Hi All (wasn't sure if this should go to r-help or bioconductor) We have recently installed R 2.0 and the Bioconductor bundle was installed using getBioC() (A systems administrator compiled it so unfortunately I'm not sure what they have done) However there appears to be a few compiling errors with a few of the affy packages This appears to be affecting affy affyPLM altcdfenvs gcrma makecdfenv simpleaffy basically when you try to attach the packages they all return errors with messages related to compilation. I've try to install myself using R CMD INSTALL packages individually but again have compilation errors I'm wondering if this a problem with the affy related packages OR more likely with the Build of R that we have been given ? [jps@bc-1-2-03 /]$ /nfs/farm/R/bin/R CMD INSTALL -l /ecs2/scratch1/jps/Jasonlibrary /ecs2/scratch1/jps/Jasonlibrary/affy_1.5.8.tar.gz For X functions to work, this machine needs to be authorised to access deskpro179:0.0. I will test this now (this may take a few seconds. This is unning remotely on a blade somewhere so I don't know much about the machine its running on: Job <576812> is submitted to default queue <normal>. <<waiting for="" dispatch="" ...="">> <<starting on="" bc-3-2-12="">> * Installing *source* package 'affy' ... creating cache ./config.cache checking how to run the C preprocessor... /lib/cpp checking for main in -lz... no updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -I/nfs/farm/R/Linux-i686/lib/R/include -D__NO_MATH_INLINES -mieee-fp -fPIC -O2 -march=pentium3 -c chipbackground.c -o chipbackground.o make: gcc: Command not found make: *** [chipbackground.o] Error 127 ERROR: compilation failed for package 'affy' other packages that came from the same bundle work fine & also packages I have obtained seperately like limma, gregmisc etc all work with this method apologies for my lack of linux/unix experiance, any help will be greatfully recieved If these errors mean anything to anyone could they explain them please all the packages mentioned appear to be looking for gcc which I'm guessing is being effected by how R was built ? best regards 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

> creating cache ./config.cache > checking how to run the C preprocessor... /lib/cpp > checking for main in -lz... no > updating cache ./config.cache > creating ./config.status > creating src/Makevars > ** libs > gcc -I/nfs/farm/R/Linux-i686/lib/R/include -D__NO_MATH_INLINES > -mieee-fp -fPIC -O2 -march=pentium3 -c chipbackground.c -o > chipbackground.o > make: gcc: Command not found > make: *** [chipbackground.o] Error 127 > ERROR: compilation failed for package 'affy' You'll need to ask your sysadmin where 'gcc' is and make sure it is in your path.