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 Your Bioconductor is out-of-date, upgrade to version 2.12 by following instructions at 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/c ontrib/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/c ontrib/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/c ontrib/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. Dan > -- > Sent via the guest posting facility at bioconductor.org. > > > ____________________________________________________________________ ____ > devteam-bioc mailing list > To unsubscribe from this mailing list send a blank email to > devteam-bioc-leave at lists.fhcrc.org > You can also unsubscribe or change your personal options at > https://lists.fhcrc.org/mailman/listinfo/devteam-bioc >

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. D. ________________________________________ From: dandante@gmail.com [dandante@gmail.com] on behalf of Dan Tenenbaum [dtenenba@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/c ontrib/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/c ontrib/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/c ontrib/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. Dan > -- > Sent via the guest posting facility at bioconductor.org. > > > ____________________________________________________________________ ____ > devteam-bioc mailing list > To unsubscribe from this mailing list send a blank email to > devteam-bioc-leave at lists.fhcrc.org > You can also unsubscribe or change your personal options at > https://lists.fhcrc.org/mailman/listinfo/devteam-bioc >