printf ' ' | fink --no-use-binary-dist --yes rebuild bioconductor-preprocessorcore-r31 2>&1 WARNING: your info file index has not been updated for 22 days. You should run 'fink selfupdate' to get the latest package descriptions. The package 'bioconductor-preprocessorcore-r31' will be built without being installed. Reading build dependency for bioconductor-preprocessorcore-r31-1.26.1-1... Reading dependency for bioconductor-preprocessorcore-r31-1.26.1-1... Reading dependency for bioconductor-preprocessorcore-r31-dev-1.26.1-1... Reading build conflict for bioconductor-preprocessorcore-r31-1.26.1-1... The following package will be rebuilt: bioconductor-preprocessorcore-r31 Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-bioconductor-preprocessorcore-r31-1.26.1-1 /sw/build.build dpkg-deb: building package `fink-buildlock-bioconductor-preprocessorcore-r31-1.26.1-1' in `/sw/build.build/fink-buildlock-bioconductor-preprocessorcore-r31-1.26.1-1_2014.08.16-11.06.11_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-bioconductor-preprocessorcore-r31-1.26.1-1_2014.08.16-11.06.11_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-bioconductor-preprocessorcore-r31-1.26.1-1. (Reading database ... 7663 files and directories currently installed.) Unpacking fink-buildlock-bioconductor-preprocessorcore-r31-1.26.1-1 (from .../fink-buildlock-bioconductor-preprocessorcore-r31-1.26.1-1_2014.08.16-11.06.11_darwin-x86_64.deb) ... Setting up fink-buildlock-bioconductor-preprocessorcore-r31-1.26.1-1 (2014.08.16-11.06.11) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.0_bwu env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/preprocessCore_1.26.1.tar.gz preprocessCore/CHANGELOG preprocessCore/DESCRIPTION preprocessCore/NAMESPACE preprocessCore/R/ preprocessCore/R/colSummarize.R preprocessCore/R/normalize.quantiles.R preprocessCore/R/plmd.R preprocessCore/R/plmr.R preprocessCore/R/quantile_extensions.R preprocessCore/R/rcModel.R preprocessCore/R/rma.background.correct.R preprocessCore/R/subColSummarize.R preprocessCore/configure preprocessCore/configure.in preprocessCore/inst/ preprocessCore/inst/include/ preprocessCore/inst/include/R_subColSummarize.h preprocessCore/inst/include/R_subColSummarize_stubs.c preprocessCore/inst/include/avg.h preprocessCore/inst/include/avg_log.h preprocessCore/inst/include/biweight.h preprocessCore/inst/include/lm.h preprocessCore/inst/include/log_avg.h preprocessCore/inst/include/log_median.h preprocessCore/inst/include/median.h preprocessCore/inst/include/median_log.h preprocessCore/inst/include/medianpolish.h preprocessCore/inst/include/plmd.h preprocessCore/inst/include/plmr.h preprocessCore/inst/include/preprocessCore_background_stubs.c preprocessCore/inst/include/preprocessCore_background_stubs.h preprocessCore/inst/include/preprocessCore_normalization_stubs.c preprocessCore/inst/include/preprocessCore_normalization_stubs.h preprocessCore/inst/include/preprocessCore_summarization_stubs.c preprocessCore/inst/include/preprocessCore_summarization_stubs.h preprocessCore/inst/include/qnorm.h preprocessCore/inst/include/rlm.h preprocessCore/inst/include/rlm_se.h preprocessCore/inst/include/rma_background4.h preprocessCore/inst/include/weightedkerneldensity_stubs.c preprocessCore/inst/include/weightedkerneldensity_stubs.h preprocessCore/man/ preprocessCore/man/colSummarize.Rd preprocessCore/man/normalize.quantiles.Rd preprocessCore/man/normalize.quantiles.in.blocks.Rd preprocessCore/man/normalize.quantiles.robust.Rd preprocessCore/man/normalize.quantiles.target.Rd preprocessCore/man/rcModelPLMd.Rd preprocessCore/man/rcModelPLMr.Rd preprocessCore/man/rcModels.Rd preprocessCore/man/rma.background.correct.Rd preprocessCore/man/subColSummarize.Rd preprocessCore/man/subrcModels.Rd preprocessCore/src/ preprocessCore/src/Makevars preprocessCore/src/Makevars.in preprocessCore/src/R_colSummarize.c preprocessCore/src/R_colSummarize.h preprocessCore/src/R_plmd_interfaces.c preprocessCore/src/R_plmr_interfaces.c preprocessCore/src/R_plmr_interfaces.h preprocessCore/src/R_rlm_interfaces.c preprocessCore/src/R_rlm_interfaces.h preprocessCore/src/R_subColSummarize.c preprocessCore/src/R_subColSummarize.h preprocessCore/src/R_subrcModel_interfaces.c preprocessCore/src/avg.c preprocessCore/src/avg.h preprocessCore/src/avg_log.c preprocessCore/src/avg_log.h preprocessCore/src/biweight.c preprocessCore/src/biweight.h preprocessCore/src/dqrls.h preprocessCore/src/init_package.c preprocessCore/src/lm.c preprocessCore/src/lm.h preprocessCore/src/log_avg.c preprocessCore/src/log_avg.h preprocessCore/src/log_median.c preprocessCore/src/log_median.h preprocessCore/src/matrix_functions.c preprocessCore/src/matrix_functions.h preprocessCore/src/median.c preprocessCore/src/median.h preprocessCore/src/median_log.c preprocessCore/src/median_log.h preprocessCore/src/medianpolish.c preprocessCore/src/medianpolish.h preprocessCore/src/plmd.c preprocessCore/src/plmd.h preprocessCore/src/plmr.c preprocessCore/src/plmr.h preprocessCore/src/psi_fns.c preprocessCore/src/psi_fns.h preprocessCore/src/qnorm.c preprocessCore/src/qnorm.h preprocessCore/src/rlm.c preprocessCore/src/rlm.h preprocessCore/src/rlm_anova.c preprocessCore/src/rlm_se.c preprocessCore/src/rlm_se.h preprocessCore/src/rma_background4.c preprocessCore/src/rma_background4.h preprocessCore/src/rma_common.c preprocessCore/src/rma_common.h preprocessCore/src/weightedkerneldensity.c preprocessCore/src/weightedkerneldensity.h preprocessCore/tests/ preprocessCore/tests/PLMdtest.R preprocessCore/tests/qnormtest.R sudo -u fink-bld [ENV] sh -c /tmp/fink.yLXuV /tmp/fink.DHb08 #!/bin/bash -ev export TMPDIR=/sw/build.build/bioconductor-preprocessorcore-r31-1.26.1-1/preprocessCore/tmp BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R pushd .. /sw/build.build/bioconductor-preprocessorcore-r31-1.26.1-1 /sw/build.build/bioconductor-preprocessorcore-r31-1.26.1-1/preprocessCore $BIN_R --verbose CMD build --no-build-vignettes preprocessCore * checking for file 'preprocessCore/DESCRIPTION' ... OK * preparing 'preprocessCore': * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'preprocessCore_1.26.1.tar.gz' /bin/rm -rf /sw/build.build/root-bioconductor-preprocessorcore-r31-1.26.1-1 /bin/mkdir -p /sw/build.build/root-bioconductor-preprocessorcore-r31-1.26.1-1/sw /bin/mkdir -p /sw/build.build/root-bioconductor-preprocessorcore-r31-1.26.1-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bioconductor-preprocessorcore-r31-1.26.1-1 sudo -u fink-bld [ENV] sh -c /tmp/fink._gwqV /tmp/fink.c_4w9 #!/bin/sh -ev BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R mkdir -p /sw/build.build/root-bioconductor-preprocessorcore-r31-1.26.1-1/sw/lib/R/3.1/site-library pushd /sw/build.build/bioconductor-preprocessorcore-r31-1.26.1-1/preprocessCore/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-bioconductor-preprocessorcore-r31-1.26.1-1/sw/lib/R/3.1/site-library preprocessCore /sw/build.build/bioconductor-preprocessorcore-r31-1.26.1-1 /sw/build.build/bioconductor-preprocessorcore-r31-1.26.1-1/preprocessCore * installing *source* package 'preprocessCore' ... checking for gcc... flag-sort -r gcc -ffor-scope checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether flag-sort -r gcc -ffor-scope accepts -g... yes checking for flag-sort -r gcc -ffor-scope option to accept ISO C89... none needed checking how to run the C preprocessor... flag-sort -r gcc -ffor-scope -E checking for library containing pthread_create... none required checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking if PTHREAD_STACK_MIN is defined... yes configure: creating ./config.status config.status: creating src/Makevars ** libs flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c R_colSummarize.c -o R_colSummarize.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c R_plmd_interfaces.c -o R_plmd_interfaces.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c R_plmr_interfaces.c -o R_plmr_interfaces.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c R_rlm_interfaces.c -o R_rlm_interfaces.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c R_subColSummarize.c -o R_subColSummarize.o R_subColSummarize.c:84:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ R_subColSummarize.c:255:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ R_subColSummarize.c:426:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ R_subColSummarize.c:596:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ R_subColSummarize.c:768:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ R_subColSummarize.c:939:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ R_subColSummarize.c:1110:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ R_subColSummarize.c:1280:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ R_subColSummarize.c:1452:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ R_subColSummarize.c:1626:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 10 warnings generated. flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o R_subrcModel_interfaces.c:141:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ R_subrcModel_interfaces.c:454:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 2 warnings generated. flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c avg.c -o avg.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c avg_log.c -o avg_log.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c biweight.c -o biweight.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c init_package.c -o init_package.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c lm.c -o lm.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c log_avg.c -o log_avg.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c log_median.c -o log_median.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c matrix_functions.c -o matrix_functions.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c median.c -o median.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c median_log.c -o median_log.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c medianpolish.c -o medianpolish.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c plmd.c -o plmd.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c plmr.c -o plmr.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c psi_fns.c -o psi_fns.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c qnorm.c -o qnorm.o qnorm.c:458:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ qnorm.c:463:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ qnorm.c:1551:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ qnorm.c:1869:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ qnorm.c:2461:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ qnorm.c:2965:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 6 warnings generated. flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c rlm.c -o rlm.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c rlm_anova.c -o rlm_anova.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c rlm_se.c -o rlm_se.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c rma_background4.c -o rma_background4.o rma_background4.c:122:26: warning: incompatible pointer types passing 'size_t *' (aka 'unsigned long *') to parameter of type 'int *' [-Wincompatible-pointer-types] KernelDensity_lowmem(x,&rows,dens_y,dens_x,&npts); ^~~~~ ./weightedkerneldensity.h:5:43: note: passing argument to parameter 'nxxx' here void KernelDensity_lowmem(double *x, int *nxxx, double *output, double *output_x, int *nout); ^ rma_background4.c:323:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 2 warnings generated. flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c rma_common.c -o rma_common.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -I/sw/include -g -O3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -g -O3 -c weightedkerneldensity.c -o weightedkerneldensity.o weightedkerneldensity.c:551:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ 1 warning generated. flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -o preprocessCore.dylib R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.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 -framework Accelerate -framework Accelerate -L/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1 -L/sw/lib/gcc4.9/lib -lgfortran -lquadmath -lm -L/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [preprocessCore.dylib] Error 1 ERROR: compilation failed for package 'preprocessCore' * removing '/sw/build.build/root-bioconductor-preprocessorcore-r31-1.26.1-1/sw/lib/R/3.1/site-library/preprocessCore' ### execution of /tmp/fink.c_4w9 failed, exit code 1 ### execution of /tmp/fink._gwqV failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-bioconductor-preprocessorcore-r31-1.26.1-1 (Reading database ... 7664 files and directories currently installed.) Removing fink-buildlock-bioconductor-preprocessorcore-r31-1.26.1-1 ... Failed: phase installing: bioconductor-preprocessorcore-r31-1.26.1-1 failed Before reporting any errors, please run "fink selfupdate" and try again. Also try using "fink configure" to set your maximum build jobs to 1 and attempt to build the package again. If you continue to have issues, please check to see if the FAQ on Fink's website solves the problem. If not, ask on one (not both, please) of these mailing lists: The Fink Users List The Fink Beginners List , with a carbon copy to the maintainer: Jack Howarth Note that this is preferable to emailing just the maintainer directly, since most fink package maintainers do not have access to all possible hardware and software configurations. Please try to include the complete error message in your report. This generally consists of a compiler line starting with e.g. "gcc" or "g++" followed by the actual error output from the compiler. Also include the following system information: Package manager version: 0.37.0 Distribution version: selfupdate-cvs Thu Jul 24 20:26:24 2014, 10.9, x86_64 Trees: local/main stable/main Xcode.app: 5.1.1 Xcode command-line tools: 6.0.0.0.1.1405597879 Max. Fink build jobs: 8