The code below results in a looping behavior with Biobase downloaded over and over again until escaped, then each downloaded instance (all in different temp folders) is installed. This behavior began about the time that R-2.9.0 was released, but I had been using R-devel prior to that without problem. My system is Debian Lenny AMD64. Output and sessionInfo() follows below. source("http://www.bioconductor.org/biocLite.R") biocLite("Biobase") > source("http://www.bioconductor.org/biocLite.R") biocLite("Biobase") source("http://www.bioconductor.org/biocLite.R") Warning messages: 1: In safeSource() : Redefining ‘biocinstall’ 2: In safeSource() : Redefining ‘biocinstallPkgGroups’ 3: In safeSource() : Redefining ‘biocinstallRepos’ > biocLite("Biobase") Running biocinstall version 2.4.10 with R version 2.9.0 Your version of R requires version 2.4 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/mkimpel/R_HOME/site- library-2.9.0' trying URL ' http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.ta r.gz' Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb) opened URL ================================================== downloaded 1.9 Mb Loading required package: utils Running biocinstall version 2.4.10 with R version 2.9.0 Your version of R requires version 2.4 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/mkimpel/R_HOME/site- library-2.9.0' trying URL ' http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.ta r.gz' Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb) opened URL ================================================== ## REPEATS UNTIL ESCAPED ================================================== downloaded 1.9 Mb Loading required package: utils Running biocinstall version 2.4.10 with R version 2.9.0 Your version of R requires version 2.4 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/mkimpel/R_HOME/site- library-2.9.0' C-c C-c Execution halted The downloaded packages are in ‘/tmp/RtmpkGuMs0/downloaded_packages’ Warning message: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'Biobase' had non-zero exit status * Installing *source* package ‘Biobase’ ... ** libs gcc -std=gnu99 -I/home/mkimpel/R_HOME/R > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base loaded via a namespace (and not attached): [1] tools_2.9.0 ------------------------------------------------------------ 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) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** [[alternative HTML version deleted]]