[BioC] AWS cluster not finding installed R packages

[Dan Tenenbaum]

On Fri, Jul 19, 2013 at 10:56 AM,  <john at enginetix.com> wrote:
> Dan,
>
> I'm just using the standard bioconductor aws ami and I'm installing some
> extra packages from CRAN. Working from R when I'm running a doSNOW cluster.
> I see that all of the nodes show up in the cluster, and I'm exporting the
> libraries as required. Unfortunately, when I run a job I receive an error
> that the packages are not found (it works if I use only local nodes). I have
> tried to load the required packages on each node... still no luck....
>

Again, difficult to say what is going on without more information,
such as a full transcript of your session. Also which AMI are you
starting (which BioC version?).

Dan


> Thank,
> John
>
> -------- Original Message --------
> Subject: Re: [BioC] AWS cluster not finding installed R packages
> From: Dan Tenenbaum <dtenenba at fhcrc.org>
> Date: Mon, July 15, 2013 7:37 am
> To: "John [guest]" <guest at bioconductor.org>
> Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>,
> john at enginetix.com
>
> On Mon, Jul 15, 2013 at 7:24 AM, John [guest] <guest at bioconductor.org>
> wrote:
>>
>> I'm building an aws cluster with bioconductor and I have to install some
>> packages from CRAN prior to the start of the run. I'm using doSNOW for the
>> parallel tasks. When I start the run I receive the error... "X Package not
>> found" where X is my installed packages. If I run on a single multicore
>> system this error is not received.
>>
>> I tried logging into each node and installing locally but I still receive
>> the same error.
>>
>> Any ideas?
>
> I think I need more information. What is the command or code you are
> using to install packages on all nodes in the cluster?
>
> How exactly did you start up the cluster?
>
> Dan
>
>
>> Thanks
>>
>> -- output of sessionInfo():
>>
>> "X Package not found"
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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