Please try again but this time do it as root instead of a regular user. Its
a common mistake.

Ivan





Ivan Gregoretti, PhD
Bioinformatics


On Fri, Sep 13, 2013 at 10:21 AM, fran vino <biocesca@gmail.com> wrote:

> Dear Bioconductor list,
>
> I installed R on UBUNTU, but now how can I install the packages in R. For
> example if I use:
>
> > source("http://bioconductor.org/biocLite.R")
> > biocLite("DEseq")
>
> It results:
>
> Warning messages:
> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘XML’ had non-zero exit status
> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘annotate’ had non-zero exit status
> 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘genefilter’ had non-zero exit status
> 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘geneplotter’ had non-zero exit status
> 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘DESeq’ had non-zero exit status
> 6: installed directory not writable, cannot update packages 'foreign',
> 'Matrix',
>   'mgcv', 'rpart', 'spatial'
>
> but if I try to install XML, it results:
>
> > package ‘XML’ is not available (for R version 3.0.1)
>
>
> How can I solve it?
>
> Thanks
>
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>
>
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