Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1553/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
preprocessCore 1.62.1  (landing page)
Ben Bolstad
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/preprocessCore
git_branch: RELEASE_3_17
git_last_commit: a1aecdf
git_last_commit_date: 2023-05-01 20:11:04 -0400 (Mon, 01 May 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

BUILD BIN results for preprocessCore on kjohnson2


To the developers/maintainers of the preprocessCore package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: preprocessCore
Version: 1.62.1
Command: rm -rf preprocessCore.buildbin-libdir && mkdir preprocessCore.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh preprocessCore_1.62.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R preprocessCore.buildbin-libdir
StartedAt: 2023-10-19 15:58:24 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 15:58:52 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 28.0 seconds
RetCode: 0
Status:   OK  
PackageFile: preprocessCore_1.62.1.tgz
PackageFileSize: 163.1 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf preprocessCore.buildbin-libdir && mkdir preprocessCore.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh preprocessCore_1.62.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R preprocessCore.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=preprocessCore.buildbin-libdir preprocessCore_1.62.1.tar.gz'
>>>>>>> 

* installing *source* package ‘preprocessCore’ ...
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... clang -arch arm64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch arm64 -E
checking for library containing pthread_create... none required
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking if PTHREAD_STACK_MIN is defined... yes
checking if R is using flexiblas... flexiblas not found. preprocessCore threading will not be disabled
configure: Enabling threading for preprocessCore
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c R_colSummarize.c -o R_colSummarize.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c R_plmd_interfaces.c -o R_plmd_interfaces.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c R_plmr_interfaces.c -o R_plmr_interfaces.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c R_rlm_interfaces.c -o R_rlm_interfaces.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c R_subColSummarize.c -o R_subColSummarize.o
R_subColSummarize.c:111:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:109:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:117:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:115:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:288:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:284:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:282:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:290:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:466:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:458:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:460:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:464:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:641:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:643:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:635:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:637:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:817:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:813:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:811:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:819:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:988:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:990:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:994:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:996:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1165:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1163:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:1171:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1169:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1337:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:1339:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1343:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1345:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1522:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1518:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1516:30: warning: variable 'buffer2' set but not used [-Wunused-but-set-variable]
  double *results, *buffer, *buffer2;
                             ^
R_subColSummarize.c:1516:21: warning: variable 'buffer' set but not used [-Wunused-but-set-variable]
  double *results, *buffer, *buffer2;
                    ^
R_subColSummarize.c:1524:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1698:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1696:30: warning: unused variable 'buffer2' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                             ^
R_subColSummarize.c:1704:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1702:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1696:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                    ^
R_subColSummarize.c:1660:14: warning: unused function 'subColSummarize_medianpolish_group' [-Wunused-function]
static void *subColSummarize_medianpolish_group(void *data){
             ^
43 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
R_subrcModel_interfaces.c:90:11: warning: unused variable 'weights' [-Wunused-variable]
  double *weights;
          ^
R_subrcModel_interfaces.c:75:11: warning: unused variable 'buffer' [-Wunused-variable]
  double *buffer, *buffer2;
          ^
R_subrcModel_interfaces.c:91:11: warning: unused variable 'se' [-Wunused-variable]
  double *se;
          ^
R_subrcModel_interfaces.c:75:20: warning: unused variable 'buffer2' [-Wunused-variable]
  double *buffer, *buffer2;
                   ^
R_subrcModel_interfaces.c:167:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subrcModel_interfaces.c:165:30: warning: unused variable 'buffer2' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                             ^
R_subrcModel_interfaces.c:165:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                    ^
R_subrcModel_interfaces.c:165:11: warning: unused variable 'results' [-Wunused-variable]
  double *results, *buffer, *buffer2;
          ^
R_subrcModel_interfaces.c:173:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subrcModel_interfaces.c:171:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subrcModel_interfaces.c:398:10: warning: unused variable 'scale' [-Wunused-variable]
  double scale=-1.0;
         ^
R_subrcModel_interfaces.c:377:11: warning: unused variable 'buffer' [-Wunused-variable]
  double *buffer, *buffer2;
          ^
R_subrcModel_interfaces.c:377:20: warning: unused variable 'buffer2' [-Wunused-variable]
  double *buffer, *buffer2;
                   ^
R_subrcModel_interfaces.c:491:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subrcModel_interfaces.c:493:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subrcModel_interfaces.c:485:30: warning: unused variable 'buffer2' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                             ^
R_subrcModel_interfaces.c:485:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                    ^
R_subrcModel_interfaces.c:487:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subrcModel_interfaces.c:485:11: warning: unused variable 'results' [-Wunused-variable]
  double *results, *buffer, *buffer2;
          ^
19 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c avg.c -o avg.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c avg_log.c -o avg_log.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c biweight.c -o biweight.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c init_package.c -o init_package.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c lm.c -o lm.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c log_avg.c -o log_avg.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c log_median.c -o log_median.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c matrix_functions.c -o matrix_functions.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c median.c -o median.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c median_log.c -o median_log.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c medianpolish.c -o medianpolish.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c plmd.c -o plmd.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c plmr.c -o plmr.o
plmr.c:82:13: warning: unused function 'XTWY_R' [-Wunused-function]
static void XTWY_R(int *rows, int *cols, double *out_weights, double *y,double *xtwy){
            ^
plmr.c:152:13: warning: unused function 'XTWX_R' [-Wunused-function]
static void XTWX_R(int *rows, int *cols, double *out_weights, double *xtwx){
            ^
plmr.c:279:13: warning: unused function 'XTWX_R_inv' [-Wunused-function]
static void XTWX_R_inv(int *rows, int *cols, double *xtwx){
            ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c psi_fns.c -o psi_fns.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c qnorm.c -o qnorm.o
qnorm.c:1905:12: warning: unused variable 'j' [-Wunused-variable]
  size_t i,j,row_mean_ind;
           ^
qnorm.c:1910:7: warning: unused variable 'non_na' [-Wunused-variable]
  int non_na;
      ^
qnorm.c:2102:14: warning: variable 'target_rows' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  } else if (isMatrix(target)){
             ^~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:936:19: note: expanded from macro 'isMatrix'
#define isMatrix                Rf_isMatrix
                                ^
qnorm.c:2115:55: note: uninitialized use occurs here
  qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows);
                                                      ^~~~~~~~~~~
qnorm.c:2102:10: note: remove the 'if' if its condition is always true
  } else if (isMatrix(target)){
         ^~~~~~~~~~~~~~~~~~~~~
qnorm.c:2083:21: note: initialize the variable 'target_rows' to silence this warning
  size_t target_rows, target_cols;
                    ^
                     = 0
qnorm.c:2504:12: warning: unused variable 'j' [-Wunused-variable]
  size_t i,j,row_mean_ind;
           ^
qnorm.c:2509:7: warning: unused variable 'non_na' [-Wunused-variable]
  int non_na;
      ^
qnorm.c:2725:14: warning: variable 'ind' set but not used [-Wunused-but-set-variable]
  size_t i,j,ind,target_ind;
             ^
qnorm.c:2823:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
  double *sample_percentiles;
          ^
qnorm.c:2824:11: warning: unused variable 'datvec' [-Wunused-variable]
  double *datvec;
          ^
qnorm.c:2957:12: warning: unused variable 'j' [-Wunused-variable]
  size_t i,j,ind,target_ind;
           ^
qnorm.c:2957:14: warning: unused variable 'ind' [-Wunused-variable]
  size_t i,j,ind,target_ind;
             ^
qnorm.c:2957:18: warning: unused variable 'target_ind' [-Wunused-variable]
  size_t i,j,ind,target_ind;
                 ^
qnorm.c:2959:14: warning: unused variable 'dimat' [-Wunused-variable]
  dataitem **dimat;
             ^
qnorm.c:2961:11: warning: unused variable 'row_mean' [-Wunused-variable]
  double *row_mean = target;
          ^
qnorm.c:2963:11: warning: unused variable 'ranks' [-Wunused-variable]
  double *ranks = (double *)Calloc((rows),double);
          ^
qnorm.c:2964:10: warning: unused variable 'samplepercentile' [-Wunused-variable]
  double samplepercentile;
         ^
qnorm.c:2965:10: warning: unused variable 'target_ind_double' [-Wunused-variable]
  double target_ind_double,target_ind_double_floor;
         ^
qnorm.c:2965:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable]
  double target_ind_double,target_ind_double_floor;
                           ^
qnorm.c:2967:7: warning: unused variable 'targetnon_na' [-Wunused-variable]
  int targetnon_na = targetrows;
      ^
qnorm.c:2968:7: warning: unused variable 'non_na' [-Wunused-variable]
  int non_na = 0;
      ^
qnorm.c:2972:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
  double *sample_percentiles;
          ^
qnorm.c:2973:11: warning: unused variable 'datvec' [-Wunused-variable]
  double *datvec;
          ^
qnorm.c:3228:14: warning: variable 'target_rows' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
  } else if (isMatrix(target)){
             ^~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:936:19: note: expanded from macro 'isMatrix'
#define isMatrix                Rf_isMatrix
                                ^
qnorm.c:3242:77: note: uninitialized use occurs here
  qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows);
                                                                            ^~~~~~~~~~~
qnorm.c:3228:10: note: remove the 'if' if its condition is always true
  } else if (isMatrix(target)){
         ^~~~~~~~~~~~~~~~~~~~~
qnorm.c:3209:21: note: initialize the variable 'target_rows' to silence this warning
  size_t target_rows, target_cols;
                    ^
                     = 0
22 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c rlm.c -o rlm.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c rlm_anova.c -o rlm_anova.o
rlm_anova.c:1235:10: warning: unused variable 'endprobe' [-Wunused-variable]
  double endprobe;
         ^
rlm_anova.c: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:1426:17: warning: unused variable 'm' [-Wunused-variable]
  double vs=0.0,m,varderivpsi=0.0; 
                ^
rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable]
  double sumpsi2=0.0;  /* sum of psi(r_i)^2 */
         ^
rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable]
  double sumderivpsi=0.0; /* sum of psi'(r_i) */
         ^
rlm_anova.c:1426:10: warning: unused variable 'vs' [-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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c rlm_se.c -o rlm_se.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c rma_background4.c -o rma_background4.o
rma_background4.c:354:10: warning: unused variable 'j' [-Wunused-variable]
  size_t j;
         ^
rma_background4.c:355:10: warning: unused variable 'param' [-Wunused-variable]
  double param[3];
         ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c rma_common.c -o rma_common.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c weightedkerneldensity.c -o weightedkerneldensity.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/preprocessCore.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so
>>>>>>> 

>>>>>>> Paths before fix:
preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so:
	preprocessCore.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so"

>>>>>>> Paths after fix:

preprocessCore.buildbin-libdir/preprocessCore/libs/preprocessCore.so:
	preprocessCore.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)