[BioC] BioConductor Affy package

[Jeff Gentry]

On Fri, 3 Jan 2003, Susan J. Miller wrote:
> =====================================================
> cd CELFILES
> R
> > library(affy)
> Error in library(affy) : This is not a valid package -- no DESCRIPTION
> exists
> =====================================================

Am I assuming correctly here that you have package affy installed in
directory CELFILES?  Or in /usr/local/lib/R/library (from below)?

If the former, and if CELFILES is not in your .libPaths() set of
locations, that would be a problem.  You could try:
library(affy,lib.loc("CELFILES")) for instance.

> Running getBioC version 1.2.3 ....

As an aside, there is a newer version of getBioC which solves some
problems, you might want to get that.  It wouldn't solve this particular
issue, but ....

> ERROR: cannot write to or create directory '/usr/local/lib/R/library'
> Error in file(file, "wb") : unable to open connection
> I looked for the liblisting file and it is readable - and it looks like
> I would need write access to /usr/local/lib/R/library for this approach
> to work so hopefully I can use library(affy) instead.  

Sure enough, if you don't have write access to that directory, it won't be
able to install the file.  You can specify parameter 'destdir' in getBioC
to be a location where you *do* have write access to, however.

-J