Variations on this problem seems to creep up a lot ... When you run expresso(), R complains about ... [ Environment hgu133acdf is not available. This environment contains needed probe location information. We will try to download and install the hgu133acdf package. Note: No specified download type, defaulting to Source [1] "Attempting to download hgu133acdf from BIOcdf/" ] So, my questions are 1) Are there cookbook instructions for making R recognize the "Environment hgu133acdf" ??? 2) What the heck does "Attempting to download hgu133acdf from BIOcdf/" mean? Wouldn't hardcoding a real URL do the trick? What do I need to do tell R where to really download the hgu133acdf file? Where is it looking? I have the directory "hgu133acdf" unzipped from the link at "http://www/bioconductor.org/data/metaData.html/" in the current working directory.

On Thu, Sep 25, 2003 at 02:11:09PM -0700, Richard Finney wrote: > Variations on this problem seems to creep up a lot ... Yes, and we are trying, right now, to figure out a better solution. But, please folks, give us the OS, the version of R and whether you are using the release or devel branch of BioC because otherwise we really have no chance of helping you. > > When you run expresso(), R complains about ... > [ > Environment hgu133acdf is not available. > This environment contains needed probe location > information. > We will try to download and install the hgu133acdf > package. > > Note: No specified download type, defaulting to Source > [1] "Attempting to download hgu133acdf from BIOcdf/" > ] > > > So, my questions are > > 1) Are there cookbook instructions for making R > recognize the "Environment hgu133acdf" ??? You can download this manually and install them manually like any other R package. > > 2) What the heck does "Attempting to download > hgu133acdf from BIOcdf/" mean? Wouldn't hardcoding > a real URL do the trick? What do I need to do tell > R where to really download the hgu133acdf file? Well, the folks in Europe, Asia or Oz might not want to wait for us to serve them up from the USA (which I know is the center of everyone's universe :-) > Where is it looking? I have the directory > "hgu133acdf" unzipped from the link at > "http://www/bioconductor.org/data/metaData.html/" in > the current working directory. > ahh, so now we see that you're on windows and btw you do need to read about install packages because unzipping them does not install them. This is covered in the R FAQ and in the Bioconductor FAQ. R has one set of package managment routines (and Bioconductor has a slightly larger set). you can try the following (provided of course you have an internet connection) library(reposTools) install.packages2("hgu133acdf") which seems to work on my windows machine. then library(hgu133cdf) and you are away > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+