[BioC] Packaging bioconductor

Giuseppe Ghibò ghibo at mandriva.com
Thu Sep 22 20:50:16 CEST 2005


I would like to build a Bioconducor Linux RPM package (I've
already did that for Bioconductor 1.4, but now Bioconductor
is at 1.6 and soon will be at 1.7...), so that it can be used
for a system-wide installation (which already have a system
wide R 2.1.1).

The problem is that currently there isn't available a single tarball for
downloading all the single bioconductor subpackages in one shot. I've seen
that in http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/
the list of package is very long and takes a lot of time do
download. One can issue a command:


and take packages from $HOME/tmp/Rtmpq<randomnumber>/downloaded_packages/
before they are removed by the installation, but also in this way the
number of packages downloaded are just a subset of the ones listed on the
page above.

The second problem is that I need also the complete list of ALL bioconductor
subpackages packages in the right order (so to satify the dependencies) so that
a set of batch commands like:

for i in	affy_1.6.7.tar.gz \
		affydata_1.4.1.tar.gz \
		affyPLM_1.3.3.tar.gz \
		...; do
	R CMD INSTALL $i -l %{buildroot}%{_libdir}/R/library

can be run to build the RPM package.
I can do that by hand looking at the order getBioC() installs the packages,
but this is very long, and at every new release of bioconductor it
would be hard to redo everything, as new package are added,
new versions too, and order might change.

Any idea?

Best regards.
Giuseppe Ghibò

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