Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

shared object ‘datatable.so’ not found #4653

Closed
loganknecht opened this issue Jul 31, 2020 · 9 comments
Closed

shared object ‘datatable.so’ not found #4653

loganknecht opened this issue Jul 31, 2020 · 9 comments
Labels
install

Comments

@loganknecht
Copy link

loganknecht commented Jul 31, 2020 •
edited
Loading

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.
@kiwiroy
Copy link
Member

kiwiroy commented Jul 31, 2020

@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?

@matthewgson
Copy link

@loganknecht Possibly related solutions:
#4581 (comment)
#4574 (comment)

@loganknecht
Copy link
Author

@kiwiroy It looks like that solved the issue!

Thank you so much for your guidance!

@biancamanago
Copy link

This worked for me too! Thank you for taking the time to answer this!

@houruiyan
Copy link

This worked for me too! Thank you! @kiwiroy

@jangorecki
Copy link
Member

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?

@kwhitney727
Copy link

Wow this helped big time, thanks @kiwiroy!

@markdanese
Copy link

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

@hermandr
Copy link

hermandr commented Oct 18, 2020 •
edited
Loading

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!

@robertdj robertdj mentioned this issue Mar 18, 2021
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
install
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
9 participants
@kiwiroy @loganknecht @jangorecki @markdanese @hermandr @kwhitney727 @matthewgson @houruiyan @biancamanago