[BioC] warning during installation of cummeRbund

[Lien Spans]

The --vanilla seemed to do the trick. 
It installed fine now. 
Thanks a lot. 

Lien 

Molecular Endocrinology Laboratory
Department of Cellular and Molecular Medicine | KU Leuven
Campus GHB O&N1 | Herestraat 49 box 901 | BE-3000 Leuven | Belgium
Phone +3216330648

________________________________________
Van: Dan Tenenbaum [dtenenba at fhcrc.org]
Verzonden: zaterdag 15 december 2012 1:28
To: Lien Spans
Cc: bioconductor at r-project.org
Onderwerp: Re: [BioC] warning during installation of cummeRbund

On Fri, Dec 14, 2012 at 5:16 AM, Lien Spans <Lien.Spans at med.kuleuven.be> wrote:
> Dear all,
>
> I'm working on RNA-seq data that I would like to analyze with the cummeRbund package.
> I have R and biocLite installed, however when I try installing the cummeRbund package, I receive an error. I googled to find out if other people had a similar problem, but didn't really find an answer.
> I first tried
>     > biocLite('cummeRbund')
>    Using R version 2.15.2, biocinstall version 2.4.13.


>    Installing Bioconductor version 2.4 packages:
>    [1] "cummeRbund"
>    Please wait...
>    Installing package(s) into ‘/home/lien/R/x86_64-pc-linux-gnu-library/2.15’
>    (as ‘lib’ is unspecified)
>    Warning message:
>    package ‘cummeRbund’ is not available (for R version 2.15.2)
>
>
> I then tried
>    > biocLite(character()) but the cummeRbund package doesn't show up in the list of all available packages.
>
> I also tried
>    > install.packages("cummeRbund", repos="http://www.omegahat.org/R", type="source")
>    Installing package(s) into ‘/home/lien/R/x86_64-pc-linux-gnu-library/2.15’
>    (as ‘lib’ is unspecified)
>    Warning message:
>    package ‘cummeRbund’ is not available (for R version 2.15.2)
>
>
> I'm not very familiar with R, so I hope this question is not too basic, but I would appreciate an answer.
>



Looks like the BiocInstaller package is not properly installed.

Try starting R like this:

R --vanilla

Then do this:

source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")

If that does not work, please email the output of the following commands:

sessionInfo()
biocinstallRepos()

Dan

> Many thanks in advance,
> Lien Spans
> Molecular Endocrinology Laboratory
> Department of Cellular and Molecular Medicine | KU Leuven
> Campus GHB O&N1 | Herestraat 49 box 901 | BE-3000 Leuven | Belgium
> Phone +3216330648
>
>         [[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