[BioC] Bioconductor, PHP, and R

[Pierre-Yves Chibon]

On Mon, 2011-11-07 at 11:25 -0800, Dan Tenenbaum wrote:
> On Mon, Nov 7, 2011 at 11:05 AM, Hussein Hijazi <hshijazi at gmail.com> wrote:
> > Thank you for the reply. Yes I have apache running. I basically installed
> > gcrma from R using the following :
> >
> >     source("http://bioconductor.org/biocLite.R")
> >     biocLite("gcrma")
> >
> 
> That is correct. What I am saying is that
> 1) R sometimes installs packages in a directory somewhere under your
> home directory. When other users run R, they cannot see this
> directory.
> 2) Your apache web server is probably not running as you; it's
> probably running as the user 'apache'. Therefore the 'apache' user
> does not have the gcrma package installed.
> 
> The solution is something like this:
> 
> if (!"gcrma" %in% installed.packages()) {
>   source("http://bioconductor.org/biocLite.R")
>   biocLite("gcrma")
> }
> library(gcrma)
> # etc etc

Are you positive you want to let your web-server installing something
retrieved from the web automatically?
Sounds quite like a security risk to me.

The solution to me is having the library installed at the system level
by the system administrator.

Pierre