BioinformaticsToolsmith/MeShClust

Compilation problem

Opened this issue · 3 comments

oliemery commented

Hello, I tried to install MeShClust using "make" after cloning the git repository on Ubuntu but this throws errors, see the log below. I tried updating gcc but this did not fix the issue.
I'd be very grateful if you could indicate me what I could do to fix this and to test MeShClust.

Log:

$laptop:/WorkingDir//MeShClust$ make
make -C src/cluster
make[1]: Entering directory /WorkingDir/MeShClust/src/cluster' rm -f bin/./src/DivergencePoint.o bin/./src/bvec.o bin/./src/GLM.o bin/./src/Histogram.o bin/./src/bvec_iterator.o bin/./src/LogTable.o bin/./src/ClusterFactory.o bin/./src/needleman_wunsch.o bin/./src/Feature.o bin/./src/Progress.o bin/./src/main.o bin/./src/Trainer.o bin/./src/Runner.o bin/./src/Matrix.o bin/./src/SingleFeature.o meshclust mkdir -p bin/./src g++ -fopenmp -O3 -march=native -g -std=c++11 -DVERSION=\"1.2.0\" -c src/DivergencePoint.cpp -o bin/./src/DivergencePoint.o mkdir -p bin/./src g++ -fopenmp -O3 -march=native -g -std=c++11 -DVERSION=\"1.2.0\" -c src/bvec.cpp -o bin/./src/bvec.o mkdir -p bin/./src g++ -fopenmp -O3 -march=native -g -std=c++11 -DVERSION=\"1.2.0\" -c src/GLM.cpp -o bin/./src/GLM.o mkdir -p bin/./src g++ -fopenmp -O3 -march=native -g -std=c++11 -DVERSION=\"1.2.0\" -c src/Histogram.cpp -o bin/./src/Histogram.o mkdir -p bin/./src g++ -fopenmp -O3 -march=native -g -std=c++11 -DVERSION=\"1.2.0\" -c src/bvec_iterator.cpp -o bin/./src/bvec_iterator.o mkdir -p bin/./src g++ -fopenmp -O3 -march=native -g -std=c++11 -DVERSION=\"1.2.0\" -c src/LogTable.cpp -o bin/./src/LogTable.o mkdir -p bin/./src g++ -fopenmp -O3 -march=native -g -std=c++11 -DVERSION=\"1.2.0\" -c src/ClusterFactory.cpp -o bin/./src/ClusterFactory.o src/ClusterFactory.cpp: In function ‘Point<T>* get_mean(std::vector<Point<T>*>&, Point<T>&, double)’: src/ClusterFactory.cpp:412:36: error: expected ‘+’, ‘*’, ‘-’, ‘&’, ‘^’, ‘|’, ‘&&’, ‘||’, ‘min’ or ‘max’ before ‘cmin’ #pragma omp parallel for reduction(cmin:result) ^ make[1]: *** [bin/./src/ClusterFactory.o] Error 1 make[1]: Leaving directory /WorkingDir/MeShClust/src/cluster'
make: *** [bin/meshclust] Error 2
$laptop:/WorkingDir/

moxgreen commented

I solved a similar problem by doing:

 conda create -n gcc_49 -c serge-sans-paille gcc_49
 conda activate gcc_49
 make CXX=g++-4.9

but then I get

bin/meshclust: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by bin/meshclust)

at runtime

hani-girgis commented

Hi. Thanks for your interest in MeShClust. Would you please try a more recent release of GCC? I would try GCC 7.x or higher. Please keep me posted.

iamTad commented

Hi, I also have similar issues installing the software (similar to op). Using gcc 4.x, I get the same error as op, so tried to compile with gcc 7.x and 8.x . However, I still get an error, granted a bit different.
meshclust_compile_err.txt

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