I am trying to install networkit 6.1 on macOS 10.15.4 with python 3.8.
I have double checked and made sure that I have all the requirements.
pip3 errors out while Building wheel for networkit (setup.py)
Here is what the error message says. After extensive Googling, I am still not sure what it means.
I would love any insight that might be provided. Here is the incredibly long error code:
pip3 install networkit
Collecting networkit
Using cached networkit-6.1.tar.gz (2.0 MB)
Requirement already satisfied: scipy in /Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages (from networkit) (1.4.1)
Requirement already satisfied: numpy in /Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages (from networkit) (1.18.1)
Building wheels for collected packages: networkit
Building wheel for networkit (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Library/Frameworks/Python.framework/Versions/3.8/bin/python3.8 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit/setup.py'"'"'; __file__='"'"'/private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-wheel-bqalgacb
cwd: /private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit/
Complete output (518 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.8
creating build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/simulation.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/sparsification.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/coloring.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/viztasks.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/graphio.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/plot.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/randomization.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/support.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/clique.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/GraphMLIO.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/linkprediction.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/partitioning.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/globals.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/graph.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/scd.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/flow.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/coarsening.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/algebraic.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/distance.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/stopwatch.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/matching.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/GEXFIO.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/generators.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/centrality.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/dynamic.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/community.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/stats.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/sampling.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/workflows.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/engineering.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/exceptions.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/structures.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/components.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/viz.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/correlation.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/nxadapter.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
creating build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_randomization.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_community.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_graphio.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_generators.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_graphtools.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_graph_traversal.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_sparsification.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_graph.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_algorithms.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
creating build/lib.macosx-10.9-x86_64-3.8/networkit/gephi
copying networkit/gephi/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/gephi
copying networkit/gephi/csv.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/gephi
copying networkit/gephi/pyclient.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/gephi
copying networkit/gephi/streaming.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/gephi
creating build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
copying networkit/profiling/plot.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
copying networkit/profiling/multiprocessing_helper.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
copying networkit/profiling/job.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
copying networkit/profiling/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
copying networkit/profiling/stat.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
copying networkit/profiling/profiling.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
creating build/lib.macosx-10.9-x86_64-3.8/networkit/test/extension
copying networkit/test/extension/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test/extension
copying networkit/test/extension/test.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test/extension
creating build/lib.macosx-10.9-x86_64-3.8/networkit/test/gephi
copying networkit/test/gephi/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test/gephi
creating build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/html
copying networkit/profiling/html/profile.html -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/html
copying networkit/profiling/html/profiling.css -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/html
copying networkit/profiling/html/measure.html -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/html
copying networkit/profiling/html/profiling.js -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/html
copying networkit/profiling/html/overlay.html -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/html
creating build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/latex
copying networkit/profiling/latex/measure.tex -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/latex
copying networkit/profiling/latex/profile.tex -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/latex
creating build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/description
copying networkit/profiling/description/descriptions.txt -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/description
running build_ext
Cython not available, but _NetworKit.cpp provided. Continue build without cythonizing
initializing NetworKit compilation with: 'cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit/build/lib.macosx-10.9-x86_64-3.8 -DCMAKE_CXX_COMPILER=c++ -DNETWORKIT_FLATINSTALL=ON -DNETWORKIT_PYTHON=/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -DNETWORKIT_PYTHON_SOABI=cpython-38-darwin /private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit'
-- The CXX compiler identification is AppleClang 11.0.3.11030032
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_CXX_FOUND)
-- Found OpenMP_CXX: -Xpreprocessor -fopenmp -I/usr/local/include (found version "3.1")
-- Found OpenMP: TRUE (found version "3.1")
-- The C compiler identification is AppleClang 11.0.3.11030032
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Performing Test TLX_CXX_HAS_CXX17
-- Performing Test TLX_CXX_HAS_CXX17 - Success
-- TLX CMAKE_CXX_FLAGS: -Wshadow -Wold-style-cast -std=c++17 -g -W -Wall -Wextra -fPIC -Wdeprecated
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- sphinx-build not found. Disable documentation targets
-- Configuring done
-- Generating done
-- Build files have been written to: /private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit/build/build_python
Build with: 'make install -j4'
Scanning dependencies of target tlx
[ 1%] Building CXX object extlibs/tlx/tlx/CMakeFiles/tlx.dir/algorithm/parallel_multiway_merge.cpp.o
[ 1%] Building CXX object extlibs/tlx/tlx/CMakeFiles/tlx.dir/backtrace.cpp.o
[ 1%] Building CXX object extlibs/tlx/tlx/CMakeFiles/tlx.dir/die/core.cpp.o
[ 1%] Building CXX object extlibs/tlx/tlx/CMakeFiles/tlx.dir/cmdline_parser.cpp.o
[ 1%] Building CXX object extlibs/tlx/tlx/CMakeFiles/tlx.dir/digest/md5.cpp.o
[ 2%] Building CXX object extlibs/tlx/tlx/CMakeFiles/tlx.dir/digest/sha1.cpp.o
[ 2%] Building CXX object extlibs/tlx/tlx/CMakeFiles/tlx.dir/digest/sha256.cpp.o
[ 2%] Building CXX object extlibs/tlx/tlx/CMakeFiles/tlx.dir/digest/sha512.cpp.o
[ 2%] Building CXX object extlibs/tlx/tlx/CMakeFiles/tlx.dir/logger/core.cpp.o
...edited for brevity....
[ 88%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/linkprediction/UDegreeIndex.cpp.o
[ 88%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/linkprediction/VDegreeIndex.cpp.o
[ 89%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/matching/LocalMaxMatcher.cpp.o
[ 89%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/matching/Matcher.cpp.o
[ 89%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/matching/Matching.cpp.o
[ 90%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/matching/PathGrowingMatcher.cpp.o
[ 90%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/overlap/HashingOverlapper.cpp.o
[ 90%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/overlap/Overlapper.cpp.o
[ 91%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/randomization/Curveball.cpp.o
[ 91%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/randomization/CurveballGlobalTradeGenerator.cpp.o
[ 91%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/randomization/CurveballImpl.cpp.o
[ 91%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/randomization/CurveballUniformTradeGenerator.cpp.o
[ 92%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/randomization/DegreePreservingShuffle.cpp.o
[ 92%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/randomization/GlobalCurveball.cpp.o
[ 92%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/scd/ApproximatePageRank.cpp.o
clang: error: unable to execute command: Segmentation fault: 11
clang: error: clang frontend command failed due to signal (use -v to see invocation)
Apple clang version 11.0.3 (clang-1103.0.32.29)
Target: x86_64-apple-darwin19.4.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
clang: note: diagnostic msg: PLEASE submit a bug report to http://developer.apple.com/bugreporter/ and include the crash backtrace, preprocessed source, and associated run script.
clang: note: diagnostic msg:
********************
PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
clang: note: diagnostic msg: /var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/DegreePreservingShuffle-57cb30.cpp
clang: note: diagnostic msg: /var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/DegreePreservingShuffle-57cb30.sh
clang: note: diagnostic msg: Crash backtrace is located in
clang: note: diagnostic msg: /Users/derycpainter/Library/Logs/DiagnosticReports/clang_<YYYY-MM-DD-HHMMSS>_<hostname>.crash
clang: note: diagnostic msg: (choose the .crash file that corresponds to your crash)
clang: note: diagnostic msg:
********************
make[2]: *** [CMakeFiles/networkit.dir/networkit/cpp/randomization/DegreePreservingShuffle.cpp.o] Error 254
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/networkit.dir/all] Error 2
make: *** [all] Error 2
Build tool returned an error, exiting setup.py
----------------------------------------
ERROR: Failed building wheel for networkit
Running setup.py clean for networkit
Failed to build networkit
Installing collected packages: networkit
Running setup.py install for networkit ... error
ERROR: Command errored out with exit status 1:
command: /Library/Frameworks/Python.framework/Versions/3.8/bin/python3.8 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit/setup.py'"'"'; __file__='"'"'/private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-record-f2ad9aq9/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /Users/derycpainter/Library/Python/3.8/include/python3.8/networkit
cwd: /private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit/
Complete output (123 lines):
running install
running build
running build_py
creating build/lib.macosx-10.9-x86_64-3.8
creating build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/simulation.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/sparsification.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/coloring.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/viztasks.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/graphio.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/plot.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/randomization.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/support.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/clique.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/GraphMLIO.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/linkprediction.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/partitioning.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/globals.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/graph.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/scd.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/flow.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/coarsening.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/algebraic.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/distance.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/stopwatch.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/matching.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/GEXFIO.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/generators.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/centrality.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/dynamic.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/community.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/stats.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/sampling.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/workflows.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/engineering.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/exceptions.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/structures.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/components.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/viz.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/correlation.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
copying networkit/nxadapter.py -> build/lib.macosx-10.9-x86_64-3.8/networkit
creating build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_randomization.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_community.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_graphio.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_generators.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_graphtools.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_graph_traversal.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_sparsification.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_graph.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
copying networkit/test/test_algorithms.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test
creating build/lib.macosx-10.9-x86_64-3.8/networkit/gephi
copying networkit/gephi/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/gephi
copying networkit/gephi/csv.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/gephi
copying networkit/gephi/pyclient.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/gephi
copying networkit/gephi/streaming.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/gephi
creating build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
copying networkit/profiling/plot.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
copying networkit/profiling/multiprocessing_helper.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
copying networkit/profiling/job.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
copying networkit/profiling/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
copying networkit/profiling/stat.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
copying networkit/profiling/profiling.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling
creating build/lib.macosx-10.9-x86_64-3.8/networkit/test/extension
copying networkit/test/extension/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test/extension
copying networkit/test/extension/test.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test/extension
creating build/lib.macosx-10.9-x86_64-3.8/networkit/test/gephi
copying networkit/test/gephi/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/networkit/test/gephi
creating build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/html
copying networkit/profiling/html/profile.html -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/html
copying networkit/profiling/html/profiling.css -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/html
copying networkit/profiling/html/measure.html -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/html
copying networkit/profiling/html/profiling.js -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/html
copying networkit/profiling/html/overlay.html -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/html
creating build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/latex
copying networkit/profiling/latex/measure.tex -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/latex
copying networkit/profiling/latex/profile.tex -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/latex
creating build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/description
copying networkit/profiling/description/descriptions.txt -> build/lib.macosx-10.9-x86_64-3.8/networkit/profiling/description
running build_ext
Cython not available, but _NetworKit.cpp provided. Continue build without cythonizing
initializing NetworKit compilation with: 'cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit/build/lib.macosx-10.9-x86_64-3.8 -DCMAKE_CXX_COMPILER=c++ -DNETWORKIT_FLATINSTALL=ON -DNETWORKIT_PYTHON=/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -DNETWORKIT_PYTHON_SOABI=cpython-38-darwin /private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit'
-- Found OpenMP_CXX: -Xpreprocessor -fopenmp -I/usr/local/include
-- Found OpenMP: TRUE
-- TLX CMAKE_CXX_FLAGS: -Wshadow -Wold-style-cast -std=c++17 -g -W -Wall -Wextra -fPIC -Wdeprecated
-- sphinx-build not found. Disable documentation targets
-- Configuring done
-- Generating done
-- Build files have been written to: /private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit/build/build_python
Build with: 'make install -j4'
[ 13%] Built target tlx
[ 15%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/randomization/DegreePreservingShuffle.cpp.o
[ 15%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/scd/GCE.cpp.o
[ 15%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/scd/PageRankNibble.cpp.o
[ 15%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/scd/SelectiveCommunityDetector.cpp.o
clang: error: unable to execute command: Segmentation fault: 11
clang: error: clang frontend command failed due to signal (use -v to see invocation)
Apple clang version 11.0.3 (clang-1103.0.32.29)
Target: x86_64-apple-darwin19.4.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
clang: note: diagnostic msg: PLEASE submit a bug report to http://developer.apple.com/bugreporter/ and include the crash backtrace, preprocessed source, and associated run script.
[ 16%] Building CXX object CMakeFiles/networkit.dir/networkit/cpp/simulation/EpidemicSimulationSEIR.cpp.o
clang: note: diagnostic msg:
********************
PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
clang: note: diagnostic msg: /var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/DegreePreservingShuffle-264185.cpp
clang: note: diagnostic msg: /var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/DegreePreservingShuffle-264185.sh
clang: note: diagnostic msg: Crash backtrace is located in
clang: note: diagnostic msg: /Users/derycpainter/Library/Logs/DiagnosticReports/clang_<YYYY-MM-DD-HHMMSS>_<hostname>.crash
clang: note: diagnostic msg: (choose the .crash file that corresponds to your crash)
clang: note: diagnostic msg:
********************
make[2]: *** [CMakeFiles/networkit.dir/networkit/cpp/randomization/DegreePreservingShuffle.cpp.o] Error 254
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/networkit.dir/all] Error 2
make: *** [all] Error 2
Build tool returned an error, exiting setup.py
----------------------------------------
ERROR: Command errored out with exit status 1: /Library/Frameworks/Python.framework/Versions/3.8/bin/python3.8 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit/setup.py'"'"'; __file__='"'"'/private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-install-khdr64cp/networkit/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/gy/2kn7_0x140z14dgv422v38jh0000gn/T/pip-record-f2ad9aq9/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /Users/derycpainter/Library/Python/3.8/include/python3.8/networkit Check the logs for full command output.
Related
I'm trying to build LUAGLM (from https://github.com/gottfriedleibniz/lua) to bind GLM library to give access in Lua using cmake. When i build, the building completes ok but the linker does not giving error:
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [glm.so] Error 1
make[1]: *** [CMakeFiles/glm.dir/all] Error 2
make: *** [all] Error 2
Above these lines there is a very long list starting with:
[ 10%] Building CXX object CMakeFiles/liblua.dir/onelua.c.o
[ 20%] Linking CXX shared library liblua54.dylib
[ 20%] Built target liblua
[ 30%] Building CXX object CMakeFiles/liblua_static.dir/onelua.c.o
[ 40%] Linking CXX static library liblua54_static.a
[ 40%] Built target liblua_static
[ 50%] Building C object CMakeFiles/lua.dir/lua.c.o
[ 60%] Linking CXX executable lua
[ 60%] Built target lua
[ 70%] Building CXX object CMakeFiles/luac.dir/onelua.c.o
[ 80%] Linking CXX executable luac
[ 80%] Built target luac
[ 90%] Building CXX object CMakeFiles/glm.dir/libs/glm_binding/lglmlib.cpp.o
[100%] Linking CXX shared module glm.so
Undefined symbols for architecture x86_64:
"glm_pushmat(lua_State*, glmMatrix const&)", referenced from:
glm_mat_add(lua_State*) in lglmlib.cpp.o
glm_mat_sub(lua_State*) in lglmlib.cpp.o
glm_mat_mul(lua_State*) in lglmlib.cpp.o
glm_mat_negate(lua_State*) in lglmlib.cpp.o
glm_mix(lua_State*) in lglmlib.cpp.o
glm_saturation(lua_State*) in lglmlib.cpp.o
glm_orthonormalize(lua_State*) in lglmlib.cpp.o
...
I'm on MacOS Intel (i386-apple-darwin11.3.0)
Not sure where to go next, do I need to edit the CMakeList somehow?
Any help much appreciated
EDIT:
The cmake error log contains the following :
Compiling the C compiler identification source file "CMakeCCompilerId.c" failed. Compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc Build flags: Id flags:
The output was: 1 ld: library not found for -lSystem clang: error: linker command failed with exit code 1 (use -v to see invocation)
Compiling the CXX compiler identification source file "CMakeCXXCompilerId.cpp" failed. Compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ Build flags: Id flags:
The output was: 1 ld: library not found for -lc++ clang: error: linker command failed with exit code 1 (use -v to see invocation)
This is actually a bug in the CMakeList.txt because the library-list for the glm.so module does not contain the liblua.
If you apply the following patch
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8cf8a1a6..6eda2a17 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
## -940,7 +940,7 ## ENDIF()
ADD_LIBRARY(glm MODULE ${SRC_LIBGLM})
TARGET_INCLUDE_DIRECTORIES(glm PRIVATE ${INCLUDE_DIRECTORIES})
-TARGET_LINK_LIBRARIES(glm PRIVATE ${LIBS})
+TARGET_LINK_LIBRARIES(glm PRIVATE ${LIBS} liblua_static)
IF( LUA_BUILD_AS_DLL )
TARGET_LINK_LIBRARIES(glm PUBLIC ${interpretor_target})
TARGET_COMPILE_DEFINITIONS(glm PRIVATE LUA_BUILD_AS_DLL)
to the freshly cloned repository and then do (inside the cloned repository):
git submodule update --init
mkdir build
cd build
cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release -DONE_LUA=ON ..
make
you should find the files glm.so, lua and luac in your build directory. At least that worked on my Intel MacBook.
Using liblua_static in the CMakeList.txt for the library glm makes sure, that the resulting glm.so does not need the liblua dynamic library but contains the required code statically. That avoids problems when loading glm.so and the liblua library not being in the library path.
I opened an issue in the GitHub repository for it. So hopefully it will get fixed for everybody soon.
Usually it'll be something like -lYourLibrary not found, if -lSystem for example is not found, try adding it to your CMakeLists.
Are you still having the issue?
I am new to Docker container and kubenetes cluster. I am trying to run following section of command using buildah
##install cmake
USER root
RUN apt-get update && apt-get -y install cmake
USER ${user}
WORKDIR $HOME
## bustools_dev
RUN git clone https://github.com/Yenaled/bustools.git && \
cd bustools && \
mkdir build && \
cd build
RUN cmake ../
RUN make
RUN cd src
RUN mv bustools bustools_dev
RUN ENV PATH=$HOME/bustools/build/src/:${PATH}
but get the following error. What am I missing here?
STEP 17: WORKDIR $HOME
WARN[0002] SHELL is not supported for OCI image format, [/bin/bash -o pipefail -c] will be ignored. Must use `docker` format
--> 770a1b90326
STEP 18: RUN git clone https://github.com/Yenaled/bustools.git && cd bustools && mkdir build && cd build
Cloning into 'bustools'...
WARN[0005] SHELL is not supported for OCI image format, [/bin/bash -o pipefail -c] will be ignored. Must use `docker` format
--> 2b87555e927
STEP 19: RUN cmake ../
CMake Error: The source directory "/home" does not appear to contain CMakeLists.txt.
Specify --help for usage, or press the help button on the CMake GUI.
error building at STEP "RUN cmake ../": error while running runtime: exit status 1
ERRO[0111] exit status 1
I'd simplify the Dockerfile to avoid the issues with the WORKDIR setup that I think are the cause of the problem:
FROM debian:11
RUN apt-get update \
&& apt-get install --assume-yes --no-install-recommends --quiet \
ca-certificates \
cmake \
git \
g++ \
make \
libzip-dev \
&& apt-get clean all
WORKDIR /usr/local/src
RUN git clone https://github.com/Yenaled/bustools.git
RUN mkdir -p /usr/local/src/bustools/build
RUN cd /usr/local/src/bustools/build \
&& cmake .. \
&& make
[...]
Output
[...]
STEP 3/6: WORKDIR /usr/local/src
--> ffb056fd5b3
STEP 4/6: RUN git clone https://github.com/Yenaled/bustools.git
Cloning into 'bustools'...
--> 83afa44c5c8
STEP 5/6: RUN mkdir -p /usr/local/src/bustools/build
--> 2e6ed328088
STEP 6/6: RUN cd /usr/local/src/bustools/build && cmake .. && make
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
release mode
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11")
-- Configuring done
-- Generating done
-- Build files have been written to: /usr/local/src/bustools/build
Scanning dependencies of target bustools_core
[ 4%] Building CXX object src/CMakeFiles/bustools_core.dir/BUSData.cpp.o
[ 8%] Building CXX object src/CMakeFiles/bustools_core.dir/Common.cpp.o
[ 13%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_capture.cpp.o
[ 17%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_clusterhist.cpp.o
[ 21%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_collapse.cpp.o
[ 26%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_correct.cpp.o
[ 30%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_count.cpp.o
[ 34%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_extract.cpp.o
[ 39%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_inspect.cpp.o
[ 43%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_linker.cpp.o
[ 47%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_main.cpp.o
[ 52%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_mash.cpp.o
[ 56%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_merge.cpp.o
[ 60%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_predict.cpp.o
[ 65%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_project.cpp.o
[ 69%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_sort.cpp.o
[ 73%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_text.cpp.o
[ 78%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_umicorrect.cpp.o
[ 82%] Building CXX object src/CMakeFiles/bustools_core.dir/bustools_whitelist.cpp.o
[ 86%] Building C object src/CMakeFiles/bustools_core.dir/roaring.c.o
[ 91%] Linking CXX static library libbustools_core.a
[ 91%] Built target bustools_core
Scanning dependencies of target bustools
[ 95%] Building CXX object src/CMakeFiles/bustools.dir/bustools_main.cpp.o
[100%] Linking CXX executable bustools
[100%] Built target bustools
--> b08bc457b5f
I tried to install tensornets in my ubuntu anaconda environment but the message bellow appears.
I installed:
numpy 1.17.0,
tensoflow 1.14.0,
pandas 1.1.5,
opencv,
keras,
cmake,
dlib
$ pip install tensornets
collecting tensornets
Using cached tensornets-0.4.6.tar.gz (651 kB)
Installing build dependencies ... done
WARNING: Missing build requirements in pyproject.toml for tensornets from https://files.pythonhosted.org/packages/71/22/2c9402bbf142b94dc39d8a3c9884690ae87706a8bc1453d6cf0630525173/tensornets-0.4.6.tar.gz#sha256=e1095082b45a06168d56450d8c8fa49780d8aef8d4d1fcc64efceadb743f9ceb.
WARNING: The project does not specify a build backend, and pip cannot fall back to setuptools without 'wheel'.
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing wheel metadata ... done
Building wheels for collected packages: tensornets
Building wheel for tensornets (PEP 517) ... error
ERROR: Command errored out with exit status 1:
command: /home/mario/miniconda3/envs/VARVO_LINUX/bin/python /home/mario/miniconda3/envs/VARVO_LINUX/lib/python3.6/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmp2bm7gwnh
cwd: /tmp/pip-install-vupow4g5/tensornets_24fc2060cce2460b9b6417949ee1e6b6
Complete output (86 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/tensornets
copying tensornets/utils.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/unet.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/inceptions.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/densenets.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/preprocess.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/capsulenets.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/tnets.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/resnets.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/nasnets.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/init.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/middles.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/version_utils.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/squeezenets.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/vggs.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/darknets.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/zf.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/layers.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/pretrained.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/mobilenets.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/ops.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/detections.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/efficientnets.py -> build/lib.linux-x86_64-3.6/tensornets
copying tensornets/wavenets.py -> build/lib.linux-x86_64-3.6/tensornets
creating build/lib.linux-x86_64-3.6/tensornets/datasets
copying tensornets/datasets/init.py -> build/lib.linux-x86_64-3.6/tensornets/datasets
copying tensornets/datasets/imagenet.py -> build/lib.linux-x86_64-3.6/tensornets/datasets
copying tensornets/datasets/voc.py -> build/lib.linux-x86_64-3.6/tensornets/datasets
copying tensornets/datasets/coco.py -> build/lib.linux-x86_64-3.6/tensornets/datasets
creating build/lib.linux-x86_64-3.6/tensornets/contrib_framework
copying tensornets/contrib_framework/init.py -> build/lib.linux-x86_64-3.6/tensornets/contrib_framework
copying tensornets/contrib_framework/arg_scope.py -> build/lib.linux-x86_64-3.6/tensornets/contrib_framework
copying tensornets/contrib_framework/variables.py -> build/lib.linux-x86_64-3.6/tensornets/contrib_framework
creating build/lib.linux-x86_64-3.6/tensornets/contrib_layers
copying tensornets/contrib_layers/utils.py -> build/lib.linux-x86_64-3.6/tensornets/contrib_layers
copying tensornets/contrib_layers/init.py -> build/lib.linux-x86_64-3.6/tensornets/contrib_layers
copying tensornets/contrib_layers/initializers.py -> build/lib.linux-x86_64-3.6/tensornets/contrib_layers
copying tensornets/contrib_layers/normalization.py -> build/lib.linux-x86_64-3.6/tensornets/contrib_layers
copying tensornets/contrib_layers/optimizers.py -> build/lib.linux-x86_64-3.6/tensornets/contrib_layers
copying tensornets/contrib_layers/layers.py -> build/lib.linux-x86_64-3.6/tensornets/contrib_layers
copying tensornets/contrib_layers/regularizers.py -> build/lib.linux-x86_64-3.6/tensornets/contrib_layers
copying tensornets/contrib_layers/summaries.py -> build/lib.linux-x86_64-3.6/tensornets/contrib_layers
copying tensornets/contrib_layers/rev_block_lib.py -> build/lib.linux-x86_64-3.6/tensornets/contrib_layers
creating build/lib.linux-x86_64-3.6/tensornets/references
copying tensornets/references/init.py -> build/lib.linux-x86_64-3.6/tensornets/references
copying tensornets/references/rcnns.py -> build/lib.linux-x86_64-3.6/tensornets/references
copying tensornets/references/yolo_utils.py -> build/lib.linux-x86_64-3.6/tensornets/references
copying tensornets/references/rpn_utils.py -> build/lib.linux-x86_64-3.6/tensornets/references
copying tensornets/references/yolos.py -> build/lib.linux-x86_64-3.6/tensornets/references
creating build/lib.linux-x86_64-3.6/tensornets/references/darkflow_utils
copying tensornets/references/darkflow_utils/init.py -> build/lib.linux-x86_64-3.6/tensornets/references/darkflow_utils
copying tensornets/references/darkflow_utils/box.py -> build/lib.linux-x86_64-3.6/tensornets/references/darkflow_utils
running egg_info
writing tensornets.egg-info/PKG-INFO
writing dependency_links to tensornets.egg-info/dependency_links.txt
writing top-level names to tensornets.egg-info/top_level.txt
reading manifest file 'tensornets.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'tensornets.egg-info/SOURCES.txt'
copying tensornets/datasets/coco.names -> build/lib.linux-x86_64-3.6/tensornets/datasets
copying tensornets/datasets/voc.names -> build/lib.linux-x86_64-3.6/tensornets/datasets
copying tensornets/references/coco.names -> build/lib.linux-x86_64-3.6/tensornets/references
copying tensornets/references/voc.names -> build/lib.linux-x86_64-3.6/tensornets/references
copying tensornets/references/darkflow_utils/init.pyc -> build/lib.linux-x86_64-3.6/tensornets/references/darkflow_utils
copying tensornets/references/darkflow_utils/box.pyc -> build/lib.linux-x86_64-3.6/tensornets/references/darkflow_utils
copying tensornets/references/darkflow_utils/get_boxes.c -> build/lib.linux-x86_64-3.6/tensornets/references/darkflow_utils
copying tensornets/references/darkflow_utils/get_boxes.pyx -> build/lib.linux-x86_64-3.6/tensornets/references/darkflow_utils
copying tensornets/references/darkflow_utils/get_boxes.so -> build/lib.linux-x86_64-3.6/tensornets/references/darkflow_utils
copying tensornets/references/darkflow_utils/nms.c -> build/lib.linux-x86_64-3.6/tensornets/references/darkflow_utils
copying tensornets/references/darkflow_utils/nms.pxd -> build/lib.linux-x86_64-3.6/tensornets/references/darkflow_utils
copying tensornets/references/darkflow_utils/nms.pyx -> build/lib.linux-x86_64-3.6/tensornets/references/darkflow_utils
copying tensornets/references/darkflow_utils/nms.so -> build/lib.linux-x86_64-3.6/tensornets/references/darkflow_utils
running build_ext
building 'tensornets.references.darkflow_utils.nms' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/tensornets
creating build/temp.linux-x86_64-3.6/tensornets/references
creating build/temp.linux-x86_64-3.6/tensornets/references/darkflow_utils
gcc -pthread -B /home/mario/miniconda3/envs/VARVO_LINUX/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-5o3ttz/overlay/lib/python3.6/site-packages/numpy/core/include -I/home/mario/miniconda3/envs/VARVO_LINUX/include/python3.6m -c tensornets/references/darkflow_utils/nms.c -o build/temp.linux-x86_64-3.6/tensornets/references/darkflow_utils/nms.o
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for tensornets
Failed to build tensornets
ERROR: Could not build wheels for tensornets which use PEP 517 and cannot be installed directly
The problem was in the gcc compiler
I followed this tutorial: https://linuxize.com/post/how-to-install-gcc-compiler-on-ubuntu-18-04/
In summary:
1.- Update
$sudo apt update
2.- Install build-essential
$sudo apt install build-essential
2.1.- Optional (documentation)
$sudo apt-get install manpages-dev
3.- Verify GCC compiler installation
$gcc --version
I am using $pip install web3 inside a python_virtual_env, but I get the error below.
Defaulting to user installation because normal site-packages is not writeable
Collecting web3
Using cached web3-5.7.0-py3-none-any.whl (460 kB)
Collecting hexbytes<1.0.0,>=0.1.0
Using cached hexbytes-0.2.0-py3-none-any.whl (5.3 kB)
Collecting jsonschema<4.0.0,>=3.0.0
Using cached jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
Collecting typing-extensions<4,>=3.7.4.1; python_version < "3.8"
Using cached typing_extensions-3.7.4.2-py3-none-any.whl (22 kB)
Collecting protobuf<4,>=3.10.0
Using cached protobuf-3.11.3-cp36-cp36m-manylinux1_x86_64.whl (1.3 MB)
Requirement already satisfied: websockets<9.0.0,>=8.1.0 in /home/ajay/.local/lib/python3.6/site-packages (from web3) (8.1)
Collecting ipfshttpclient<1,>=0.4.12
Using cached ipfshttpclient-0.4.12-py2.py3-none-any.whl (157 kB)
Requirement already satisfied: requests<3.0.0,>=2.16.0 in /usr/lib/python3/dist-packages (from web3) (2.18.4)
Collecting eth-abi<3.0.0,>=2.0.0b6
Using cached eth_abi-2.1.1-py3-none-any.whl (27 kB)
Requirement already satisfied: eth-hash[pycryptodome]<1.0.0,>=0.2.0 in /home/ajay/.local/lib/python3.6/site-packages (from web3) (0.2.0)
Collecting lru-dict<2.0.0,>=1.1.6
Using cached lru-dict-1.1.6.tar.gz (9.4 kB)
Collecting eth-account<0.5.0,>=0.4.0
Using cached eth_account-0.4.0-py3-none-any.whl (26 kB)
Requirement already satisfied: eth-typing<3.0.0,>=2.0.0 in /home/ajay/.local/lib/python3.6/site-packages (from web3) (2.2.1)
Collecting eth-utils<2.0.0,>=1.8.4
Using cached eth_utils-1.8.4-py3-none-any.whl (23 kB)
Collecting attrs>=17.4.0
Using cached attrs-19.3.0-py2.py3-none-any.whl (39 kB)
Collecting importlib-metadata; python_version < "3.8"
Using cached importlib_metadata-1.6.0-py2.py3-none-any.whl (30 kB)
Requirement already satisfied: setuptools in /home/ajay/.local/lib/python3.6/site-packages (from jsonschema<4.0.0,>=3.0.0->web3) (46.1.3)
Requirement already satisfied: six>=1.11.0 in /usr/lib/python3/dist-packages (from jsonschema<4.0.0,>=3.0.0->web3) (1.11.0)
Processing /home/ajay/.cache/pip/wheels/d1/8a/1c/32ab9017418a2c64e4fbaf503c08648bed2f8eb311b869a464/pyrsistent-0.16.0-cp36-cp36m-linux_x86_64.whl
Collecting multiaddr>=0.0.7
Using cached multiaddr-0.0.9-py2.py3-none-any.whl (16 kB)
Processing /home/ajay/.cache/pip/wheels/43/95/c9/c9f7a3f9dc34ebd851739148bd5b42ab35618ea0808388647c/parsimonious-0.8.1-py3-none-any.whl
Requirement already satisfied: pycryptodome<4,>=3.6.6; extra == "pycryptodome" in /home/ajay/.local/lib/python3.6/site-packages (from eth-hash[pycryptodome]<1.0.0,>=0.2.0->web3) (3.9.7)
Collecting eth-rlp<1,>=0.1.2
Using cached eth_rlp-0.1.2-py3-none-any.whl (6.5 kB)
Collecting rlp<2,>=1.0.0
Using cached rlp-1.2.0-py2.py3-none-any.whl (19 kB)
Collecting attrdict<3,>=2.0.0
Using cached attrdict-2.0.1-py2.py3-none-any.whl (9.9 kB)
Collecting eth-keys<0.3.0,>=0.2.1
Using cached eth_keys-0.2.4-py3-none-any.whl (24 kB)
Collecting eth-keyfile<0.6.0,>=0.5.0
Using cached eth_keyfile-0.5.1-py3-none-any.whl (8.3 kB)
Collecting cytoolz<1.0.0,>=0.10.1; implementation_name == "cpython"
Using cached cytoolz-0.10.1.tar.gz (475 kB)
Collecting zipp>=0.5
Using cached zipp-3.1.0-py3-none-any.whl (4.9 kB)
Processing /home/ajay/.cache/pip/wheels/35/f3/7e/e67e5ecf7e79b875e840bee3258c29ade8bffd56542d9c9c39/varint-1.0.2-py3-none-any.whl
Collecting base58
Using cached base58-2.0.0-py3-none-any.whl (6.0 kB)
Collecting netaddr
Using cached netaddr-0.7.19-py2.py3-none-any.whl (1.6 MB)
Requirement already satisfied: toolz>=0.8.0 in /home/ajay/.local/lib/python3.6/site-packages (from cytoolz<1.0.0,>=0.10.1; implementation_name == "cpython"->eth-utils<2.0.0,>=1.8.4->web3) (0.10.0)
Building wheels for collected packages: lru-dict, cytoolz
Building wheel for lru-dict (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-j__tim18/lru-dict/setup.py'"'"'; __file__='"'"'/tmp/pip-install-j__tim18/lru-dict/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-023_93_d
cwd: /tmp/pip-install-j__tim18/lru-dict/
Complete output (12 lines):
running bdist_wheel
running build
running build_ext
building 'lru' extension
creating build
creating build/temp.linux-x86_64-3.6
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.6m -c lru.c -o build/temp.linux-x86_64-3.6/lru.o
lru.c:1:10: fatal error: Python.h: No such file or directory
#include <Python.h>
^~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for lru-dict
Running setup.py clean for lru-dict
Building wheel for cytoolz (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-j__tim18/cytoolz/setup.py'"'"'; __file__='"'"'/tmp/pip-install-j__tim18/cytoolz/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-o4caiffl
cwd: /tmp/pip-install-j__tim18/cytoolz/
Complete output (57 lines):
ALERT: Cython not installed. Building without Cython.
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/compatibility.py -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/_signatures.py -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/_version.py -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/__init__.py -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/utils_test.py -> build/lib.linux-x86_64-3.6/cytoolz
creating build/lib.linux-x86_64-3.6/cytoolz/curried
copying cytoolz/curried/operator.py -> build/lib.linux-x86_64-3.6/cytoolz/curried
copying cytoolz/curried/exceptions.py -> build/lib.linux-x86_64-3.6/cytoolz/curried
copying cytoolz/curried/__init__.py -> build/lib.linux-x86_64-3.6/cytoolz/curried
copying cytoolz/recipes.pyx -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/utils.pyx -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/itertoolz.pyx -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/dicttoolz.pyx -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/functoolz.pyx -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/__init__.pxd -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/dicttoolz.pxd -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/itertoolz.pxd -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/recipes.pxd -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/utils.pxd -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/cpython.pxd -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/functoolz.pxd -> build/lib.linux-x86_64-3.6/cytoolz
creating build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_tlz.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_doctests.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_curried.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_signatures.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/dev_skip_test.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_curried_toolzlike.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_functoolz.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_recipes.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_inspect_args.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_dicttoolz.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_dev_skip_test.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_embedded_sigs.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_compatibility.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_utils.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_none_safe.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_serialization.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_itertoolz.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_docstrings.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
running build_ext
building 'cytoolz.dicttoolz' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/cytoolz
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.6m -c cytoolz/dicttoolz.c -o build/temp.linux-x86_64-3.6/cytoolz/dicttoolz.o
cytoolz/dicttoolz.c:17:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for cytoolz
Running setup.py clean for cytoolz
Failed to build lru-dict cytoolz
Installing collected packages: cytoolz, eth-utils, hexbytes, attrs, zipp, importlib-metadata, pyrsistent, jsonschema, typing-extensions, protobuf, varint, base58, netaddr, multiaddr, ipfshttpclient, parsimonious, eth-abi, lru-dict, rlp, eth-rlp, attrdict, eth-keys, eth-keyfile, eth-account, web3
Running setup.py install for cytoolz ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-j__tim18/cytoolz/setup.py'"'"'; __file__='"'"'/tmp/pip-install-j__tim18/cytoolz/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-1xzorhvi/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/ajay/.local/include/python3.6m/cytoolz
cwd: /tmp/pip-install-j__tim18/cytoolz/
Complete output (57 lines):
ALERT: Cython not installed. Building without Cython.
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/compatibility.py -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/_signatures.py -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/_version.py -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/__init__.py -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/utils_test.py -> build/lib.linux-x86_64-3.6/cytoolz
creating build/lib.linux-x86_64-3.6/cytoolz/curried
copying cytoolz/curried/operator.py -> build/lib.linux-x86_64-3.6/cytoolz/curried
copying cytoolz/curried/exceptions.py -> build/lib.linux-x86_64-3.6/cytoolz/curried
copying cytoolz/curried/__init__.py -> build/lib.linux-x86_64-3.6/cytoolz/curried
copying cytoolz/recipes.pyx -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/utils.pyx -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/itertoolz.pyx -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/dicttoolz.pyx -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/functoolz.pyx -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/__init__.pxd -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/dicttoolz.pxd -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/itertoolz.pxd -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/recipes.pxd -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/utils.pxd -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/cpython.pxd -> build/lib.linux-x86_64-3.6/cytoolz
copying cytoolz/functoolz.pxd -> build/lib.linux-x86_64-3.6/cytoolz
creating build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_tlz.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_doctests.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_curried.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_signatures.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/dev_skip_test.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_curried_toolzlike.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_functoolz.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_recipes.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_inspect_args.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_dicttoolz.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_dev_skip_test.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_embedded_sigs.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_compatibility.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_utils.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_none_safe.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_serialization.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_itertoolz.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
copying cytoolz/tests/test_docstrings.py -> build/lib.linux-x86_64-3.6/cytoolz/tests
running build_ext
building 'cytoolz.dicttoolz' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/cytoolz
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.6m -c cytoolz/dicttoolz.c -o build/temp.linux-x86_64-3.6/cytoolz/dicttoolz.o
cytoolz/dicttoolz.c:17:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-j__tim18/cytoolz/setup.py'"'"'; __file__='"'"'/tmp/pip-install-j__tim18/cytoolz/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-1xzorhvi/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/ajay/.local/include/python3.6m/cytoolz Check the logs for full command output.
Why is that and how can I fix it?
Just rerun after:
sudo apt-get install python3-dev
fatal error: Python.h: No such file or directory
So I'm trying to install lxml on my machine, and I can't seem to get it to work.
I've got Windows 8.1 64-bit and python 3.5
I've used both
pip install lxml
and
easy_install lxml
I keep getting this error message:
C:\Users\jgarber\Downloads>pip install readability-lxml --upgrade Requirement already up-to-date: readability-lxml in c:\python\lib\site-packages\ readability_lxml-0.6.2-py3.5.egg Requirement already up-to-date: chardet in c:\python\lib\site-packages (from rea dability-lxml) Collecting lxml (from readability-lxml) Using cached lxml-3.6.4.tar.gz Requirement already up-to-date: cssselect in c:\python\lib\site-packages\csssele ct-1.0.0-py3.5.egg (from readability-lxml) Installing collected packages: lxml Running setup.py install for lxml ... error
Complete output from command c:\python\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\jgarber\\AppData\\Local\\Temp\\pip-build-bypbiu8j\ \lxml\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().r eplace('\r\n', '\n'), __file__, 'exec'))" install --record C:\Users\jgarber\AppD ata\Local\Temp\pip-j8svsde4-record\install-record.txt
--single-version-externall y-managed --compile:
Building lxml version 3.6.4.
Building without Cython.
ERROR: b"'xslt-config' is not recognized as an internal or external command, \r\noperable program or batch file.\r\n"
** make sure the development packages of libxml2 and libxslt are installed *
*
Using build configuration of libxslt
running install
running build
running build_py
creating build
creating build\lib.win32-3.5
creating build\lib.win32-3.5\lxml
copying src\lxml\builder.py -> build\lib.win32-3.5\lxml
copying src\lxml\cssselect.py -> build\lib.win32-3.5\lxml
copying src\lxml\doctestcompare.py -> build\lib.win32-3.5\lxml
copying src\lxml\ElementInclude.py -> build\lib.win32-3.5\lxml
copying src\lxml\pyclasslookup.py -> build\lib.win32-3.5\lxml
copying src\lxml\sax.py -> build\lib.win32-3.5\lxml
copying src\lxml\usedoctest.py -> build\lib.win32-3.5\lxml
copying src\lxml\_elementpath.py -> build\lib.win32-3.5\lxml
copying src\lxml\__init__.py -> build\lib.win32-3.5\lxml
creating build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\__init__.py -> build\lib.win32-3.5\lxml\includes
creating build\lib.win32-3.5\lxml\html
copying src\lxml\html\builder.py -> build\lib.win32-3.5\lxml\html
copying src\lxml\html\clean.py -> build\lib.win32-3.5\lxml\html
copying src\lxml\html\defs.py -> build\lib.win32-3.5\lxml\html
copying src\lxml\html\diff.py -> build\lib.win32-3.5\lxml\html
copying src\lxml\html\ElementSoup.py -> build\lib.win32-3.5\lxml\html
copying src\lxml\html\formfill.py -> build\lib.win32-3.5\lxml\html
copying src\lxml\html\html5parser.py -> build\lib.win32-3.5\lxml\html
copying src\lxml\html\soupparser.py -> build\lib.win32-3.5\lxml\html
copying src\lxml\html\usedoctest.py -> build\lib.win32-3.5\lxml\html
copying src\lxml\html\_diffcommand.py -> build\lib.win32-3.5\lxml\html
copying src\lxml\html\_html5builder.py -> build\lib.win32-3.5\lxml\html
copying src\lxml\html\_setmixin.py -> build\lib.win32-3.5\lxml\html
copying src\lxml\html\__init__.py -> build\lib.win32-3.5\lxml\html
creating build\lib.win32-3.5\lxml\isoschematron
copying src\lxml\isoschematron\__init__.py -> build\lib.win32-3.5\lxml\isosc hematron
copying src\lxml\lxml.etree.h -> build\lib.win32-3.5\lxml
copying src\lxml\lxml.etree_api.h -> build\lib.win32-3.5\lxml
copying src\lxml\includes\c14n.pxd -> build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\config.pxd -> build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\dtdvalid.pxd -> build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\etreepublic.pxd -> build\lib.win32-3.5\lxml\includ es
copying src\lxml\includes\htmlparser.pxd -> build\lib.win32-3.5\lxml\include s
copying src\lxml\includes\relaxng.pxd -> build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\schematron.pxd -> build\lib.win32-3.5\lxml\include s
copying src\lxml\includes\tree.pxd -> build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\uri.pxd -> build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\xinclude.pxd -> build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\xmlerror.pxd -> build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\xmlparser.pxd -> build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\xmlschema.pxd -> build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\xpath.pxd -> build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\xslt.pxd -> build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\etree_defs.h -> build\lib.win32-3.5\lxml\includes
copying src\lxml\includes\lxml-version.h -> build\lib.win32-3.5\lxml\include s
creating build\lib.win32-3.5\lxml\isoschematron\resources
creating build\lib.win32-3.5\lxml\isoschematron\resources\rng
copying src\lxml\isoschematron\resources\rng\iso-schematron.rng -> build\lib .win32-3.5\lxml\isoschematron\resources\rng
creating build\lib.win32-3.5\lxml\isoschematron\resources\xsl
copying src\lxml\isoschematron\resources\xsl\RNG2Schtrn.xsl -> build\lib.win 32-3.5\lxml\isoschematron\resources\xsl
copying src\lxml\isoschematron\resources\xsl\XSD2Schtrn.xsl -> build\lib.win 32-3.5\lxml\isoschematron\resources\xsl
creating build\lib.win32-3.5\lxml\isoschematron\resources\xsl\iso-schematron
-xslt1
copying src\lxml\isoschematron\resources\xsl\iso-schematron-xslt1\iso_abstra ct_expand.xsl -> build\lib.win32-3.5\lxml\isoschematron\resources\xsl\iso-schema tron-xslt1
copying src\lxml\isoschematron\resources\xsl\iso-schematron-xslt1\iso_dsdl_i nclude.xsl -> build\lib.win32-3.5\lxml\isoschematron\resources\xsl\iso-schematro n-xslt1
copying src\lxml\isoschematron\resources\xsl\iso-schematron-xslt1\iso_schema tron_message.xsl -> build\lib.win32-3.5\lxml\isoschematron\resources\xsl\iso-sch ematron-xslt1
copying src\lxml\isoschematron\resources\xsl\iso-schematron-xslt1\iso_schema tron_skeleton_for_xslt1.xsl -> build\lib.win32-3.5\lxml\isoschematron\resources\ xsl\iso-schematron-xslt1
copying src\lxml\isoschematron\resources\xsl\iso-schematron-xslt1\iso_svrl_f or_xslt1.xsl -> build\lib.win32-3.5\lxml\isoschematron\resources\xsl\iso-schemat ron-xslt1
copying src\lxml\isoschematron\resources\xsl\iso-schematron-xslt1\readme.txt
-> build\lib.win32-3.5\lxml\isoschematron\resources\xsl\iso-schematron-xslt1
running build_ext
building 'lxml.etree' extension
creating build\temp.win32-3.5
creating build\temp.win32-3.5\Release
creating build\temp.win32-3.5\Release\src
creating build\temp.win32-3.5\Release\src\lxml
C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Isrc\lxml\includes
-Ic:\python\include -Ic:\python\in clude "-IC:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" "-IC:\P rogram Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt" "-IC:\Program File s (x86)\Windows Kits\8.1\include\shared" "-IC:\Program Files (x86)\Windows Kits\
8.1\include\um" "-IC:\Program Files (x86)\Windows Kits\8.1\include\winrt" /Tcsrc \lxml\lxml.etree.c /Fobuild\temp.win32-3.5\Release\src\lxml\lxml.etree.obj -w
cl : Command line warning D9025 : overriding '/W3' with '/w'
lxml.etree.c
src\lxml\includes\etree_defs.h(14): fatal error C1083: Cannot open include f ile: 'libxml/xmlversion.h': No such file or directory
Compile failed: command 'C:\\Program Files (x86)\\Microsoft Visual Studio 14 .0\\VC\\BIN\\cl.exe' failed with exit status 2
creating Users
creating Users\jgarber
creating Users\jgarber\AppData
creating Users\jgarber\AppData\Local
creating Users\jgarber\AppData\Local\Temp
C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -I/usr/include/libxml2 "-IC:\Program Files (x86)\Micro soft Visual Studio 14.0\VC\INCLUDE" "-IC:\Program Files (x86)\Windows Kits\10\in clude\10.0.10240.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\8.1\include\shar ed" "-IC:\Program Files (x86)\Windows Kits\8.1\include\um" "-IC:\Program Files ( x86)\Windows Kits\8.1\include\winrt" /TcC:\Users\jgarber\AppData\Local\Temp\xmlX PathInit_qrahzea.c /FoUsers\jgarber\AppData\Local\Temp\xmlXPathInit_qrahzea.obj
xmlXPathInit_qrahzea.c
C:\Users\jgarber\AppData\Local\Temp\xmlXPathInit_qrahzea.c(1): fatal error C 1083: Cannot open include file: 'libxml/xpath.h': No such file or directory
****************************************************************************
*****
Could not find function xmlCheckVersion in library libxml2. Is libxml2 insta lled?
****************************************************************************
*****
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio 14.0\\VC\\B IN\\cl.exe' failed with exit status 2
---------------------------------------- Command "c:\python\python.exe -u -c "import setuptools, tokenize;__file__='C:\\U sers\\jgarber\\AppData\\Local\\Temp\\pip-build-bypbiu8j\\lxml\\setup.py';exec(co mpile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __ file__, 'exec'))" install --record C:\Users\jgarber\AppData\Local\Temp\pip-j8svs de4-record\install-record.txt --single-version-externally-managed
--compile" fai led with error code 1 in C:\Users\jgarber\AppData\Local\Temp\pip-build-bypbiu8j\ lxml\
I have also tried downloading the .whl from http://www.lfd.uci.edu/~gohlke/pythonlibs/#lxml and attempted to manually install the wheel but receive this error message:
C:\Users\jgarber\Downloads>pip install lxml-3.6.4-cp35-cp35m-win_amd64.whl
lxml-3.6.4-cp35-cp35m-win_amd64.whl is not a supported wheel on this platform.
even with the python -m pip install statement.
At this point I'm not sure what I'm missing, any help would be greatly appreciated.
By default, Python will install as 32-bit on Windows, even on 64-bit systems. Therefore, to match this, you must select the wheel for 32-bit systems.
You can verify that your Python interpreter is 32-bit, because the REPL will look like this when starting:
Python 3.5.2 (v3.5.2:4def2a2901a5, Jun 25 2016, 22:01:18) [MSC v.1900 32 bit (Intel)] on win32
You should pick the lxml-3.6.4-cp35-cp35m-win32.whl package for Python 3.5 on Windows (unless you explicitly selected 64-bit when downloading Python) which should solve your issue.
They fixed this issue as of lxml version 4.2.5.
If you are still getting this issue, see if your requirements file specifies a specific version of lxml. If so, you should be able to fix the problem by updating the specified version to 4.2.5 or above.