magick
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Published
20 hours ago •
ropensci
ropensci
installing fails after updating gcc/g++ to either 7 or 8 on ubuntu 16.04
We've been using ubuntu 16 without issue for a while, following the instructions, including installing from:
add-apt-repository -y ppa:cran/imagemagick
however due to some other scientific software we attempted to update and change the default compiler toolchain to the 8 series for gcc/g++
Now installing runs into the following:
[1] "Found pkg-config cflags and libs!"
[2] "Using PKG_CFLAGS=-fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6-I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6"
[3] "Using PKG_LIBS=-lMagick++-6.Q16 -lMagickWand-6.Q16 -lMagickCore-6.Q16"
[4] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o"
[5] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c animation.cpp -o animation.o"
[6] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c attributes.cpp -o attributes.o"
[7] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c base.cpp -o base.o"
[8] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c color.cpp -o color.o"
[9] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c composite.cpp -o composite.o"
[10] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c config.cc -o config.o"
[11] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g-O2 -c convolve.cpp -o convolve.o"
[12] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c device.cpp -o device.o"
[13] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c edges.cpp -o edges.o"
[14] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c edit.cpp -o edit.o"
[15] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c fonts.cpp -o fonts.o"
[16] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c options.cpp -o options.o"
[17] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c properties.cpp -o properties.o"
[18] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c resize.cpp -o resize.o"
[19] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic-g -O2 -c segment.cpp -o segment.o"
[20] "g++ -std=gnu++11 -I\\\"/opt/R/3.6.1/lib/R/include\\\" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I\\\"/data/home/devinp/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include\\\" -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c transformations.cpp -o transformations.o"
[21] "g++ -std=gnu++11 -shared -L/opt/R/3.6.1/lib/R/lib -L/usr/local/lib -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/3.6.1/lib/R/lib -lR"
[22] "Error: package or namespace load failed for ‘magick’ in dyn.load(file, DLLpath = DLLpath, ...):"
[23] " unable to load shared object '/tmp/GSAPGATLMODY/00LOCK-magick/00new/magick/libs/magick.so':"
[24] " /tmp/GSAPGATLMODY/00LOCK-magick/00new/magick/libs/magick.so: undefined symbol: _ZNK6Magick8GeometrycvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEv"
[25] "Error: loading failed"
[26] "Execution halted"
I've poked around, with issue such as #54 but am not really familiar enough with c++/makevars to make judgements about what might need to be changed.
Any suggestions/thoughts about possible resolution(s)?
Thanks
@dpastoor I am experimenting the same issue, under Fedora 32, did you happen to solve this?
@dpastoor I am experimenting the same issue, under Fedora 32, did you happen to solve this?
Nevermind, fresh compiling/install of R 4.0.2 "patched" fixed the issue.