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###
### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL preprocessCore
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/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/home/biocbuild/bbs-3.22-bioc/R/lib -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/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/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)
