[BioC] AWS cluster not finding installed R packages

[john at enginetix.com]

   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....

   Thank,

   John

   -------- Original Message --------
   Subject: Re: [BioC] AWS cluster not finding installed R packages
   From: Dan Tenenbaum <[1]dtenenba at fhcrc.org>
   Date: Mon, July 15, 2013 7:37 am
   To: "John [guest]" <[2]guest at bioconductor.org>
   Cc: "[3]bioconductor at r-project.org" <[4]bioconductor at r-project.org>,
   [5]john at enginetix.com
   On Mon, Jul 15, 2013 at 7:24 AM, John [guest] <[6]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 [7]bioconductor.org.
   >
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References

   1. mailto:dtenenba at fhcrc.org
   2. mailto:guest at bioconductor.org
   3. mailto:bioconductor at r-project.org
   4. mailto:bioconductor at r-project.org
   5. mailto:john at enginetix.com
   6. mailto:guest at bioconductor.org
   7. http://bioconductor.org/
   8. mailto:Bioconductor at r-project.org
   9. https://stat.ethz.ch/mailman/listinfo/bioconductor
  10. http://news.gmane.org/gmane.science.biology.informatics.conductor