Hi Sean, Thanks a lot! I tried biocLite() earlier and then switched to R CMD INSTALL. I just did it once again and got: (1) For server 1, > source('http://bioconductor.org/biocLite.R') > biocLite('cghFLasso') Running biocinstall version 2.1.8 with R version 2.6.0 Your version of R requires version 2.1 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/allen/R/x86_64-redhat-linux-gnu-library/2.6' trying URL 'http://cran.fhcrc.org/src/contrib/cghFLasso_0.1-2.tar.gz' Content type 'application/x-gzip' length 142390 bytes (139 Kb) opened URL ================================================== downloaded 139 Kb ERROR: failed to lock directory '/mnt/sc03/genomics/home/allen/R/x86_64-redhat-linux-gnu-library/2.6' for modifying Try removing '/mnt/sc03/genomics/home/allen/R/x86_64-redhat-linux-gnu- library/2.6/00LOCK' The downloaded packages are in /tmp/Rtmp2UkIQF/downloaded_packages Warning message: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'cghFLasso' had non-zero exit status > (2) For server 2, > source('http://bioconductor.org/biocLite.R') > biocLite('cghFLasso') Running biocinstall version 2.0.8 with R version 2.5.0 Your version of R requires version 2.0 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/allen/lib/R' trying URL 'http://cran.fhcrc.org/src/contrib/cghFLasso_0.1-2.tar.gz' Content type 'application/x-gzip' length 142390 bytes opened URL ================================================== downloaded 139Kb * Installing *source* package 'cghFLasso' ... /usr/local/lib/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter: Permission denied ERROR: configuration failed for package 'cghFLasso' ** Removing '/home/allen/lib/R/cghFLasso' The downloaded packages are in /tmp/RtmpbuM77p/downloaded_packages Warning messages: 1: installation of package 'cghFLasso' had non-zero exit status in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, 2: cannot create HTML package index in: tools:::unix.packages.html(.Library) > Thanks a lot! Allen On Nov 10, 2007 4:13 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Nov 10, 2007 3:52 PM, affy snp <affysnp at="" gmail.com=""> wrote: > > Dear list, > > > > Hello! My name is Allen Shore, a graduate student at Wistar > > Institute in Philadelphia. I am trying to use cghFLasso to > > analyze a bunch of Affy SNP array data for identifying > > copy number variations. > > > > I had no problem with installing cghFLasso package on > > windows desketop. But I did have trouble with installing > > on the server (unix system). > > > > I tried two servers and got the following errors. > > > > For Server1: > > > > [shoreallen at madison download]$ R CMD INSTALL cghFLasso_0.1-2.tar.gz > > * Installing to library '/home/allen/lib/R' > > * Installing *source* package 'cghFLasso' ... > > /usr/local/lib/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter: > > Permission denied > > ERROR: configuration failed for package 'cghFLasso' > > ** Removing '/home/allen/lib/R/cghFLasso' > > Hi, Allen. > > This looks like a permissions problem. Typically, if R is installed > as root, the directories for packages are owned by root. > > Now, a couple of suggestions: > > 1) USE biocLite() whenever possible. It will typically do the right > thing by getting the correct package for your os and R package from > the correct repository as well as dependencies. Also, if you are not > the Root user, it will use R to ask you for a location that makes > sense to install packages into in your local directory. > > 2) If possible, ask a root user to install the packages (again, using > biocLite()) as the root user so that everyone on your machine has > access. > > 3) While it seems silly to do all the time, include sessionInfo for > ALL emails if there is ANY doubt about what machine, OS, R version, or > loaded packages are being used. I have never seen anyone faulted for > including sessionInfo unnecessarily. > > So, try: > > source('http://bioconductor.org/biocLite.R') > biocLite('bghFLasso') > > and let us know how it went if you have problems. > > Sean >