[pkg-bioc] Re: Genetics Program

[Dirk Eddelbuettel]

On 12 December 2005 at 13:30, Steffen Moeller wrote:
| > At any rate, I am not willing to spend time *_daily_* on this project. I
| > think we need a volunteer here, perhaps someone willing to become a
| > Debian developer who is not yet maintaining other packages.
| 
| I want to thank Dirk for providing the detailed information. From my 
| perspective I am mostly thinking about the BioConductor packages and the CRAN 
| packages would be coming with it. For BioConductor, with most users executing 
| >source("http://www.bioconductor.org/getBioC.R")
| within R for an automated install, a preparation of prebuilt packages through 
| Debian to my perception might be very very close or better than what a 
| regular user or a novice expects. Debian would allow to omit the build 
| environments and the libraries would be in place with no manual care. Dirk 
| pointed out very vividly that this does not hold for several of the packages 
| in CRAN. The gain is mostly for novices and power users who are distributing 
| their software over many machines.
| 
| Would the following be acceptable? The script today caters for the distinction 
| of the distributions in contrib and main, depending on the license. 
| Analogously we could have a default distribution in experimental. We would 
| still go through all the packages distributed in CRAN and BioConductor.org, 
| but move any we do not consider as up to a certain standard for inclusion 
| with a Debian main into experimental. A package's move from experimental -> 
| main on alioth could then be initiated by the upstream maintainer, 
| improvements to the script or the addition of requirements to Debian.
| 
| Today's script takes some time, indeed, though I am with Rafael, the Debian 
| BioC maintainers shoud have things either mostly automated or should not be 
| doing it. Improvements should mostly be done to the upstream packages 
| whenever appropriate.

We could add do that, or start with the newer biocLite from Bioconductor.org:
	source("http://www.bioconductor.org/biocLite.R")
as per http://www.bioconductor.org/docs/install-howto.html to create on big
r-bioc-lite-all package (better name needed ...). Or even build all of these,
and then have debian/rules split it.  You'd have to be creative to define an
.orig.tar.gz that matches the conventions of Debian, though.

But that is independent of work we'd need to do on the Debianization of CRAN
and BioC. Doing this may remove resources from other things, but it may add
focus and interest from the bio/genetics community to Debian.

In a nutshell, if you want to do that, why not if you find a sponsor etc pp.

Cheers, Dirk

-- 
Hell, there are no rules here - we're trying to accomplish something. 
                                                  -- Thomas A. Edison