[R] Installing Bioconductor on R
Arunkumar R
arajendr at orca.st.usm.edu
Tue Oct 18 18:52:33 CEST 2005
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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