[BioC] installing problem - preprocessCore, affy on linux platform

Thu Sep 4 00:12:29 CEST 2008

I am having trouble installing some bioconductor packages (but not all)
on an openSUSE 11.0 platform. For example, I cannot install
preprocessCore or affy, genefilter, matchprobes, vsn, gcrma, simpleaffy,
affyPLM but I can install Biobase.  Below is an example of my attempting
to install preprocessCore using biocLite.R.  I've tried using
install.packages() and gotten the same error messages

I would REALLY appreciate some help - I've been struggling with this for
over a year.

Thanks,
Laura Read - Research Scientist, Nathan Kline Institute, Orangeburg, NY

LINUX distribution:  openSUSE 11.0
R version 2.7.2 (2008-08-25)

Hardware: Dell Precision PWS690
Intel(R) Xeon(R) CPU
X5355 @ 2.66GHZ, 16 GB of RAM
64

> source("http://www.bioconductor.org/biocLite.R")
> biocLite("preprocessCore")
Running biocinstall version 2.2.10 with R version 2.7.2
Your version of R requires version 2.2 of BioConductor.
trying URL
'http://bioconductor.org/packages/2.2/bioc/src/contrib/preprocessCore_1.
2.1.tar.gz'
Content type 'application/x-gzip' length 108435 bytes (105 Kb)
opened URL
==================================================
downloaded 105 Kb

* Installing *source* package 'preprocessCore' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for pthread_create in -lpthread... yes
checking if we can use pthreads... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c R_colSummarize.c -o R_colSummarize.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c R_rlm_interfaces.c -o R_rlm_interfaces.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c R_subColSummarize.c -o R_subColSummarize.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c avg.c -o avg.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c avg_log.c -o avg_log.o

gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c biweight.c -o biweight.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c init_package.c -o init_package.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c lm.c -o lm.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c log_avg.c -o log_avg.o

gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c log_median.c -o log_median.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c median.c -o median.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c median_log.c -o median_log.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c medianpolish.c -o medianpolish.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c plmd.c -o plmd.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c plmr.c -o plmr.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c psi_fns.c -o psi_fns.o

gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c qnorm.c -o qnorm.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c rlm.c -o rlm.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c rlm_anova.c -o rlm_anova.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c rlm_se.c -o rlm_se.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c rma_background4.c -o rma_background4.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c rma_common.c -o rma_common.o
gcc -std=gnu99 -I/usr/lib64/R/include  -I/usr/local/include   -g -O2
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1
-DUSE_PTHREADS=1 -fpic  -O -c weightedkerneldensity.c -o
weightedkerneldensity.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o preprocessCore.so
R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o
R_rlm_interfaces.o R_subColSummarize.o avg.o avg_log.obiweight.o
init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o
median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o
rlm_anova.o rlm_se.o rma_background4.o rma_common.o
weightedkerneldensity.o -lpthread  -lpthread -lgfortran -lm
-L/usr/lib64/R/lib -lRlapack -L/usr/lib64/R/lib -lRblas
-L/usr/lib64/R/lib -lR
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/l
d: cannot find -lgfortran
collect2: ld returned 1 exit status
make: *** [preprocessCore.so] Error 1
chmod: cannot access `/usr/lib64/R/library/preprocessCore/libs/*': No
such file or directory
ERROR: compilation failed for package 'preprocessCore'
** Removing '/usr/lib64/R/library/preprocessCore'

The downloaded packages are in
        /tmp/RtmprnVyNm/downloaded_packages
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'preprocessCore' had non-zero exit status

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