Carlos Ortega
2023-Sep-25 08:06 UTC
[R] data.table installation on intel macOS Ventura 13.6
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 at gmail.com> wrote:> On Sun, 24 Sep 2023 23:42:14 +0000 > Naresh Gurbuxani <naresh_gurbuxani at 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 at r-project.org. > > -- > Best regards, > Ivan > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
Naresh Gurbuxani
2023-Sep-26 09:49 UTC
[R] data.table installation on intel macOS Ventura 13.6
> 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 at 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 at gmail.com> wrote: > On Sun, 24 Sep 2023 23:42:14 +0000 > Naresh Gurbuxani <naresh_gurbuxani at 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 at r-project.org. > > -- > Best regards, > Ivan > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.