[R] data.table installation on intel macOS Ventura 13.6
Naresh Gurbuxani
n@re@h_gurbux@n| @end|ng |rom hotm@||@com
Tue Sep 26 11:49:15 CEST 2023
> Sys.info()
sysname
"Darwin"
release
"22.6.0"
version
"Darwin Kernel Version 22.6.0: Fri Sep 15 13:39:52 PDT 2023; root:xnu-8796.141.3.700.8~1/RELEASE_X86_64"
nodename
[deleted]
machine
"x86_64"
login
[deleted]
user
[deleted]
effective_user
[deleted]
My Makevars file:
CPPFLAGS += -Xclang -fopenmp
LDFLAGS += -lomp
Using brew, I installed libomp
data.table is not installed on my machine. In fresh R session:
> install.packages("data.table", repos = "https://cran.r-project.org")
Installing package into ‘/usr/local/lib/R/4.3/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/data.table_1.14.8.tar.gz'
Content type 'application/x-gzip' length 5338582 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
zlib 1.2.11 is available ok
*** OpenMP not supported! data.table uses OpenMP to automatically
*** parallelize operations like sorting, grouping, file reading, etc.
*** For details on how to install the necessary toolchains on your OS see:
*** https://github.com/Rdatatable/data.table/wiki/Installation
*** Continuing installation without OpenMP support...
** libs
using C compiler: ‘Homebrew clang version 17.0.1’
using SDK: ‘’
clang -I"/usr/local/Cellar/r/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -Xclang -fopenmp -fPIC -g -O2 -c assign.c -o assign.o
[several lines deleted]
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/4.3.1/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/xz/lib -L/usr/local/lib -lomp -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 -L/usr/local/Cellar/r/4.3.1/lib/R/lib -lR -lintl -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
ld: library 'omp' not found
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [data.table.so] Error 1
ERROR: compilation failed for package ‘data.table’
* removing ‘/usr/local/lib/R/4.3/site-library/data.table’
The downloaded source packages are in
‘/private/var/folders/97/5377j5_d207fshvjz_pz7szw0000gn/T/RtmpjZgIo0/downloaded_packages’
Warning message:
In install.packages("data.table", repos = "https://cran.r-project.org") :
installation of package ‘data.table’ had non-zero exit status
I delete above two lines from my Makevars fiie, which is now empty. Now reinstall data.table.
> install.packages("data.table", repos = "https://cran.r-project.org")
Installing package into ‘/usr/local/lib/R/4.3/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/data.table_1.14.8.tar.gz'
Content type 'application/x-gzip' length 5338582 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
zlib 1.2.11 is available ok
R CMD SHLIB supports OpenMP without any extra hint
** libs
using C compiler: ‘Homebrew clang version 17.0.1’
using SDK: ‘’
clang -I"/usr/local/Cellar/r/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -g -O2 -c assign.c -o assign.o
[several lines deleted]
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/4.3.1/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/xz/lib -L/usr/local/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 -L/usr/local/Cellar/r/4.3.1/lib/R/lib -lR -lintl -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 =
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 /usr/local/lib/R/4.3/site-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)
> library(data.table)
data.table 1.14.8 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.
**********
> On Sep 25, 2023, at 4:06 AM, Carlos Ortega <coforfe using gmail.com> wrote:
>
> Hi,
>
> Yes, on Mac, it takes a while to even get the build to allow data.table to be used on multithread.
>
> See this installation guide which has sections specially dedicated for Mac.
> • https://github.com/Rdatatable/data.table/wiki/Installation
>
> You will see that you will most likely have to modify the "Makevars" file to include the paths of different compilers.
>
> Thank you,
> Carlos.
>
> On Mon, Sep 25, 2023 at 9:41 AM Ivan Krylov <krylov.r00t using gmail.com> wrote:
> On Sun, 24 Sep 2023 23:42:14 +0000
> Naresh Gurbuxani <naresh_gurbuxani using hotmail.com> wrote:
>
> > Instruction on this site do not apply to Ventura 13.6
>
> What happens whey you try to follow them?
>
> The data.table maintainers have prepared the following guide:
> <https://github.com/Rdatatable/data.table/wiki/Support>. In particular,
> in order to help us help you, you need to include your actions, their
> expected and actual results. Without that, you're effectively asking
> someone to write a personal tutorial for you, which is not a good use
> of anyone's time.
>
> If you don't get an answer here and don't find anything useful on
> StackOverflow when searching for [data.table], try
> R-SIG-Mac using r-project.org.
>
> --
> Best regards,
> Ivan
>
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