linker error on mac clang-17: symbol not found in flat namespace '___kmpc_barrier' · Issue #6622 · Rdatatable/data.table · GitHub

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

Does it work if you Sys.setenv(PKG_LIBS='-fopenmp') first? If yes, we might need an export PKG_LIBS="${PKG_LIBS} -fopenmp" here too:

data.table/configure

Line 128 in 546259d

export PKG_CFLAGS="${PKG_CFLAGS} -fopenmp"

(Interesting how it previously worked when compiling with -fopenmp but linking without it. This is probably better handled by someone with a Mac.)

Does it work if you Sys.setenv(PKG_LIBS='-fopenmp') first?

Works in my case (macOS 14.6.1 M1). Thanks!

Does it work if you Sys.setenv(PKG_LIBS='-fopenmp') first?

Yes, it does!

Interesting how it previously worked when compiling with -fopenmp but linking without it.

I'm not sure that it did--previous installations from source of data table on my mac have always started up with a message along the lines of "this installation was compiled without openmp support and is running in single-threaded mode, go complain to Apple"

Here it is in full:

data.table 1.15.4 using 1 threads (see ?getDTthreads). Latest news: r-datatable.com

This installation of data.table has not detected OpenMP support. It should still work but in single-threaded mode.
This is a Mac. Please read https://mac.r-project.org/openmp/. Please engage with Apple and ask them for support. Check r-datatable.com for updates, and our Mac instructions here: https://github.com/Rdatatable/data.table/wiki/Installation. After several years of many reports of installation problems on Mac, it's time to gingerly point out that there have been no similar problems on Windows or Linux.

Ok so on my R4.4 installation, we take a different branch and hit a similar error that seems resistant to the workaround:

% R

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
[...]
> install.packages('data.table', type = 'source')
--- Please select a CRAN mirror for use in this session ---
[selected 0-cloud]
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’ ...

Full output

** 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" ... yes
** libs
using C compiler: ‘Homebrew clang version 19.1.3’
using SDK: ‘’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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   -Xclang -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 -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 -lomp -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
PKG_CFLAGS = -Xclang -fopenmp
PKG_LIBS = -lomp -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 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-data.table/00new/data.table/libs/data_table.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-data.table/00new/data.table/libs/data_table.so, 0x0006): symbol not found in flat namespace '___kmpc_dispatch_deinit'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/data.table’

The downloaded source packages are in
	‘/private/var/folders/sr/lw2ng95s3mj1qsqtdxywzjvc0000gn/T/RtmpHgVbPN/downloaded_packages’
Warning message:
In install.packages("data.table", type = "source") :
  installation of package ‘data.table’ had non-zero exit status

Though this time the particular symbol we fail to find is ___kmpc_dispatch_deinit.

Interesting. The flags seem correct according to the OpenMP on Mac page, but the workaround is apparently not needed and doesn't work with the Homebrew toolchain. Is this R build also from Homebrew?

I suppose we'll have to update the configure test to not only compile a shared library with R CMD SHLIB but also try to load it before declaring the test successful.

It looks like the same workaround should work because the configure script only appends to the user-provided PKG_CFLAGS and PKG_LIBS environment variables, and yet it doesn't. Hard to figure out without running sh -x configure on a real Mac.

It looks like the same workaround should work because the configure script only appends to the user-provided PKG_CFLAGS and PKG_LIBS environment variables, and yet it doesn't. Hard to figure out without running sh -x configure on a real Mac.

Well, doing this produces a third scenario for me, in which all of the checks fail.

* checking if R installation supports OpenMP with "-Xclang -fopenmp" ... + CPPFLAGS='-I/opt/homebrew/opt/llvm/include -Xclang -fopenmp'
+ PKG_LIBS=-lomp
+ /bin/R CMD SHLIB test-omp.c
+ echo no
no
+ printf %s '* checking if R installation supports OpenMP with "-fopenmp" ... '
* checking if R installation supports OpenMP with "-fopenmp" ... + CPPFLAGS='-I/opt/homebrew/opt/llvm/include -fopenmp'
+ /bin/R CMD SHLIB test-omp.c
+ echo no
no
++ uname -m
+ '[' arm64 = arm64 ']'
+ HOMEBREW_PREFIX=/opt/homebrew
+ '[' -e /opt/homebrew/opt/libomp ']'
+ printf %s '* checking if libomp installation at /opt/homebrew/opt/libomp can be used... '
* checking if libomp installation at /opt/homebrew/opt/libomp can be used... + LIBOMP_INCLUDE='-I/opt/homebrew/opt/libomp/include -Xclang -fopenmp'
+ LIBOMP_LINK='-L/opt/homebrew/opt/libomp/lib -lomp'
+ -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -L/opt/homebrew/opt/libomp/lib -lomp test-omp.c
+ echo no
no
+ export R_OPENMP_ENABLED=0

--though it occurs to me that I do have some R makevars set, which could be affecting things

% cat ~/.R/Makevars
FC = /opt/homebrew/bin/gfortran
FLIBS = -L/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/current/ -lgfortran -lquadmath -lm

Although I don't see how they'd account for the difference between R4.2 and R4.4

Ah, it's probably the fact that R4.3 changed the default C(++) standard to C(++)17. R4.3 behaves the same as R4.4 for me.

Sorry, forgot to mention that configure relies on R_HOME=`R RHOME` being set.

dgealow@Dans-P4-MacBook-Pro data.table % export R_HOME=$(R RHOME) 
dgealow@Dans-P4-MacBook-Pro data.table % echo $R_HOME            
/Library/Frameworks/R.framework/Resources
dgealow@Dans-P4-MacBook-Pro data.table % zsh -x configure                                                                                                                       
+configure:4> CC=+configure:4> /Library/Frameworks/R.framework/Resources/bin/R CMD config CC
+configure:4> CC='clang -arch arm64' 
+configure:5> CFLAGS=+configure:5> /Library/Frameworks/R.framework/Resources/bin/R CMD config CFLAGS
+configure:5> CFLAGS='-falign-functions=64 -Wall -g -O2' 
+configure:7> echo 'CC=clang -arch arm64'
+configure:8> echo 'CFLAGS=-falign-functions=64 -Wall -g -O2'
+configure:11> case clang -arch arm64 (gcc*)
+configure:22> msg=0 
+configure:23> NOZLIB=1 
+configure:24> pkg-config --version
+configure:25> [ 0 -ne 0 ']'
+configure:29> pkg-config --exists zlib
+configure:30> [ 0 -ne 0 ']'
+configure:34> NOZLIB=0 
+configure:35> lib=+configure:35> pkg-config --libs zlib
+configure:35> lib=-lz 
+configure:36> cflag=+configure:36> pkg-config --cflags zlib
+configure:36> cflag='' 
+configure:37> expr -- -lz : '.*-lz$'
+configure:38> [ 0 -ne 0 ']'
+configure:50> [ 0 -ne 0 ']'
+configure:67> version=+configure:67> pkg-config --modversion zlib
+configure:67> version=1.2.11 
+configure:68> echo 'zlib 1.2.11 is available ok'
zlib 1.2.11 is available ok
+configure:78> cat
+configure:163> detect_openmp
+detect_openmp:2> uname
+detect_openmp:2> [ Darwin '=' Linux ']'
+detect_openmp:25> uname
+detect_openmp:25> [ Darwin '=' Darwin ']'
+detect_openmp:28> printf %s '* checking if R installation supports OpenMP with "-Xclang -fopenmp" ... '
* checking if R installation supports OpenMP with "-Xclang -fopenmp" ... +detect_openmp:29> CPPFLAGS='-I/opt/homebrew/opt/llvm/include -Xclang -fopenmp' PKG_LIBS=-lomp /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB test-omp.c
+detect_openmp:30> echo yes
yes
+detect_openmp:31> export PKG_CFLAGS=' -Xclang -fopenmp'
+detect_openmp:32> export PKG_LIBS=' -lomp'
+detect_openmp:33> export R_OPENMP_ENABLED=1
+detect_openmp:34> return
+configure:165> rm -f test-omp.c test-omp.o test-omp.so a.out
+configure:167> [ 1 '=' 0 ']'
+configure:177> sed -e 's|@openmp_cflags@|$(SHLIB_OPENMP_CFLAGS)|' src/Makevars.in
+configure:181> sed -e 's|@PKG_CFLAGS@| -Xclang -fopenmp|' src/Makevars
+configure:181> mv src/Makevars.tmp src/Makevars
+configure:182> sed -e 's|@PKG_LIBS@| -lomp|' src/Makevars
+configure:182> mv src/Makevars.tmp src/Makevars
+configure:185> [ 0 '=' 1 ']'
+configure:190> sed -e 's|@zlib_cflags@||' src/Makevars
+configure:190> mv src/Makevars.tmp src/Makevars
+configure:191> sed -e 's|@zlib_libs@|-lz|' src/Makevars
+configure:191> mv src/Makevars.tmp src/Makevars
+configure:194> exit 0

(/Library/Frameworks/R.framework/Resources symlinks into whichever R version I have selected as current with the handy Rswitch utility -- 4.3 for the above, though 4.4 yields similar results)

Thanks! What's the difference if you additionally set PKG_CFLAGS=-fopenmp PKG_LIBS=-fopenmp before running sh -x configure?

Confirmed. It installs correctly with clang 16.0.0, which can be found in Command Line Tools for Xcode 16.2.

Wow, thank you so much @twitched! I was able to install with clang 16.0.0. To be clear, here is what I did:

Install clang 16 from homebrew: brew install llvm@16
Install data.table using clang 16.0.0 via either:
a. Adding CC=/opt/homebrew/opt/llvm@16/bin/clang to your .R/Makevars
OR
b. Temporarily using clang 16.0.0 only for data.table installation using the withr package:

withr::with_makevars(
  c(CC = "/opt/homebrew/opt/llvm@16/bin/clang"),
  install.packages("data.table", type = "source", repos = c(CRAN = "https://cloud.r-project.org/"))
)

Wow, thank you so much @twitched! I was able to install with clang 16.0.0. To be clear, here is what I did:

Install clang 16 from homebrew: brew install llvm@16

Install data.table using clang 16.0.0 via either:
a. Adding CC=/opt/homebrew/opt/llvm@16/bin/clang to your .R/Makevars
OR
b. Temporarily using clang 16.0.0 only for data.table installation using the withr package:

withr::with_makevars(
c(CC = "/opt/homebrew/opt/llvm@16/bin/clang"),
install.packages("data.table", type = "source", repos = c(CRAN = "https://cloud.r-project.org/"))
)

This worked for me too.

.R/Makevars

# Apple Silicon Macs LDFLAGS += -L/opt/homebrew/opt/libomp/lib -lomp CPPFLAGS += -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp

CPPFLAGS += -I/opt/homebrew/opt/gettext/include
LDFLAGS += -L/opt/homebrew/opt/gettext/lib
CC=/opt/homebrew/opt/llvm@16/bin/clang

Installation log

❯ Rscript -e "install.packages('data.table', type='source')" Installing package into ‘/Users/eyayaw/Library/R/arm64/4.5/library’ (as ‘lib’ is unspecified) trying URL 'https://packagemanager.rstudio.com/all/latest/src/contrib/data.table_1.17.8.tar.gz' Content type 'binary/octet-stream' length 5744656 bytes (5.5 MB) ================================================== downloaded 5.5 MB

installing source package ‘data.table’ ...
** this is package ‘data.table’ version ‘1.17.8’
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
zlib 1.2.12 is available ok
checking if R installation supports OpenMP with "-Xclang -fopenmp" ... yes
** libs
using C compiler: ‘Homebrew clang version 16.0.6’
using SDK: ‘MacOSX26.0.sdk’
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c assign.c -o assign.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c between.c -o between.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c bmerge.c -o bmerge.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c chmatch.c -o chmatch.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c cj.c -o cj.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c coalesce.c -o coalesce.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c dogroups.c -o dogroups.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fastmean.c -o fastmean.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fcast.c -o fcast.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fifelse.c -o fifelse.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fmelt.c -o fmelt.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c forder.c -o forder.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c frank.c -o frank.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fread.c -o fread.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c freadR.c -o freadR.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c froll.c -o froll.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c frollR.c -o frollR.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c frolladaptive.c -o frolladaptive.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fsort.c -o fsort.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fwrite.c -o fwrite.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c fwriteR.c -o fwriteR.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c gsumm.c -o gsumm.o
gsumm.c:1177:38: warning: implicit conversion from 'long long' to 'long double' changes value from 9223372036854775807 to 9223372036854775808 [-Wimplicit-const-int-float-conversion]
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'
#define INT64_MAX 9223372036854775807LL
^~~~~~~~~~~~~~~~~~~~~
1 warning generated.
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c idatetime.c -o idatetime.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c ijoin.c -o ijoin.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c inrange.c -o inrange.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c nafill.c -o nafill.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c negate.c -o negate.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c nqrecreateindices.c -o nqrecreateindices.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c openmp-utils.c -o openmp-utils.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c programming.c -o programming.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c quickselect.c -o quickselect.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c rbindlist.c -o rbindlist.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c reorder.c -o reorder.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c shift.c -o shift.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c snprintf.c -o snprintf.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c subset.c -o subset.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c transpose.c -o transpose.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c types.c -o types.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c uniqlist.c -o uniqlist.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c vecseq.c -o vecseq.o
/opt/homebrew/opt/llvm@16/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp -I/opt/homebrew/opt/gettext/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c wrappers.c -o wrappers.o
/opt/homebrew/opt/llvm@16/bin/clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -L/opt/homebrew/opt/libomp/lib -lomp -L/opt/homebrew/opt/gettext/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 -lomp -lz -F/Library/Frameworks/R.framework/.. -framework R
ld: warning: ignoring duplicate libraries: '-lomp'
PKG_CFLAGS = -Xclang -fopenmp
PKG_LIBS = -lomp -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/eyayaw/Library/R/arm64/4.5/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
** 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 (data.table)

The downloaded source packages are in
‘/private/var/folders/rs/rprvvwqd59j4cw51g1bb48dr0000gn/T/RtmpzzbGdy/downloaded_packages’

hi! I am having the same issue on github actions, with macos-latest image (same as macos-15 since its release 2 weeks ago). Downgrading to macos-14 image works, consistent with the comment about that downgrading clang works. tdhock/atime#94
This is in the context of running atime tests, one of the cases involves data.table.

Downgrading is a nice temporary work-around, but we should eventually try to get data.table compiling with the newer compilers, right?

So this is perhaps interesting news for this issue, because we could perhaps use github actions with os: macos-15 to test this issue with data.table compilation scripts? Anyone willing to give it a try? @aitap ?

this is not a bug in clang. it is a bug in data.table. vllm had the same problem, and fixed it via this PR vllm-project/vllm#16086 which we may use as inspiration for our fix. that pr removes these two flags "-Xpreprocessor"
"-fopenmp"

Any updates on this issue?

I think I am having the same problem:

> sessionInfo()
R version 4.5.2 (2025-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.7.3

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/London
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.5.2    tools_4.5.2       rstudioapi_0.18.0
> install.packages("data.table", type = "source")
trying URL 'https://cran.rstudio.com/src/contrib/data.table_1.18.2.1.tar.gz'
Content type 'application/x-gzip' length 6023973 bytes (5.7 MB)
==================================================
downloaded 5.7 MB

* installing *source* package ‘data.table’ ...
** this is package ‘data.table’ version ‘1.18.2.1’
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
zlib 1.2.12 is available ok
* checking if R installation supports OpenMP with "-Xclang -fopenmp" ... yes
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
using SDK: ‘MacOSX26.2.sdk’
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c assign.c -o assign.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c between.c -o between.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c bmerge.c -o bmerge.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c chmatch.c -o chmatch.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c cj.c -o cj.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c coalesce.c -o coalesce.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c dogroups.c -o dogroups.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fastmean.c -o fastmean.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fcast.c -o fcast.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fifelse.c -o fifelse.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fmelt.c -o fmelt.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c forder.c -o forder.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c frank.c -o frank.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fread.c -o fread.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c freadR.c -o freadR.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c froll.c -o froll.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c frollR.c -o frollR.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c frolladaptive.c -o frolladaptive.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c frollapply.c -o frollapply.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fsort.c -o fsort.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fwrite.c -o fwrite.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fwriteR.c -o fwriteR.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c gsumm.c -o gsumm.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c hash.c -o hash.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c idatetime.c -o idatetime.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c ijoin.c -o ijoin.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c inrange.c -o inrange.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c mergelist.c -o mergelist.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c nafill.c -o nafill.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c negate.c -o negate.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c nqrecreateindices.c -o nqrecreateindices.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c openmp-utils.c -o openmp-utils.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c programming.c -o programming.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c quickselect.c -o quickselect.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c rbindlist.c -o rbindlist.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c reorder.c -o reorder.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c shellsort.c -o shellsort.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c shift.c -o shift.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c snprintf.c -o snprintf.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c subset.c -o subset.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c transpose.c -o transpose.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c types.c -o types.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c uniqlist.c -o uniqlist.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.c -o utils.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c vecseq.c -o vecseq.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c wrappers.c -o wrappers.o
/usr/bin/clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -L/opt/homebrew/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 frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fvisibility=hidden -lomp -lz -F/Library/Frameworks/R.framework/.. -framework R
PKG_CFLAGS = -fvisibility=hidden -Xclang -fopenmp
PKG_LIBS = -fvisibility=hidden -lomp -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 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 '/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-data.table/00new/data.table/libs/data_table.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-data.table/00new/data.table/libs/data_table.so, 0x0006): symbol not found in flat namespace '___kmpc_dispatch_deinit'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/data.table’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/data.table’
The downloaded source packages are in
	‘/private/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T/RtmpLEsYgZ/downloaded_packages’
Warning message:
In utils::install.packages("data.table", type = "source") :
  installation of package ‘data.table’ had non-zero exit status

The Sys.setenv(PKG_LIBS='-fopenmp') trick does not work for me.

> Sys.setenv(PKG_LIBS='-fopenmp')
> install.packages("data.table", type = "source")
trying URL 'https://cran.rstudio.com/src/contrib/data.table_1.18.2.1.tar.gz'
Content type 'application/x-gzip' length 6023973 bytes (5.7 MB)
==================================================
downloaded 5.7 MB

* installing *source* package ‘data.table’ ...
** this is package ‘data.table’ version ‘1.18.2.1’
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
zlib 1.2.12 is available ok
* checking if R installation supports OpenMP with "-Xclang -fopenmp" ... yes
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.3.2)’
using SDK: ‘MacOSX26.2.sdk’
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c assign.c -o assign.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c between.c -o between.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c bmerge.c -o bmerge.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c chmatch.c -o chmatch.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c cj.c -o cj.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c coalesce.c -o coalesce.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c dogroups.c -o dogroups.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fastmean.c -o fastmean.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fcast.c -o fcast.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fifelse.c -o fifelse.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fmelt.c -o fmelt.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c forder.c -o forder.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c frank.c -o frank.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fread.c -o fread.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c freadR.c -o freadR.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c froll.c -o froll.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c frollR.c -o frollR.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c frolladaptive.c -o frolladaptive.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c frollapply.c -o frollapply.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fsort.c -o fsort.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fwrite.c -o fwrite.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c fwriteR.c -o fwriteR.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c gsumm.c -o gsumm.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c hash.c -o hash.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c idatetime.c -o idatetime.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c ijoin.c -o ijoin.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c inrange.c -o inrange.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c mergelist.c -o mergelist.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c nafill.c -o nafill.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c negate.c -o negate.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c nqrecreateindices.c -o nqrecreateindices.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c openmp-utils.c -o openmp-utils.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c programming.c -o programming.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c quickselect.c -o quickselect.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c rbindlist.c -o rbindlist.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c reorder.c -o reorder.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c shellsort.c -o shellsort.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c shift.c -o shift.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c snprintf.c -o snprintf.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c subset.c -o subset.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c transpose.c -o transpose.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c types.c -o types.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c uniqlist.c -o uniqlist.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.c -o utils.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c vecseq.c -o vecseq.o
/usr/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/opt/homebrew/include   -fvisibility=hidden  -Xclang -fopenmp   -fPIC  -falign-functions=64 -Wall -g -O2  -c wrappers.c -o wrappers.o
/usr/bin/clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -L/opt/homebrew/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 frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fvisibility=hidden -fopenmp -lomp -lz -F/Library/Frameworks/R.framework/.. -framework R
clang: error: unsupported option '-fopenmp'
make: *** [data.table.so] Error 1
ERROR: compilation failed for package ‘data.table’
* removing ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/data.table’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/data.table’

My Makevars file looks like:

# Set Fortran compilers
F77=/usr/local/bin/gfortran
FC=/usr/local/bin/gfortran
FLIBS=-L/usr/local/bin/gfortran

# Set C/C++ compilers (clang/clang++)
# Set compilers
CC=/usr/bin/clang
CXX=/usr/bin/clang++

# OpenMP support (multithreading)
# Homebrew libomp + correct Apple clang flags
# -Xpreprocessor is required on newer macOS/clang
# CPPFLAGS += -I/opt/homebrew/opt/libomp/include -Xpreprocessor -fopenmp
# LDFLAGS  += -L/opt/homebrew/opt/libomp/lib -lomp -Wl,-rpath,/opt/homebrew/opt/libomp/lib

# Homebrew headers & libs (for libintl.h, etc.)
# * Required for data.table / Matrix / other source installs on R >= 4.5
CPPFLAGS += -I/opt/homebrew/include
LDFLAGS  += -L/opt/homebrew/lib

Any advice would be welcome!

Using the llvm clang 16 works - see the instructions in the message above #6622 (comment)

@edwardlavender, the toolchain currently installed on your Mac is incompatible with the toolchain used to compile the CRAN builds of R-4.5.2 and packages. Thankfully, you can just install the binary package from CRAN, which nowadays includes OpenMP support, and avoid having to hunt around for Xcode 14.2/14.3 (see the version requirements at https://mac.r-project.org/).

Thank you for the advice!

Hi! Having the same issue here, but I do need to build from source because I use renv and when I restore an old project with a slightly older data.table, then the error above occurs. I tried installing from source with the latest data.table and it doesn't work.

I am bit lost in the thread, so I not sure what the current solution would be.

R version 4.5.2 (2025-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Tahoe 26.3

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/London
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.5.2

I installed the latest CLI tools with xcode-select --install. I don't have a Makevars and I using the CRAN build of R.

Output of R CMD config --all

Details

CC = clang -arch arm64 -std=gnu2x
CFLAGS = -falign-functions=64 -Wall -g -O2
CPICFLAGS = -fPIC
CPPFLAGS = -I/opt/R/arm64/include
CC17 = clang -arch arm64 -std=gnu17
C17FLAGS = -falign-functions=64 -Wall -g -O2
CC23 = clang -arch arm64 -std=gnu2x
C23FLAGS = -falign-functions=64 -Wall -g -O2
CC90 = clang -arch arm64 -std=gnu90
C90FLAGS = -falign-functions=64 -Wall -g -O2
CC99 = clang -arch arm64 -std=gnu99
C99FLAGS = -falign-functions=64 -Wall -g -O2
CXX = clang++ -arch arm64 -std=gnu++17
CXXFLAGS = -falign-functions=64 -Wall -g -O2
CXXPICFLAGS = -fPIC
CXX11 = clang++ -arch arm64
CXX11STD = -std=gnu++11
CXX11FLAGS = -falign-functions=64 -Wall -g -O2
CXX11PICFLAGS = -fPIC
CXX14 = clang++ -arch arm64
CXX14STD = -std=gnu++14
CXX14FLAGS = -falign-functions=64 -Wall -g -O2
CXX14PICFLAGS = -fPIC
CXX17 = clang++ -arch arm64
CXX17STD = -std=gnu++17
CXX17FLAGS = -falign-functions=64 -Wall -g -O2
CXX17PICFLAGS = -fPIC
CXX20 = clang++ -arch arm64
CXX20STD = -std=gnu++20
CXX20FLAGS = -falign-functions=64 -Wall -g -O2
CXX20PICFLAG =
CXX23 = clang++ -arch arm64
CXX23STD = -std=gnu++23
CXX23FLAGS = -falign-functions=64 -Wall -g -O2
CXX23PICFLAGS = -fPIC
CXX26 = clang++ -arch arm64
CXX26STD = -std=gnu++26
CXX26FLAGS = -falign-functions=64 -Wall -g -O2
CXX26PICFLAGS = -fPIC
DYLIB_EXT = .dylib
DYLIB_LD = clang -arch arm64 -std=gnu2x
DYLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup
FC = /opt/gfortran/bin/gfortran -arch arm64
FFLAGS = -Wall -g -O2
FPICFLAGS = -fPIC
FLIBS = -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath
FCFLAGS = -Wall -g -O2
SAFE_FFLAGS = -Wall -g -O2
OBJC = clang -arch arm64
OBJCFLAGS = -falign-functions=64 -Wall -g -O2 -fobjc-exceptions
JAVA = /usr/bin/java
JAVAC = /usr/bin/javac
JAVAH = /usr/bin/javah
JAR = /usr/bin/jar
JAVA_HOME = /Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home
JAVA_LIBS = -L/Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home/lib/server -ljvm
JAVA_CPPFLAGS = -I/Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home/include/darwin
LDFLAGS = -L/opt/R/arm64/lib
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = clang++ -arch arm64 -std=gnu++17
SHLIB_CXXLDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup
SHLIB_CXX11LD = clang++ -arch arm64 -std=gnu++11
SHLIB_CXX11LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup
SHLIB_CXX14LD = clang++ -arch arm64 -std=gnu++14
SHLIB_CXX14LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup
SHLIB_CXX17LD = clang++ -arch arm64 -std=gnu++17
SHLIB_CXX17LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup
SHLIB_CXX20LD = clang++ -arch arm64 -std=gnu++20
SHLIB_CXX20LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup
SHLIB_CXX23LD = clang++ -arch arm64 -std=gnu++23
SHLIB_CXX23LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup
HLIB_CXX26LD =
SHLIB_CXX266DFLAGS =
SHLIB_EXT = .so
SHLIB_FFLAGS =
SHLIB_LD = clang -arch arm64 -std=gnu2x
SHLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup
TCLTK_CPPFLAGS = -I/opt/R/arm64/include -I/opt/R/arm64/include -I/usr/X11R6/include
TCLTK_LIBS = -L/opt/R/arm64/lib -ltcl8.6 -L/opt/R/arm64/lib -ltk8.6 -L/usr/X11R6/lib -lX11 -Wl,-weak-lXss -lXext
BLAS_LIBS = -L/Library/Frameworks/R.framework/Resources/lib -lRblas
LAPACK_LIBS = -L/Library/Frameworks/R.framework/Resources/lib -lRlapack
MAKE = make
LIBnn = lib
AR = ar
NM = /usr/bin/nm -B
RANLIB = ranlib
LTO =
LTO_FC =
LTO_LD =

## The following variables are defunct
CPP CXXCPP

EDIT: So, this worked for me:

Installed libraries with https://mac.r-project.org/bin/ (not sure they are needed for data.table but they are needed for other packages)
- source("https://mac.R-project.org/bin/install.R")
- install.libs("all")
Installed OpenMP with https://mac.thecoatlessprofessor.com/macrtools/ (It creates Makevars too, with CPPFLAGS += -Xclang -fopenmp LDFLAGS += -lomp)
brew install llvm@16

Installed data.table from source with:

withr::with_makevars(
  c(CC = "/opt/homebrew/opt/llvm@16/bin/clang"),
  install.packages("data.table", type = "source", repos = c(CRAN = "https://cloud.r-project.org/"))
)

It works. BUT the Makevars break compilation of other packages (like Matrix).

Thank you for sharing your experience!

I installed the latest CLI tools with xcode-select --install.

Is is possible to install Xcode 14.2/14.3 on macOS Tahoe 26.3? That's the only supported toolchain for the CRAN build of R-4.5 for macOS.

R 4.5.2 for macOS arm64 (which is what I have) requires Xcode 16, but I installed Xcode 26 and it worked fine. (I don't think Xcode 16 works on Tahoe, I've seen people reporting errors after installing it).

As far as I know there are no breaking changes between Xcode 16 and 26 (which is the following release despite the number jump), so maybe that's why it works fine but not sure?

linker error on mac clang-17: symbol not found in flat namespace '___kmpc_barrier' · Issue #6622 · Rdatatable/data.table · GitHub

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linker error on mac clang-17: symbol not found in flat namespace '___kmpc_barrier' #6622

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linker error on mac clang-17: symbol not found in flat namespace '___kmpc_barrier' · Issue #6622 · Rdatatable/data.table · GitHub

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linker error on mac clang-17: symbol not found in flat namespace '___kmpc_barrier' #6622

Description

Minimal reproducible example

Workaround

Output of sessionInfo()

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