[R] Installing Bioconductor on R

From: Arunkumar R <arajendr_at_orca.st.usm.edu>
Date: Wed 19 Oct 2005 - 02:52:33 EST


hi all,

           Am new to R. I am having problems installing Bioconductor package in R on fedora core 4 running on AMD64 bit machine.

this is the error message I get :

gcc -shared -L/usr/local/lib -o affyPLM.so avg_log.o biweight.o 
chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o 
idealmismatch.o LESN.o lm.o lm_threestep.o log_avg.o matrix_functions.o 
median_logPM.o medianPM.o medianpolish.o nthLargestPM.o PLM_modelmatrix.o preprocess.o psi_fns.o qnorm.o qnorm_probeset.o rlm_anova.o rlm.o rlm_PLM.o rlm_se.o rlm_threestep.o rma_background2.o rma_common.o rma_PLM.o rmaPLM_pseudo.o SCAB.o scaling.o threestep.o threestep_common.o threestep_PLM.o threestep_summary.o threestep_summary_methods.o transfns.o weightedkerneldensity.o -L/usr/lib64/R/lib -lRlapack -lblas -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -lblas
collect2: ld returned 1 exit status
make: *** [affyPLM.so] Error 1
ERROR: compilation failed for package 'affyPLM' ** Removing '/usr/lib64/R/library/affyPLM' ** Restoring previous '/usr/lib64/R/library/affyPLM'

The downloaded packages are in

         /tmp/RtmpY18969/downloaded_packages Warning message:
installation of package 'affyPLM' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy",

I get these error messages after I type these commands on R :

source("http://www.bioconductor.org/biocLite.R") biocLite()

when I search for blas , I get this :

$ locate blas | grep so
/usr/lib/libgslcblas.so.0
/usr/lib/libgslcblas.so.0.0.0
/usr/lib64/libblas.so.3.0
/usr/lib64/libblas.so.3.0.3
/usr/lib64/libblas.so.3

do I need to install blas or make some changes in the configuration file in the bioconductor package.

Thanks
Arun



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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Wed Oct 19 03:24:32 2005

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