############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL preprocessCore ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’ * installing *source* package ‘preprocessCore’ ... ** this is package ‘preprocessCore’ version ‘1.71.2’ ** using staged installation 'config' variable 'CPP' is defunct checking for gcc... gcc -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 gcc -std=gnu2x accepts -g... yes checking for gcc -std=gnu2x option to enable C11 features... none needed checking how to run the C preprocessor... gcc -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... yes configure: Enabling threading for preprocessCore configure: Using __pthread_get_minstack configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c R_colSummarize.c -o R_colSummarize.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c R_plmd_interfaces.c -o R_plmd_interfaces.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c R_plmr_interfaces.c -o R_plmr_interfaces.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c R_rlm_interfaces.c -o R_rlm_interfaces.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c R_subColSummarize.c -o R_subColSummarize.o R_subColSummarize.c: In function ‘R_subColSummarize_avg_log’: R_subColSummarize.c:133:9: warning: unused variable ‘j’ [-Wunused-variable] 133 | int i,j; | ^ R_subColSummarize.c:131:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable] 131 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:127:8: warning: unused variable ‘cur_rows’ [-Wunused-variable] 127 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:125:21: warning: unused variable ‘buffer’ [-Wunused-variable] 125 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function ‘R_subColSummarize_log_avg’: R_subColSummarize.c:309:9: warning: unused variable ‘j’ [-Wunused-variable] 309 | int i,j; | ^ R_subColSummarize.c:307:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable] 307 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:303:8: warning: unused variable ‘cur_rows’ [-Wunused-variable] 303 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:301:21: warning: unused variable ‘buffer’ [-Wunused-variable] 301 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function ‘R_subColSummarize_avg’: R_subColSummarize.c:488:9: warning: unused variable ‘j’ [-Wunused-variable] 488 | int i,j; | ^ R_subColSummarize.c:486:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable] 486 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:482:8: warning: unused variable ‘cur_rows’ [-Wunused-variable] 482 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:480:21: warning: unused variable ‘buffer’ [-Wunused-variable] 480 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function ‘R_subColSummarize_biweight_log’: R_subColSummarize.c:668:9: warning: unused variable ‘j’ [-Wunused-variable] 668 | int i,j; | ^ R_subColSummarize.c:666:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable] 666 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:662:8: warning: unused variable ‘cur_rows’ [-Wunused-variable] 662 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:660:21: warning: unused variable ‘buffer’ [-Wunused-variable] 660 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function ‘R_subColSummarize_biweight’: R_subColSummarize.c:847:9: warning: unused variable ‘j’ [-Wunused-variable] 847 | int i,j; | ^ R_subColSummarize.c:845:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable] 845 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:841:8: warning: unused variable ‘cur_rows’ [-Wunused-variable] 841 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:839:21: warning: unused variable ‘buffer’ [-Wunused-variable] 839 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function ‘R_subColSummarize_median_log’: R_subColSummarize.c:1027:9: warning: unused variable ‘j’ [-Wunused-variable] 1027 | int i,j; | ^ R_subColSummarize.c:1025:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable] 1025 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:1021:8: warning: unused variable ‘cur_rows’ [-Wunused-variable] 1021 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:1019:21: warning: unused variable ‘buffer’ [-Wunused-variable] 1019 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function ‘R_subColSummarize_log_median’: R_subColSummarize.c:1205:9: warning: unused variable ‘j’ [-Wunused-variable] 1205 | int i,j; | ^ R_subColSummarize.c:1203:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable] 1203 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:1199:8: warning: unused variable ‘cur_rows’ [-Wunused-variable] 1199 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:1197:21: warning: unused variable ‘buffer’ [-Wunused-variable] 1197 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function ‘R_subColSummarize_median’: R_subColSummarize.c:1382:9: warning: unused variable ‘j’ [-Wunused-variable] 1382 | int i,j; | ^ R_subColSummarize.c:1380:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable] 1380 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:1376:8: warning: unused variable ‘cur_rows’ [-Wunused-variable] 1376 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:1374:21: warning: unused variable ‘buffer’ [-Wunused-variable] 1374 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function ‘R_subColSummarize_medianpolish_log’: R_subColSummarize.c:1564:9: warning: unused variable ‘j’ [-Wunused-variable] 1564 | int i,j; | ^ R_subColSummarize.c:1562:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable] 1562 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:1558:8: warning: unused variable ‘cur_rows’ [-Wunused-variable] 1558 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:1556:30: warning: variable ‘buffer2’ set but not used [-Wunused-but-set-variable] 1556 | double *results, *buffer, *buffer2; | ^~~~~~~ R_subColSummarize.c:1556:21: warning: variable ‘buffer’ set but not used [-Wunused-but-set-variable] 1556 | double *results, *buffer, *buffer2; | ^~~~~~ R_subColSummarize.c: In function ‘R_subColSummarize_medianpolish’: R_subColSummarize.c:1747:9: warning: unused variable ‘j’ [-Wunused-variable] 1747 | int i,j; | ^ R_subColSummarize.c:1745:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable] 1745 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:1741:8: warning: unused variable ‘cur_rows’ [-Wunused-variable] 1741 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:1739:30: warning: unused variable ‘buffer2’ [-Wunused-variable] 1739 | double *results, *buffer, *buffer2; | ^~~~~~~ R_subColSummarize.c:1739:21: warning: unused variable ‘buffer’ [-Wunused-variable] 1739 | double *results, *buffer, *buffer2; | ^~~~~~ R_subColSummarize.c: At top level: R_subColSummarize.c:1703:14: warning: ‘subColSummarize_medianpolish_group’ defined but not used [-Wunused-function] 1703 | static void *subColSummarize_medianpolish_group(void *data){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o R_subrcModel_interfaces.c: In function ‘sub_rcModelSummarize_medianpolish_group’: R_subrcModel_interfaces.c:103:11: warning: unused variable ‘se’ [-Wunused-variable] 103 | double *se; | ^~ R_subrcModel_interfaces.c:102:11: warning: unused variable ‘weights’ [-Wunused-variable] 102 | double *weights; | ^~~~~~~ R_subrcModel_interfaces.c:87:20: warning: unused variable ‘buffer2’ [-Wunused-variable] 87 | double *buffer, *buffer2; | ^~~~~~~ R_subrcModel_interfaces.c:87:11: warning: unused variable ‘buffer’ [-Wunused-variable] 87 | double *buffer, *buffer2; | ^~~~~~ R_subrcModel_interfaces.c: In function ‘R_sub_rcModelSummarize_medianpolish’: R_subrcModel_interfaces.c:185:9: warning: unused variable ‘j’ [-Wunused-variable] 185 | int i,j; | ^ R_subrcModel_interfaces.c:183:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable] 183 | int ncur_rows; | ^~~~~~~~~ R_subrcModel_interfaces.c:179:8: warning: unused variable ‘cur_rows’ [-Wunused-variable] 179 | int *cur_rows; | ^~~~~~~~ R_subrcModel_interfaces.c:177:30: warning: unused variable ‘buffer2’ [-Wunused-variable] 177 | double *results, *buffer, *buffer2; | ^~~~~~~ R_subrcModel_interfaces.c:177:21: warning: unused variable ‘buffer’ [-Wunused-variable] 177 | double *results, *buffer, *buffer2; | ^~~~~~ R_subrcModel_interfaces.c:177:11: warning: unused variable ‘results’ [-Wunused-variable] 177 | double *results, *buffer, *buffer2; | ^~~~~~~ R_subrcModel_interfaces.c: In function ‘sub_rcModelSummarize_plm_group’: R_subrcModel_interfaces.c:413:10: warning: unused variable ‘scale’ [-Wunused-variable] 413 | double scale=-1.0; | ^~~~~ R_subrcModel_interfaces.c:392:20: warning: unused variable ‘buffer2’ [-Wunused-variable] 392 | double *buffer, *buffer2; | ^~~~~~~ R_subrcModel_interfaces.c:392:11: warning: unused variable ‘buffer’ [-Wunused-variable] 392 | double *buffer, *buffer2; | ^~~~~~ R_subrcModel_interfaces.c: In function ‘R_sub_rcModelSummarize_plm’: R_subrcModel_interfaces.c:510:9: warning: unused variable ‘j’ [-Wunused-variable] 510 | int i,j; | ^ R_subrcModel_interfaces.c:508:7: warning: unused variable ‘ncur_rows’ [-Wunused-variable] 508 | int ncur_rows; | ^~~~~~~~~ R_subrcModel_interfaces.c:504:8: warning: unused variable ‘cur_rows’ [-Wunused-variable] 504 | int *cur_rows; | ^~~~~~~~ R_subrcModel_interfaces.c:502:30: warning: unused variable ‘buffer2’ [-Wunused-variable] 502 | double *results, *buffer, *buffer2; | ^~~~~~~ R_subrcModel_interfaces.c:502:21: warning: unused variable ‘buffer’ [-Wunused-variable] 502 | double *results, *buffer, *buffer2; | ^~~~~~ R_subrcModel_interfaces.c:502:11: warning: unused variable ‘results’ [-Wunused-variable] 502 | double *results, *buffer, *buffer2; | ^~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c avg.c -o avg.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c avg_log.c -o avg_log.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c biweight.c -o biweight.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c lm.c -o lm.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c log_avg.c -o log_avg.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c log_median.c -o log_median.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c matrix_functions.c -o matrix_functions.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c median.c -o median.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c median_log.c -o median_log.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c medianpolish.c -o medianpolish.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c plmd.c -o plmd.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c plmr.c -o plmr.o plmr.c:279:13: warning: ‘XTWX_R_inv’ defined but not used [-Wunused-function] 279 | static void XTWX_R_inv(int *rows, int *cols, double *xtwx){ | ^~~~~~~~~~ plmr.c:152:13: warning: ‘XTWX_R’ defined but not used [-Wunused-function] 152 | static void XTWX_R(int *rows, int *cols, double *out_weights, double *xtwx){ | ^~~~~~ plmr.c:82:13: warning: ‘XTWY_R’ defined but not used [-Wunused-function] 82 | static void XTWY_R(int *rows, int *cols, double *out_weights, double *y,double *xtwy){ | ^~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c psi_fns.c -o psi_fns.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c qnorm.c -o qnorm.o qnorm.c: In function ‘qnorm_c_l’: qnorm.c:613:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 613 | error("ERROR; return code from pthread_join(thread #%d) is %d, exit status for thread was %d\n", | ~^ | | | int | %ld 614 | i, returnCode, *((int *) status)); | ~ | | | size_t {aka long unsigned int} qnorm.c:634:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 634 | error("ERROR; return code from pthread_join(thread #%d) is %d, exit status for thread was %d\n", | ~^ | | | int | %ld 635 | i, returnCode, *((int *) status)); | ~ | | | size_t {aka long unsigned int} qnorm.c: In function ‘qnorm_c_determine_target_l’: qnorm.c:2028:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 2028 | error("ERROR; return code from pthread_join(thread #%d) is %d, exit status for thread was %d\n", | ~^ | | | int | %ld 2029 | i, returnCode, *((int *) status)); | ~ | | | size_t {aka long unsigned int} qnorm.c:1931:7: warning: unused variable ‘non_na’ [-Wunused-variable] 1931 | int non_na; | ^~~~~~ qnorm.c:1926:12: warning: unused variable ‘j’ [-Wunused-variable] 1926 | size_t i,j,row_mean_ind; | ^ qnorm.c: In function ‘qnorm_c_determine_target_via_subset_l’: qnorm.c:2631:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 2631 | error("ERROR; return code from pthread_join(thread #%d) is %d, exit status for thread was %d\n", | ~^ | | | int | %ld 2632 | i, returnCode, *((int *) status)); | ~ | | | size_t {aka long unsigned int} qnorm.c:2533:7: warning: unused variable ‘non_na’ [-Wunused-variable] 2533 | int non_na; | ^~~~~~ qnorm.c:2528:12: warning: unused variable ‘j’ [-Wunused-variable] 2528 | size_t i,j,row_mean_ind; | ^ qnorm.c: In function ‘using_target_via_subset_part1’: qnorm.c:2752:14: warning: variable ‘ind’ set but not used [-Wunused-but-set-variable] 2752 | size_t i,j,ind,target_ind; | ^~~ qnorm.c: In function ‘using_target_via_subset_part2’: qnorm.c:2851:11: warning: unused variable ‘datvec’ [-Wunused-variable] 2851 | double *datvec; | ^~~~~~ qnorm.c:2850:11: warning: unused variable ‘sample_percentiles’ [-Wunused-variable] 2850 | double *sample_percentiles; | ^~~~~~~~~~~~~~~~~~ qnorm.c: In function ‘using_target_via_subset’: qnorm.c:3000:11: warning: unused variable ‘datvec’ [-Wunused-variable] 3000 | double *datvec; | ^~~~~~ qnorm.c:2999:11: warning: unused variable ‘sample_percentiles’ [-Wunused-variable] 2999 | double *sample_percentiles; | ^~~~~~~~~~~~~~~~~~ qnorm.c:2995:7: warning: unused variable ‘non_na’ [-Wunused-variable] 2995 | int non_na = 0; | ^~~~~~ qnorm.c:2994:7: warning: unused variable ‘targetnon_na’ [-Wunused-variable] 2994 | int targetnon_na = targetrows; | ^~~~~~~~~~~~ qnorm.c:2992:28: warning: unused variable ‘target_ind_double_floor’ [-Wunused-variable] 2992 | double target_ind_double,target_ind_double_floor; | ^~~~~~~~~~~~~~~~~~~~~~~ qnorm.c:2992:10: warning: unused variable ‘target_ind_double’ [-Wunused-variable] 2992 | double target_ind_double,target_ind_double_floor; | ^~~~~~~~~~~~~~~~~ qnorm.c:2991:10: warning: unused variable ‘samplepercentile’ [-Wunused-variable] 2991 | double samplepercentile; | ^~~~~~~~~~~~~~~~ qnorm.c:2990:11: warning: unused variable ‘ranks’ [-Wunused-variable] 2990 | double *ranks = (double *)R_Calloc((rows),double); | ^~~~~ qnorm.c:2988:11: warning: unused variable ‘row_mean’ [-Wunused-variable] 2988 | double *row_mean = target; | ^~~~~~~~ qnorm.c:2986:14: warning: unused variable ‘dimat’ [-Wunused-variable] 2986 | dataitem **dimat; | ^~~~~ qnorm.c:2984:18: warning: unused variable ‘target_ind’ [-Wunused-variable] 2984 | size_t i,j,ind,target_ind; | ^~~~~~~~~~ qnorm.c:2984:14: warning: unused variable ‘ind’ [-Wunused-variable] 2984 | size_t i,j,ind,target_ind; | ^~~ qnorm.c:2984:12: warning: unused variable ‘j’ [-Wunused-variable] 2984 | size_t i,j,ind,target_ind; | ^ qnorm.c: In function ‘R_qnorm_using_target’: qnorm.c:2139:3: warning: ‘target_rows’ may be used uninitialized [-Wmaybe-uninitialized] 2139 | qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ qnorm.c:2107:10: note: ‘target_rows’ was declared here 2107 | size_t target_rows, target_cols; | ^~~~~~~~~~~ qnorm.c: In function ‘R_qnorm_using_target_via_subset’: qnorm.c:3272:3: warning: ‘target_rows’ may be used uninitialized [-Wmaybe-uninitialized] 3272 | qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ qnorm.c:3239:10: note: ‘target_rows’ was declared here 3239 | size_t target_rows, target_cols; | ^~~~~~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c rlm.c -o rlm.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c rlm_anova.c -o rlm_anova.o rlm_anova.c: In function ‘rlm_fit_anova_given_probe_effects_engine’: rlm_anova.c:1235:10: warning: unused variable ‘endprobe’ [-Wunused-variable] 1235 | double endprobe; | ^~~~~~~~ rlm_anova.c: In function ‘rlm_compute_se_anova_given_probe_effects’: rlm_anova.c:1426:19: warning: unused variable ‘varderivpsi’ [-Wunused-variable] 1426 | double vs=0.0,m,varderivpsi=0.0; | ^~~~~~~~~~~ rlm_anova.c:1426:17: warning: unused variable ‘m’ [-Wunused-variable] 1426 | double vs=0.0,m,varderivpsi=0.0; | ^ rlm_anova.c:1426:10: warning: unused variable ‘vs’ [-Wunused-variable] 1426 | double vs=0.0,m,varderivpsi=0.0; | ^~ rlm_anova.c:1419:10: warning: unused variable ‘scale’ [-Wunused-variable] 1419 | double scale=0.0; | ^~~~~ rlm_anova.c:1418:10: warning: unused variable ‘Kappa’ [-Wunused-variable] 1418 | double Kappa=0.0; /* A correction factor */ | ^~~~~ rlm_anova.c:1417:10: warning: unused variable ‘sumderivpsi’ [-Wunused-variable] 1417 | double sumderivpsi=0.0; /* sum of psi'(r_i) */ | ^~~~~~~~~~~ rlm_anova.c:1415:10: warning: unused variable ‘sumpsi2’ [-Wunused-variable] 1415 | double sumpsi2=0.0; /* sum of psi(r_i)^2 */ | ^~~~~~~ rlm_anova.c:1414:10: warning: unused variable ‘k1’ [-Wunused-variable] 1414 | double k1 = psi_k; /* was 1.345; */ | ^~ rlm_anova.c: In function ‘rlm_wfit_anova_given_probe_effects_engine’: rlm_anova.c:1505:10: warning: unused variable ‘endprobe’ [-Wunused-variable] 1505 | double endprobe; | ^~~~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c rlm_se.c -o rlm_se.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c rma_background4.c -o rma_background4.o rma_background4.c: In function ‘rma_bg_correct’: rma_background4.c:370:10: warning: unused variable ‘param’ [-Wunused-variable] 370 | double param[3]; | ^~~~~ rma_background4.c:369:10: warning: unused variable ‘j’ [-Wunused-variable] 369 | size_t j; | ^ rma_background4.c: In function ‘R_rma_bg_correct’: rma_background4.c:527:12: warning: ‘PMcopy’ may be used uninitialized [-Wmaybe-uninitialized] 527 | return PMcopy; | ^~~~~~ rma_background4.c:500:13: note: ‘PMcopy’ was declared here 500 | SEXP dim1,PMcopy; | ^~~~~~ gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c rma_common.c -o rma_common.o gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 -DINFER_MIN_STACKSIZE=1 -fpic -g -O2 -Wall -Werror=format-security -c weightedkerneldensity.c -o weightedkerneldensity.o gcc -std=gnu2x -shared -L/usr/local/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 -llapack -L/home/rapidbuild/bbs-3.22-bioc-rapid/R/lib -lRblas -lgfortran -lm -lquadmath installing to /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-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)