I am getting a problem installing shap in jupyter notebook, it is showing the following error, Running setup.py install for shap ... error. While shap is getting installed from the terminal without any problem. Please help. I am using : - pip install shap, also I am unable to use conda. Using pip install conda also shows the error of the same kind:- Building wheel for pycosat (setup.py) ... error, Running setup.py install for pycosat ... error.
The following is the error that I am facing while using pip install shap:-
Collecting shap
Using cached shap-0.35.0.tar.gz (273 kB)
Requirement already satisfied: numpy in /home/kv/snap/jupyter/common/lib/python3.7/site-packages (from shap) (1.18.2)
Requirement already satisfied: scipy in /home/kv/snap/jupyter/common/lib/python3.7/site-packages (from shap) (1.4.1)
Requirement already satisfied: scikit-learn in home/kv/snap/jupyter/common/lib/python3.7/site-packages (from shap) (0.22.2.post1)
Requirement already satisfied: pandas in /home/kv/snap/jupyter/common/lib/python3.7/site-packages (from shap) (1.0.3)
Requirement already satisfied: tqdm>4.25.0 in /home/kv/snap/jupyter/common/lib/python3.7/site-packages (from shap) (4.45.0)
Requirement already satisfied: joblib>=0.11 in /home/kv/snap/jupyter/common/lib/python3.7/site-packages (from scikit-learn->shap) (0.14.1)
Requirement already satisfied: python-dateutil>=2.6.1 in /snap/jupyter/6/lib/python3.7/site-packages (from pandas->shap) (2.8.0)
Requirement already satisfied: pytz>=2017.2 in /home/kv/snap/jupyter/common/lib/python3.7/site-packages (from pandas->shap) (2019.3)
Requirement already satisfied: six>=1.5 in /snap/jupyter/6/lib/python3.7/site-packages (from python-dateutil>=2.6.1->pandas->shap) (1.12.0)
Building wheels for collected packages: shap
Building wheel for shap (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /snap/jupyter/6/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-vla3cytp/shap/setup.py'"'"'; file='"'"'/tmp/pip-install-vla3cytp/shap/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-1shy2q7c
cwd: /tmp/pip-install-vla3cytp/shap/
Complete output (71 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/shap
copying shap/datasets.py -> build/lib.linux-x86_64-3.7/shap
copying shap/init.py -> build/lib.linux-x86_64-3.7/shap
copying shap/common.py -> build/lib.linux-x86_64-3.7/shap
creating build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/partition.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/tf_utils.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/explainer.py -> build/lib.linux-x86_64-3.7/shap/explainers copying shap/explainers/sampling.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/mimic.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/linear.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/pytree.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/permutation.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/init.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/gradient.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/additive.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/kernel.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/tree.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/bruteforce.py -> build/lib.linux-x86_64-3.7/shap/explainers
creating build/lib.linux-x86_64-3.7/shap/explainers/other
copying shap/explainers/other/treegain.py -> build/lib.linux-x86_64-3.7/shap/explainers/other
copying shap/explainers/other/coefficent.py -> build/lib.linux-x86_64-3.7/shap/explainers/other
copying shap/explainers/other/lime.py -> build/lib.linux-x86_64-3.7/shap/explainers/other
copying shap/explainers/other/maple.py -> build/lib.linux-x86_64-3.7/shap/explainers/other
copying shap/explainers/other/init.py -> build/lib.linux-x86_64-3.7/shap/explainers/other
copying shap/explainers/other/random.py -> build/lib.linux-x86_64-3.7/shap/explainers/other
creating build/lib.linux-x86_64-3.7/shap/explainers/deep
copying shap/explainers/deep/deep_tf.py -> build/lib.linux-x86_64-3.7/shap/explainers/deep
copying shap/explainers/deep/deep_pytorch.py -> build/lib.linux-x86_64- 3.7/shap/explainers/deep
copying shap/explainers/deep/init.py -> build/lib.linux-x86_64-3.7/shap/explainers/deep
creating build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/colorconv.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/colors.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/waterfall.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/monitoring.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/partial_dependence.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/force_matplotlib.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/embedding.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/text.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/summary.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/image.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/decision.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/init.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/dependence.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/bar.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/force.py -> build/lib.linux-x86_64-3.7/shap/plots
creating build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/models.py -> build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/methods.py -> build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/measures.py -> build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/plots.py -> build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/metrics.py -> build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/init.py -> build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/experiments.py -> build/lib.linux-x86_64-3.7/shap/benchmark
creating build/lib.linux-x86_64-3.7/shap/plots/resources
copying shap/plots/resources/logoSmallGray.png -> build/lib.linux-x86_64-3.7/shap/plots/resources
copying shap/plots/resources/bundle.js -> build/lib.linux-x86_64-3.7/shap/plots/resources
copying shap/tree_shap.h -> build/lib.linux-x86_64-3.7/shap
running build_ext
numpy.get_include() /home/kv/snap/jupyter/common/lib/python3.7/site-packages/numpy/core/include
building 'shap._cext' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/shap
gcc -pthread -B /home/filipe/miniconda3/envs/JUPYTER/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/snap/jupyter/6/include/python3.7m -I/home/kv/snap/jupyter/common/lib/python3.7/site-packages/numpy/core/include -c shap/_cext.cc -o build/temp.linux-x86_64-3.7/shap/_cext.o
unable to execute 'gcc': No such file or directory
error: command 'gcc' failed with exit status 1
ERROR: Failed building wheel for shap
Running setup.py clean for shap
Failed to build shap
Installing collected packages: shap
Running setup.py install for shap ... error
ERROR: Command errored out with exit status 1:
command: /snap/jupyter/6/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-vla3cytp/shap/setup.py'"'"'; __file__='"'"'/tmp/pip-install-vla3cytp/shap/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-tt70qus_/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/kv/snap/jupyter/common/include/python3.7m/shap
cwd: /tmp/pip-install-vla3cytp/shap/
Complete output (71 lines):
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/shap
copying shap/datasets.py -> build/lib.linux-x86_64-3.7/shap
copying shap/__init__.py -> build/lib.linux-x86_64-3.7/shap
copying shap/common.py -> build/lib.linux-x86_64-3.7/shap
creating build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/partition.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/tf_utils.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/explainer.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/sampling.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/mimic.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/linear.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/pytree.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/permutation.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/__init__.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/gradient.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/additive.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/kernel.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/tree.py -> build/lib.linux-x86_64-3.7/shap/explainers
copying shap/explainers/bruteforce.py -> build/lib.linux-x86_64-3.7/shap/explainers
creating build/lib.linux-x86_64-3.7/shap/explainers/other
copying shap/explainers/other/treegain.py -> build/lib.linux-x86_64-
3.7/shap/explainers/other
copying shap/explainers/other/coefficent.py -> build/lib.linux-x86_64-
3.7/shap/explainers/other
copying shap/explainers/other/lime.py -> build/lib.linux-x86_64-3.7/shap/explainers/other
copying shap/explainers/other/maple.py -> build/lib.linux-x86_64-3.7/shap/explainers/other
copying shap/explainers/other/__init__.py -> build/lib.linux-x86_64-
3.7/shap/explainers/other
copying shap/explainers/other/random.py -> build/lib.linux-x86_64-3.7/shap/explainers/other
creating build/lib.linux-x86_64-3.7/shap/explainers/deep
copying shap/explainers/deep/deep_tf.py -> build/lib.linux-x86_64-3.7/shap/explainers/deep
copying shap/explainers/deep/deep_pytorch.py -> build/lib.linux-x86_64-
3.7/shap/explainers/deep
copying shap/explainers/deep/__init__.py -> build/lib.linux-x86_64-3.7/shap/explainers/deep
creating build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/colorconv.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/colors.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/waterfall.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/monitoring.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/partial_dependence.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/force_matplotlib.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/embedding.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/text.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/summary.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/image.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/decision.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/__init__.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/dependence.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/bar.py -> build/lib.linux-x86_64-3.7/shap/plots
copying shap/plots/force.py -> build/lib.linux-x86_64-3.7/shap/plots
creating build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/models.py -> build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/methods.py -> build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/measures.py -> build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/plots.py -> build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/metrics.py -> build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/__init__.py -> build/lib.linux-x86_64-3.7/shap/benchmark
copying shap/benchmark/experiments.py -> build/lib.linux-x86_64-3.7/shap/benchmark
creating build/lib.linux-x86_64-3.7/shap/plots/resources
copying shap/plots/resources/logoSmallGray.png -> build/lib.linux-x86_64-3.7/shap/plots/resources
copying shap/plots/resources/bundle.js -> build/lib.linux-x86_64-3.7/shap/plots/resources
copying shap/tree_shap.h -> build/lib.linux-x86_64-3.7/shap
running build_ext
numpy.get_include() /home/kv/snap/jupyter/common/lib/python3.7/site-packages/numpy/core/include
building 'shap._cext' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/shap
gcc -pthread -B /home/filipe/miniconda3/envs/JUPYTER/compiler_compat -Wl,--sysroot=/ -Wsign-
compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/snap/jupyter/6/include/python3.7m -I/home/kv/snap/jupyter/common/lib/python3.7/site-packages/numpy/core/include -c shap/_cext.cc -o build/temp.linux-x86_64-3.7/shap/_cext.o
unable to execute 'gcc': No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /snap/jupyter/6/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-vla3cytp/shap/setup.py'"'"'; file='"'"'/tmp/pip-install-vla3cytp/shap/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-tt70qus_/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/kv/snap/jupyter/common/include/python3.7m/shap Check the logs for full command output.
Note: you may need to restart the kernel to use updated packages.
