[BioC] [devteam-bioc] Failure to update to Bioconductor 2.12 from bioconductor 2.11

Das, D. D.Das at uu.nl
Mon Aug 5 18:34:24 CEST 2013

Hi all,

Thanks guys for the reply. I understand that the console output in RStudio shows R version 2.15.3 but that is where the problem lies.
I don't have any installation of R2.15 on my system ( not sure if I uninstalled it properly or just deleted the folders and shortcuts).

Dilemma : Currently I am using R3.0.1 and if I use the same " > source("http://bioconductor.org/biocLite.R") "  code on R3.0.1 it confirms that R is using Bioconductor 2.12.
But in R-studio it is always showing R2.15.3 as dependency for the GUI.

(i)  Also I installed Revolution R enterprise 6.2 after installing R3.01 and Rstudio. Its installation directory shows R2.15 in one of the sub directories.Maybe thats why it uses R 2.15.3
(ii)  I went to registry editor on windows 7 ultimate and found 2 keys named R2.15.3  along with R3.0.1 keys. 

So in short what I understand is that somehow R-Studio and Revolution R 6.2 both are bound to use R2.15 rather than R3.0.1 on my laptop.

Solution :  I uninstalled revolution R 6.2 and deleted the registry keys through regedit and reopened Rstudio the console output confirms use of R3.0.1

Possible cause : I think the revolution R6.2 installation made Rstudio bound to use R2.15.3 rather than the already installed R3.0.1.

Anyways thanks guys for the replies. It is solved now. I will take care of the R versions being installed while installing any otehr GUI or dependency software.

Regards to the team/James.


From: dandante at gmail.com [dandante at gmail.com] on behalf of Dan Tenenbaum [dtenenba at fhcrc.org]
Sent: Monday, August 05, 2013 4:29 PM
To: diyanah [guest]
Cc: bioconductor at r-project.org; Das, D.; BiocInstaller Maintainer
Subject: Re: [devteam-bioc] Failure to update to Bioconductor 2.12 from bioconductor 2.11

On Mon, Aug 5, 2013 at 1:50 AM, Maintainer <maintainer at bioconductor.org> wrote:
> Bioconductor does not update itself form 2.11 to 2.12 although I am using the latest R version of 3.0.1.
> Please help...
> Thanks in advance.
> D.
>  -- output of sessionInfo():
>> source("http://bioconductor.org/biocLite.R")
> Your Bioconductor is out-of-date, upgrade to version 2.12 by following instructions at
> http://bioconductor.org/install.
> Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
>> biocLite()
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi'
> Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15
> trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/Biobase_2.18.0.zip'
> Content type 'application/zip' length 2346708 bytes (2.2 Mb)
> opened URL
> downloaded 2.2 Mb
> trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/IRanges_1.16.6.zip'
> Content type 'application/zip' length 2048190 bytes (2.0 Mb)
> opened URL
> downloaded 2.0 Mb
> trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/AnnotationDbi_1.20.7.zip'
> Content type 'application/zip' length 4200978 bytes (4.0 Mb)
> opened URL
> downloaded 4.0 Mb
> package ‘Biobase’ successfully unpacked and MD5 sums checked
> package ‘IRanges’ successfully unpacked and MD5 sums checked
> package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked

This output suggests you are using R 2.15. Maybe you have more than
one version of R on your machine?

At any rate, if you start R 3.0.1, biocLite() will automatically
install the appropriate (BioC 2.12) packages.


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