[BioC] Packaging bioconductor

Seth Falcon sfalcon at fhcrc.org
Thu Sep 22 22:22:16 CEST 2005

Hi Giuseppe,

On 22 Sep 2005, ghibo at mandriva.com wrote:
> 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.

For a few reasons, you may find the most convenient thing to do is to
mirror the Bioconductor package repositories on your local systems.
There are some notes on how to access our rsync server here:

> 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) 

install.packages is not smart enough to resolve dependencies
(recursively) and determine a correct installation order.  As long as
every required package is in one of the repositories given in the
repos arg, things will Just Work.  This is how the getBioC and
biocLite functions work.

So I would recommend creating local CRAN-style repositories via rsync
and then install the packages from inside R using install.packages so
that you don't have to worry about the depedencies and such.

Hope that helps.

+ seth

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