Hello everybody, on installation of the current bioconductor packages (on fedora core 4, R version 2.2.0) no errors are appearing and everything seems fine, but it ends with the following output: The downloaded packages are in /tmp/Rtmpf12484/downloaded_packages Warning message: 'CRAN.packages' is deprecated. Use 'available.packages' instead. See help("Deprecated") There's nothing to find in the given tmp directory, so finally nothing seems to be stored or installed. The message is the same whether I use biocLite.R or getBioC.R, default or with own lib and destdir parameters. I've googled a while and searched through this mailing list archive to find similar problems, but I didn't find anything useful to me. Does anyone know how to solve this installation problem ? Bart Hooghe, PhD student BioIT, VIB UGent Belgium

Hi Bart, On 20 Jan 2006, barth at dmbr.ugent.be wrote: > on installation of the current bioconductor packages (on fedora core > 4, R version 2.2.0) no errors are appearing and everything seems > fine, but it ends with the following output: > > The downloaded packages are in /tmp/Rtmpf12484/downloaded_packages > Warning message: 'CRAN.packages' is deprecated. Use > available.packages' instead. See help("Deprecated") Thanks for pointing this out. The warning message indicates that we need to update a part of the installation scripts, but it should not have an effect on behavior at this time. > There's nothing to find in the given tmp directory, so finally > nothing seems to be stored or installed. Hmm, did you try simply loading one of the Bioc packages from inside R? For example, library("Biobase") On second thought, it might be most useful to inspect the locations where packages would most likely have been installed: .libPaths() I say most likely, because if your environment had R_LIBS set, R would have used that, but most likely, whatever .libPaths() reports will be where packages will have been installed. -- + seth