############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf preprocessCore.buildbin-libdir && mkdir preprocessCore.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh preprocessCore_1.62.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R preprocessCore.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=preprocessCore.buildbin-libdir preprocessCore_1.62.1.tar.gz' >>>>>>> * installing *source* package ‘preprocessCore’ ... ** using staged installation 'config' variable 'CPP' is defunct checking for gcc... clang -arch x86_64 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 clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 option to accept ISO C89... none needed checking how to run the C preprocessor... clang -arch x86_64 -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 checking if R is using flexiblas... flexiblas not found. preprocessCore threading will not be disabled configure: Enabling threading for preprocessCore configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c R_colSummarize.c -o R_colSummarize.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c R_plmd_interfaces.c -o R_plmd_interfaces.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c R_plmr_interfaces.c -o R_plmr_interfaces.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c R_rlm_interfaces.c -o R_rlm_interfaces.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c R_subColSummarize.c -o R_subColSummarize.o R_subColSummarize.c:115:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:117:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:109:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:111:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:284:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:288:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:290:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:282:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:458:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:460:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:464:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:466:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:641:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:643:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:635:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:637:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:811:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:813:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:819:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:817:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:996:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:994:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:990:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:988:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:1163:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:1165:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:1169:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:1171:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1345:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1343:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:1339:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:1337:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:1522:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:1518:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:1516:30: warning: variable 'buffer2' set but not used [-Wunused-but-set-variable] double *results, *buffer, *buffer2; ^ R_subColSummarize.c:1516:21: warning: variable 'buffer' set but not used [-Wunused-but-set-variable] double *results, *buffer, *buffer2; ^ R_subColSummarize.c:1524:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1704:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1702:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:1698:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:1696:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subColSummarize.c:1696:30: warning: unused variable 'buffer2' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subColSummarize.c:1660:14: warning: unused function 'subColSummarize_medianpolish_group' [-Wunused-function] static void *subColSummarize_medianpolish_group(void *data){ ^ 43 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o R_subrcModel_interfaces.c:91:11: warning: unused variable 'se' [-Wunused-variable] double *se; ^ R_subrcModel_interfaces.c:90:11: warning: unused variable 'weights' [-Wunused-variable] double *weights; ^ R_subrcModel_interfaces.c:75:20: warning: unused variable 'buffer2' [-Wunused-variable] double *buffer, *buffer2; ^ R_subrcModel_interfaces.c:75:11: warning: unused variable 'buffer' [-Wunused-variable] double *buffer, *buffer2; ^ R_subrcModel_interfaces.c:171:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subrcModel_interfaces.c:173:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subrcModel_interfaces.c:165:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subrcModel_interfaces.c:165:11: warning: unused variable 'results' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subrcModel_interfaces.c:165:30: warning: unused variable 'buffer2' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subrcModel_interfaces.c:167:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subrcModel_interfaces.c:398:10: warning: unused variable 'scale' [-Wunused-variable] double scale=-1.0; ^ R_subrcModel_interfaces.c:377:20: warning: unused variable 'buffer2' [-Wunused-variable] double *buffer, *buffer2; ^ R_subrcModel_interfaces.c:377:11: warning: unused variable 'buffer' [-Wunused-variable] double *buffer, *buffer2; ^ R_subrcModel_interfaces.c:493:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subrcModel_interfaces.c:487:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subrcModel_interfaces.c:485:30: warning: unused variable 'buffer2' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subrcModel_interfaces.c:485:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subrcModel_interfaces.c:485:11: warning: unused variable 'results' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subrcModel_interfaces.c:491:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ 19 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c avg.c -o avg.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c avg_log.c -o avg_log.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c biweight.c -o biweight.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c lm.c -o lm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c log_avg.c -o log_avg.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c log_median.c -o log_median.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c matrix_functions.c -o matrix_functions.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c median.c -o median.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c median_log.c -o median_log.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c medianpolish.c -o medianpolish.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c plmd.c -o plmd.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c plmr.c -o plmr.o plmr.c:82:13: warning: unused function 'XTWY_R' [-Wunused-function] static void XTWY_R(int *rows, int *cols, double *out_weights, double *y,double *xtwy){ ^ plmr.c:152:13: warning: unused function 'XTWX_R' [-Wunused-function] static void XTWX_R(int *rows, int *cols, double *out_weights, double *xtwx){ ^ plmr.c:279:13: warning: unused function 'XTWX_R_inv' [-Wunused-function] static void XTWX_R_inv(int *rows, int *cols, double *xtwx){ ^ 3 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c psi_fns.c -o psi_fns.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c qnorm.c -o qnorm.o qnorm.c:1905:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,row_mean_ind; ^ qnorm.c:1910:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na; ^ qnorm.c:2102:14: warning: variable 'target_rows' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] } else if (isMatrix(target)){ ^~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:936:19: note: expanded from macro 'isMatrix' #define isMatrix Rf_isMatrix ^ qnorm.c:2115:55: note: uninitialized use occurs here qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows); ^~~~~~~~~~~ qnorm.c:2102:10: note: remove the 'if' if its condition is always true } else if (isMatrix(target)){ ^~~~~~~~~~~~~~~~~~~~~ qnorm.c:2083:21: note: initialize the variable 'target_rows' to silence this warning size_t target_rows, target_cols; ^ = 0 qnorm.c:2504:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,row_mean_ind; ^ qnorm.c:2509:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na; ^ qnorm.c:2725:14: warning: variable 'ind' set but not used [-Wunused-but-set-variable] size_t i,j,ind,target_ind; ^ qnorm.c:2823:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] double *sample_percentiles; ^ qnorm.c:2824:11: warning: unused variable 'datvec' [-Wunused-variable] double *datvec; ^ qnorm.c:2957:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,ind,target_ind; ^ qnorm.c:2957:14: warning: unused variable 'ind' [-Wunused-variable] size_t i,j,ind,target_ind; ^ qnorm.c:2957:18: warning: unused variable 'target_ind' [-Wunused-variable] size_t i,j,ind,target_ind; ^ qnorm.c:2959:14: warning: unused variable 'dimat' [-Wunused-variable] dataitem **dimat; ^ qnorm.c:2961:11: warning: unused variable 'row_mean' [-Wunused-variable] double *row_mean = target; ^ qnorm.c:2963:11: warning: unused variable 'ranks' [-Wunused-variable] double *ranks = (double *)Calloc((rows),double); ^ qnorm.c:2964:10: warning: unused variable 'samplepercentile' [-Wunused-variable] double samplepercentile; ^ qnorm.c:2965:10: warning: unused variable 'target_ind_double' [-Wunused-variable] double target_ind_double,target_ind_double_floor; ^ qnorm.c:2965:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable] double target_ind_double,target_ind_double_floor; ^ qnorm.c:2967:7: warning: unused variable 'targetnon_na' [-Wunused-variable] int targetnon_na = targetrows; ^ qnorm.c:2968:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na = 0; ^ qnorm.c:2972:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] double *sample_percentiles; ^ qnorm.c:2973:11: warning: unused variable 'datvec' [-Wunused-variable] double *datvec; ^ qnorm.c:3228:14: warning: variable 'target_rows' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] } else if (isMatrix(target)){ ^~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:936:19: note: expanded from macro 'isMatrix' #define isMatrix Rf_isMatrix ^ qnorm.c:3242:77: note: uninitialized use occurs here qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows); ^~~~~~~~~~~ qnorm.c:3228:10: note: remove the 'if' if its condition is always true } else if (isMatrix(target)){ ^~~~~~~~~~~~~~~~~~~~~ qnorm.c:3209:21: note: initialize the variable 'target_rows' to silence this warning size_t target_rows, target_cols; ^ = 0 22 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c rlm.c -o rlm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c rlm_anova.c -o rlm_anova.o rlm_anova.c:1235:10: warning: unused variable 'endprobe' [-Wunused-variable] double endprobe; ^ rlm_anova.c:1426:17: warning: unused variable 'm' [-Wunused-variable] double vs=0.0,m,varderivpsi=0.0; ^ rlm_anova.c:1426:10: warning: unused variable 'vs' [-Wunused-variable] double vs=0.0,m,varderivpsi=0.0; ^ rlm_anova.c:1414:10: warning: unused variable 'k1' [-Wunused-variable] double k1 = psi_k; /* was 1.345; */ ^ rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable] double sumderivpsi=0.0; /* sum of psi'(r_i) */ ^ rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable] double sumpsi2=0.0; /* sum of psi(r_i)^2 */ ^ rlm_anova.c:1426:19: warning: unused variable 'varderivpsi' [-Wunused-variable] double vs=0.0,m,varderivpsi=0.0; ^ rlm_anova.c:1418:10: warning: unused variable 'Kappa' [-Wunused-variable] double Kappa=0.0; /* A correction factor */ ^ rlm_anova.c:1419:10: warning: unused variable 'scale' [-Wunused-variable] double scale=0.0; ^ rlm_anova.c:1505:10: warning: unused variable 'endprobe' [-Wunused-variable] double endprobe; ^ 10 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c rlm_se.c -o rlm_se.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c rma_background4.c -o rma_background4.o rma_background4.c:354:10: warning: unused variable 'j' [-Wunused-variable] size_t j; ^ rma_background4.c:355:10: warning: unused variable 'param' [-Wunused-variable] double param[3]; ^ 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c rma_common.c -o rma_common.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -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 -falign-functions=64 -Wall -g -O2 -c weightedkerneldensity.c -o weightedkerneldensity.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o preprocessCore.so 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 -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.17-bioc/meat/preprocessCore.buildbin-libdir/00LOCK-preprocessCore/00new/preprocessCore/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (preprocessCore) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so >>>>>>> >>>>>>> Paths before fix: preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so: preprocessCore.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so" install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so" install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so" >>>>>>> Paths after fix: preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so: preprocessCore.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)