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

Auke Booij auke at tulcod.com
Fri Jul 9 09:53:58 CEST 2010

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

Thanks again,
Auke Booij / tulcod.

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