[BioC] installation packages

[Dan Tenenbaum]

----- Original Message -----
> From: "fran vino" <biocesca at gmail.com>
> To: bioconductor at r-project.org
> Sent: Friday, September 13, 2013 7:21:31 AM
> Subject: [BioC] installation packages
> 
> 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?
> 

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. 
The other package failures you saw were probably because XML was not installed. 

The "6: installed directory not writable, cannot update packages" is just a warning and you can ignore it.
It's talking about core R packages which are typically installed in a directory that ordinary users can't write to. If you want, you can run biocLite() as root to update those packages.

Dan


> Thanks
> 
> 	[[alternative HTML version deleted]]
> 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor