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

Marc Carlson mcarlson at fhcrc.org
Fri Jul 9 18:23:33 CEST 2010

Hi Auke,

Thanks to Martins generous hint, I think I have this fixed.  There were
some default behaviors in a package we depend on that were opening these
databases so that they could be written to (even though nothing was
being written there).  If you grab the very latest version of
AnnotationDbi, you can try to see if its working any better for you. 
The latest version is already available in the svn repository, but you
should be able to get the latest tarball from our website/build system
within the next 24 hours or so.


On 07/09/2010 12:53 AM, Auke Booij wrote:
> On Fri, Jul 9, 2010 at 12:37 AM, Marc Carlson <mcarlson at fhcrc.org> wrote:
>> Hi Auke,
> Hi Marc,
>> The installer should place the contents of "inst/extdata" into "extdata"
>> of your installed library, but that is about it.  There *IS* a
>> dependency however that is logged in the DESCRIPTION file.  Each chip
>> package requires that an "org" package be installed in order for it to
>> work.  So for example, this package "zebrafish.db_2.4.1.tar.gz "
>> requires the "org.Dr.eg.db".  And the message below seems to be
>> complaining that the database in "org.Dr.eg.db" is not available.  It
>> does not need to write to this DB, but it does need to be able to read
>> it.  Did you install the org packages and other dependencies 1st?
> I most definitely have that package installed. The package manager
> resolves all dependencies. As far as I'm concerned, the error is
> pretty clear: something's trying to open a file with write
> permissions, and that's prohibited. Could it be that the org.Dr.eg.db
> is opened with write permissions, even though nothing is really
> written? If so, could that be fixed or will I need a workaround?
>> Also is there a specific reason why is biocLite() is not your preferred
>> way to install bioconductor packages?  It handles all of these issues
>> for you and installs requested packages (and resolves dependencies).
> No, there is no specific reason for me not to use biocLite, but then
> again, I personally don't seek anything in Bioconductor at all. I'm
> working on enabling virtually all users of Gentoo Linux to install
> CRAN and Bioconductor packages using their regular package manager,
> which I think offers some obvious conceptual advantages. Perhaps one
> of the bigger issues with biocLite() some Gentoo purists may have is
> that it installs files without the package manager knowing anything
> about those files, and some users consider that evil. Another serious
> advantage would be dependency resolution for external packages, like
> for CRAN's gsl package, but I have yet to find a package with external
> dependencies in Bioconductor.
>> http://www.bioconductor.org/docs/install/
> Yes, I've seen that, and I've actually scavenged the (two) repository
> locations by reading biocLite() and friends :-)
> So, to sum it up, could it be that the database is opened with write
> permissions, but nothing is actually written, and is it possible at
> all to fix this, or is this inherent in the way R reads sqlite
> databases?
> Thanks again,
> Auke Booij / tulcod.

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