linker error on mac clang-17: symbol not found in flat namespace '___kmpc_barrier' #6622
Description
This issue may be a result of #6418 causing openmp support to be detected, and data.table to be compiled, but not linked with -fopenmp.
Minimal reproducible example
dgealow@Dans-P4-MacBook-Pro ~ % R
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
[...]
> install.packages('data.table')
Installing package into ‘/Users/dgealow/Library/R/arm64/4.2/library’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
[selected 0-cloud]
There is a binary version available but the source version is later:
binary source needs_compilation
data.table 1.15.4 1.16.2 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘data.table’
Full output
trying URL 'https://cloud.r-project.org/src/contrib/data.table_1.16.2.tar.gz'
Content type 'application/x-gzip' length 5490076 bytes (5.2 MB)
==================================================
downloaded 5.2 MB
* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
zlib 1.2.11 is available ok
* checking if R installation supports OpenMP with "-Xclang -fopenmp" ... no
* checking if R installation supports OpenMP with "-fopenmp" ... yes
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c assign.c -o assign.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c between.c -o between.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c bmerge.c -o bmerge.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c chmatch.c -o chmatch.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c cj.c -o cj.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c coalesce.c -o coalesce.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c dogroups.c -o dogroups.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fastmean.c -o fastmean.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fcast.c -o fcast.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fifelse.c -o fifelse.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fmelt.c -o fmelt.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c forder.c -o forder.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c frank.c -o frank.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fread.c -o fread.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c freadR.c -o freadR.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c froll.c -o froll.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c frollR.c -o frollR.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c frolladaptive.c -o frolladaptive.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fsort.c -o fsort.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fwrite.c -o fwrite.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fwriteR.c -o fwriteR.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c gsumm.c -o gsumm.o
gsumm.c:1173:38: warning: implicit conversion from 'long long' to 'long double' changes value from 9223372036854775807 to 9223372036854775808 [-Wimplicit-const-int-float-conversion]
1173 | ansd[i] = (ISNAN(s[i]) || s[i]>INT64_MAX || s[i]<=INT64_MIN) ? NA_INTEGER64 : (int64_t)s[i];
| ~^~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX15.sdk/usr/include/stdint.h:94:26: note: expanded from macro 'INT64_MAX'
94 | #define INT64_MAX 9223372036854775807LL
| ^~~~~~~~~~~~~~~~~~~~~
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c idatetime.c -o idatetime.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c ijoin.c -o ijoin.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c inrange.c -o inrange.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c nafill.c -o nafill.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c negate.c -o negate.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c nqrecreateindices.c -o nqrecreateindices.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c openmp-utils.c -o openmp-utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c programming.c -o programming.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c quickselect.c -o quickselect.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c rbindlist.c -o rbindlist.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c reorder.c -o reorder.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c shift.c -o shift.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c snprintf.c -o snprintf.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c subset.c -o subset.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c transpose.c -o transpose.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c types.c -o types.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c uniqlist.c -o uniqlist.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c vecseq.c -o vecseq.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c wrappers.c -o wrappers.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 data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -single_module is obsolete
ld: warning: -multiply_defined is obsolete
ld: warning: -single_module is obsolete
ld: warning: -multiply_defined is obsolete
PKG_CFLAGS = -fopenmp
PKG_LIBS = -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /Users/dgealow/Library/R/arm64/4.2/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘data.table’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/dgealow/Library/R/arm64/4.2/library/00LOCK-data.table/00new/data.table/libs/data_table.so':
dlopen(/Users/dgealow/Library/R/arm64/4.2/library/00LOCK-data.table/00new/data.table/libs/data_table.so, 0x0006): symbol not found in flat namespace '___kmpc_barrier'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/dgealow/Library/R/arm64/4.2/library/data.table’
* restoring previous ‘/Users/dgealow/Library/R/arm64/4.2/library/data.table’
The downloaded source packages are in
‘/private/var/folders/sr/lw2ng95s3mj1qsqtdxywzjvc0000gn/T/Rtmp0Drt3Z/downloaded_packages’
Warning message:
In install.packages("data.table") :
installation of package ‘data.table’ had non-zero exit status
>
Workaround
Sys.setenv(PKG_LIBS='-fopenmp') before installing the package, as suggested by aitap below along with a possible package-level solution.
Output of sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.1.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.3