[Bioc-devel] bioc AMI: permissions in R-libs

[Obenchain, Valerie]

I've regenerated the release (3.3) and devel (3.4) AMIs. New links are
live on the website:

  http://www.bioconductor.org/help/bioconductor-cloud-ami/#ami_ids

The approach we took was to install R (with no recommended packages) as
root in /usr/local. In theory, these packages should not be updated
until the next R release so biocLite() should never ask about them. All
other packages are installed in /home/ubuntu/R-libs all owned by ubuntu.
I've done some preliminary testing and all looks good as far as
permissions. Let me know if you run into other problems.

Valerie

On 08/24/2016 04:45 AM, Simon Anders wrote:
> Hi
>
> I'm currently working with the Bioconductor Amazon Machine Instance
> (AMI) for Bioc 3.3 (ami-64d43409) and wanted to install additional
> packages with biocLite(). This failed because about half of the
> sub-directories in ~/R-libs are not owned by the standard user 'ubuntu'
> but by root. 
>
> Can this be easily fixed in the existing AMI? (I mean, can one just
> run a 'chown' and save it as a new AMI?) If so, this might be useful.
>
>
> Thanks
>
>   Simon
>
>
> --
> | Dr. Simon Anders, Dipl.-Phys.
> | Group Leader, Institute for Molecular Medicine Finland (FIMM)
> | https://www.fimm.fi/en/research/groups/anders
>
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> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



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