I have just installed R 2.0.1 on our Solaris8 system, and when I try to run getBioC, the following errors occur. Can someone suggest a solution to this problem? > source("http://www.bioconductor.org/getBioC.R") > getBioC() Running getBioC version 1.2.69.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. [1] "Attempting to download affy from http://www.bioconductor.org/repository/release1.5/package/Source" [1] "Download complete." [1] "Installing affy" * Installing *source* package 'affy' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -g -O2 -c chipbackground.c -o chipbackground.o gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -g -O2 -c getall_locations.c -o getall_locations.o gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -g -O2 -c mas5calls.c -o mas5calls.o gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -g -O2 -c qnorm.c -o qnorm.o gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -g -O2 -c read_abatch.c -o read_abatch.o gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -g -O2 -c rma2.c -o rma2.o gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -g -O2 -c rma_background2.c -o rma_background2.o gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fPIC -g -O2 -c rma_common.c -o rma_common.o gcc -G -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o qnorm.o read_abatch.o rma2.o rma_background2.o rma_common.o -lz ** R ** data ** demo ** inst ** save image [1] TRUE [1] TRUE Error in library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, : 'Biobase' is not a valid package -- installed < 2.0.0? Execution halted Broken Pipe ERROR: execution of package source for 'affy' failed ** Removing '/usr/local/lib/R/library/affy' ** Restoring previous '/usr/local/lib/R/library/affy' -- Thanks, -susan Susan J. Miller Biotechnology Computing Facility Arizona Research Laboratories Bio West 228 University of Arizona Tucson, AZ 85721 (520) 626-2597

Hi Susan, "Susan J. Miller" <sjmiller@email.arizona.edu> writes: > I have just installed R 2.0.1 on our Solaris8 system, and when I try > to run getBioC, the following errors occur. Can someone suggest a > solution to this problem? > > Error in library(package, character.only = TRUE, logical = TRUE, > warn.conflicts = warn.conflicts, : > 'Biobase' is not a valid package -- installed < 2.0.0? > Execution halted This looks like the type of error one would see if R is finding an old version of Biobase on the system. Is that possible? Did you install over an existing R install? + seth

"Susan J. Miller" <sjmiller@email.arizona.edu> writes: >> This looks like the type of error one would see if R is finding an >> old >> version of Biobase on the system. Is that possible? > > In the DESCRIPTION file for Biobase it says: > > Package: Biobase [snip] > Built: R 1.9.1; sparc-sun-solaris2.8; 2005-01-24 16:31:07; unix So this is a stale version of the Biobase package and this is the cause of your problem. >> Did you install over an existing R install? > > Yes, I did (R version 1.9.1). Is there some sort of cleanup I should > have done? We need better documentation on this. Since you had Bioconductor installed already, I think using update.packages2 from reposTools would have helped. At this point, I'm not sure what the best course of action is because you may have a mix of new and old? Here are things you could try: * Try to use update.packages2 * To be safe, you can remove all Bioconductor packages from your package library (just rm -r the package directories). Be careful not to remove the packages that come with R. * Another option would be to nuke the package library entirely and reinstall R and then run getBioC. We are working on making this sort of upgrade process *much* easier and less error prone in the next release (coming in mid May). Best, + seth

"Susan J. Miller" <sjmiller@email.arizona.edu> writes: > Hi Again Seth, > > Looks like you hit the nail on the head. I removed the Biobase > directory and ran getBioC again and everything looks good. > > Thanks a lot Excellent! + seth