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install_graph_tool.txt
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install_graph_tool.txt
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Install graph-tool to visualize the network:
1. Search https://anaconda.org/anaconda/anaconda-navigator the channel for graph-tool.
For example, the channel named 'vgauthier' https://anaconda.org/vgauthier/graph-tool for os x 64
2. Install dependencies and graph-tool in a conda virtual environment
2.2 conda install pygobject -c conda-forge
2.1 conda install gtk3 -c pkgw-forge
2.3 conda install matplotlib -c conda-forge
2.4 conda install graph-tool -c vgauthier
3. brew install graph-tool --with-python3
3. python > import graph_tool
ImportError: dlopen(/Users/chjiang/miniconda3/envs/netsci/lib/python3.6/site-packages/graph_tool/libgraph_tool_core.so, 9): Library not loaded: @rpath/libboost_python3.dylib
Referenced from: /Users/chjiang/miniconda3/envs/netsci/lib/python3.6/site-packages/graph_tool/libgraph_tool_core.so
Reason: image not found
3.1 Find all dependencies of libgraph_tool_core.so
otool -L /Users/chjiang/miniconda3/envs/netsci/lib/python3.6/site-packages/graph_tool/libgraph_tool_core.so
@rpath/libpython3.6m.dylib (compatibility version 3.6.0, current version 3.6.0)
@rpath/libboost_iostreams.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libboost_python3.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libboost_regex.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libboost_context.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libboost_coroutine.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libexpat.1.dylib (compatibility version 8.0.0, current version 8.7.0)
@rpath/libomp.dylib (compatibility version 5.0.0, current version 5.0.0)
@rpath/libgmp.10.dylib (compatibility version 14.0.0, current version 14.2.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 400.9.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.0.0)
3.2 Find the place of
@rpath/libboost_python3.dylib
3.3 Change the install name of the dependency
install_name_tool -change @rpath/libboost_python3.dylib /Users/chjiang/miniconda3/pkgs/boost-1.66.0-py36_1/lib/libboost_python3.dylib /Users/chjiang/miniconda3/envs/netsci/lib/python3.6/site-packages/graph_tool/libgraph_tool_core.so
4. python > import graph_tool
ImportError: dlopen(/Users/chjiang/miniconda3/envs/netsci/lib/python3.6/site-packages/graph_tool/libgraph_tool_core.so, 9): Symbol not found: __ZNK5boost16re_detail_10660031cpp_regex_traits_implementationIcE17transform_primaryEPKcS4_
Referenced from: /Users/chjiang/miniconda3/envs/netsci/lib/python3.6/site-packages/graph_tool/libgraph_tool_core.so
Expected in: /Users/chjiang/miniconda3/envs/netsci/lib/libboost_regex.dylib
in /Users/chjiang/miniconda3/envs/netsci/lib/python3.6/site-packages/graph_tool/libgraph_tool_core.so
5. brew install --build-from-source -with-openmp --with-python3 graph-tool
otool /Users/chjiang/miniconda3/lib/libgdk-3.0.dylib
install_name_tool -change @rpath/libgdk_pixbuf-2.0.0.dylib /Users/chjiang/miniconda3/lib/libgdk_pixbuf-2.0.0.dylib libgdk-3.0.dylib