title: Error installing SHAP package in virtual environment pycharm MAC
body: <p>I am working on a project in pycharm which is in a virtual environment on Mac OS. I have been trying to install the SHAP package unfortunately it is not working out. Below is the full error message. There seems to be a problem with an SDK that does not seem to exist, but when I install the package outside of the virtual environment I do not encounter any problem.</p>
  <pre><code>Collecting shap
    Using cached shap-0.35.0.tar.gz (273 kB)
  Requirement already satisfied: numpy in /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/lib/python3.7/site-packages (from shap) (1.19.0)
  Requirement already satisfied: scipy in /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/lib/python3.7/site-packages (from shap) (1.5.1)
  Requirement already satisfied: scikit-learn in /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/lib/python3.7/site-packages (from shap) (0.23.1)
  Requirement already satisfied: pandas in /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/lib/python3.7/site-packages (from shap) (1.0.5)
  Requirement already satisfied: tqdm&gt;4.25.0 in /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/lib/python3.7/site-packages (from shap) (4.48.0)
  Requirement already satisfied: joblib&gt;=0.11 in /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/lib/python3.7/site-packages (from scikit-learn-&gt;shap) (0.16.0)
  Requirement already satisfied: threadpoolctl&gt;=2.0.0 in /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/lib/python3.7/site-packages (from scikit-learn-&gt;shap) (2.1.0)
  Requirement already satisfied: python-dateutil&gt;=2.6.1 in /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/lib/python3.7/site-packages (from pandas-&gt;shap) (2.8.1)
  Requirement already satisfied: pytz&gt;=2017.2 in /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/lib/python3.7/site-packages (from pandas-&gt;shap) (2020.1)
  Requirement already satisfied: six&gt;=1.5 in /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/lib/python3.7/site-packages (from python-dateutil&gt;=2.6.1-&gt;pandas-&gt;shap) (1.15.0)
  Using legacy setup.py install for shap, since package 'wheel' is not installed.
  Installing collected packages: shap
      Running setup.py install for shap: started
      Running setup.py install for shap: finished with status 'error'
  
      ERROR: Command errored out with exit status 1:
       command: /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '&quot;'&quot;'/private/var/folders/gk/rzy7hgz11nxcx5y0bjgsndx40000gn/T/pycharm-packaging/shap/setup.py'&quot;'&quot;'; __file__='&quot;'&quot;'/private/var/folders/gk/rzy7hgz11nxcx5y0bjgsndx40000gn/T/pycharm-packaging/shap/setup.py'&quot;'&quot;';f=getattr(tokenize, '&quot;'&quot;'open'&quot;'&quot;', open)(__file__);code=f.read().replace('&quot;'&quot;'\r\n'&quot;'&quot;', '&quot;'&quot;'\n'&quot;'&quot;');f.close();exec(compile(code, __file__, '&quot;'&quot;'exec'&quot;'&quot;'))' install --record /private/var/folders/gk/rzy7hgz11nxcx5y0bjgsndx40000gn/T/pip-record-92beasur/install-record.txt --single-version-externally-managed --compile --install-headers /Users/geilerloui/Documents/GitHub/churn_dashboard/venv/include/site/python3.7/shap
           cwd: /private/var/folders/gk/rzy7hgz11nxcx5y0bjgsndx40000gn/T/pycharm-packaging/shap/
      Complete output (83 lines):
      /usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long_description_content_type'
        warnings.warn(msg)
      running install
      running build
      running build_py
      creating build
      creating build/lib.macosx-10.14-x86_64-3.7
      creating build/lib.macosx-10.14-x86_64-3.7/shap
      copying shap/datasets.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap
      copying shap/__init__.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap
      copying shap/common.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap
      creating build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/tree.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/partition.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/kernel.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/explainer.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/bruteforce.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/gradient.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/linear.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/__init__.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/mimic.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/permutation.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/sampling.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/additive.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/tf_utils.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      copying shap/explainers/pytree.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers
      creating build/lib.macosx-10.14-x86_64-3.7/shap/explainers/other
      copying shap/explainers/other/coefficent.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers/other
      copying shap/explainers/other/maple.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers/other
      copying shap/explainers/other/lime.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers/other
      copying shap/explainers/other/__init__.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers/other
      copying shap/explainers/other/random.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers/other
      copying shap/explainers/other/treegain.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers/other
      creating build/lib.macosx-10.14-x86_64-3.7/shap/explainers/deep
      copying shap/explainers/deep/__init__.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers/deep
      copying shap/explainers/deep/deep_pytorch.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers/deep
      copying shap/explainers/deep/deep_tf.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/explainers/deep
      creating build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/force_matplotlib.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/force.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/embedding.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/monitoring.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/colorconv.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/__init__.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/decision.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/waterfall.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/summary.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/text.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/dependence.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/bar.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/image.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/partial_dependence.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      copying shap/plots/colors.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots
      creating build/lib.macosx-10.14-x86_64-3.7/shap/benchmark
      copying shap/benchmark/metrics.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/benchmark
      copying shap/benchmark/models.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/benchmark
      copying shap/benchmark/methods.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/benchmark
      copying shap/benchmark/__init__.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/benchmark
      copying shap/benchmark/measures.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/benchmark
      copying shap/benchmark/plots.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/benchmark
      copying shap/benchmark/experiments.py -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/benchmark
      creating build/lib.macosx-10.14-x86_64-3.7/shap/plots/resources
      copying shap/plots/resources/bundle.js -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots/resources
      copying shap/plots/resources/logoSmallGray.png -&gt; build/lib.macosx-10.14-x86_64-3.7/shap/plots/resources
      copying shap/tree_shap.h -&gt; build/lib.macosx-10.14-x86_64-3.7/shap
      warning: build_py: byte-compiling is disabled, skipping.
      
      running build_ext
      numpy.get_include() /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/lib/python3.7/site-packages/numpy/core/include
      building 'shap._cext' extension
      creating build/temp.macosx-10.14-x86_64-3.7
      creating build/temp.macosx-10.14-x86_64-3.7/shap
      Compiling with an SDK that doesn't seem to exist: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
      Please check your Xcode installation
      x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -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 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/include -I/usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/lib/python3.7/site-packages/numpy/core/include -c shap/_cext.cc -o build/temp.macosx-10.14-x86_64-3.7/shap/_cext.o
      clang-4.0: warning: no such sysroot directory: '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk' [-Wmissing-sysroot]
      In file included from shap/_cext.cc:3:
      In file included from /usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/include/python3.7m/Python.h:25:
      /anaconda3/bin/../include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file not found
      #include_next &lt;stdio.h&gt;
                    ^~~~~~~~~
      1 error generated.
      error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1
      ----------------------------------------
  ERROR: Command errored out with exit status 1: /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '&quot;'&quot;'/private/var/folders/gk/rzy7hgz11nxcx5y0bjgsndx40000gn/T/pycharm-packaging/shap/setup.py'&quot;'&quot;'; __file__='&quot;'&quot;'/private/var/folders/gk/rzy7hgz11nxcx5y0bjgsndx40000gn/T/pycharm-packaging/shap/setup.py'&quot;'&quot;';f=getattr(tokenize, '&quot;'&quot;'open'&quot;'&quot;', open)(__file__);code=f.read().replace('&quot;'&quot;'\r\n'&quot;'&quot;', '&quot;'&quot;'\n'&quot;'&quot;');f.close();exec(compile(code, __file__, '&quot;'&quot;'exec'&quot;'&quot;'))' install --record /private/var/folders/gk/rzy7hgz11nxcx5y0bjgsndx40000gn/T/pip-record-92beasur/install-record.txt --single-version-externally-managed --compile --install-headers /Users/xxxxxx/Documents/GitHub/churn_dashboard/venv/include/site/python3.7/shap Check the logs for full command output.
  </code></pre>