We are using the newest version of Bioconductor (1.9) to perform an Affy microarray analysis on some mouse chips. When we start using the "expresso" command to normalize the signal intensity, we get the following error statement: "mkdir: "/usr/local/R-2.4.0/lib/R/library/00LOCK": Permission denied ERROR: failed to lock directory '/usr/local/R-2.4.0/lib/R/library' for modifying The downloaded packages are in /tmp/Rtmpi41v2y/downloaded_packages Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain Mouse430_2 Library - package mouse4302cdf not installed Data for package affy did not contain mouse4302cdf Library - package mouse4302cdf not installed In addition: Warning messages: 1: installation of package 'mouse4302cdf' had non-zero exit status in: install.packages(cdfname, lib = lib, repos = Biobase:::biocReposList(), 2: cannot create HTML package index in: tools:::unix.packages.html(.Library)" We downloaded "mouse4302cdf_1.12.0.tar.gz", but we cannot install it. We tried to use the following R commands to install this package: install.packages("mouse4302cdf") install.packages2("mouse4302cdf") attach(mouse4302cdf) biocLite("mouse4302cdf") We also tried installing the "getBioC" package from the www.bioconductor.org/download . Thank you for your help.

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20061024/ f9f55ddd/attachment.pl

Hi Melissa, It appears your sysadmin is pretty responsive (you do have the newest release of R installed after all), so you may be able to take Li and Kasper's advice. However, there is a simple option you can take that will allow you to install an arbitrary number of packages without having to bother the sysadmin every time you want to add another. Just create a directory somewhere that you do have privileges (e.g., /home/<melissa's home="">/R_library) and then use .libPaths() to set this as a library. You will also need to create a .Rprofile file in your home directory as well, so every time you start R it will know about the library. The .Rprofile file will only need to contain one line: .libPaths("/home/<melissa's home="">/R_library") You could also add source("http://www.bioconductor.org/biocLite.R") so you can use biocLite() to install things without having to explicitly source the function every time. I have this in my .Rprofile because I get really tired of typing the above line every time I want to install something. Best, Jim Melissa Paczkowski wrote: > We are using the newest version of Bioconductor (1.9) to perform an Affy > microarray analysis on some mouse chips. When we start using the "expresso" > command to normalize the signal intensity, we get the following error statement: > > "mkdir: "/usr/local/R-2.4.0/lib/R/library/00LOCK": Permission denied > ERROR: failed to lock directory '/usr/local/R-2.4.0/lib/R/library' for modifying > > The downloaded packages are in > /tmp/Rtmpi41v2y/downloaded_packages > Error in getCdfInfo(object) : Could not obtain CDF environment, problems > encountered: > Specified environment does not contain Mouse430_2 > Library - package mouse4302cdf not installed > Data for package affy did not contain mouse4302cdf > Library - package mouse4302cdf not installed > In addition: Warning messages: > 1: installation of package 'mouse4302cdf' had non-zero exit status in: > install.packages(cdfname, lib = lib, repos = Biobase:::biocReposList(), > 2: cannot create HTML package index in: tools:::unix.packages.html(.Library)" > > We downloaded "mouse4302cdf_1.12.0.tar.gz", but we cannot install it. We tried > to use the following R commands to install this package: > > install.packages("mouse4302cdf") > install.packages2("mouse4302cdf") > attach(mouse4302cdf) > biocLite("mouse4302cdf") > > We also tried installing the "getBioC" package from the > www.bioconductor.org/download . > > Thank you for your help. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20061025/ 32110f5c/attachment.pl

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20061025/ ee4cf77f/attachment.pl