[BioC] A question about installation of cghFLasso package

[Sean Davis]

On Nov 10, 2007 4:21 PM, affy snp <affysnp at gmail.com> wrote:
> Hi Sean,
>
> Thanks a lot!
>
> I tried biocLite() earlier and then switched to R CMD INSTALL.
>
> I just did it once again and got:
>
> (1) For server 1,
>
> > source('http://bioconductor.org/biocLite.R')
> > biocLite('cghFLasso')
> Running biocinstall version 2.1.8 with R version 2.6.0
> Your version of R requires version 2.1 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   argument 'lib' is missing: using
> '/home/allen/R/x86_64-redhat-linux-gnu-library/2.6'
> trying URL 'http://cran.fhcrc.org/src/contrib/cghFLasso_0.1-2.tar.gz'
> Content type 'application/x-gzip' length 142390 bytes (139 Kb)
> opened URL
> ==================================================
> downloaded 139 Kb
>
> ERROR: failed to lock directory
> '/mnt/sc03/genomics/home/allen/R/x86_64-redhat-linux-gnu-library/2.6'
> for modifying
> Try removing '/mnt/sc03/genomics/home/allen/R/x86_64-redhat-linux-gnu-library/2.6/00LOCK'

So, did you try removing that file?

> (2) For server 2,
>
> > source('http://bioconductor.org/biocLite.R')
> > biocLite('cghFLasso')
> Running biocinstall version 2.0.8 with R version 2.5.0
> Your version of R requires version 2.0 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>          argument 'lib' is missing: using '/home/allen/lib/R'
> trying URL 'http://cran.fhcrc.org/src/contrib/cghFLasso_0.1-2.tar.gz'
> Content type 'application/x-gzip' length 142390 bytes
> opened URL
> ==================================================
> downloaded 139Kb
>
> * Installing *source* package 'cghFLasso' ...
> /usr/local/lib/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter:
> Permission denied
> ERROR: configuration failed for package 'cghFLasso'
> ** Removing '/home/allen/lib/R/cghFLasso'

Can you install ANY packages on this machine?  This looks like the R
installation procedure is broken, perhaps because of permissions.
Unless you are the system administrator on this machine, I think you
will need to find some local help.  Also, perhaps someone else on this
list has another idea, but since this is R-2.5.0, it might be better
to simply reinstall a newer version of R.

Sean