Hi I'm having difficulty using the R CMD INSTALL command with the affy package, I can use it with any other package from Bioconductor except any of the affy package versions: hoyle[jps]55: /usr/local/bin/R CMD INSTALL -l /nfs/team85/jps/R_dictyostelium/library /nfs/team85/jps/R_dictyostelium/affy_1.3.27.tar.gz * 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 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c chipbackground.c -o chipbackground.o gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -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 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c qnorm.c -o qnorm.o gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -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 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c rma2.c -o rma2.o gcc -I/usr/local/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -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 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c rma_common.c -o rma_common.o gcc -shared -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o qnorm.o read_abatch.o rma2.o rma_background2.o rma_common.o -lz ** R ** data ** demo ** inst ** save image [1] FALSE Warning message: There is no package called 'Biobase' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, [1] TRUE [1] TRUE Error in getClass(Class, where = topenv(parent.frame())) : "MIAME" is not a defined class Execution halted ERROR: execution of package source for 'affy' failed ** Removing '/.automount/babel/root/nfs/jps/R_dictyostelium/Jasonlibrary/affy' ** Restoring previous '/.automount/babel/root/nfs/jps/R_dictyostelium/Jasonlibrary/affy' It's asking for Biobase, WHICH OF COURSE I HAVE ALREADY INSTALLED and the correct version I've tried all these versions with the same outcome affy_1.3.23.tar.gz affy_1.3.27.tar.gz affy_1.4.4.tar.gz currently have biobase version 1.4.1 installed any ideas would greatfully be received thanks Jason -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919