James, Further to where one can find the annotation data. I notice that when I install R2.3.1 on my Windows computer, the Select Repositories option shows 4 sites, CRAN, CRAN(extras), Bioconductor and Omegahat. If I add the following line: BioCMData BiocMetaData http://www.bioconductor.org/packages/data/annotation FALSE TRUE TRUE FALSE (This is one long line) to the repositories file in my R-2.3.1\etc subdirectory, I then have an extra repository listed, called BiocMetaData and I can then (provided I select it as a repository) see all the annotation data packages listed when I use Install Packages from the Packages Menu of the RGui. Can this repository option be added automatically to the Repositories file when R is installed Keith Satterley WEHI James W. MacDonald wrote: > Hi Daniel, > > Daniel Gatti wrote: > >>O/S: Linux >>arch : i686 >>R version : 2.2.1 >> >>I'm using the install.packages() command to install Bioconductor >>libraries to my home directory. I can install functional packages like >>"safe" and "GOstats". But when I try to install annotation packages, it >>tells me that it can't find them in given repository. I'm using >>repos="http://www.bioconductor.org". What repository should I use for >>the annotation packages? >> >>install.packages("hgu133a", lib = "~/Rlib", >>repos="http://www.bioconductor.org") > > > It's easier to use biocLite() instead. > > source("http://www.bioconductor.org/biocLite.R") > biocLite("hgu133a") > > HTH, > > Jim > > > >>Warning in download.packages(pkgs, destdir = tmpd, available = >>available, : >> no package 'hgu133a' at the repositories >> >>Dan Gatti >>UNC-CH >> >>_______________________________________________ >>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 > > >

Daniel Gatti wrote: > Daniel Gatti wrote: > > >> O/S: Linux > >> arch : i686 > >> R version : 2.2.1 > >> > >> I'm using the install.packages() command to install Bioconductor > >> libraries to my home directory. I can install functional packages like > >> "safe" and "GOstats". But when I try to install annotation packages, it > >> tells me that it can't find them in given repository. I'm using > >> repos="http://www.bioconductor.org". What repository should I use for > >> the annotation packages? > >> > >> install.packages("hgu133a", lib = "~/Rlib", > >> repos="http://www.bioconductor.org") > > >It's easier to use biocLite() instead. > > > >source("http://www.bioconductor.org/biocLite.R") > >biocLite("hgu133a") > > biocLite installs in the R library directory on the server. That's not true. biocLite() is simply a wrapper to install.packages() that among other things sets the correct repositories to iterate through. All you have to do is pass a lib argument and it will install wherever you want, just like install.packages(). > biocLite("affy", lib="C:/Documents and Settings/dd1/Desktop/test") Running getBioC version 0.1.6 with R version 2.3.0 Running biocinstall version 1.8.4 with R version 2.3.0 Your version of R requires version 1.8 of Bioconductor. trying URL 'http://bioconductor.org/packages/1.8/bioc/bin/windows/contrib/2.3/aff y_1.10.0.zip' Content type 'application/zip' length 2230953 bytes opened URL downloaded 2178Kb package 'affy' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\dd1\Local Settings\Temp\RtmpM8Sbqb\downloaded_packages updating HTML package descriptions > dir("C:/Documents and Settings/dd1/Desktop/test") [1] "affy" -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Daniel Gatti wrote: > Daniel Gatti wrote: > > >> O/S: Linux > >> arch : i686 > >> R version : 2.2.1 > >> > >> I'm using the install.packages() command to install Bioconductor > >> libraries to my home directory. I can install functional packages like > >> "safe" and "GOstats". But when I try to install annotation packages, it > >> tells me that it can't find them in given repository. I'm using > >> repos="http://www.bioconductor.org". What repository should I use for > >> the annotation packages? > >> > >> install.packages("hgu133a", lib = "~/Rlib", > >> repos="http://www.bioconductor.org") > > >It's easier to use biocLite() instead. > > > >source("http://www.bioconductor.org/biocLite.R") > >biocLite("hgu133a") > > biocLite installs in the R library directory on the server. Hi Daniel, This is what it does by default. But you can specify your own library directory with the 'lib' arg: > source('http://bioconductor.org/biocLite.R') > biocLite('Biobase', lib='my_lib_dir') In fact, all the arguments that can be used with the install.packages() function can also be used with biocLite(). I don't think this is documented on the Bioconductor website. It probably should (and will be soon). Sorry for that... Best, H. -- ------------------------ Hervé Pagès E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319