Hi everyone, I am working on R 2.0 installed in Windows 2000. I tried to download 'affy' package. No apparent error message appears, although there is a message that says 'dependencies NA are not available'. When I try to load the package it complains (please see below). What is going on? Any idea is appreciated. Could you please include my own e-mail address (not just the Bioconductor's) in the reply. Thank you. Melania > local({a<- CRAN.packages(CRAN=getOption("BIOC")) + install.packages(select.list(a[,1],,TRUE), .libPaths()[1], available=a, CRAN=getOption("BIOC"), dependencies=TRUE)}) trying URL `http://www.bioconductor.org/bin/windows/contrib/2.0/PACKAGES' Content type `text/plain' length 36813 bytes opened URL downloaded 35Kb dependencies 'NA' are not available trying URL `http://www.bioconductor.org/bin/windows/contrib/2.0/affy_1.4.32.zip' Content type `application/zip' length 1414189 bytes opened URL downloaded 1381Kb package 'affy' successfully unpacked and MD5 sums checked Delete downloaded files (y/N)? y updating HTML package descriptions > library(affy) Error in library(affy) : 'affy' is not a valid package -- installed < 2.0.0? Melania Rm 15-433, ext 4886 Fax: (416) 946-2048 This e-mail may contain confidential and/or privileged infor...{{dropped}}

You would be better off using reposTools functions rather than R-base functions for getting and installing packages. Here you are installing the release version of affy on R-2.0.0, which is an incompatible combination. Try library(reposTools) install.packages2("affy", develOK=TRUE) HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Pintilie, Melania" <melania.pintilie@uhn.on.ca> 10/28/04 10:26 AM >>> Hi everyone, I am working on R 2.0 installed in Windows 2000. I tried to download 'affy' package. No apparent error message appears, although there is a message that says 'dependencies NA are not available'. When I try to load the package it complains (please see below). What is going on? Any idea is appreciated. Could you please include my own e-mail address (not just the Bioconductor's) in the reply. Thank you. Melania > local({a<- CRAN.packages(CRAN=getOption("BIOC")) + install.packages(select.list(a[,1],,TRUE), .libPaths()[1], available=a, CRAN=getOption("BIOC"), dependencies=TRUE)}) trying URL `http://www.bioconductor.org/bin/windows/contrib/2.0/PACKAGES' Content type `text/plain' length 36813 bytes opened URL downloaded 35Kb dependencies 'NA' are not available trying URL `http://www.bioconductor.org/bin/windows/contrib/2.0/affy_1.4.32.zip' Content type `application/zip' length 1414189 bytes opened URL downloaded 1381Kb package 'affy' successfully unpacked and MD5 sums checked Delete downloaded files (y/N)? y updating HTML package descriptions > library(affy) Error in library(affy) : 'affy' is not a valid package -- installed < 2.0.0? Melania Rm 15-433, ext 4886 Fax: (416) 946-2048 This e-mail may contain confidential and/or privileged infor...{{dropped}} _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.