[BioC] bioconductor installation problem

[hpages at fhcrc.org]

Hi Olivier,

It looks like there was some internet access problem to me.
Can you open this links

  http://bioconductor.org/packages/2.1/bioc/src/contrib/PACKAGES

If it works, can you try biocLite() again?

Cheers,
H.

Quoting Olivier RICHE <o.riche at ulster.ac.uk>:

> Hi,
> 
> I am trying to install Bioconductor on the latest version of R (2.6.0) 
> and I get error messages (see below) about the repository. I am trying 
> to install using the method described there : 
> http://www.bioconductor.org/docs/install-howto.html
> 
> Is there a problem with the repository at the moment?
> 
>  > source("http://bioconductor.org/biocLite.R")
>  > biocLite()
> Running biocinstall version 2.1.8 with R version 2.6.0
> Your version of R requires version 2.1 of Bioconductor.
> Will install the following packages:
> [1] "affy" "affydata" "affyPLM" "annaffy" "annotate"
> [6] "Biobase" "Biostrings" "DynDoc" "gcrma" "genefilter"
> [11] "geneplotter" "hgu95av2" "limma" "marray" "matchprobes"
> [16] "multtest" "ROC" "vsn" "xtable" "affyQCReport"
> Please wait...
> 
> Warning: unable to access index for repository 
> http://bioconductor.org/packages/2.1/bioc/src/contrib
> Warning: unable to access index for repository 
> http://bioconductor.org/packages/2.1/data/annotation/src/contrib
> Warning: unable to access index for repository 
> http://bioconductor.org/packages/2.1/data/experiment/src/contrib
> Warning: unable to access index for repository 
> http://bioconductor.org/packages/2.1/extra/src/contrib
> Warning: unable to access index for repository 
> http://cran.fhcrc.org/src/contrib
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies = 
> dependencies, :
> packages ‘affy’, ‘affydata’, ‘affyPLM’, ‘annaffy’, ‘annotate’, 
> ‘Biobase’, ‘Biostrings’, ‘DynDoc’, ‘gcrma’, ‘genefilter’, ‘geneplotter’, 
> ‘hgu95av2’, ‘limma’, ‘marray’, ‘matchprobes’, ‘multtest’, ‘ROC’, ‘vsn’, 
> ‘xtable’, ‘affyQCReport’ are not available
> 
> Thank you for your help
> 
> Regards
> 
> Olivier
> 
> -- 
>  Olivier RICHE, Computing officer
>  University of Ulster, School of Biomedical Sciences,
>  Cromore Road, Coleraine BT52 1SA, Northern Ireland
>  http://www.systemsbiology.ulster.ac.uk
>  phone: +44-(0)28-70-323205 
> 
> ----
> 
> I am prepared to die, but there is no cause for which I am prepared to kill.
> -- Gandhi
> 
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