[BioC] File permission failures when building Bioconductor on AMD64/Opteron

[Michael Redmond]

This problem has been resolved. It was found to be an obscure 
interaction between selinx security and the AFS files system that we use.
Thanks
Mike Redmond
----

Michael Redmond wrote:
> I get the following error when building on Opteron:
> 
> mv: cannot create regular file 
> `/afs/.cs.wisc.edu/unsup/R-2.1.1/@sys/lib/R/library/reposTools/R/all.rda': 
> Permission denied
> 
> This happens with many packages associated in affy, but with reposTools, 
> no all.rda file is created. Then other packages fail to install.
> 
> Doing this same type of install on the same type of file system (afs) 
> with i386 Linux works fine.
> 
> Since the install operation for reposTools recreates the associated 
> directories, I can't preset 777 or 666 permissions in advance. However, 
> the permissions appear adequate for me as the owner to complete the 
> install.
> 
> It is not clear if this is a bioconductor problem, an R problem or a 
> problem with our AFS file system, but any advice would be appreciated.
> 
> Thanks
> M. Redmond
> UW-Madison Statistics
> 
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