Hi, I am having trouble getting packages in Bioconductor installed. It looks like affy is the one causing the trouble, and that's the one I actually need, too... I am working under Linux, with R 1.8.1 beta. I copy the report of the intallation below in this email. Any help would be very much appreciated. Thank you, Julia > source("http://www.bioconductor.org/getBioC.R") > getBioC(relLevel="release", destdir="/var/tmp/juliab/RLibs", libName="affy") Running getBioC version 1.2.46.... 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. Synching your local package management information ... Packages which have been removed: tkWidgets affy affyPLM Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download tkWidgets from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing tkWidgets" * Installing *source* package 'tkWidgets' ... ** R ** inst ** save image [1] TRUE Error in setIs("character", "characterORMIAME", where = where) : Class "character" is sealed; new superclasses can not be defined, except by setClassUnion Error in firstlib(which.lib.loc, package) : cannot load DynDoc without Biobase Error: Package DynDoc unavailable Execution halted ERROR: execution of package source for 'tkWidgets' failed ** Removing '/var/tmp/juliab/RLibs/tkWidgets' Warning message: Installation of package tkWidgets had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) [1] "Attempting to download affy from http://www.bioconductor.org/repository/release1.3/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/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c chipbackground.c -o chipbackground.o gcc -I/usr/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c getall_locations.c -o getall_locations.o gcc -I/usr/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c qnorm.c -o qnorm.o gcc -I/usr/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c read_abatch.c -o read_abatch.o gcc -I/usr/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c rma2.c -o rma2.o gcc -I/usr/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c rma_background2.c -o rma_background2.o gcc -I/usr/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c rma_common.c -o rma_common.o gcc -shared -o affy.so chipbackground.o getall_locations.o qnorm.o read_abatch.o rma2.o rma_background2.o rma_common.o -lz -L/usr/lib/R/bin -lR ** R ** data ** demo ** inst ** save image Error in setIs("character", "characterORMIAME", where = where) : Class "character" is sealed; new superclasses can not be defined, except by setClassUnion [1] FALSE [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 '/var/tmp/juliab/RLibs/affy' Warning message: Installation of package affy had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) [1] "Attempting to download affyPLM from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing affyPLM" * Installing *source* package 'affyPLM' ... ** libs gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c LESN.c -o LESN.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c SCAB.c -o SCAB.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c avg_log.c -o avg_log.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c biweight.c -o biweight.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c chipbackground.c -o chipbackground.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c do_PLMrlm.c -o do_PLMrlm.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c idealmismatch.c -o idealmismatch.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c lm.c -o lm.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c lm_threestep.c -o lm_threestep.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c log_avg.c -o log_avg.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c medianPM.c -o medianPM.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c median_logPM.c -o median_logPM.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c medianpolish.c -o medianpolish.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c nthLargestPM.c -o nthLargestPM.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c preprocess.c -o preprocess.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c psi_fns.c -o psi_fns.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c qnorm.c -o qnorm.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c qnorm_probeset.c -o qnorm_probeset.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c rlm.c -o rlm.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c rlm_PLM.c -o rlm_PLM.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c rlm_se.c -o rlm_se.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c rlm_threestep.c -o rlm_threestep.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c rma_background2.c -o rma_background2.ogcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c rma_common.c -o rma_common.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c scaling.c -o scaling.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c threestep.c -o threestep.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c threestep_common.c -o threestep_common.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c threestep_summary.c -o threestep_summary.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c threestep_summary_methods.c -o threestep_summary_methods.o gcc -I/usr/lib/R/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c weightedkerneldensity.c -o weightedkerneldensity.o gcc -shared -o affyPLM.so LESN.o SCAB.o avg_log.o biweight.o chipbackground.o do_PLMrlm.o idealmismatch.o lm.o lm_threestep.o log_avg.o medianPM.o median_logPM.o medianpolish.o nthLargestPM.o preprocess.o psi_fns.o qnorm.o qnorm_probeset.o rlm.o rlm_PLM.o rlm_se.o rlm_threestep.o rma_background2.o rma_common.o scaling.o threestep.o threestep_common.o threestep_summary.o threestep_summary_methods.o weightedkerneldensity.o -L/usr/lib/R/bin -lRlapack -lblas -L/usr/lib/R/bin -lR ** R ** inst ** save image [1] TRUE Error in setIs("character", "characterORMIAME", where = where) : Class "character" is sealed; new superclasses can not be defined, except by setClassUnion [1] FALSE Error: package affy was built for sparc-sun-solaris2.7 Execution halted ERROR: execution of package source for 'affyPLM' failed ** Removing '/var/tmp/juliab/RLibs/affyPLM' Warning message: Installation of package affyPLM had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) >From URL: http://www.bioconductor.org/repository/release1.3/package/Source tkWidgets version 1.3.0 affy version 1.3.26 affyPLM version 1.0.0 Packages that were not updated: Biobase annotate genefilter geneplotter edd ROC multtest pamr limma MAGEML siggenes globaltest vsn affycomp affydata annaffy matchprobes gcrma makecdfenv >