Thank you Levi and Julie, I had the same problem last week also but it did not seem to get in the way of my work. Per your suggestion, I tried biocLite("BiocUpgrade") and it worked fine just now on Linux Ubuntu 13.04. The upgrade, however, removed the arrayQualityMetrics package I have been working with and I got a "Non-zero exit status" message. To fix that, I started R as root user, re-installed biocLite("arrayQualityMetrics"). The package and everything else is working fine now. Lisa On Thu, Oct 24, 2013 at 10:03 AM, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> wrote: > Hugo, > > I had similar problem a week ago. Here is my work around. > > First download the latest version of the BiocInstaller package, then > upgrades all currently installed packages to the latest repositories using > the following commands. > source("http://bioconductor.org/biocLite.R") > biocLite("BiocUpgrade") > > Hope this helps. > > Best regards, > > Julie > > > On 10/24/13 9:32 AM, "A M Torres, Hugo" <hugo.am.torres@usp.br> wrote: > > > Hi, > > > > I am following the upgrade instructions here: > > http://master.bioconductor.org/install/#update-bioconductor- packages > > > > But I keep getting biocLite 2.12 instead of 2.13 **no matter which > mirror > > I choose.** > > > > > > Any clues? > > > > R > > > > R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" > > Copyright (C) 2013 The R Foundation for Statistical Computing > > Platform: x86_64-pc-linux-gnu (64-bit) > > > > R is free software and comes with ABSOLUTELY NO WARRANTY. > > You are welcome to redistribute it under certain conditions. > > Type 'license()' or 'licence()' for distribution details. > > > > Natural language support but running in an English locale > > > > R is a collaborative project with many contributors. > > Type 'contributors()' for more information and > > 'citation()' on how to cite R or R packages in publications. > > > > Type 'demo()' for some demos, 'help()' for on-line help, or > > 'help.start()' for an HTML browser interface to help. > > Type 'q()' to quit R. > > > > R » source("http://bioconductor.org/biocLite.R") > > Your Bioconductor is out-of-date, upgrade to version 2.13 by following > > instructions > > at http://bioconductor.org/install. > > R » biocLite() > > BioC_mirror: http://www.bioconductor.org > > Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.0.2. > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]