You're right the 'apache' user does not have the gcrma package installed
because when I added the if statement in my R script that gets called by
php to check for gcrma I got the following output:
Using R version 2.11.1, biocinstall version 2.6.10. Installing Bioconductor
version 2.6 packages: [1] "gcrma" Please wait...
The page just stays like that with out running any code after the
if-statement.
Is there a way to install it directly on the apache user server?

On Mon, Nov 7, 2011 at 2:25 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> On Mon, Nov 7, 2011 at 11:05 AM, Hussein Hijazi <hshijazi@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
>
> Dan
>
>
>
>
> > Is this the right installation?
> >
> >
> >
> > On Mon, Nov 7, 2011 at 2:00 PM, Dan Tenenbaum <dtenenba@fhcrc.org>
> wrote:
> >>
> >> On Mon, Nov 7, 2011 at 10:57 AM, hussein bazzi [guest]
> >> <guest@bioconductor.org> wrote:
> >> >
> >> > I'm calling some R script in php and it works fine. However when I
> call
> >> > an R script that is using a bio-conductor package the script doesn't
> run.
> >> > Specifically I have the following script which works perfectly fine
> in R but
> >> > when I call it from php it doesn't. Note that when I call a script
> that
> >> > doesn't use the bio-conductor package it works fine.
> >> >
> >> > library(gcrma) //It stops before it hits the first line
> >> > print("b")
> >> > Data <- ReadAffy()
> >> > eset <- rma(Data)
> >> > write.exprs(eset, file="NormalizedDate.txt")
> >> >
> >> >
> >> >
> >> >  -- output of sessionInfo():
> >> >
> >> > This is my input:
> >> >
> >> >
> >> > library(gcrma) //It stops before it hits the first line
> >> > print("b")
> >> > Data <- ReadAffy()
> >> > eset <- rma(Data)
> >> > write.exprs(eset, file="NormalizedDate.txt")
> >> >
> >> >
> >>
> >> What user is your web server (presumably apache) running as?
> >> Does that user have the gcrma package installed?
> >>
> >> Dan
> >>
> >>
> >> >
> >> > --
> >> > Sent via the guest posting facility at bioconductor.org.
> >> >
> >> > _______________________________________________
> >> > Bioconductor mailing list
> >> > Bioconductor@r-project.org
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives:
> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >
> >
> >
>

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