Re: Packaging r-bioc-simpleaffy
On 28/02/11 14:09, Charles Plessy wrote:
Le Mon, Feb 28, 2011 at 12:55:58AM +0000, Tony Travis a écrit :
It is what Debian and Ubuntu have in common that attracted me to
Debian-Med. The people here have been very helpful indeed, but the
Debian politics I've witnessed recently are a wake-up call to me.
What is the big deal about the fact that we set up two Bioconductor
repo's?
Hi Tony,
I think that there is a confusion between Policy and politics :)
Hi, Charles.
I believe that 'policy' is generally a good thing, as a statement of
intent. My wake-up call is about Debian politics, by which I mean the
way that Debian makes collective decisions. I'm new to all this and I
must admit that I find political correctness an obstacle to progress.
Please don't misunderstand - I believe in FLOSS, and I support Debian
policy. However, I'm now rather more aware than I was that the biggest
difference between Debian and Ubuntu is their underlying politics :-)
Debian packages are hand made and eye-reviewed, this is one core procedure
that can not be changed without changing Debian's identity.
OK, I understand that better now.
The Biocoductor cran2deb repository is a great achievement that I hope we
will support and advertise appropriately, through packages in our archive
and documentation on our website.
This is mostly Steffen's work, but I'm grateful to Debian-Med for
organizing the 'sprint' in Travemuende where I was able to raise the
topic and get real help from you all to create an Ubuntu repository.
Steffen's message in [🔎] 4D5D0F30.30700@gmx.de">http://lists.debian.org/[🔎] 4D5D0F30.30700@gmx.de suggests
that there will be a more general announcement. This would be a good
candidate for being added to our website in its news section:
http://www.debian.org/devel/debian-med/News/
Yes, I think that would help us publicise our efforts to re-package
Bioconductor automatically for Debian/Ubuntu using cran2deb.
Likewise, detailed instructions could be added to our website… Suggestions
welcome !
Ah, detailed instructions... That will be a work in progress ;-)
In parallell, I think that it will be complementary to distribute some
Bioconductor packages in Debian itself, in particular some that fit well
with in our tasks.
I'm not sure how useful that would be, because even re-packaging one
Bioconductor simpleaffy package, and its dependencies is not trivial.
Most users import Bioconductor libraries from the main Bioconductor
repository, or a mirror, into their local R instance from source using
bioclite. What incentive would there be for people to install a few
manually comitted deb packages from Debian-Med instead of adding an
external APT repository with most/all Bioconductor deb's available?
What I think might be more useful is packaging cran2deb itself, and
documenting how to use it to create a Bioconductor deb repository.
Bye,
Tony.
Reply to: