantage in interpreting the en_DE here (or be completely
misled). From how I read Karsten's and Andreas's replies, they are full
of sympathy and harmony with us and our cran2debbing. Karsten came to
accept that a separate repository for CRAN and BioConductor may be
preferable for Debian and Ubuntu to have, since even with the biannual
updates of Ubuntu one wants to update the applications, not the complete
OS. The installation from either source should be somehow "orthogonal"
and not be bound to e.g. 10.04 LTS.
What Karsten was saying is that if there is such a demand for separate
repositories, e.g. Debian has "non-free" offered itself, but there is the
independent repository for multimedia already, then the core Debian people
should start some head scratching on how Debian could develop further to
start integrating those better. This would also help e.g. the repositories
for skype, Opera, Eucalyptus, Mozilla.org, ... donno. This
"beyond Debian Med" was thus meant to support us. And I think Karsten
is right.
My personal interest for the moment is mostly on the scientific
functionality of the packages we provided. The deeper integration
of external repositories will also happen without me ;) The testing
we cannot do alone.
Best,
Steffen
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