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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1589/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
preprocessCore 1.68.0  (landing page)
Ben Bolstad
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/preprocessCore
git_branch: RELEASE_3_20
git_last_commit: fa0e33e
git_last_commit_date: 2024-10-29 09:21:09 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


INSTALL results for preprocessCore on merida1

To the developers/maintainers of the preprocessCore package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/preprocessCore.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: 1.68.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL preprocessCore
StartedAt: 2024-12-19 15:03:09 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 15:03:39 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 30.4 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL preprocessCore
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘preprocessCore’ ...
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... clang -arch x86_64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch x86_64 -E
checking for library containing pthread_create... none required
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking if PTHREAD_STACK_MIN is defined... yes
checking if R is using flexiblas... flexiblas not found. preprocessCore threading will not be disabled
configure: Enabling threading for preprocessCore
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c R_colSummarize.c -o R_colSummarize.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c R_plmd_interfaces.c -o R_plmd_interfaces.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c R_plmr_interfaces.c -o R_plmr_interfaces.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c R_rlm_interfaces.c -o R_rlm_interfaces.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c R_subColSummarize.c -o R_subColSummarize.o
R_subColSummarize.c: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:111:8: 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:284:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:288:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:290:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
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: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: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:637:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:635:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c: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:817:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_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:988:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:990:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1165:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1169:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1171:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1163:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer;
                    ^
R_subColSummarize.c:1343:7: 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: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:1702:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subColSummarize.c:1704:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subColSummarize.c:1696:21: warning: unused variable 'buffer' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                    ^
R_subColSummarize.c:1696:30: warning: unused variable 'buffer2' [-Wunused-variable]
  double *results, *buffer, *buffer2;
                             ^
R_subColSummarize.c:1698:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subColSummarize.c:1660:14: warning: unused function 'subColSummarize_medianpolish_group' [-Wunused-function]
static void *subColSummarize_medianpolish_group(void *data){
             ^
43 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
R_subrcModel_interfaces.c:75:20: warning: unused variable 'buffer2' [-Wunused-variable]
  double *buffer, *buffer2;
                   ^
R_subrcModel_interfaces.c:91:11: warning: unused variable 'se' [-Wunused-variable]
  double *se;
          ^
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:173:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subrcModel_interfaces.c:165:11: warning: unused variable 'results' [-Wunused-variable]
  double *results, *buffer, *buffer2;
          ^
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:167:8: warning: unused variable 'cur_rows' [-Wunused-variable]
  int *cur_rows;
       ^
R_subrcModel_interfaces.c:171:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
R_subrcModel_interfaces.c:377:11: warning: unused variable 'buffer' [-Wunused-variable]
  double *buffer, *buffer2;
          ^
R_subrcModel_interfaces.c:377:20: warning: unused variable 'buffer2' [-Wunused-variable]
  double *buffer, *buffer2;
                   ^
R_subrcModel_interfaces.c:398:10: warning: unused variable 'scale' [-Wunused-variable]
  double scale=-1.0;
         ^
R_subrcModel_interfaces.c:485:11: warning: unused variable 'results' [-Wunused-variable]
  double *results, *buffer, *buffer2;
          ^
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:493:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j;
        ^
R_subrcModel_interfaces.c:491:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
  int ncur_rows;
      ^
19 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c avg.c -o avg.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c avg_log.c -o avg_log.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c biweight.c -o biweight.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c init_package.c -o init_package.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c lm.c -o lm.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c log_avg.c -o log_avg.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c log_median.c -o log_median.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c matrix_functions.c -o matrix_functions.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c median.c -o median.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c median_log.c -o median_log.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c medianpolish.c -o medianpolish.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c plmd.c -o plmd.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c plmr.c -o plmr.o
plmr.c:82:13: warning: unused function 'XTWY_R' [-Wunused-function]
static void XTWY_R(int *rows, int *cols, double *out_weights, double *y,double *xtwy){
            ^
plmr.c:152:13: warning: unused function 'XTWX_R' [-Wunused-function]
static void XTWX_R(int *rows, int *cols, double *out_weights, double *xtwx){
            ^
plmr.c:279:13: warning: unused function 'XTWX_R_inv' [-Wunused-function]
static void XTWX_R_inv(int *rows, int *cols, double *xtwx){
            ^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c psi_fns.c -o psi_fns.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c qnorm.c -o qnorm.o
qnorm.c:596:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
               i, returnCode, *((int *) status));
               ^
qnorm.c:617:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
               i, returnCode, *((int *) status));
               ^
qnorm.c:2005:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
               i, returnCode, *((int *) status));
               ^
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:945:19: 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:2605:9: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
               i, returnCode, *((int *) status));
               ^
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 *)R_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:945:19: 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
26 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c rlm.c -o rlm.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c rlm_anova.c -o rlm_anova.o
rlm_anova.c:1235:10: warning: unused variable 'endprobe' [-Wunused-variable]
  double endprobe;
         ^
rlm_anova.c:1414:10: warning: unused variable 'k1' [-Wunused-variable]
  double k1 = psi_k;   /*  was 1.345; */
         ^
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:1418:10: warning: unused variable 'Kappa' [-Wunused-variable]
  double Kappa=0.0;      /* A correction factor */
         ^
rlm_anova.c:1426:19: warning: unused variable 'varderivpsi' [-Wunused-variable]
  double vs=0.0,m,varderivpsi=0.0; 
                  ^
rlm_anova.c:1419:10: warning: unused variable 'scale' [-Wunused-variable]
  double scale=0.0;
         ^
rlm_anova.c:1426:17: warning: unused variable 'm' [-Wunused-variable]
  double vs=0.0,m,varderivpsi=0.0; 
                ^
rlm_anova.c:1426:10: warning: unused variable 'vs' [-Wunused-variable]
  double vs=0.0,m,varderivpsi=0.0; 
         ^
rlm_anova.c:1505:10: warning: unused variable 'endprobe' [-Wunused-variable]
  double endprobe;
         ^
10 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c rlm_se.c -o rlm_se.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c rma_background4.c -o rma_background4.o
rma_background4.c:354:10: warning: unused variable 'j' [-Wunused-variable]
  size_t j;
         ^
rma_background4.c:355:10: warning: unused variable 'param' [-Wunused-variable]
  double param[3];
         ^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c rma_common.c -o rma_common.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include  -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC  -falign-functions=64 -Wall -g -O2  -c weightedkerneldensity.c -o weightedkerneldensity.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-preprocessCore/00new/preprocessCore/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (preprocessCore)