preprocessCore 1.45.0
Ben Bolstad
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/preprocessCore |
| Branch: master |
| Last Commit: 59d073d |
| Last Changed Date: 2018-10-30 11:54:26 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] | |
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### Running command:
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### rm -rf preprocessCore.buildbin-libdir && mkdir preprocessCore.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh preprocessCore_1.45.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R preprocessCore.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=preprocessCore.buildbin-libdir preprocessCore_1.45.0.tar.gz'
>>>>>>>
* installing *source* package ‘preprocessCore’ ...
checking for gcc... clang
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 accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -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
configure: Enabling threading for preprocessCore
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c R_colSummarize.c -o R_colSummarize.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c R_plmd_interfaces.c -o R_plmd_interfaces.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c R_plmr_interfaces.c -o R_plmr_interfaces.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c R_rlm_interfaces.c -o R_rlm_interfaces.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c R_subColSummarize.c -o R_subColSummarize.o
R_subColSummarize.c:105:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:103:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:99:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:97:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:273:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:271:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:267:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:265:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:442:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:444:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:438:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:436:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:614:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:616:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:608:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:610:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:787:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:785:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:779:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:781:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:951:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:959:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:957:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:953:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1121:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:1123:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1127:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:1129:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1292:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1290:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer;
^
R_subColSummarize.c:1298:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1296:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:1470:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:1466:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1472:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1647:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subColSummarize.c:1645:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subColSummarize.c:1641:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subColSummarize.c:1639:30: warning: unused variable 'buffer2' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subColSummarize.c:1639:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subColSummarize.c:1603:14: warning: unused function 'subColSummarize_medianpolish_group' [-Wunused-function]
static void *subColSummarize_medianpolish_group(void *data){
^
41 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
R_subrcModel_interfaces.c:80:11: warning: unused variable 'se' [-Wunused-variable]
double *se;
^
R_subrcModel_interfaces.c:79:11: warning: unused variable 'weights' [-Wunused-variable]
double *weights;
^
R_subrcModel_interfaces.c:64:11: warning: unused variable 'buffer' [-Wunused-variable]
double *buffer, *buffer2;
^
R_subrcModel_interfaces.c:64:20: warning: unused variable 'buffer2' [-Wunused-variable]
double *buffer, *buffer2;
^
R_subrcModel_interfaces.c:156:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subrcModel_interfaces.c:160:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subrcModel_interfaces.c:162:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subrcModel_interfaces.c:154:11: warning: unused variable 'results' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subrcModel_interfaces.c:154:30: warning: unused variable 'buffer2' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subrcModel_interfaces.c:154:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subrcModel_interfaces.c:361:11: warning: unused variable 'buffer' [-Wunused-variable]
double *buffer, *buffer2;
^
R_subrcModel_interfaces.c:361:20: warning: unused variable 'buffer2' [-Wunused-variable]
double *buffer, *buffer2;
^
R_subrcModel_interfaces.c:382:10: warning: unused variable 'scale' [-Wunused-variable]
double scale=-1.0;
^
R_subrcModel_interfaces.c:475:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
int ncur_rows;
^
R_subrcModel_interfaces.c:477:9: warning: unused variable 'j' [-Wunused-variable]
int i,j;
^
R_subrcModel_interfaces.c:471:8: warning: unused variable 'cur_rows' [-Wunused-variable]
int *cur_rows;
^
R_subrcModel_interfaces.c:469:30: warning: unused variable 'buffer2' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subrcModel_interfaces.c:469:21: warning: unused variable 'buffer' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
R_subrcModel_interfaces.c:469:11: warning: unused variable 'results' [-Wunused-variable]
double *results, *buffer, *buffer2;
^
19 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c avg.c -o avg.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c avg_log.c -o avg_log.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c biweight.c -o biweight.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c init_package.c -o init_package.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c lm.c -o lm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c log_avg.c -o log_avg.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c log_median.c -o log_median.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c matrix_functions.c -o matrix_functions.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c median.c -o median.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c median_log.c -o median_log.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c medianpolish.c -o medianpolish.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c plmd.c -o plmd.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c psi_fns.c -o psi_fns.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c qnorm.c -o qnorm.o
qnorm.c:1882:12: warning: unused variable 'j' [-Wunused-variable]
size_t i,j,row_mean_ind;
^
qnorm.c:1887:7: warning: unused variable 'non_na' [-Wunused-variable]
int non_na;
^
qnorm.c:2074:14: 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:1446:19: note: expanded from macro 'isMatrix'
#define isMatrix Rf_isMatrix
^
qnorm.c:2087:55: note: uninitialized use occurs here
qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows);
^˜˜˜˜˜˜˜˜˜˜
qnorm.c:2074:10: note: remove the 'if' if its condition is always true
} else if (isMatrix(target)){
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
qnorm.c:2055:21: note: initialize the variable 'target_rows' to silence this warning
size_t target_rows, target_cols;
^
= 0
qnorm.c:2476:12: warning: unused variable 'j' [-Wunused-variable]
size_t i,j,row_mean_ind;
^
qnorm.c:2481:7: warning: unused variable 'non_na' [-Wunused-variable]
int non_na;
^
qnorm.c:2790:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
double *sample_percentiles;
^
qnorm.c:2791:11: warning: unused variable 'datvec' [-Wunused-variable]
double *datvec;
^
qnorm.c:2924:12: warning: unused variable 'j' [-Wunused-variable]
size_t i,j,ind,target_ind;
^
qnorm.c:2924:14: warning: unused variable 'ind' [-Wunused-variable]
size_t i,j,ind,target_ind;
^
qnorm.c:2924:18: warning: unused variable 'target_ind' [-Wunused-variable]
size_t i,j,ind,target_ind;
^
qnorm.c:2926:14: warning: unused variable 'dimat' [-Wunused-variable]
dataitem **dimat;
^
qnorm.c:2928:11: warning: unused variable 'row_mean' [-Wunused-variable]
double *row_mean = target;
^
qnorm.c:2930:11: warning: unused variable 'ranks' [-Wunused-variable]
double *ranks = (double *)Calloc((rows),double);
^
qnorm.c:2931:10: warning: unused variable 'samplepercentile' [-Wunused-variable]
double samplepercentile;
^
qnorm.c:2932:10: warning: unused variable 'target_ind_double' [-Wunused-variable]
double target_ind_double,target_ind_double_floor;
^
qnorm.c:2932:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable]
double target_ind_double,target_ind_double_floor;
^
qnorm.c:2934:7: warning: unused variable 'targetnon_na' [-Wunused-variable]
int targetnon_na = targetrows;
^
qnorm.c:2935:7: warning: unused variable 'non_na' [-Wunused-variable]
int non_na = 0;
^
qnorm.c:2939:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
double *sample_percentiles;
^
qnorm.c:2940:11: warning: unused variable 'datvec' [-Wunused-variable]
double *datvec;
^
qnorm.c:3191:14: 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:1446:19: note: expanded from macro 'isMatrix'
#define isMatrix Rf_isMatrix
^
qnorm.c:3205:77: note: uninitialized use occurs here
qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows);
^˜˜˜˜˜˜˜˜˜˜
qnorm.c:3191:10: note: remove the 'if' if its condition is always true
} else if (isMatrix(target)){
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
qnorm.c:3172:21: note: initialize the variable 'target_rows' to silence this warning
size_t target_rows, target_cols;
^
= 0
21 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c rlm.c -o rlm.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -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:1419:10: warning: unused variable 'scale' [-Wunused-variable]
double scale=0.0;
^
rlm_anova.c:1418:10: warning: unused variable 'Kappa' [-Wunused-variable]
double Kappa=0.0; /* A correction factor */
^
rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable]
double sumderivpsi=0.0; /* sum of psi'(r_i) */
^
rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable]
double sumpsi2=0.0; /* sum of psi(r_i)^2 */
^
rlm_anova.c:1426:10: 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:1426:19: warning: unused variable 'varderivpsi' [-Wunused-variable]
double vs=0.0,m,varderivpsi=0.0;
^
rlm_anova.c:1505:10: warning: unused variable 'endprobe' [-Wunused-variable]
double endprobe;
^
10 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c rlm_se.c -o rlm_se.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c rma_background4.c -o rma_background4.o
rma_background4.c:342:10: warning: unused variable 'j' [-Wunused-variable]
size_t j;
^
rma_background4.c:343:10: warning: unused variable 'param' [-Wunused-variable]
double param[3];
^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c rma_common.c -o rma_common.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -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 -Wall -g -O2 -c weightedkerneldensity.c -o weightedkerneldensity.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/preprocessCore.buildbin-libdir/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
* DONE (preprocessCore)
>>>>>>>
>>>>>>> FIXING LINKS FOR preprocessCore.buildbin-libdir/preprocessCore/libs//preprocessCore.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs//preprocessCore.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs//preprocessCore.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs//preprocessCore.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs//preprocessCore.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs//preprocessCore.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs//preprocessCore.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs//preprocessCore.so"