Dear BioConductor gurus, On a Windows XP (SP2) machine, when I use the package Affy (R 2.0.1, bioconductor 1.5), the following error message appears: _______________________________________________________________ >library(affy) >AB<-ReadAffy("D:/newdata.CEL") >pmData<-pm(AB) Note: You did not specify a download type. Using a default value of: Win32 This will be fine for almost all users [1] "Attempting to download hgu133plus2cdf from http://www.bioconductor.org/data/cdfenvs/repos/" [1] "Download complete." [1] "Installing hgu133plus2cdf" Note: Running R version 2.0.1 and package hgu133plus2cdf was built for R version 2.0.0 , installing anyway. Error in library("hgu133plus2cdf", lib.loc = "C:/PROGRA~1/R/rw2001/library") : There is no package called 'hgu133plus2cdf' In addition: Warning messages: 1: error -1 in extracting from zip file 2: Installation of package hgu133plus2cdf had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) __________________________________________________________________ But we have updated all package when was installing R 2.0.1. Does anyone know what is the problem? Thank you. Jufen Zhou

Hi Jufen, "Jufen Zhou" <jfzhou@ucdavis.edu> writes: > On a Windows XP (SP2) machine, when I use the package Affy (R 2.0.1, > bioconductor 1.5), the following error message appears: > >>library(affy) >>AB<-ReadAffy("D:/newdata.CEL") >>pmData<-pm(AB) > Note: You did not specify a download type. Using a default value of: > Win32 > This will be fine for almost all users > [1] "Attempting to download hgu133plus2cdf from > http://www.bioconductor.org/data/cdfenvs/repos/" > [1] "Download complete." > [1] "Installing hgu133plus2cdf" > Note: Running R version 2.0.1 and package hgu133plus2cdf was built for R > version 2.0.0 > , installing anyway. This message is, I believe, separate from the error. It is saying that the data package hgu133plus2cdf was built with R 2.0.0. It _should_ work just fine with R 2.0.1. > > Error in library("hgu133plus2cdf", lib.loc > = "C:/PROGRA~1/R/rw2001/library") : > There is no package called 'hgu133plus2cdf' > In addition: Warning messages: > 1: error -1 in extracting from zip file > 2: Installation of package hgu133plus2cdf had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) I suspect this is library path issue. Can you look and see if the hgu133plus2cdf package was installed to C:/PROGRA~1/R/rw2001/library on your machine? If you see a directory there called hgu133plus2cdf, then it was installed. If you don't see it, I wonder if you also have a R/rw2000/library where it did get installed. + seth