[pkg-bioc] BioConductor

[Dirk Eddelbuettel]

Andreas,

On 16 March 2009 at 16:25, Andreas Tille wrote:
| I would like to have some clarification, what exactly is packaged in the
| pkg-bioc group.  At LinuxTage Chemnitz I've got some interesting hint to

Nothing, really.

The name is a historical accident as Matt Hope once set up a project to
automatically create Debian packages from BioC sources for R. That then
merged with my earlier efforts of 'cran2deb'.  Matt more or less dropped out;
Steffen, David and I then had a Perl-coded 'top-down' apprach that managed to
package 1500 or so packages from CRAN and BioC. This was largely driven by
David who was then a PhD studen at Muenster. We presented that at useR 2007
and NETTAB and may have gotten a paper out of it (Steffen: did that ever get
published in 'formal' sense ?).

The work basically stopped then.  End of story. It was unmainable code. But
we learned a lesson or two.

And then... during last year's GSoC, Charles Blundell built a new cran2deb,
built 'bottom-up' and re-using a ton more R code as well as some ideas from
my simple CRANberries CRAN RSS summaries feed (in 200 lines of R and single
blosxom call).  Charles and I are still working on it.  CRAN administrators
in Vienna gave us a Xen slice on one of their hosts, and we currently build
around 1570 package from CRAN for both i386 and amd64 (and refuse to build
few dozen for murky license reasons).  We hope to have more to show during
useR 2009 in Rennes.

Our plan is to basically render all manually maintained r-cran-* packages
inside Debian obsolete [at least for the arches we support] by providing a
complete and up-to-date archive to apt-get'able package.  In short, we want
CRAN to provide for Debian what it already provides for Windows: binaries for
an easier user experience.

Given that we are talking about 1600 source package and a growth rate of over
40% per year (see my presentations page and the recent MFA talk for a chart),
I (personally) have no intention of pushing these into Debian.  You just
can't babysit that many packages on all the autobuilders, library
transitions, ... or even walking them through the NEW queue.

| BioConductor and I have seen that there is a really interesting collection
| of R packages at
| 
|      http://www.bioconductor.org/packages/release/bioc/

Yes, BioC is very impressive, and very widely used in Bioinformatics. Lots of
nice things there eg for visualization. Check out hexbin, for example. I
think that is finally on CRAN too.

| I know that there is an Alioth project concerning packaging of
| BioConductor at
| 
|      http://alioth.debian.org/projects/pkg-bioc/
| 
| but in SVN
| 
|      http://svn.debian.org/wsvn/pkg-bioc/trunk/packages/?rev=0&sc=0
| 
| I can only see a package of r-cran-qtl - which is actually not at
| BioConductor page (or at least I did not found it there).
| 
| If I try to follow the advise how to obtain BioConductor packages
| given at
| 
|      http://wiki.debian.org/AliothPkgBioc
| 
| and just try
| 
|      sh ./r_pkg_prepare.sh --create-all --eu
| 
| I get a file autogenerate-variable.out and when I continue with
| 
| $ ./r_pkg_update.pl --doupdate --dobuilderupdate
| Can't locate Graph/Directed.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl . /usr/share/R/share/perl ../tools-ng) at debtag.pm line 140.
| BEGIN failed--compilation aborted at debtag.pm line 140.
| Compilation failed in require at ./r_pkg_update.pl line 161.
| BEGIN failed--compilation aborted at ./r_pkg_update.pl line 161.
| 
| so I guess something is wrong.
| 
| My suspicion is that this stuf was not touched for a while because
| the scripts contain a version string "2.1" for BioConductor and upstream
| mentions 2.3 as stable and 2.4 as devel.
| 
| So could you please give a short summary about the current status of
| this BioConductor stuff here on the list to perhaps coordinate things
| to some extend?

There is none. See above.

The new cran2deb is on R-Forge.r-project.org, and one fellow already managed
to set up an instance local to his lab. Now Charles and I think it is too
early for that but heck.

Cheers, Dirk


| Thank you very much for your effort so far
| 
|         Andreas.
| 
| -- 
| http://fam-tille.de
| 

-- 
Three out of two people have difficulties with fractions.