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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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 [[alternative HTML version deleted]]

Hi Catherine -- Cathrine Mitchell wrote: > 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.ta r.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? I think this is pointing to an issue with your R installation per se; it thinks that it will link to a system-supplied liblapack, but cannot find one. It would have decided or been told to use a system-supplied lapack when R was configured and installed. It might be that there is a liblapack available % locate liblapack and if so your system can be configured to find it (details of configuring your system are best delegated to your local sys. admin if this is mostly gibberish to you). I think that someone would have fairly deliberately had to set lapack to liblapack, rather than using R's buiilt-in libRlapack. Martin > * 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_IDEN TIFICATION=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 > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor