Dear BioC, How can I install all metaData available (including CDF,Probe and Annotation) information from URL: http://www.bioconductor.org/packages/data/annotation/stable/src/contri b/html/ I am doing follwoing, and I get all latest results from that URL. But somehow , I get error msg. as shown below. Please, help me if someone have done this before or point me in to right direction. #================= # some pkgs I have already installed, long time ago manually by downloading .gz file, out of 240 > allnew <- getReposEntry("http://www.bioconductor.org/packages/data/annotation/st able/src/contrib") > update.packages2(repEntry=allnew) Note: argument `lib' is missing: using /usr/local/lib/R/library Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Warning message: cannot open: HTTP status was `404 Not Found' Note: http://www.bioconductor.org/data/metaData/src/contrib does not seem to have a valid repository, skipping Warning message: Failed to read replisting at http://www.bioconductor.org/data/metaData/src/contrib in: getReplisting(repURL, repFile, method = method) Warning message: cannot open: HTTP status was `403 Forbidden' Note: http://www.bioconductor.org/repository/devel/package/Win32 does not seem to have a valid repository, skipping Error in agrep(nfPkgs[i], availPkgs) : pattern must be a non-empty character string In addition: Warning message: Failed to read replisting at http://www.bioconductor.org/repository/devel/package/Win32 in: getReplisting(repURL, repFile, method = method) #=========================== Thank you in advance, Saurin Jani

Saurin Jani wrote: > Dear BioC, > > How can I install all metaData available (including > CDF,Probe and Annotation) information from URL: library(reposTools) reps <- repositories() ## choose either 10 or 11, depending on your OS install.packages2(repEntry=reps) Should do the trick. Best, Jim -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623