Hi, My OS is Mac OS X Server 10.4.8 I've got a fully functional R-2.3.1/bioconductor instance and decided to try installing R-2.4.0 in a different location. the R-2.4.0 appears fine but the bioconductor packages dislike the kernel version. The error is: ----- Error: package 'affy' was built for universal-apple-darwin8.8.1 ------ my version is: #uname -a Darwin luria.mit.edu 8.8.0 Darwin Kernel Version 8.8.0: Fri Sep 8 17:18:57 PDT 2006; root:xnu-792.12.6.obj~1/RELEASE_PPC Power Macintosh powerpc In addition to affy, Biobase has also been tried and produced an identical error. this is what the error looks like: --------------------------- R version 2.4.0 (2006-10-03) Copyright .... an HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] > source("http://www.bioconductor.org/getBioC.R") > getBioC("affy") Running getBioC version 0.1.8 with R version 2.4.0 Running biocinstall version 1.9.9 with R version 2.4.0 Your version of R requires version 1.9 of Bioconductor. trying URL 'http://bioconductor.org/packages/1.9/bioc/bin/macosx/ universal/contrib/2.4/affy_1.12.1.tgz' Content type 'application/x-gzip' length 1575163 bytes opened URL ================================================== downloaded 1538Kb The downloaded packages are in /tmp/RtmpEK32vV/downloaded_packages > library(affy) Error: package 'affy' was built for universal-apple-darwin8.8.1 ------------------------- does anyone have any advice? thanks charlie

Sean Davis <sdavis2 at="" mail.nih.gov=""> writes: > On Friday 08 December 2006 09:28, Charlie Whittaker wrote: >> Hi, >> My OS is Mac OS X Server 10.4.8 >> >> I've got a fully functional R-2.3.1/bioconductor instance and decided >> to try installing R-2.4.0 in a different location. >> >> the R-2.4.0 appears fine but the bioconductor packages dislike the >> kernel version. The error is: >> ----- >> Error: package 'affy' was built for universal-apple-darwin8.8.1 > > I don't think there is a guarantee that packages built on one version of R > will work with another. It looks like this is the case with the affy > package. You will probably need to reinstall bioconductor under > 2.4.0. In fact, for binary packages, there is almost a guarantee that packages will _only_ work with the version of R for which they are intended. Sorry about that. >From an R 2.4 session, try: source("http://bioconductor.org/biocLite.R") biocLite("affy") + seth

On Friday 08 December 2006 09:28, Charlie Whittaker wrote: > Hi, > My OS is Mac OS X Server 10.4.8 > > I've got a fully functional R-2.3.1/bioconductor instance and decided > to try installing R-2.4.0 in a different location. > > the R-2.4.0 appears fine but the bioconductor packages dislike the > kernel version. The error is: > ----- > Error: package 'affy' was built for universal-apple-darwin8.8.1 I don't think there is a guarantee that packages built on one version of R will work with another. It looks like this is the case with the affy package. You will probably need to reinstall bioconductor under 2.4.0. Sean