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

[Rongkun Shen]

Thanks so much, Martin. I followed your instruction and it did give v2.9 
for biocinstallRepos() using R --vanilla. But using R without --vanilla, 
the problem came back.

Then I found that the .RData is restored everytime when I launch R. So I 
deleted .RData and everything goes well.

I really appreciate your help!

Best regards,
--Rongkun


On 2011-11-13 Sun 1:12 PM, Martin Morgan wrote:
> 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.
>>
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>