[BioC] Bioconductor, PHP, and R

[Sean Davis]

Hi, Hussein.

There are several ways to get this done, but all of them probably
require someone with admin access.  The simplest option is to have the
administrator install things are the system level.  Alternatively, you
could have the admin install the software as the apache user; how you
do that will depend a bit on the system you are using.

Sean


On Mon, Nov 7, 2011 at 2:43 PM, Hussein Hijazi <hshijazi at gmail.com> wrote:
> 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 at fhcrc.org> 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
>>
>> Dan
>>
>>
>>
>>
>> > Is this the right installation?
>> >
>> >
>> >
>> > On Mon, Nov 7, 2011 at 2:00 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
>> wrote:
>> >>
>> >> On Mon, Nov 7, 2011 at 10:57 AM, hussein bazzi [guest]
>> >> <guest at 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 at 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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