[BioC] installing problem - preprocessCore, affy on linux platform
Kasper Daniel Hansen
khansen at stat.berkeley.edu
Thu Sep 4 01:44:42 CEST 2008
Install gfortran (a fortran compiler)
Kasper
On Sep 3, 2008, at 3:12 PM, Read, Laura wrote:
> 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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