[BioC] AWS cluster not finding installed R packages
john at enginetix.com
john at enginetix.com
Fri Jul 19 19:56:37 CEST 2013
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
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