Peng, If you are still having this problem then source("http://bioconductor.org/biocLite.R") update.packages(repos = biocinstallRepos()) will prompt you for updating all the out of date packages. Patrick Peng Yu wrote: > Hi Patrick, > > The problem was because that the BioC packages were not updated. It > seems that the problem is solved after all the packages are updated. > > Regards, > Peng > > On Wed, Aug 5, 2009 at 4:55 PM, Patrick Aboyoun<paboyoun at="" fhcrc.org=""> wrote: > >> Peng, >> We don't have any utility to check the version numbers of all installed >> packages because as long as you don't install the development version of >> BioC with the release version of R and you routinely run the commands >> >> biocLite(<<character vector="" of="" package="" names="">>) >> >> to install packages and >> >> update.packages(repos = biocinstallRepos()) >> >> to update the BioC packages you will be current for your version of R. >> >> Could you put your current situation in context? How have you been managing >> your packages and what is the current state of your R installation? >> >> >> Patrick >> >> >> >> Peng Yu wrote: >> >>> Hi Patrick, >>> >>> Would you please let me know what is the command to check the BioC >>> version? >>> >>> Regards, >>> Peng >>> >>> On Wed, Aug 5, 2009 at 12:02 PM, Patrick Aboyoun<paboyoun at="" fhcrc.org=""> >>> wrote: >>> >>> >>>> Peng, >>>> In addition to the versioning of R and Bioconductor packages, we also >>>> version the biocLite.R script on biocondunctor.org >>>> >>>> "biocinstall version 2.4.11" because we sometimes change the behavior of >>>> the >>>> functions in that script, such as which BioC packages are recommended, so >>>> providing the printout that you gave is ideal for us to pinpoint problems >>>> users encounter. >>>> >>>> >>>> Patrick >>>> >>>> >>>> Sean Davis wrote: >>>> >>>> >>>>> On Wed, Aug 5, 2009 at 12:14 PM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: >>>>> >>>>> >>>>> >>>>> >>>>>> Hi, >>>>>> >>>>>> I got the following message. I don't understand what it means. Can >>>>>> somebody let me know its meaning? >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> source("http://bioconductor.org/biocLite.R") >>>>>>> biocLite("pd.mogene.1.0.st.v1") >>>>>>> >>>>>>> >>>>>>> >>>>>> Running biocinstall version 2.4.11 with R version 2.9.0 >>>>>> Your version of R requires version 2.4 of Bioconductor. >>>>>> >>>>>> >>>>>> >>>>>> >>>>> Version 2.4 is the current release of bioconductor. biocLite() will do >>>>> the >>>>> right thing, generally. What you want to try to avoid is mixing >>>>> bioconductor versions together. If you use biocLite() all the time, you >>>>> shouldn't have any problems. >>>>> >>>>> Sean >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >>>>> >>>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >