Many thanks Seth! That script helped a lot. One more question. After installing a new version of R, for example 2.3.1, the command biocLite() should let you install the default subset of packages listed in the new release (BC v. 1.8) that are built with the newly installed R, shouldn't it? Thanks again! Jianping --On Thursday, August 10, 2006 7:50 AM -0700 Seth Falcon <sfalcon at="" fhcrc.org=""> wrote: > Hi Jianping, > > Jianping Jin <jjin at="" email.unc.edu=""> writes: >> We are running R-2.3.1/BioConductor on a Sun machine. I am wondering how >> I can check which version of BioConductor, 1.8 or 1.7 for example, was >> installed? Do I need to check package(s) of my interest by >> packageDescription() and see what version of R this package was >> built with? > > Packages in a Bioconductor release do not share a common version > number. As a result, you will want to verify installed package > versions against the version number that is part of a given release. > > You can use packageDescription to find the installed package version. > > You can browse the package version number in a particular release > here: > > http://www.bioconductor.org/packages/bioc/1.7/src/contrib/html/ > http://www.bioconductor.org/packages/1.8/bioc/ > > You can also pull the package information from the online repositories > using available.packages and then do comparisons in R. > > [below, untested outline of how to go about this] > > bioc18 = > available.packages(contrib.url("http://www.bioconductor.org/packages /1.8/ > bioc/")) instPkgs = installed.packages() > commonPkgs = intersect(rownames(bioc18), rownames(instPkgs)) > mapply(function(x, y) compareVersion(x, y), > instPkgs[commonPkgs, "Version"], > bioc18[commonPkgs, "Version"]) > > + seth > > _______________________________________________ > 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 ################################## Jianping Jin Ph.D. Bioinformatics scientist Center for Bioinformatics Room 3133 Bioinformatics building CB# 7104 University of Chapel Hill Chapel Hill, NC 27599 Phone: (919)843-6105 FAX: (919)843-3103 E-Mail: jjin at email.unc.edu

On 8/10/06, Seth Falcon <sfalcon at="" fhcrc.org=""> wrote: > Jianping Jin <jjin at="" email.unc.edu=""> writes: > > > Many thanks Seth! That script helped a lot. > > > > One more question. After installing a new version of R, for example > > 2.3.1, the command biocLite() should let you install the default > > subset of packages listed in the new release (BC v. 1.8) that are > > built with the newly installed R, shouldn't it? > > Yes, that's the idea. But not always what you want ;) I find myself having to install Bioc devel on R stable sometimes (since I don't always have access to R devel - lagging behind when the R versions get bumped up). In other words, I would use the version of R to infer the version of Bioc. /H > > _______________________________________________ > 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 >

On 8/10/06, Seth Falcon <sfalcon at="" fhcrc.org=""> wrote: > "Henrik Bengtsson" <hb at="" stat.berkeley.edu=""> writes: > > But not always what you want ;) I find myself having to install Bioc > > devel on R stable sometimes (since I don't always have access to R > > devel - lagging behind when the R versions get bumped up). > > Mixing BioC devel with R-release is for advanced users and is not > supported. If you do this often, you could edit your own copy of > biocLite to make it more convenient. > > > In other words, I would use the version of R to infer the version of > > Bioc. > > only if you have only used biocLite for installing packages. Won't be > reliable if you've manually downloaded things. Oopps, I missed a "not" there. Good catch. /H > > _______________________________________________ > 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 >