Thanks for your quick reply. However, I've already install R 2.14.0 -- please see my sessionInfo. Best regards, --Rongkun On 2011-11-13 Sun 12:08 PM, Dan Tenenbaum wrote: > > > On Nov 13, 2011 11:51 AM, "Rongkun Shen [guest]" > <guest@bioconductor.org <mailto:guest@bioconductor.org="">> 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! > > > > By the way, there is no problem to install bioc 2.9 in Ubuntu > > 10.04LTS. > > BioC 2.8 works with R 2.13 and BioC 2.9 works with R 2.14. If you want > to use BioC 2.9, install R 2.14. > Dan > > > > 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 > <http: bioconductor.org="">. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

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. >> >> _______________________________________________ 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 >