I tried following the instructions here: https://github.com/Rdatatable/data.table/wiki/Installation
and also the advice here: installing data.table on macOS
but have been stuck so far.
I am running Big Sur 11.2 on an Apple M1 chip.
My sessionInfo() looks like this
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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_4.0.3 tools_4.0.3
(so I gather this is running under Rosetta).
If I install.packages("data.table"), it works, but I get notified that OpenMP is not supported and data.table is single threaded.
So I try install.packages("data.table", type = "source") and I get this:
trying URL 'https://cran.rstudio.com/src/contrib/data.table_1.13.6.tar.gz'
Content type 'application/x-gzip' length 5303120 bytes (5.1 MB)
==================================================
downloaded 5.1 MB
* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
*** pkg-config is not installed.
*** Compilation will now be attempted and if it works you can ignore this message. In
*** particular, this should be the case on Mac where zlib is built in.
*** However, if compilation fails, try 'locate zlib.h zconf.h' and ensure the zlib
*** development library is installed :
*** deb: zlib1g-dev (Debian, Ubuntu, ...)
*** rpm: zlib-devel (Fedora, EPEL, ...)
*** There is a zlib in brew for OSX but the built in zlib should work.
*** Note that zlib is required to compile R itself so you may find the advice in the R-admin
*** guide helpful regarding zlib. On Debian/Ubuntu, zlib1g-dev is a dependency of r-base as
*** shown by 'apt-cache showsrc r-base | grep ^Build-Depends | grep zlib', and therefore
*** 'sudo apt-get build-dep r-base' should be sufficient too.
*** To silence this message, please ensure that :
*** 1) 'pkg-config --exists zlib' succeeds (i.e. $? -eq 0)
*** 2) 'pkg-config --libs zlib' contains -lz
*** Compilation will now be attempted ...
R CMD SHLIB supports OpenMP without any extra hint
** libs
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c assign.c -o assign.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c between.c -o between.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c bmerge.c -o bmerge.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c chmatch.c -o chmatch.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c cj.c -o cj.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c coalesce.c -o coalesce.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c dogroups.c -o dogroups.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fastmean.c -o fastmean.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fcast.c -o fcast.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fifelse.c -o fifelse.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fmelt.c -o fmelt.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c forder.c -o forder.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frank.c -o frank.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fread.c -o fread.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c freadR.c -o freadR.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c froll.c -o froll.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frollR.c -o frollR.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frolladaptive.c -o frolladaptive.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fsort.c -o fsort.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwrite.c -o fwrite.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwriteR.c -o fwriteR.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c gsumm.c -o gsumm.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c ijoin.c -o ijoin.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c init.c -o init.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c inrange.c -o inrange.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nafill.c -o nafill.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nqrecreateindices.c -o nqrecreateindices.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c openmp-utils.c -o openmp-utils.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c quickselect.c -o quickselect.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c rbindlist.c -o rbindlist.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c reorder.c -o reorder.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c shift.c -o shift.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c snprintf.c -o snprintf.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c subset.c -o subset.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c transpose.c -o transpose.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c types.c -o types.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c uniqlist.c -o uniqlist.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c utils.c -o utils.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c vecseq.c -o vecseq.o
/opt/homebrew/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c wrappers.c -o wrappers.o
/opt/homebrew/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/opt/homebrew/Cellar/gettext/0.21/lib -L/opt/homebrew/opt/llvm/lib -Wl,-rpath,/opt/homebrew/opt/llvm/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 ijoin.o init.o inrange.o nafill.o nqrecreateindices.o openmp-utils.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: ignoring file /Library/Frameworks/R.framework/R, building for macOS-arm64 but attempting to link with file built for macOS-x86_64
PKG_CFLAGS =
PKG_LIBS = -lz
if [ "data.table.so" != "datatable.so" ]; then mv data.table.so datatable.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id datatable.so datatable.so; fi
installing to /Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/00LOCK-data.table/00new/data.table/libs/datatable.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-data.table/00new/data.table/libs/datatable.so, 6): no suitable image found. Did find:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-data.table/00new/data.table/libs/datatable.so: mach-o, but wrong architecture
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-data.table/00new/data.table/libs/datatable.so: mach-o, but wrong architecture
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/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/4b/2jtbyjzd1w5gsdm_g_jcpr2h0000gn/T/RtmpW0NKyv/downloaded_packages’
Problems:
(1) It says pkg-config not installed. But it is, in /opt/homebrew/bin/pkg-config.
(2) It seems like it's trying to compile for my chip, not for the translated x86_84 chip. But RStudio is running on Rosetta.
My Makevars looks like this:
LLVM_LOC = /opt/homebrew/opt/llvm
CC=$(LLVM_LOC)/bin/clang -fopenmp
CXX=$(LLVM_LOC)/bin/clang++ -fopenmp
# -O3 should be faster than -O2 (default) level optimisation ..
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L/opt/homebrew/Cellar/gettext/0.21/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/opt/homebrew/Cellar/gettext/0.21/include -I$(LLVM_LOC)/include
I've also tried with gfortran, to no success.
