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Installation failing on macOS #21

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BBQuercus opened this issue Oct 2, 2019 · 9 comments
Closed

Installation failing on macOS #21

BBQuercus opened this issue Oct 2, 2019 · 9 comments

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@BBQuercus
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Continuation of my pull request #20.

I wasn't able to reproduce the error with pip (probably delete all dependencies in python / locally). I was able to generate an error running python setup.py install from the master. This was all it output. If I manage to get the same through pip directly, I'll make sure to add it here.

$ python setup.py install

running install
running bdist_egg
running egg_info
writing stardist.egg-info/PKG-INFO
writing dependency_links to stardist.egg-info/dependency_links.txt
writing requirements to stardist.egg-info/requires.txt
writing top-level names to stardist.egg-info/top_level.txt
reading manifest file 'stardist.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'stardist.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.14-x86_64/egg
running install_lib
running build_py
creating build/lib.macosx-10.14-x86_64-3.7
creating build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/plot.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/version.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/rays3d.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/nms.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/matching.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/utils.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
creating build/lib.macosx-10.14-x86_64-3.7/stardist/models
copying stardist/models/model3d.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/models
copying stardist/models/model2d.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/models
copying stardist/models/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/models
copying stardist/models/base.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/models
creating build/lib.macosx-10.14-x86_64-3.7/stardist/geometry
copying stardist/geometry/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/geometry
copying stardist/geometry/geom3d.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/geometry
copying stardist/geometry/geom2d.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/geometry
creating build/lib.macosx-10.14-x86_64-3.7/stardist/kernels
copying stardist/kernels/stardist2d.cl -> build/lib.macosx-10.14-x86_64-3.7/stardist/kernels
copying stardist/kernels/stardist3d.cl -> build/lib.macosx-10.14-x86_64-3.7/stardist/kernels
running build_ext
building 'stardist.lib.stardist2d' extension
Warning: Can't read registry to find the necessary compiler setting
Make sure that Python modules winreg, win32api or win32con are installed.
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers

creating build/temp.macosx-10.14-x86_64-3.7
creating build/temp.macosx-10.14-x86_64-3.7/stardist
creating build/temp.macosx-10.14-x86_64-3.7/stardist/lib
compile options: '-I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
extra options: '-std=c++11 -fopenmp'
clang: stardist/lib/clipper.cpp
clang: stardist/lib/stardist2d.cpp
clang: clang: error: unsupported option '-fopenmp'error: unsupported option '-fopenmp'

compiling with OpenMP support failed, re-trying without
building 'stardist.lib.stardist2d' extension
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers

compile options: '-I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
extra options: '-std=c++11'
clang: stardist/lib/stardist2d.cpp
clang: stardist/lib/clipper.cpp
In file included from stardist/lib/stardist2d.cpp:5:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: 
      "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API
      NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
1 warning generated.
creating build/lib.macosx-10.14-x86_64-3.7/stardist/lib
clang++ -bundle -undefined dynamic_lookup build/temp.macosx-10.14-x86_64-3.7/stardist/lib/stardist2d.o build/temp.macosx-10.14-x86_64-3.7/stardist/lib/clipper.o -L/usr/local/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/sqlite/lib -o build/lib.macosx-10.14-x86_64-3.7/stardist/lib/stardist2d.cpython-37m-darwin.so
building 'stardist.lib.stardist3d' extension
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers

creating build/temp.macosx-10.14-x86_64-3.7/stardist/lib/qhull_src
creating build/temp.macosx-10.14-x86_64-3.7/stardist/lib/qhull_src/src
creating build/temp.macosx-10.14-x86_64-3.7/stardist/lib/qhull_src/src/libqhullcpp
creating build/temp.macosx-10.14-x86_64-3.7/stardist/lib/qhull_src/src/libqhull_r
compile options: '-I/usr/local/lib/python3.7/site-packages/numpy/core/include -Istardist/lib/qhull_src/src -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
extra options: '-std=c++11 -fopenmp'
clang: stardist/lib/stardist3d.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/RoadError.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullVertex.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullRidge.cpp
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullPointSet.cpp
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullFacetSet.cpp
clang: stardist/lib/qhull_src/src/libqhull_r/user_r.c
clang: stardist/lib/qhull_src/src/libqhullcpp/Qhull.cpp
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
clang: stardist/lib/qhull_src/src/libqhull_r/random_r.c
clang: stardist/lib/qhull_src/src/libqhull_r/poly2_r.c
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
clang: stardist/lib/qhull_src/src/libqhull_r/libqhull_r.c
clang: stardist/lib/qhull_src/src/libqhull_r/geom_r.c
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
compiling with OpenMP support failed, re-trying without
building 'stardist.lib.stardist3d' extension
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers

compile options: '-I/usr/local/lib/python3.7/site-packages/numpy/core/include -Istardist/lib/qhull_src/src -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
extra options: '-std=c++11'
clang: stardist/lib/stardist3d.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/RoadError.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullVertex.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullRidge.cpp
In file included from stardist/lib/stardist3d.cpp:6:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: 
      "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API
      NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
stardist/lib/stardist3d.cpp:949:24: warning: unused variable 'scores' [-Wunused-variable]
   const float * const scores = (float*) PyArray_DATA(arr_scores);
                       ^
clang: stardist/lib/qhull_src/src/libqhullcpp/RboxPoints.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullStat.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullQh.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullSet.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullPoints.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullVertexSet.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullPointSet.cpp
2 warnings generated.
clang: stardist/lib/qhull_src/src/libqhullcpp/usermem_r-cpp.cpp
stardist/lib/qhull_src/src/libqhullcpp/usermem_r-cpp.cpp:42:13: warning: explicitly assigning value
      of variable of type 'int' to itself [-Wself-assign]
    exitcode= exitcode;
    ~~~~~~~~^ ~~~~~~~~
1 warning generated.
clang: stardist/lib/qhull_src/src/libqhullcpp/RoadLogEvent.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullFacetSet.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/Qhull.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullPoint.cpp
clang: stardist/lib/qhull_src/src/libqhull_r/user_r.c
error: invalid argument '-std=c++11' not allowed with 'C'
clang: stardist/lib/qhull_src/src/libqhull_r/random_r.c
error: invalid argument '-std=c++11' not allowed with 'C'
clang: stardist/lib/qhull_src/src/libqhull_r/poly2_r.c
error: invalid argument '-std=c++11' not allowed with 'C'
clang: stardist/lib/qhull_src/src/libqhull_r/libqhull_r.c
error: invalid argument '-std=c++11' not allowed with 'C'
clang: stardist/lib/qhull_src/src/libqhull_r/geom_r.c
error: invalid argument '-std=c++11' not allowed with 'C'
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullFacetList.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/PointCoordinates.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullHyperplane.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/QhullFacet.cpp
clang: stardist/lib/qhull_src/src/libqhullcpp/Coordinates.cpp
error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/lib/python3.7/site-packages/numpy/core/include -Istardist/lib/qhull_src/src -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c stardist/lib/qhull_src/src/libqhull_r/user_r.c -o build/temp.macosx-10.14-x86_64-3.7/stardist/lib/qhull_src/src/libqhull_r/user_r.o -std=c++11" failed with exit status 1
@BBQuercus BBQuercus mentioned this issue Oct 2, 2019
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@maweigert
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Hi,

This seems to be a different (expected) error as you use clang and not gcc.

Does is build when specifying gcc explicitely?

CC="gcc-8" CXX="g++-8" python setup.py install

@BBQuercus
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Doesn't seem to change much:

$ CC="gcc-8" CXX="g++-8" python setup.py install 

running install
running bdist_egg
running egg_info
writing stardist.egg-info/PKG-INFO
writing dependency_links to stardist.egg-info/dependency_links.txt
writing requirements to stardist.egg-info/requires.txt
writing top-level names to stardist.egg-info/top_level.txt
reading manifest file 'stardist.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'stardist.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.14-x86_64/egg
running install_lib
running build_py
running build_ext
building 'stardist.lib.stardist3d' extension
Warning: Can't read registry to find the necessary compiler setting
Make sure that Python modules winreg, win32api or win32con are installed.
C compiler: gcc-8 -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers

compile options: '-I/usr/local/lib/python3.7/site-packages/numpy/core/include -Istardist/lib/qhull_src/src -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
extra options: '-std=c++11 -fopenmp'
gcc-8: stardist/lib/stardist3d.cpp
gcc-8: stardist/lib/qhull_src/src/libqhullcpp/RoadError.cpp
gcc-8: stardist/lib/qhull_src/src/libqhullcpp/QhullRidge.cpp
gcc-8: stardist/lib/qhull_src/src/libqhullcpp/QhullVertex.cpp
gcc-8: stardist/lib/qhull_src/src/libqhullcpp/QhullPointSet.cpp
gcc-8: stardist/lib/qhull_src/src/libqhullcpp/Qhull.cpp
gcc-8: stardist/lib/qhull_src/src/libqhullcpp/QhullFacetSet.cpp
gcc-8: stardist/lib/qhull_src/src/libqhull_r/user_r.c
gcc-8: stardist/lib/qhull_src/src/libqhull_r/poly2_r.c
gcc-8: stardist/lib/qhull_src/src/libqhull_r/random_r.c
gcc-8: stardist/lib/qhull_src/src/libqhull_r/libqhull_r.c
gcc-8: stardist/lib/qhull_src/src/libqhull_r/geom_r.c
compiling with OpenMP support failed, re-trying without
building 'stardist.lib.stardist3d' extension
C compiler: gcc-8 -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers

compile options: '-I/usr/local/lib/python3.7/site-packages/numpy/core/include -Istardist/lib/qhull_src/src -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
extra options: '-std=c++11'
gcc-8: stardist/lib/stardist3d.cpp
gcc-8: stardist/lib/qhull_src/src/libqhullcpp/QhullVertex.cpp
gcc-8: stardist/lib/qhull_src/src/libqhullcpp/RoadError.cpp
gcc-8: stardist/lib/qhull_src/src/libqhullcpp/QhullRidge.cpp
gcc-8: stardist/lib/qhull_src/src/libqhullcpp/QhullPointSet.cpp
gcc-8: stardist/lib/qhull_src/src/libqhullcpp/QhullFacetSet.cpp
gcc-8: stardist/lib/qhull_src/src/libqhullcpp/Qhull.cpp
gcc-8: stardist/lib/qhull_src/src/libqhull_r/user_r.c
gcc-8: stardist/lib/qhull_src/src/libqhull_r/random_r.c
gcc-8: stardist/lib/qhull_src/src/libqhull_r/poly2_r.c
gcc-8: stardist/lib/qhull_src/src/libqhull_r/libqhull_r.c
gcc-8: stardist/lib/qhull_src/src/libqhull_r/geom_r.c
error: Command "gcc-8 -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/lib/python3.7/site-packages/numpy/core/include -Istardist/lib/qhull_src/src -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c stardist/lib/stardist3d.cpp -o build/temp.macosx-10.14-x86_64-3.7/stardist/lib/stardist3d.o -std=c++11" failed with exit status 127

@maweigert
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Could you do the following (and post the output)?

CC="gcc-8" CXX="g++-8" python setup.py clean --all install

@BBQuercus
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Sure:

$ CC="gcc-8" CXX="g++-8" python setup.py clean --all install

running clean
removing 'build/temp.macosx-10.14-x86_64-3.7' (and everything under it)
removing 'build/lib.macosx-10.14-x86_64-3.7' (and everything under it)
removing 'build/bdist.macosx-10.14-x86_64' (and everything under it)
'build/scripts-3.7' does not exist -- can't clean it
running install
running bdist_egg
running egg_info
writing stardist.egg-info/PKG-INFO
writing dependency_links to stardist.egg-info/dependency_links.txt
writing requirements to stardist.egg-info/requires.txt
writing top-level names to stardist.egg-info/top_level.txt
reading manifest file 'stardist.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'stardist.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.14-x86_64/egg
running install_lib
running build_py
creating build/lib.macosx-10.14-x86_64-3.7
creating build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/plot.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/version.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/rays3d.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/nms.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/matching.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
copying stardist/utils.py -> build/lib.macosx-10.14-x86_64-3.7/stardist
creating build/lib.macosx-10.14-x86_64-3.7/stardist/models
copying stardist/models/model3d.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/models
copying stardist/models/model2d.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/models
copying stardist/models/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/models
copying stardist/models/base.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/models
creating build/lib.macosx-10.14-x86_64-3.7/stardist/geometry
copying stardist/geometry/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/geometry
copying stardist/geometry/geom3d.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/geometry
copying stardist/geometry/geom2d.py -> build/lib.macosx-10.14-x86_64-3.7/stardist/geometry
creating build/lib.macosx-10.14-x86_64-3.7/stardist/kernels
copying stardist/kernels/stardist2d.cl -> build/lib.macosx-10.14-x86_64-3.7/stardist/kernels
copying stardist/kernels/stardist3d.cl -> build/lib.macosx-10.14-x86_64-3.7/stardist/kernels
running build_ext
building 'stardist.lib.stardist2d' extension
Warning: Can't read registry to find the necessary compiler setting
Make sure that Python modules winreg, win32api or win32con are installed.
C compiler: gcc-8 -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers

creating build/temp.macosx-10.14-x86_64-3.7
creating build/temp.macosx-10.14-x86_64-3.7/stardist
creating build/temp.macosx-10.14-x86_64-3.7/stardist/lib
compile options: '-I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
extra options: '-std=c++11 -fopenmp'
gcc-8: stardist/lib/stardist2d.cpp
gcc-8: stardist/lib/clipper.cpp
compiling with OpenMP support failed, re-trying without
building 'stardist.lib.stardist2d' extension
C compiler: gcc-8 -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers

compile options: '-I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
extra options: '-std=c++11'
gcc-8: stardist/lib/clipper.cpp
gcc-8: stardist/lib/stardist2d.cpp
error: Command "gcc-8 -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c stardist/lib/clipper.cpp -o build/temp.macosx-10.14-x86_64-3.7/stardist/lib/clipper.o -std=c++11" failed with exit status 127

@maweigert
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What's the output of which gcc-8 and gcc-8 --version?

@BBQuercus
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Both of them return nothing / command not found. Only with ggc-9 do I get /usr/local/bin/gcc-9 or gcc-9 (Homebrew GCC 9.1.0) 9.1.0 Copyright (C) 2019 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE..

@maweigert
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Ok, so gcc-8 was not installed :) If you do brew install gcc@8 it should work again. But as you already have gcc-9, there is no need for that anyway.

Btw, as tensorflow does not support GPUs on OSX, running stardist on OSX is very very slow. So I would only use it to play around a bit with the non-training parts.

@BBQuercus
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Perfect. I'm aware of the GPU issue. I'm just testing things out before I 'outsource' my training onto a VM.

@maweigert
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Great! Let us know if you run into troubles.

@m-albert m-albert mentioned this issue Feb 7, 2020
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