[Bioc-devel] Installation process for affymetrix databases (*.db packages)

Auke Booij auke at tulcod.com
Thu Jul 8 11:37:41 CEST 2010

Hello, I'm a Google Summer of Code student working for Gentoo to
integrate installation of R packages into the package manager. Up
until now, progress has been steady and I've run into little true
issues. I'm using the R tools to build and install packages wherever
applicable. Most CRAN packages install fine right now, so I'm now
working on bioconductor, making sure your packages can be installed
using a package manager as well.

Now, it seems the *.db packages are giving me some headaches. They
open up an existing sqlite database file on the disk and try to write
to it, or so it seems. Writing directly to installed files is not
really supported by the package managers of gentoo, and it can usually
be argued against indeed. Packages can, in principle, only read from
disk and create new files to be added to the system. However, I'm not
really into Bioconductor and its software, and I'd like to hear your
idea behind this process. What do the sqlite databases contain, how
are they used (from a user perspective), what data is added to them by
the *.db packages? Perhaps most importantly, can't this additional
data be in a separate database file?

Thanks for your thoughts,
Auke Booij / tulcod.

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