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

Question

install.packages("data.table")
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/data.table_1.12.8.tgz'
Content type 'application/x-gzip' length 2117137 bytes (2.0 MB)
downloaded 2.0 MB
The downloaded binary packages are in
    /var/folders/r1/1rsn2y0j78v907qgv0btm_fm0000gn/T//RtmppBu3UK/downloaded_packages

updating to the latest development version using provided code:

data.table::update.dev.pkg()

The printed console:

Warning: unable to access index for repository https://Rdatatable.gitlab.io/data.table/bin/macosx/el-capitan/contrib/3.5:
  cannot open URL 'https://Rdatatable.gitlab.io/data.table/bin/macosx/el-capitan/contrib/3.5/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 5189945 bytes (4.9 MB)
==================================================
downloaded 4.9 MB

* installing *source* package ‘data.table’ ...
*** 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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -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/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: 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/3.5/Resources/library/data.table’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/data.table’

The downloaded source packages are in
    ‘/private/var/folders/r1/1rsn2y0j78v907qgv0btm_fm0000gn/T/RtmppBu3UK/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

What is wrong with this ‘datatable.so’ not found? And I didn't find any posting related to datatable.so so far.

FYI: I've followed all instruction here when first problem (the gettext issue) solved, the datatable.so did not. I've went through all related/possible post and followed all the instruction including brewing, clang, gfortan etc. But nothing seems to be working.

I'm trying to use 'fcase' as provided in the answer to my previous question here.

Answer 1

The problem you are facing is compilation package from source on macOS. It is known to be causing much more troubles than on other platforms. We have a dedicated wiki page: https://github.com/Rdatatable/data.table/wiki/Installation

As you mentioned you followed those instructions. If they were not sufficient to solve your configuration, please do submit issue in github repository describing your current setup, Makevars, compiler, version.