[BioC] installation packages

[Steve Lianoglou]

Hi,

On Thu, Sep 19, 2013 at 4:09 AM, fran vino <biocesca at gmail.com> wrote:
> Hi thanks for your suggestions.
>
> I performed the command as root instead of a regular user, how you said
> me.. When I performed:
>
>
>  > biocLite(“XML”), it resulted:
>
>
>  Warning message:
>
> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>
> installation of package ‘XML’ had non-zero exit status

You should go back to the email that Dan wrote to you.

The installation of the XML package is likely failing because you are
missing an essential library on your system -- it's not related to R.

This is what was said:

"""The XML problem is probably because you are missing system dependencies:
Try this at the unix command line:

sudo apt-get install -y libcurl-dev libxml2-dev

Then try installing XML again."""

Assuming you are running a debian-like version of linux, you will need
to install those *-dev packages *on your system*! Run those `sudo
apt-get` command from your terminal (not in R) so that the proper
libraries (headers) for libcurl ad libxml2 are on your system, then
reinstall RCurl via biocLite using R.

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech