[BioC] Problems installing Genominator and GenomeGraphs

[Dan Tenenbaum]

Hello Jose,

On Tue, Apr 3, 2012 at 12:21 PM, Jose Lopez [guest]
<guest at bioconductor.org> wrote:
>
> I already used
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("Genominator")
> Warning messages:
> 1: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package 'RCurl' had non-zero exit status
> 2: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package 'biomaRt' had non-zero exit status
> 3: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package 'GenomeGraphs' had non-zero exit status
> 4: In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package 'Genominator' had non-zero exit status
>
> I already tried with others packages and had no problem.
>
> Apparently is the biomaRt package, when tried to install it directly, I had the same problem. What do I need to do?

What makes you say that biomaRt is the problem? It looks like RCurl is
the problem.

But...what are your CRAN and Bioconductor mirrors set to? What happens
if you start R as follows:

R --vanilla

Try that and let us know if it works.


Also, as always, we recommend working with the latest release version
of R (2.15) if possible.

Thanks,
Dan


>
> Thank you.
>
>  -- output of sessionInfo():
>
> R version 2.12.1 (2010-12-16)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.12.1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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