[BioC] trouble with installing biomaRt in R-2.15

[Steve Lianoglou]

Hi,

On Fri, Dec 14, 2012 at 8:29 AM, chawla <chawla at bio.ntnu.no> wrote:
> Hi
> In R 2.15.2
> I try to install biomaRt and Rcurl by
> source("http://bioconductor.org/biocLite.R")
> biocLite("biomaRt")
>
> And I get the error below after some lines of processing:
>
> ERROR: compilation failed for package 'RCurl'
> * removing
> '/gpfs/norstore_trd/user/chawla/R/x86_64-unknown-linux-gnu-library/2.15/RCurl'

As this error message indicates, your problem is with the RCurl
library -- not biomaRt (yet).

Try installing RCurl by itself first.

Also:

> The downloaded source packages are in
>      '/tmp/RtmpiW2q4W/downloaded_packages'
> Warning messages:
> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>    installation of package 'RCurl' had non-zero exit status
> 2: installed directory not writable, cannot update packages 'Matrix',
> 'nlme',
>    'rpart', 'survival'

It seems you have another problem which is related to the permission
settings on the directory that holds your installed packages --
specifically, it seems like you don't have the write permissions to
write to it.

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact