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

Marc Carlson mcarlson at fhcrc.org
Thu Jul 8 22:21:19 CEST 2010

Hi Auke,

Why is it that you think these packages are writing to these SQLite
databases?  They should not be doing so.  Their purpose is only to be
annotation packages and they make use of a relational database simply to
represent biological data.


On 07/08/2010 02:37 AM, Auke Booij wrote:
> 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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