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ropensci / magick

Magic, madness, heaven, sin
https://docs.ropensci.org/magick
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installing fails after updating gcc/g++ to either 7 or 8 on ubuntu 16.04 #218

Open dpastoor opened 4 years ago

dpastoor commented 4 years ago

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

drelo commented 4 years ago

@dpastoor I am experimenting the same issue, under Fedora 32, did you happen to solve this?

drelo commented 4 years ago

@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.