[pkg-bioc] Re: Genetics Program

[Dirk Eddelbuettel]

On 13 December 2005 at 10:13, Steffen Moeller wrote:
| > 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.

Yes, individual packages is probably better as it matches to orig.tar.gz
files and fits the build process structure.
| 
| > 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 

We would need to make it __very clear__ that this is a private archive with
no claims to Debianness whatsoever.

And even that is still very murky if the files come from a .debian.org
server. People will get confused.  So I think this needs a little more
thought and a clearer definition of what standards if any we are shooting
for.  What is you goal?  Pass 'R CMD check' (a given) but also pass lintian?

| 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") 

What you mean "for sponsoring" ?  I cannot really sponsor any more packages
and be responsive to my packages as well as those. I have to draw a line
somewhere, and I am afraid I have to draw it at "I cannot build 120 BioC
packages for you". Or even 40, to take a number for some subset.

| means NO (or "not yet") - at least for me - and this will not change when I 
| eventually become a DD.

In general, I am not entirely clear I understand what you wrote in this large
paragraph. Could you try again in different wording, and I get a shower and
some coffee ? (just did a morning run so may lack blood near the brain ...)

| 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.

Hm, you're an alioth member so you can already write, create dirs, build an
apt-getable structure as you like.  You don't Rafael for that -- but he has
of course the most experience in that given all his excellent Octave work.

Dirk, glad to see all this bioc/cran momentum !!

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