Data.table: shared object ‘datatable.so’ not found
Introduction
Hello there!
I'm having some issues getting the data.table package installed.
Session Info
This is my session information
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin19.6.0 (64-bit)
Running under: macOS Catalina 10.15.6
Matrix products: default
BLAS: /Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2/lib/libRblas.dylib
LAPACK: /Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2/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_4.0.2
Install Command
install.packages("data.table",
repos = "https://cloud.r-project.org")
Error Output
This is the error output I'm receiving
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/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2/library/data.table’
The downloaded source packages are in
‘/private/var/folders/p1/5x96dz_s2jn6nk6k0tpw4ftc0000gn/T/Rtmp6sRwrd/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Full Installation Output
now dyn.load("/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2/library/tools/libs/tools.so") ...
system (cmd0): /Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2/bin/R CMD INSTALL
Garbage collection 3 = 2+0+1 (level 0) ...
24.0 Mbytes of cons cells used (68%)
15.4 Mbytes of vectors used (24%)
Garbage collection 4 = 3+0+1 (level 0) ...
24.3 Mbytes of cons cells used (69%)
15.5 Mbytes of vectors used (24%)
Garbage collection 5 = 4+0+1 (level 0) ...
24.6 Mbytes of cons cells used (70%)
15.5 Mbytes of vectors used (24%)
Garbage collection 6 = 5+0+1 (level 0) ...
25.5 Mbytes of cons cells used (72%)
16.8 Mbytes of vectors used (26%)
Garbage collection 7 = 6+0+1 (level 0) ...
27.0 Mbytes of cons cells used (76%)
17.4 Mbytes of vectors used (27%)
Garbage collection 8 = 7+0+1 (level 0) ...
27.0 Mbytes of cons cells used (76%)
17.4 Mbytes of vectors used (27%)
Garbage collection 9 = 8+0+1 (level 0) ...
27.0 Mbytes of cons cells used (76%)
17.4 Mbytes of vectors used (27%)
Garbage collection 10 = 9+0+1 (level 0) ...
27.0 Mbytes of cons cells used (76%)
17.4 Mbytes of vectors used (27%)
Garbage collection 11 = 10+0+1 (level 0) ...
27.0 Mbytes of cons cells used (76%)
17.4 Mbytes of vectors used (27%)
Garbage collection 12 = 11+0+1 (level 0) ...
27.0 Mbytes of cons cells used (76%)
17.4 Mbytes of vectors used (27%)
Garbage collection 13 = 12+0+1 (level 0) ...
27.7 Mbytes of cons cells used (78%)
19.9 Mbytes of vectors used (31%)
trying URL 'https://cloud.r-project.org/src/contrib/data.table_1.13.0.tar.gz'
Content type 'application/x-gzip' length 5273400 bytes (5.0 MB)
==================================================
downloaded 5.0 MB
foundpkgs: data.table, /var/folders/p1/5x96dz_s2jn6nk6k0tpw4ftc0000gn/T//Rtmp6sRwrd/downloaded_packages/data.table_1.13.0.tar.gz
Garbage collection 14 = 13+0+1 (level 0) ...
28.1 Mbytes of cons cells used (79%)
20.3 Mbytes of vectors used (32%)
files: /var/folders/p1/5x96dz_s2jn6nk6k0tpw4ftc0000gn/T//Rtmp6sRwrd/downloaded_packages/data.table_1.13.0.tar.gz
* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
gcc 11.0.3
*** 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
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c assign.c -o assign.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c between.c -o between.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c bmerge.c -o bmerge.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c chmatch.c -o chmatch.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c cj.c -o cj.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c coalesce.c -o coalesce.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c dogroups.c -o dogroups.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c fastmean.c -o fastmean.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c fcast.c -o fcast.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c fifelse.c -o fifelse.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c fmelt.c -o fmelt.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c forder.c -o forder.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c frank.c -o frank.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c fread.c -o fread.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c freadR.c -o freadR.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c froll.c -o froll.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c frollR.c -o frollR.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c frolladaptive.c -o frolladaptive.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c fsort.c -o fsort.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c fwrite.c -o fwrite.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c fwriteR.c -o fwriteR.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c gsumm.c -o gsumm.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ijoin.c -o ijoin.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c init.c -o init.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c inrange.c -o inrange.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c nafill.c -o nafill.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c nqrecreateindices.c -o nqrecreateindices.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c openmp-utils.c -o openmp-utils.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c quickselect.c -o quickselect.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c rbindlist.c -o rbindlist.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c reorder.c -o reorder.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c shift.c -o shift.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c snprintf.c -o snprintf.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c subset.c -o subset.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c transpose.c -o transpose.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c types.c -o types.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c uniqlist.c -o uniqlist.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c utils.c -o utils.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c vecseq.c -o vecseq.o
gcc -I"/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2_INSTALL/lib/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c wrappers.c -o wrappers.o
gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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 -lintl -Wl,-framework -Wl,CoreFoundation
installing to /Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2/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 ‘/Users/lknecht/Repositories/FAUST_Nextflow_Desktop/electron_faust_nextflow_desktop/app/binaries/r/r-mac/4.0.2/library/data.table’
The downloaded source packages are in
‘/private/var/folders/p1/5x96dz_s2jn6nk6k0tpw4ftc0000gn/T/Rtmp6sRwrd/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Attempted Workarounds
I thought this might be related to zlib so I uninstalled and reinstalled using
brew install zlib
That didn't change anything.
Potential Linked Issues
I am not sure if these are related?
4650
4640
Plea For Help
Any guidance is appreciated on this! I have no idea what I'm doing wrong.
install
loganknecht
All 9 comments
@loganknecht I can reproduce on 10.15.6 with 4.0.2 by deactivating pkgconfig and/or zlib (I use MacPorts). Is pkg-config installed and available in your $PATH and does brew install pkg-config help?
kiwiroy
on 31 Jul 2020
👍8
@loganknecht Possibly related solutions:
https://github.com/Rdatatable/data.table/issues/4581#issuecomment-659976021
https://github.com/Rdatatable/data.table/issues/4574#issuecomment-660146163
matthewgson
on 31 Jul 2020
@kiwiroy It looks like that solved the issue!
Thank you so much for your guidance!
loganknecht
on 3 Aug 2020
This worked for me too! Thank you for taking the time to answer this!
biancamanago
on 6 Sep 2020
This worked for me too! Thank you! @kiwiroy
houruiyan
on 21 Sep 2020
Thanks for providing feedback.
Note that you are welcome to improve our Installation wiki (git skills are not required there, edition is via web ui).
Maybe we should have a simplified MacOSX section in installation wiki, and then if that doesn't work, a link to separate page MacOSX specific listing examples of working configurations?
jangorecki
on 21 Sep 2020
Wow this helped big time, thanks @kiwiroy!
kwhitney727
on 14 Oct 2020
brew install pkg-config worked for me. I am on Mac 10.14.6 and was getting the following error at the very end of the installation process (all else seemed fine)
installing to /Library/Frameworks/R.framework/Versions/3.6/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
markdanese
on 16 Oct 2020
Hi I am encountering the same error but my OS is Ubuntu 16.04
Instead of "brew install pkg-config" what should I run to fix this?
Update:
I ran apt-get install -y pkg-config
It worked!
hermandr
on 18 Oct 2020
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Most helpful comment
@loganknecht I can reproduce on
10.15.6with4.0.2by deactivatingpkgconfigand/orzlib(I use MacPorts). Ispkg-configinstalled and available in your$PATHand doesbrew install pkg-confighelp?