Dear all, I have problem installing Bioconductor, 'lumi' package on my Linux box. What's wrong with it? Is there any other way I can install them? > source('http://bioconductor.org/biocLite.R') > biocLite('lumi') Running biocinstall version 2.3.9 with R version 2.8.0 Your version of R requires version 2.3 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/gundala/R/x86_64-pc-linux-gnu-library/2.6' trying URL 'http://bioconductor.org/packages/2.3/bioc/src/contrib/lumi _1.8.3.tar.gz' Content type 'application/x-gzip' length 6834945 bytes (6.5 Mb) opened URL ================================================== downloaded 6.5 Mb * Installing *source* package 'lumi' ... ** R ** data ** inst ** preparing package for lazy loading Loading required package: annotate Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: AnnotationDbi Loading required package: DBI Loading required package: RSQLite Loading required package: xtable Loading required package: affy Loading required package: affyio Loading required package: preprocessCore Loading required package: mgcv This is mgcv 1.4-1 Error: package 'affy' does not have a name space Execution halted ERROR: lazy loading failed for package 'lumi' ** Removing '/home/gundala/R/x86_64-pc-linux-gnu-library/2.6/lumi' The downloaded packages are in /tmp/Rtmp2VaJzZ/downloaded_packages Warning message: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'lumi' had non-zero exit status - Gundala Viswanath Jakarta - Indonesia

Hello Gundula, this might be a problem of conflicting package versions. I presume that this line indicates that some Bioconductor packages are older versions matching the outdated R-2.6 > argument 'lib' is missing: using > '/home/gundala/R/x86_64-pc-linux-gnu-library/2.6' To make sure that all the required packages are up to date and can work with each other, I suggest you do the following: 1.) define an environment variable R_LIBS, for example by adding the following to the file $HOME/.bashrc: R_LIBS=$HOME/rpacks export R_LIBS and create that directory $HOME/rpacks. 2.) do a fresh Bioc install, using biocLite(), and this time the packages will be installed into the just created directory. 3.) Whenever you update the version of R that you are working with, follow the instructions for updating Bioc packages to the current version, to be found at the bottom of this page: http://www.bioconductor.org/docs/install Once these steps are done, the installation of "lumi" and other released packages should work. If the error persists, please get back to the list and provide the output of sessionInfo() following the error. Best regards, Joern