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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL preprocessCore
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* 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:117:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:115:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:111:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:109:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
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: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:460:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:458:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:466:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:464:7: 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:641:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:637:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:635:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:817:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_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:994:7: 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:988:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:990:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1165:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1163:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:1171:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1169:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:1337:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:1339:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1343:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:1345:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1524:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1522:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:1516:21: warning: variable 'buffer' set but not used [-Wunused-but-set-variable]
double *results, *buffer, *buffer2;
^
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:1702:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:1704:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1698:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1696:30: warning: unused variable 'buffer2' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subColSummarize.c:1696:21: warning: unused variable 'buffer' [-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:75:11: warning: unused variable 'buffer' [-Wunused-variable]
double *buffer, *buffer2;
^
R_subrcModel_interfaces.c:75:20: warning: unused variable 'buffer2' [-Wunused-variable]
double *buffer, *buffer2;
^
R_subrcModel_interfaces.c:90:11: warning: unused variable 'weights' [-Wunused-variable]
double *weights;
^
R_subrcModel_interfaces.c:173:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subrcModel_interfaces.c:171:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
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:167:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subrcModel_interfaces.c:165:30: warning: unused variable 'buffer2' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subrcModel_interfaces.c:377:11: warning: unused variable 'buffer' [-Wunused-variable]
double *buffer, *buffer2;
^
R_subrcModel_interfaces.c:377:20: warning: unused variable 'buffer2' [-Wunused-variable]
double *buffer, *buffer2;
^
R_subrcModel_interfaces.c:398:10: warning: unused variable 'scale' [-Wunused-variable]
double scale=-1.0;
^
R_subrcModel_interfaces.c:493:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subrcModel_interfaces.c:491:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
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;
^
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:1426:19: warning: unused variable 'varderivpsi' [-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:1426:17: warning: unused variable 'm' [-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: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 /Library/Frameworks/R.framework/Versions/4.3-x86_64/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)
