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