[BioC] Bioconductor, PHP, and R

Xavier de Pedro xavier.depedro at vhir.org
Thu Nov 10 12:13:55 CET 2011


[I think that this is my first message to this list, after a few months 
of silently reading many threads and slowly learning...]

Another option is to have some permission checking at php level. For 
instance, this is what it was introduced in Tiki Wiki CMS/Groupware a 
few years ago, and then, you can allow Tiki site admins of the web site 
to install those packages for you (or for themselves) through the web 
interface (a wiki page with a PluginR call).

That was partly shown in the last UseR2011 conference, with an example 
of a custom php-based web 2.0 interface for custom R scripts to produce 
HeatMaps, which required extra packages from Bioconductor.



Those potentially interested, there is a free workshop shceduled for 
next week at the 3rd Spanish UseR meeting, in order to teach how to 
create safe web 2.0 interfaces for their R scritps.




On 07/11/11 20:41, Pierre-Yves Chibon wrote:
> 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
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