Jim, Thanks for your advice. Your little code snippet might me a good inclusion in the "how to install bioconductor" page of the website under "how to update your packages". It is perhaps obvious to an experienced user, but may be very helpful to many, as it was to me. I'm posting this as a new thread on the main list just so your response is seen by others who may find it useful. Mark --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ****************************************************************** James MacDonald wrote: > Hi Mark, > > I think a much easier and safer way to update is as follows: > > source("http://www.bioconductor.org/biocLite.R") > > ## I just have the above in my .Rprofile file, so biocLite() is always > there for me. > > biocLite("Biobase") > repos <- biocReposList() > update.packages(repos=repos, ask=FALSE) > > this will get all CRAN and BioC packages, and got me correctly updated > this morning. > > Probably the problem with your script is you are hitting the IL mirror, > and it might be out of synch with fhcrc. Try the above and see if it helps. > > Best, > > Jim > -- --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please)