Data.table: Ошибка при установке из исходников на macOS

Созданный на 1 мая 2020 · 27Комментарии · Источник: Rdatatable/data.table

Я выполнил все инструкции на https://github.com/Rdatatable/data.table/wiki/Installation и выполнил поиск в StackOverflow, но не могу получить data.table для установки из источника (для поддержки OpenMP) на Mac 10.14.6. с R4.0. Я продолжаю получать эту ошибку, когда пытаюсь установить из источника:

> install.packages("data.table", type="source", Ncpus = 7)
trying URL 'https://cran.us.r-project.org/src/contrib/data.table_1.12.8.tar.gz'
Content type 'application/octet-stream' length 4948391 bytes (4.7 MB)
==================================================
downloaded 4.7 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
** 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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c cj.c -o cj.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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c coalesce.c -o coalesce.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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fifelse.c -o fifelse.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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fread.c -o fread.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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c freadR.c -o freadR.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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c froll.c -o froll.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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frollR.c -o frollR.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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frolladaptive.c -o frolladaptive.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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwriteR.c -o fwriteR.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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nafill.c -o nafill.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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nqrecreateindices.c -o nqrecreateindices.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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c types.c -o types.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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c utils.c -o 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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -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 -Wl,-rpath,/usr/local/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 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: unknown option: -platform_version
clang-10: 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 ‘/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/fs/7z2xwjxx0vn3kj7x7khc06980000gp/T/RtmpyDidEl/downloaded_packages’

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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_4.0.0 tools_4.0.0    packrat_0.5.0

platform-specific

Источник

jrf1111

Самый полезный комментарий

Неважно. Я разобрался и могу установить с поддержкой многопоточности. Мне пришлось изменить свой файл .R/Makevars . Вот новое содержание:

LDFLAGS= -L/usr/local/clang4/lib
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/gfortran/bin/g++
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++

LLVM_LOC = /usr/local/opt/llvm
CC=/usr/local/gfortran/bin/gcc -fopenmp
CXX=/usr/local/gfortran/bin/g++ -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/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include

jrf1111 1 мая 2020

😄2 👍1

Все 27 Комментарий

Можете ли вы попробовать gcc вместо clang?

Только что заметил это недавно
https://github.com/su/R-mac-dev
Не смотрел, потому что у меня нет Mac, но, возможно, это будет полезно

jangorecki 1 мая 2020

Извини, я в этом новичок. Как мне вместо этого использовать gcc?

jrf1111 1 мая 2020

LDFLAGS= -L/usr/local/clang4/lib
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/gfortran/bin/g++
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++

LLVM_LOC = /usr/local/opt/llvm
CC=/usr/local/gfortran/bin/gcc -fopenmp
CXX=/usr/local/gfortran/bin/g++ -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/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include

jrf1111 1 мая 2020

😄2 👍1

@ jrf1111 спасибо за решение, закрываю

jangorecki 1 мая 2020

Извините за беспокойство, но я пытаюсь расшифровать решение, так как у меня такая же проблема (да, новичок)

Каким образом наличие llvm и использование других компиляторов C (не тех, что в llvm, которые тоже выдают эту странную ошибку в первом посте) решают проблему? Если у меня нет этого gfortran, но я действительно выполнил все инструкции https://github.com/Rdatatable/data.table/wiki/Installation#openmp -enabled-compiler-for-mac, но с ручной установкой, что я должен писать в Makevars, чтобы data.table работал в многопоточном режиме?

eacabbi 5 мая 2020

Я перешел на gfortran по https://mac.r-project.org/tools/ , https://cran.r-project.org/bin/macosx/tools/ , настроил .R/Makevars вот так

FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=/usr/local/gfortran/bin/gcc
CXX=/usr/local/gfortran/bin/g++
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++

LLVM_LOC = /usr/local/gfortran
CC=$(LLVM_LOC)/bin/gcc -fopenmp
CXX=$(LLVM_LOC)/bin/g++ -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/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include

и теперь, пока я пытаюсь установить версию разработчика из репозитория, я получаю

data.table::update.dev.pkg()
Warning: unable to access index for repository https://Rdatatable.gitlab.io/data.table/bin/macosx/contrib/4.0:
cannot open URL 'https://Rdatatable.gitlab.io/data.table/bin/macosx/contrib/4.0/PACKAGES'
Package which is only available in source form, and may need compilation of C/C++/Fortran:
‘data.table’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package ‘data.table’

trying URL 'https://Rdatatable.gitlab.io/data.table/src/contrib/data.table_1.12.9.tar.gz'
Content type 'application/gzip' length 5195275 bytes (5.0 MB)

downloaded 5.0 MB

installing source package ‘data.table’ ...
** using staged installation
*** pkg-config is not installed.
*** Compilation will now be attempted and if it works you can ignore this message. 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, ...)
*** brew: zlib (OSX)
*** 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 ...
** libs
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c assign.c -o assign.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c between.c -o between.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c bmerge.c -o bmerge.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c chmatch.c -o chmatch.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c cj.c -o cj.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c coalesce.c -o coalesce.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c dogroups.c -o dogroups.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fastmean.c -o fastmean.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fcast.c -o fcast.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fifelse.c -o fifelse.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fmelt.c -o fmelt.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c forder.c -o forder.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frank.c -o frank.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fread.c -o fread.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c freadR.c -o freadR.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c froll.c -o froll.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frollR.c -o frollR.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frolladaptive.c -o frolladaptive.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fsort.c -o fsort.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwrite.c -o fwrite.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwriteR.c -o fwriteR.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c gsumm.c -o gsumm.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c ijoin.c -o ijoin.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c init.c -o init.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c inrange.c -o inrange.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nafill.c -o nafill.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nqrecreateindices.c -o nqrecreateindices.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c openmp-utils.c -o openmp-utils.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c quickselect.c -o quickselect.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c rbindlist.c -o rbindlist.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c reorder.c -o reorder.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c shift.c -o shift.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c subset.c -o subset.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c transpose.c -o transpose.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c types.c -o types.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c uniqlist.c -o uniqlist.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c utils.c -o utils.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c vecseq.c -o vecseq.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c wrappers.c -o wrappers.o
/usr/local/gfortran/bin/gcc -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/gfortran/lib -Wl,-rpath,/usr/local/gfortran/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 subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
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 library.dynam(lib, package, package.lib):
shared object ‘datatable.so’ not found
Error: loading failed
Execution halted
ERROR: loading failed
removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/data.table’
restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/data.table’
The downloaded source packages are in
‘/private/var/folders/z7/r94g4j6j4z33r99np7kwns2nwz14jw/T/RtmppDABFK/downloaded_packages’
R data.table package has been updated to NA (1.12.8)
Warning message:
In utils::install.packages(pkg, repos = repo, type = type, lib = lib, :
installation of package ‘data.table’ had non-zero exit status

Версия CRAN работает, но с одним потоком. Существует поток stackoverflow об этом https://stackoverflow.com/questions/59658131/error-package-or-namespace-load-failed-for-data-table-in-library-dynamlib-p, который не дает полезного ответа.

eacabbi 5 мая 2020

Возможно, вам потребуется использовать gfortran версии 6.3.0, доступную здесь: https://github.com/fxcoudert/gfortran-for-macOS/releases/tag/6.3

jrf1111 5 мая 2020

Не забудьте также обновить файл Makevars.
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm

jrf1111 5 мая 2020

К сожалению нет. Проблема сохраняется как с gfortran 6.3.0, так и с 8.2.0

eacabbi 5 мая 2020

Вы удалили предыдущую установку data.table? А вы ставили версию CRAN вместо версии для разработчиков?

jrf1111 5 мая 2020

Да, конечно. Я попробовал со всеми из них и получил тот же результат: ошибка с версией разработчика, успешная установка, но один поток с CRAN (спасибо, что попытались помочь!)

eacabbi 5 мая 2020

Похоже, между вашим файлом Makevars и моим все еще есть несколько отличий. Попробуйте просто заменить весь файл Makevars тем, что я использовал:

LDFLAGS= -L/usr/local/clang4/lib
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/gfortran/bin/g++
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++

LLVM_LOC = /usr/local/opt/llvm
CC=/usr/local/gfortran/bin/gcc -fopenmp
CXX=/usr/local/gfortran/bin/g++ -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/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include

jrf1111 5 мая 2020

перезапустил, последовал вашему совету, теперь работает. Спасибо!!!

eacabbi 5 мая 2020

Рад, что смог помочь!

jrf1111 5 мая 2020

Следуя приведенным выше предложениям, я получил следующие ошибки

[1] "en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8"
Ошибка: не удалось загрузить пакет или пространство имен для 'data.table' в library.dynam (lib, package, package.lib):
общий объект 'datatable.so' не найден
Ошибка: загрузка не удалась
Выполнение остановлено
ОШИБКА: загрузка не удалась

Какие-либо предложения?

likanzhan 11 мая 2020

@likanzhan выглядит другой проблемой, создайте новую проблему и поместите все входные и выходные данные попытки установки во вновь запущенный сеанс R.

jangorecki 11 мая 2020

@jangorecki

install.packages("data.table", type = "source",  repos = "https://Rdatatable.gitlab.io/data.table")
Installing package into ‘/Users/lzhan/R’
(as ‘lib’ is unspecified)
trying URL 'https://Rdatatable.gitlab.io/data.table/src/contrib/data.table_1.12.9.tar.gz'
Content type 'application/gzip' length 5195275 bytes (5.0 MB)

downloaded 5.0 MB

[1] "en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8"
* installing *source* package ‘data.table’ ...
** using staged installation
*** pkg-config is not installed.
*** Compilation will now be attempted and if it works you can ignore this message. 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, ...)
***   brew: zlib (OSX)
*** 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 ...
** libs
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c assign.c -o assign.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c between.c -o between.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c bmerge.c -o bmerge.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c chmatch.c -o chmatch.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c cj.c -o cj.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c coalesce.c -o coalesce.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c dogroups.c -o dogroups.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fastmean.c -o fastmean.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fcast.c -o fcast.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fifelse.c -o fifelse.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fmelt.c -o fmelt.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c forder.c -o forder.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frank.c -o frank.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fread.c -o fread.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c freadR.c -o freadR.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c froll.c -o froll.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frollR.c -o frollR.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frolladaptive.c -o frolladaptive.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fsort.c -o fsort.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwrite.c -o fwrite.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwriteR.c -o fwriteR.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c gsumm.c -o gsumm.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c ijoin.c -o ijoin.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c init.c -o init.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c inrange.c -o inrange.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nafill.c -o nafill.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nqrecreateindices.c -o nqrecreateindices.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c openmp-utils.c -o openmp-utils.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c quickselect.c -o quickselect.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c rbindlist.c -o rbindlist.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c reorder.c -o reorder.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c shift.c -o shift.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c subset.c -o subset.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c transpose.c -o transpose.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c types.c -o types.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c uniqlist.c -o uniqlist.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c utils.c -o utils.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c vecseq.c -o vecseq.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c wrappers.c -o wrappers.o
/usr/local/gfortran/bin/gcc -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 -Wl,-rpath,/usr/local/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 subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/lzhan/R/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
[1] "en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8"
** help
*** installing help indices
** building package indices
[1] "en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8"
** installing vignettes
** testing if installed package can be loaded from temporary location
[1] "en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8"
Error: package or namespace load failed for ‘data.table’ in library.dynam(lib, package, package.lib):
 shared object ‘datatable.so’ not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/lzhan/R/data.table’

The downloaded source packages are in
    ‘/private/var/folders/qz/0srg88cd2459h1cbn623wrt00000gq/T/Rtmpgzby8h/downloaded_packages’
Warning message:
In install.packages("data.table", type = "source", repos = "https://Rdatatable.gitlab.io/data.table") :
  installation of package ‘data.table’ had non-zero exit status

Спасибо !

likanzhan 12 мая 2020

Приведенное ниже решение сработало для меня:

LDFLAGS= -L/usr/local/clang4/lib
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/gfortran/bin/g++
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++

LLVM_LOC = /usr/local/opt/llvm
CC=/usr/local/gfortran/bin/gcc -fopenmp
CXX=/usr/local/gfortran/bin/g++ -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/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include

daynefiler 2 июн. 2020

@jangorecki Было бы полезно обновить файл Makevars на установочной вики - спасибо вам и команде Rdatatable!

daynefiler 2 июн. 2020

В чем дело, пришлось переустанавливать Каталину с нуля. Я обнаружил, что llvm по-прежнему не работает, тогда как установка .Makevars с компиляторами gfortran (как указано выше, но также и для версии 8.2.0) помогает.

Ни разу не удалось пройти компиляцию с llvm, как в Мохаве, так и в Каталине.

eacabbi 2 июн. 2020

У меня также возникла эта проблема с использованием как файла .R / Makevars, предложенного на странице readme (который сообщает о стандартной ошибке внизу этой страницы и привел меня сюда), так и с кодом @daynefiler выше. Это генерирует этот вывод:

> install.packages("data.table", type = "source",
+                  repos = "https://Rdatatable.gitlab.io/data.table")
trying URL 'https://Rdatatable.gitlab.io/data.table/src/contrib/data.table_1.12.9.tar.gz'
Content type 'application/gzip' length 5208337 bytes (5.0 MB)
==================================================
downloaded 5.0 MB

* installing *source* package ‘data.table’ ...
** using staged installation
*** pkg-config is not installed.
*** Compilation will now be attempted and if it works you can ignore this message. 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, ...)
***   brew: zlib (OSX)
*** 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 ...
** libs
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c assign.c -o assign.o
/bin/sh: /usr/local/gfortran/bin/gcc: No such file or directory
make: *** [assign.o] Error 127
ERROR: compilation failed for package ‘data.table’
* 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/8n/wm3qzjnn2dx4l_lznyk0fthr00_bd1/T/Rtmp1SObio/downloaded_packages’

Установка с использованием обычных пакетов install.packages ("data.table") работает, но приводит к многоядерной проблеме, которую пытается решить это исправление.

FarMar 30 июн. 2020

@FarMar, не могли бы вы проверить, работает ли у вас install.packages("data.table", type="source") ? Похоже, ваш компилятор неправильно определен в Makevars.

jangorecki 30 июн. 2020

@jangorecki Это работает с удаленным файлом Makevar, но выдает ошибку «нет ошибки OpenMP», как и репозиторий CRAN. Это не удается с файлом Makevars, подробно описанным @ jrf1111 и в ответах @daynefiler выше

FarMar 30 июн. 2020

@FarMar Прежде чем пытаться скомпилировать data.table с помощью пользовательских Makevars, убедитесь, что он что-то компилирует. Под чем угодно я подразумеваю пакет со скомпилированным кодом. В противном случае проблема на самом деле не связана с кодом data.table. Как только ваш компилятор сможет что-либо скомпилировать, может возникнуть проблема data.table при сбое компиляции.

Если вы хотите следовать по пути этого потока, вам, вероятно, потребуется установить недостающее программное обеспечение или настроить пути, чтобы Makevars отсюда правильно указывал компилятор.
В противном случае вы можете вернуться к точке, где работает ваш компилятор, затем попробуйте следовать https://github.com/Rdatatable/data.table/wiki/Installation wiki, а затем, когда он не удастся, открыть новую проблему с вашими Makevars и вывести .

В обоих случаях вам нужно убедиться, что компиляция работает с чем угодно.
Чтобы убедиться в этом, вы можете попробовать установить любой пакет с скомпилированным кодом. У меня есть набор игрушек "Привет, мир от C", которого должно хватить

install.packages("r.gitlab.ci", repos="https://jangorecki.gitlab.io/r.gitlab.ci")

при установке пакета из CRAN вам необходимо добавить type="source" потому что CRAN имеет двоичные файлы Mac, которые по умолчанию будут использоваться, а не исходники пакетов.

jangorecki 30 июн. 2020

@FarMar обратите внимание на эту строку вывода вашей установки

/ usr / local / gfortran / bin / gcc: нет такого файла или каталога

Это означает, что ваша машина настроена на поиск gcc по этому пути: /usr/local/gfortran/bin/gcc

Вы можете проверить, существует ли этот файл на вашем компьютере. У меня есть gcc на Mac (но, к сожалению, я не совсем уверен, как он туда попал, надеюсь, это вики по установке).

Лично я использую llvm на Mac в /usr/local/opt/llvm который я установил из вики установки.

В любом случае он должен быть определен как CC в вашем ~/.R/Makevars .

Надеюсь, это поможет.

MichaelChirico 30 июн. 2020

В противном случае вы можете вернуться к точке, где работает ваш компилятор, затем попробуйте следовать https://github.com/Rdatatable/data.table/wiki/Installation wiki, а затем, когда он не удастся, открыть новую проблему с вашими Makevars и вывести .

@jangorecki Я пойду по этому маршруту. Кажется, я прерываю компиляцию из-за первого редактирования Markevars в вашем файле readme. Мне не удалось скомпилировать ваш тест с нестандартным Makevars , без него отлично работает.

FarMar 30 июн. 2020

👍1

всем привет - спасибо за эту ветку! Я выполнил инструкции по установке macOS, используя llvm из brew, но не смог установить этот пакет с помощью

install.packages("data.table", type = "source", repos = "https://Rdatatable.gitlab.io/data.table")

компиляция всегда терпела неудачу с этой ошибкой:

Error: package or namespace load failed for ‘data.table’ in library.dynam(lib, package, package.lib):
 shared object ‘datatable.so’ not found

После нескольких ударов головой по клавиатуре я обнаружил, что это предупреждение оказалось довольно полезным:

** using staged installation
*** pkg-config is not installed.
*** Compilation will now be attempted and if it works you can ignore this message. 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, ...)
***   brew: zlib (OSX)
*** 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 ...

в моем случае locate не сработало. Я попробовал locate zlib.h zconf.h и получил

WARNING: The locate database (/var/db/locate.database) does not exist.
To create the database, run the following command:

  sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.locate.plist

моя машина почти новая, возможно, поэтому я получил это сообщение. во всяком случае, я выполнил эту команду launchctl load и подождал несколько минут, после чего locate смог найти несколько мест, где zlib.h и zconf.h находились на моем система. с этим на месте исходная установка работала как шарм.

РЕЗЮМЕ: может быть излишним, но у меня сработало выполнение этих brew установок перед установкой data.table из источника:

brew update
brew install llvm pkg-config zlib gettext

затем создайте базу данных для locate :

sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.locate.plist

и используйте файл ~/.R/Makevars со страницы установки с дополнительным флагом компилятора C ++ для zlib :

LLVM_LOC = /usr/local/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/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/libi -L/usr/local/opt/zlib/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/usr/local/opt/zlib/include

надеюсь, это может спасти кого-то от головной боли в будущем!