[pkg-bioc] Re: Genetics Program

[Steffen Moeller]

Am Montag 12 Dezember 2005 14:20 schrieb 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.
In my mind I saw the creation of individual packages for the data environments 
and regular packages. Then, something analogous to the r-recommended package 
could specify subsets of packages.

> 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.
I tend to disagree. And I am not fully convinced we'd need full Debian 
compliance immediately. IMHO a reliable repository would for now be suficient 
and more than a single person should have access to it. The latter is the 
reason I do not set it up from here.

> In a nutshell, if you want to do that, why not if you find a sponsor etc
> pp.
I sketched the individual packaging of BioC + CRAN packages which I forsee to 
lead us towards a preparation of packages for an inclusion with Debian. No 
sponsor would be involved, with access to the external repository granted. I 
will not ask anybody else but you for sponsoring, your NO (or "not yet") 
means NO (or "not yet") - at least for me - and this will not change when I 
eventually become a DD.

Rafael, if you read this mail to this end and Dirk agrees to this plan, please 
ask the Alioth maintainers for the possibility of an upload.

Cheers,

Steffen