Hi,

I am having some trouble installing the affy and preprocessCore packages on
my machine. I am using R 2.9.0 and am running Ubuntu Hardy Heron (I think).
I have read the already existing posts on this subject, installed gfortran,
gcc etc and nothing works. could anyone please help me?

This is my output when trying to install affy or preprocessCore:

> biocLite("affy")
Running biocinstall version 2.4.11 with R version 2.9.0
Your version of R requires version 2.4 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  argument 'lib' is missing: using
'/home/cathy/R/i486-pc-linux-gnu-library/2.6'
also installing the dependency ‘preprocessCore’

trying URL '
http://bioconductor.org/packages/2.4/bioc/src/contrib/preprocessCore_1.6.0.tar.gz
'
Content type 'application/x-gzip' length 114221 bytes (111 Kb)
opened URL
==================================================
downloaded 111 Kb

trying URL '
http://bioconductor.org/packages/2.4/bioc/src/contrib/affy_1.22.0.tar.gz'
Content type 'application/x-gzip' length 1154328 bytes (1.1 Mb)
opened URL
==================================================
downloaded 1.1 Mb

* 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/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c R_colSummarize.c -o R_colSummarize.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c R_rlm_interfaces.c -o R_rlm_interfaces.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c R_subColSummarize.c -o R_subColSummarize.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c avg.c -o avg.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c avg_log.c -o avg_log.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c biweight.c -o biweight.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c init_package.c -o init_package.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c lm.c -o lm.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c log_avg.c -o log_avg.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c log_median.c -o log_median.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c median.c -o median.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c median_log.c -o median_log.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c medianpolish.c -o medianpolish.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c plmd.c -o plmd.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c plmr.c -o plmr.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c qnorm.c -o qnorm.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c rlm.c -o rlm.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c rlm_anova.c -o rlm_anova.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c rlm_se.c -o rlm_se.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c rma_background4.c -o rma_background4.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c rma_common.c -o rma_common.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -std=gnu99 -shared -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.o biweight.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
-llapack -lblas -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
collect2: ld returned 1 exit status
make: *** [preprocessCore.so] Error 1
ERROR: compilation failed for package ‘preprocessCore’
* Removing ‘/home/cathy/R/i486-pc-linux-gnu-library/2.6/preprocessCore’
* Installing *source* package ‘affy’ ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1      -fpic  -g -O2 -c
chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1      -fpic  -g -O2 -c
getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1      -fpic  -g -O2 -c
mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1      -fpic  -g -O2 -c
rma2.c -o rma2.o
rma2.c:109:29: error: rma_background4.h: No such file or directory
rma2.c:120:45: error: preprocessCore_background_stubs.c: No such file or
directory
rma2.c:121:48: error: preprocessCore_normalization_stubs.c: No such file or
directory
rma2.c:122:48: error: preprocessCore_summarization_stubs.c: No such file or
directory
rma2.c:124:31: error: R_subColSummarize.h: No such file or directory
rma2.c:125:37: error: R_subColSummarize_stubs.c: No such file or directory
rma2.c: In function ‘do_RMA2’:
rma2.c:134: warning: implicit declaration of function
‘R_subColSummarize_medianpolish_log’
rma2.c:134: warning: assignment makes pointer from integer without a cast
rma2.c: In function ‘rma_c_call’:
rma2.c:186: warning: implicit declaration of function ‘qnorm_c’
rma2.c: In function ‘rma_c_complete’:
rma2.c:247: warning: implicit declaration of function ‘rma_bg_correct’
make: *** [rma2.o] Error 1
ERROR: compilation failed for package ‘affy’
* Removing ‘/home/cathy/R/i486-pc-linux-gnu-library/2.6/affy’

The downloaded packages are in
    ‘/tmp/RtmpmOti7W/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'preprocessCore' had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'affy' had non-zero exit status

> biocLite("preprocessCore")
Running biocinstall version 2.4.11 with R version 2.9.0
Your version of R requires version 2.4 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  argument 'lib' is missing: using
'/home/cathy/R/i486-pc-linux-gnu-library/2.6'
trying URL '
http://bioconductor.org/packages/2.4/bioc/src/contrib/preprocessCore_1.6.0.tar.gz
'
Content type 'application/x-gzip' length 114221 bytes (111 Kb)
opened URL
==================================================
downloaded 111 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/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c R_colSummarize.c -o R_colSummarize.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c R_plmd_interfaces.c -o R_plmd_interfaces.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c R_plmr_interfaces.c -o R_plmr_interfaces.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c R_rlm_interfaces.c -o R_rlm_interfaces.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c R_subColSummarize.c -o R_subColSummarize.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c avg.c -o avg.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c avg_log.c -o avg_log.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c biweight.c -o biweight.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c init_package.c -o init_package.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c lm.c -o lm.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c log_avg.c -o log_avg.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c log_median.c -o log_median.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c median.c -o median.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c median_log.c -o median_log.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c medianpolish.c -o medianpolish.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c plmd.c -o plmd.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c plmr.c -o plmr.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c qnorm.c -o qnorm.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c rlm.c -o rlm.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c rlm_anova.c -o rlm_anova.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c rlm_se.c -o rlm_se.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c rma_background4.c -o rma_background4.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c rma_common.c -o rma_common.o
gcc -std=gnu99 -I/usr/share/R/include     -g -O2  -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic  -g -O2
-c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -std=gnu99 -shared -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.o biweight.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
-llapack -lblas -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
collect2: ld returned 1 exit status
make: *** [preprocessCore.so] Error 1
ERROR: compilation failed for package ‘preprocessCore’
* Removing ‘/home/cathy/R/i486-pc-linux-gnu-library/2.6/preprocessCore’

The downloaded packages are in
    ‘/tmp/RtmpmOti7W/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'preprocessCore' had non-zero exit status

> sessionInfo()
R version 2.9.0 (2009-04-17)
i486-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.9.0

Thank you very much
Cathrine

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