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install fails from "undefined symbol" #300

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install fails from "undefined symbol"#300
@tedmoorman

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@tedmoorman
tedmoorman
opened on Feb 12, 2021

I get pretty far into the install and then receive the following error:

Error: package or namespace load failed for ‘magick’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/R/x86_64-pc-linux-gnu-library/3.5/magick/libs/magick.so':
  /home/R/x86_64-pc-linux-gnu-library/3.5/magick/libs/magick.so: undefined symbol: _ZN6Magick5Image5writeEPNS_4BlobERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm

Here is the entire installation:

Installing package into ‘/home/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
* installing *source* package ‘magick’ ...
** package ‘magick’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6  
Using PKG_LIBS=-lMagick++-6.Q16 -lMagickWand-6.Q16 -lMagickCore-6.Q16  
** libs
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c animation.cpp -o animation.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c attributes.cpp -o attributes.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c base.cpp -o base.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c color.cpp -o color.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c composite.cpp -o composite.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c config.cc -o config.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c convolve.cpp -o convolve.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c device.cpp -o device.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c edges.cpp -o edges.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c edit.cpp -o edit.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c fonts.cpp -o fonts.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c options.cpp -o options.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c properties.cpp -o properties.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c resize.cpp -o resize.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c segment.cpp -o segment.o
g++ -std=gnu++11 -I"/opt/R/R-3.5.3/lib64/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/ImageMagick-6   -I"/home/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2 -c transformations.cpp -o transformations.o
g++ -std=gnu++11 -shared -L/opt/R/R-3.5.3/lib64/R/lib -L/usr/local/lib64 -o magick.so RcppExports.o animation.o attributes.o base.o color.o composite.o config.o convolve.o device.o edges.o edit.o fonts.o options.o properties.o resize.o segment.o transformations.o -lMagick++-6.Q16 -lMagickWand-6.Q16 -lMagickCore-6.Q16 -L/opt/R/R-3.5.3/lib64/R/lib -lR
installing to /home/R/x86_64-pc-linux-gnu-library/3.5/magick/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 ‘magick’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/R/x86_64-pc-linux-gnu-library/3.5/magick/libs/magick.so':
  /home/R/x86_64-pc-linux-gnu-library/3.5/magick/libs/magick.so: undefined symbol: _ZN6Magick5Image5writeEPNS_4BlobERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/R/x86_64-pc-linux-gnu-library/3.5/magick’
Warning in install.packages :
  installation of package ‘/home/package_files/magick_2.2.tar.gz’ had non-zero exit status

Here is the session info:

R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

Matrix products: default
BLAS: /opt/R/R-3.5.3/lib64/R/lib/libRblas.so
LAPACK: /opt/R/R-3.5.3/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6        packrat_0.4.9-1   digest_0.6.25     later_1.1.0.1     mime_0.9         
 [6] R6_2.5.0          lifecycle_0.2.0   xtable_1.8-4      magrittr_2.0.1    rlang_0.4.10     
[11] promises_1.1.1    leaflet_2.0.4.1   ellipsis_0.3.0    tools_3.5.3       htmlwidgets_1.5.3
[16] crosstalk_1.1.1   shiny_1.6.0       httpuv_1.5.4      fastmap_1.0.1     compiler_3.5.3   
[21] htmltools_0.5.1

Activity

jeroen

jeroen commented on Feb 12, 2021

@jeroen
jeroen
on Feb 12, 2021 · edited by jeroen
Member

You have an ABI mismatch between your compiler and ImageMagick. I'm guessing you're not using the stock g++ from RHEL, or from Red Hat Developer Toolset? Try compiling with /usr/bin/g++.

tedmoorman

tedmoorman commented on Feb 12, 2021

@tedmoorman
tedmoorman
on Feb 12, 2021
Author

I'm definitely not of the server/admin side of things. Could you please let me know how to specific that path with {r} configure.args = in the {r} install.packages() function? Right now, I just I'm just using {r} install.packages("~/package_files/magick_2.6.0.tar.gz", repos=NULL, type="source", dependencies = TRUE) . Thanks for taking a look at this!

jeroen

jeroen commented on Feb 12, 2021

@jeroen
jeroen
on Feb 12, 2021
Member

We can't fix your global R settings from the package. Maybe you try running this in your shell:

echo "CXX11=/usr/bin/g++" > ~/.R/Makevars

And after that try again installing magick.

tedmoorman

tedmoorman commented on Feb 16, 2021

@tedmoorman
tedmoorman
on Feb 16, 2021
Author

Thank you so much @jeroen! I ended up changing that environmental variable in my .Rprofile. The install had no issues. Cheers.

tedmoorman
closed this as completedon Feb 16, 2021
jeroen
mentioned this on Apr 30, 2021
lidongyu16

lidongyu16 commented on Apr 12, 2022

@lidongyu16
lidongyu16
on Apr 12, 2022

Thank you so much @jeroen! I ended up changing that environmental variable in my .Rprofile. The install had no issues. Cheers.

I meet the exactly the same problems , I want to know how to change "that environmental variable" in my .Rprofile. Thank you very much.

tedmoorman

tedmoorman commented on Apr 19, 2022

@tedmoorman
tedmoorman
on Apr 19, 2022
Author

Thank you so much @jeroen! I ended up changing that environmental variable in my .Rprofile. The install had no issues. Cheers.

I meet the exactly the same problems , I want to know how to change "that environmental variable" in my .Rprofile. Thank you very much.

I'm thinking this was a change to the "Makevars" file located in ~/.R/Makevars. Try adding the following line: CXX11=/usr/bin/g++ and hopefully that will solve your problem.

ixxmu
mentioned this on Dec 11, 2022
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        Issue actions
          install fails from "undefined symbol" · Issue #300 · ropensci/magick