############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL preprocessCore ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘preprocessCore’ ... ** this is package ‘preprocessCore’ version ‘1.71.2’ ** using staged installation 'config' variable 'CPP' is defunct checking for gcc... clang -arch arm64 -std=gnu2x 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 the compiler supports GNU C... yes checking whether clang -arch arm64 -std=gnu2x accepts -g... yes checking for clang -arch arm64 -std=gnu2x option to enable C11 features... none needed checking how to run the C preprocessor... clang -arch arm64 -std=gnu2x -E checking for library containing pthread_create... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for stdlib.h... (cached) yes checking if PTHREAD_STACK_MIN is defined... yes checking if __pthread_get_minstack can be used... no configure: Enabling threading for preprocessCore configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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:125:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:127:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:131:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:133:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:301:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:303:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:307:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:309:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:480:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:482:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:486:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:488:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:660:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:662:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:666:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:668:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:839:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:841:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:845:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:847:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1019:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:1021:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:1025:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:1027:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1197:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:1199:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:1203:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:1205:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1374:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer; ^ R_subColSummarize.c:1376:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:1380:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:1382:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1556:21: warning: variable 'buffer' set but not used [-Wunused-but-set-variable] double *results, *buffer, *buffer2; ^ R_subColSummarize.c:1556:30: warning: variable 'buffer2' set but not used [-Wunused-but-set-variable] double *results, *buffer, *buffer2; ^ R_subColSummarize.c:1558:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:1562:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:1564:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1739:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subColSummarize.c:1739:30: warning: unused variable 'buffer2' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subColSummarize.c:1741:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subColSummarize.c:1745:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:1747:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1703:14: warning: unused function 'subColSummarize_medianpolish_group' [-Wunused-function] static void *subColSummarize_medianpolish_group(void *data){ ^ 43 warnings generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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:87:11: warning: unused variable 'buffer' [-Wunused-variable] double *buffer, *buffer2; ^ R_subrcModel_interfaces.c:87:20: warning: unused variable 'buffer2' [-Wunused-variable] double *buffer, *buffer2; ^ R_subrcModel_interfaces.c:102:11: warning: unused variable 'weights' [-Wunused-variable] double *weights; ^ R_subrcModel_interfaces.c:103:11: warning: unused variable 'se' [-Wunused-variable] double *se; ^ R_subrcModel_interfaces.c:177:11: warning: unused variable 'results' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subrcModel_interfaces.c:177:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subrcModel_interfaces.c:177:30: warning: unused variable 'buffer2' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subrcModel_interfaces.c:179:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subrcModel_interfaces.c:183:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subrcModel_interfaces.c:185:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subrcModel_interfaces.c:392:11: warning: unused variable 'buffer' [-Wunused-variable] double *buffer, *buffer2; ^ R_subrcModel_interfaces.c:392:20: warning: unused variable 'buffer2' [-Wunused-variable] double *buffer, *buffer2; ^ R_subrcModel_interfaces.c:413:10: warning: unused variable 'scale' [-Wunused-variable] double scale=-1.0; ^ R_subrcModel_interfaces.c:502:11: warning: unused variable 'results' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subrcModel_interfaces.c:502:21: warning: unused variable 'buffer' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subrcModel_interfaces.c:502:30: warning: unused variable 'buffer2' [-Wunused-variable] double *results, *buffer, *buffer2; ^ R_subrcModel_interfaces.c:504:8: warning: unused variable 'cur_rows' [-Wunused-variable] int *cur_rows; ^ R_subrcModel_interfaces.c:508:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subrcModel_interfaces.c:510:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ 19 warnings generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c avg.c -o avg.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c biweight.c -o biweight.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c lm.c -o lm.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c median.c -o median.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c medianpolish.c -o medianpolish.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c plmd.c -o plmd.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c qnorm.c -o qnorm.o qnorm.c:614:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] i, returnCode, *((int *) status)); ^ qnorm.c:635:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] i, returnCode, *((int *) status)); ^ qnorm.c:2029:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] i, returnCode, *((int *) status)); ^ qnorm.c:1926:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,row_mean_ind; ^ qnorm.c:1931:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na; ^ qnorm.c:2126:14: 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:977:19: note: expanded from macro 'isMatrix' #define isMatrix Rf_isMatrix ^ qnorm.c:2139:55: note: uninitialized use occurs here qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows); ^~~~~~~~~~~ qnorm.c:2126:10: note: remove the 'if' if its condition is always true } else if (isMatrix(target)){ ^~~~~~~~~~~~~~~~~~~~~ qnorm.c:2107:21: note: initialize the variable 'target_rows' to silence this warning size_t target_rows, target_cols; ^ = 0 qnorm.c:2632:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] i, returnCode, *((int *) status)); ^ qnorm.c:2528:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,row_mean_ind; ^ qnorm.c:2533:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na; ^ qnorm.c:2752:14: warning: variable 'ind' set but not used [-Wunused-but-set-variable] size_t i,j,ind,target_ind; ^ qnorm.c:2850:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] double *sample_percentiles; ^ qnorm.c:2851:11: warning: unused variable 'datvec' [-Wunused-variable] double *datvec; ^ qnorm.c:2984:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,ind,target_ind; ^ qnorm.c:2984:14: warning: unused variable 'ind' [-Wunused-variable] size_t i,j,ind,target_ind; ^ qnorm.c:2984:18: warning: unused variable 'target_ind' [-Wunused-variable] size_t i,j,ind,target_ind; ^ qnorm.c:2986:14: warning: unused variable 'dimat' [-Wunused-variable] dataitem **dimat; ^ qnorm.c:2988:11: warning: unused variable 'row_mean' [-Wunused-variable] double *row_mean = target; ^ qnorm.c:2990:11: warning: unused variable 'ranks' [-Wunused-variable] double *ranks = (double *)R_Calloc((rows),double); ^ qnorm.c:2991:10: warning: unused variable 'samplepercentile' [-Wunused-variable] double samplepercentile; ^ qnorm.c:2992:10: warning: unused variable 'target_ind_double' [-Wunused-variable] double target_ind_double,target_ind_double_floor; ^ qnorm.c:2992:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable] double target_ind_double,target_ind_double_floor; ^ qnorm.c:2994:7: warning: unused variable 'targetnon_na' [-Wunused-variable] int targetnon_na = targetrows; ^ qnorm.c:2995:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na = 0; ^ qnorm.c:2999:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] double *sample_percentiles; ^ qnorm.c:3000:11: warning: unused variable 'datvec' [-Wunused-variable] double *datvec; ^ qnorm.c:3258:14: 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:977:19: note: expanded from macro 'isMatrix' #define isMatrix Rf_isMatrix ^ qnorm.c:3272:77: note: uninitialized use occurs here qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows); ^~~~~~~~~~~ qnorm.c:3258:10: note: remove the 'if' if its condition is always true } else if (isMatrix(target)){ ^~~~~~~~~~~~~~~~~~~~~ qnorm.c:3239:21: note: initialize the variable 'target_rows' to silence this warning size_t target_rows, target_cols; ^ = 0 26 warnings generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c rlm.c -o rlm.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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:1414:10: warning: unused variable 'k1' [-Wunused-variable] double k1 = psi_k; /* was 1.345; */ ^ rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable] double sumpsi2=0.0; /* sum of psi(r_i)^2 */ ^ rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable] double sumderivpsi=0.0; /* sum of psi'(r_i) */ ^ 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:1426:10: warning: unused variable 'vs' [-Wunused-variable] double vs=0.0,m,varderivpsi=0.0; ^ rlm_anova.c:1426:17: warning: unused variable 'm' [-Wunused-variable] double vs=0.0,m,varderivpsi=0.0; ^ rlm_anova.c:1426:19: warning: unused variable 'varderivpsi' [-Wunused-variable] double vs=0.0,m,varderivpsi=0.0; ^ rlm_anova.c:1505:10: warning: unused variable 'endprobe' [-Wunused-variable] double endprobe; ^ 10 warnings generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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:369:10: warning: unused variable 'j' [-Wunused-variable] size_t j; ^ rma_background4.c:370:10: warning: unused variable 'param' [-Wunused-variable] double param[3]; ^ 2 warnings generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=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 arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c weightedkerneldensity.c -o weightedkerneldensity.o clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/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)