Re: Short report on Debian at UseR! 2007 conference at Iowa State Univ.
Hi Soeren, Hi Steffen
Now back from a short vacation in Michigan, I'll chime in on the ongoing
discussion.
On 18 August 2007 at 22:45, Soeren Sonnenburg wrote:
| On Sat, 2007-08-18 at 14:44 +0200, Steffen Moeller wrote:
| > On Saturday 18 August 2007 12:36:41 Soeren Sonnenburg wrote:
| > > On Tue, 2007-08-14 at 21:26 -0500, Dirk Eddelbuettel wrote:
| [...]
| > > esoteric/brand new research/unstable R-packes. However I would want to
| > > see the more mature bioconductor packages in debian...
| >
| > Again, I think we can agree on this,
|
| OK great.
Yes, we all agree on 'more is better' as well as on 'maybe these should not
be in debian' as two thousand machine generated packages.
| One could of course start with the core/essential packages and then
| slowly increase the package number. Robert Gentlemen suggested to start
| with the packages in BioCLite, which is
|
| affy affydata affyPLM annaffy annotate Biobase Biostrings DynDoc gcrma
| genefilter geneplotter hgu95av2 limma marray matchprobes multtest
| reposTools ROC vsn xtable.
|
| What do yo think?
Yes, and as an aside, these could of course be maintained 'by hand' as well
just like our current 50 or 60 CRAN packages. For Debian proper, this may be
better than the machine generated ones. BioC is high-profile enough that we
may find a few volunteers to join a packaging group on Alioth.
So getting 'core BioC' into Debian is actually a different task. Maybe
someone should pursue it (and I won't necessarily jump in as I am more on the
CRAN side of things).
But yes, this would be a good thing.
| > Btw, wouldn't you be interested to join our effort? I'd offer sponsoring
| > SHOGUN for Debian as a compensation :-)
|
| Indeed I am interested, but I don't have any experience with debian+R
| other than from packaging shogun-r. So I wonder whether for there exist
Look at any of my existing r-cran-* packages, and you see that they use a
_very_ formulaic approach which is even distilled into a one-line
debian/rules files, thanks to a) the standardization at the R package level
(that, interestingly enough, is inspired by Debian) and b) the magic powers
of cdbs which we use in the file /usr/share/R/debian/r-cran.mk --- which does
all the actual package building and installing and provides the code for the
one-liner calling it. So the key really is that Debian Policy is embedded in
the is r-cran.mk file. The other debian/* files are standard.
| general cdbs helpers for r & bioc. Also I am still confused that
| r-base-dev contains no header files (they are all in r-base-core) and
Well, Doug chose the name years ago; r-base-dev is meant to provide all
dependencies so that R users can do call install.packages() from R and not
fall over because headers and libs such as readline or curses are missing; it
is not a -dev package in the normal sense (which doesn't work for R as R is
not a library you compile against).
| that all the libR.so has no SO name (at least
| objdump -p /usr/lib/R/lib/libR.so | grep SO does not report anything).
Because ld.so does not see /usr/lib/R/lib as it doesn't need to know about it
(as one typically does not compile against it). [ You have a harder job with
shogun and a better example for you would be Ggobi and r-cran-rggobi so look
there instead of comparing with random CRAN package that are called into R --
I believe you call R into Shogun so the flow is different requiring a
different setup. ]
| So from my understanding the only build dependency is r-base-core, but
| how does one ensure smooth upgrades when switching to new (potentially
| incompatible) R releases?
I don't follow exactly what the questions is. Maybe take this to private
mail?
Good to be discussing R on debian-devel :)
Cheers, Dirk
--
Three out of two people have difficulties with fractions.
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