Can't install data.table package on MacOS 10.12+ using clang - r

Question

Thanks for clicking in. I've been trying to solve this for hours but nothing seem to work.
My operating system: MacOS sierra OS version: 10.12.3
R version: 3.3.3
I've followed the data.table download instruction here: https://github.com/Rdatatable/data.table/wiki/Installation
But it's still not working
the error message is as below:
*> install.packages("data.table", type = "source",
+ repos = "http://Rdatatable.github.io/data.table")
嘗試 URL 'http://Rdatatable.github.io/data.table/src/contrib/data.table_1.10.5.tar.gz'
Content type 'application/octet-stream' length 2843331 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
* installing *source* package ‘data.table’ ...
** libs
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c assign.c -o assign.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c between.c -o between.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c bmerge.c -o bmerge.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c chmatch.c -o chmatch.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c dogroups.c -o dogroups.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c fastmean.c -o fastmean.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c fcast.c -o fcast.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c fmelt.c -o fmelt.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c forder.c -o forder.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c frank.c -o frank.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c fread.c -o fread.o
fread.c:64:19: warning: unused variable 'TypeName' [-Wunused-const-variable]
static const char TypeName[NUMTYPE][10] = {"LGL","INT","INT64","REAL","STR","NULL"}; // for messages and errors
^
1 warning generated.
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c fsort.c -o fsort.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c fwrite.c -o fwrite.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c gsumm.c -o gsumm.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c ijoin.c -o ijoin.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c init.c -o init.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c inrange.c -o inrange.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c openmp-utils.c -o openmp-utils.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c quickselect.c -o quickselect.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c rbindlist.c -o rbindlist.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c reorder.c -o reorder.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c shift.c -o shift.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c subset.c -o subset.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c transpose.c -o transpose.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c uniqlist.c -o uniqlist.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c vecseq.c -o vecseq.o
/usr/local/opt/llvm/bin/clang -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -Wall -mtune=core2 -g -O2 -c wrappers.c -o wrappers.o
/usr/local/opt/llvm/bin/clang -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -o data.table.so assign.o between.o bmerge.o chmatch.o dogroups.o fastmean.o fcast.o fmelt.o forder.o frank.o fread.o fsort.o fwrite.o gsumm.o ijoin.o init.o inrange.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o uniqlist.o vecseq.o wrappers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
mv data.table.so datatable.so
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id datatable.so datatable.so; fi
installing to /Library/Frameworks/R.framework/Versions/3.3/Resources/library/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
Error in dyn.load(file, DLLpath = DLLpath, ...) :
無法載入共享物件 '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table/libs/datatable.so' ：
dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table/libs/datatable.so, 6): Library not loaded: #rpath/libomp.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table/libs/datatable.so
Reason: image not found
錯誤: loading failed
停止執行
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table’
Warning in install.packages :
installation of package ‘data.table’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/n3/4f7rv1dj4ys_1z2hwh95z79h0000gn/T/RtmplcaPNQ/downloaded_packages’*

Answer 1

The first is a warning about a no longer used variable as of a few days ago since you are installing the latest development version (which is fine) :
fread.c:64:19: warning: unused variable 'TypeName' [-Wunused-const-variable]
static const char TypeName[NUMTYPE][10]
That's a correct warning and I'll remove that variable.
The second is the error :
Error in dyn.load(file, DLLpath = DLLpath, ...) :
無法載入共享物件 '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table/libs/datatable.so' ：
dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table/libs/datatable.so, 6):
Library not loaded: #rpath/libomp.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table/libs/datatable.so
Reason: image not found
Other people are finding that too on MacOS and seem to be having some success with the solutions here using gcc instead of clang. The problems appears to be clang on MacOS, not data.table. No problems have been reported on Linux or Windows.