[BioC] try to install bioc v2.9 but always get v2.8 in centos 5.1

[Martin Morgan]

On 11/13/2011 11:50 AM, Rongkun Shen [guest] wrote:
>
> Hi, I installed R 2.14.0 and tried to install bioc 2.9 in centos 5.1
> 64bit. It turned out that it always got bioc b2.8 installed. I wonder
> if there is anyway to force install bioc 2.9. Thanks!

Probably a little more information needed; it sounds like an alternative 
repository is being used, perhaps set on your system in a .Rprofile? Try

  R --vanilla

and then

   source('http://bioconductor.org/biocLite.R')

and

   biocinstallRepos()

I get

 > biocinstallRepos()
                                                   BioCsoft
            "http://www.bioconductor.org/packages/2.9/bioc"
                                                       CRAN
                                    "http://cran.fhcrc.org"
                                                    BioCann
"http://www.bioconductor.org/packages/2.9/data/annotation"
                                                    BioCexp
"http://www.bioconductor.org/packages/2.9/data/experiment"
                                                  BioCextra
           "http://www.bioconductor.org/packages/2.9/extra"

You? If the version '2.9' is different, and you are not setting 
repositories yourself, what does the following produce?

 > tools:::.BioC_version_associated_with_R_version
[1] ‘2.9’

Martin

>
> By the way, there is no problem to install bioc 2.9 in Ubuntu
> 10.04LTS.
>
> Best, Rongkun Shen
>
> -- output of sessionInfo():
>
> R version 2.14.0 (2011-10-31) Platform: x86_64-unknown-linux-gnu
> (64-bit)
>
> locale: [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C [3]
> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8 [5]
> LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C
> LC_NAME=C [9] LC_ADDRESS=C               LC_TELEPHONE=C [11]
> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages: [1] stats     graphics  grDevices utils
> datasets  methods   base
>
> other attached packages: [1] BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached): [1] tools_2.14.0
>
>
> -- Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________ 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


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793