[pkg-bioc] Re: Google SoC R project

[Dirk Eddelbuettel]

Hi Chris,

You just caught me before going to bed :)

On 21 April 2006 at 21:10, Christian Bird wrote:
| Dirk,
| 
| I'm interested in applying for Google's summer of code and
| implementing a debian package generator for CRAN packages.  I'm a C.S.
| Ph.D. student at UC Davis and I use both R and python quite a bit for

[ Off-topic: Do you know that R Core member Duncan Temple-Lang is now at UC
Davis, in the stats dept?  I guess you probably do ... ]

| my research (and of course, use debian).  I saw automatic package
| generation of CRAN packages as a suggestion and it's something that
| would directly help me in my work so I'm interested in it.  I have two
| questions for you.  First, have many other people contacted you about

Nope, you're number one. Only posted two days ago though...

| working on this?  Second, is it possible to get a bit more detail
| regarding what you're wanting exactly?  Is it just automatic packaging
| of the packages or is there more to the equation (regression testing,
| etc.).  Thanks for any info you can provide.

The page(s) on alioth and the corresponding mailing list archives may help
you.

In essence, several years Albrecht Gebhard ago wrote a perl hack to build
SuSE package off CRAN. That later landed in Detlef Steuer's lap as Albrecht
moved on to Debian. Maybe two years ago I grabbed that script and turned it
into a Debian hack -- and generated packages for my Quantian distro. I then
joined forces with Matt who had started an alioth project for BioC.  The BioC
/ CRAN project is still on alioth (and you could join that _now_ irrespective
of what happens with SoC, get an alioth id and I will add you), and a few
good folks have sinced joined and pushed the script further. It is in version
control and the wiki pages have some notes on current statis.

It is still a pretty simple Perl hack. Given how easily CRAN packages build
(given how regularised they are with their own QA and unit-like testing...)
it is mostly a matter of mapping Depends etc. And polishing so that it runs
daily in an automated manner.

I also do not know how likely we are to get this approved a) within Debian
and b) with Google. I *did* learn that the R Core group had been approached
(presumably directly by Google) so we may have a chance with a proposal.

Not sure if we can flesh this out so that it maps to your PhD research.  But
we can definitely do _something_.  I have meant for so long to create a
process that follows daily CRAN updates, builds new debs, summarizes changes
to a mailing list (or rss feed) etc.  Not hard -- but I just haven't found
the time with work, 70+ Debian packages, Quantian ...

I'll see this to the pkg-bioc list where I had dropped a note about the SoC
idea.

Cheers, Dirk

| 
| -- Chris
| 
| --
| Christian Bird
| cabird at gmail.com

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