Third party package scikit-bio will not install OS-X

[markesiddall]

What were you trying to do?

Add a third party package scikit-bio

What steps did you take to trigger the issue?

When adding scikit-bio to the third party packages, it fails when adding the hdmedians dependency.

What did you expect to happen?

No response

What actually happened?

---

ERROR: Failed building wheel for scikit-bio
Building wheel for hdmedians (PEP 517): started
Building wheel for hdmedians (PEP 517): finished with status 'error'
ERROR: Command errored out with exit status 1:
command: '/Users/leechman/Library/Application Support/mu/mu_venv-38-20210414-201211/bin/python' '/Users/leechman/Library/Application Support/mu/mu_venv-38-20210414-201211/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py' build_wheel /var/folders/qk/xrvbjk6x7hv3jgfv89qfl5h80000gq/T/tmppbmjmote
cwd: /private/var/folders/qk/xrvbjk6x7hv3jgfv89qfl5h80000gq/T/pip-install-xuu1ll3a/hdmedians_2057b0ac733a4a359714220f1ab3e979
Complete output (22 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-cpython-38
creating build/lib.macosx-10.9-x86_64-cpython-38/hdmedians
copying hdmedians/init.py -> build/lib.macosx-10.9-x86_64-cpython-38/hdmedians
copying hdmedians/medoid.py -> build/lib.macosx-10.9-x86_64-cpython-38/hdmedians
creating build/lib.macosx-10.9-x86_64-cpython-38/hdmedians/tests
copying hdmedians/tests/init.py -> build/lib.macosx-10.9-x86_64-cpython-38/hdmedians/tests
copying hdmedians/tests/test_geomedian.py -> build/lib.macosx-10.9-x86_64-cpython-38/hdmedians/tests
copying hdmedians/tests/test_medoid.py -> build/lib.macosx-10.9-x86_64-cpython-38/hdmedians/tests
running build_ext
cythoning hdmedians/geomedian.pyx to hdmedians/geomedian.c
/private/var/folders/qk/xrvbjk6x7hv3jgfv89qfl5h80000gq/T/pip-build-env-2hvtwufc/overlay/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /private/var/folders/qk/xrvbjk6x7hv3jgfv89qfl5h80000gq/T/pip-install-xuu1ll3a/hdmedians_2057b0ac733a4a359714220f1ab3e979/hdmedians/geomedian.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
building 'hdmedians.geomedian' extension
creating build/temp.macosx-10.9-x86_64-cpython-38
creating build/temp.macosx-10.9-x86_64-cpython-38/hdmedians
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wno-nullability-completeness -Wno-expansion-to-defined -fPIC -I/var/folders/dd/xb3jz0tj133_hgnvdttctwxc0000gn/T/tmpur2z_3yt/tools/deps/include -I/var/folders/dd/xb3jz0tj133_hgnvdttctwxc0000gn/T/tmpur2z_3yt/tools/deps/include/ncursesw -I/var/folders/dd/xb3jz0tj133_hgnvdttctwxc0000gn/T/tmpur2z_3yt/tools/deps/lib/libffi-3.2.1/include -I/var/folders/dd/xb3jz0tj133_hgnvdttctwxc0000gn/T/tmpur2z_3yt/tools/deps/include/uuid -F/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks -Werror=unguarded-availability-new -I/private/var/folders/qk/xrvbjk6x7hv3jgfv89qfl5h80000gq/T/pip-build-env-2hvtwufc/overlay/lib/python3.8/site-packages/numpy/core/include "-I/Users/leechman/Library/Application Support/mu/mu_venv-38-20210414-201211/include" "-I/Applications/Mu Editor.app/Contents/Resources/Python/include/python3.8" -c hdmedians/geomedian.c -o build/temp.macosx-10.9-x86_64-cpython-38/hdmedians/geomedian.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command '/usr/bin/clang' failed with exit code 1

ERROR: Failed building wheel for hdmedians
Failed to build scikit-bio hdmedians
ERROR: Could not build wheels for scikit-bio, hdmedians which use PEP 517 and cannot be installed directly

FINISHED

Operating System Version

OS-X 10.13.6

Mu Version

1.1.0 beta 3

Other Info

No response

Editor Log

---

ERROR: Failed building wheel for scikit-bio
Building wheel for hdmedians (PEP 517): started
Building wheel for hdmedians (PEP 517): finished with status 'error'
ERROR: Command errored out with exit status 1:
command: '/Users/leechman/Library/Application Support/mu/mu_venv-38-20210414-201211/bin/python' '/Users/leechman/Library/Application Support/mu/mu_venv-38-20210414-201211/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py' build_wheel /var/folders/qk/xrvbjk6x7hv3jgfv89qfl5h80000gq/T/tmppbmjmote
cwd: /private/var/folders/qk/xrvbjk6x7hv3jgfv89qfl5h80000gq/T/pip-install-xuu1ll3a/hdmedians_2057b0ac733a4a359714220f1ab3e979
Complete output (22 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-cpython-38
creating build/lib.macosx-10.9-x86_64-cpython-38/hdmedians
copying hdmedians/init.py -> build/lib.macosx-10.9-x86_64-cpython-38/hdmedians
copying hdmedians/medoid.py -> build/lib.macosx-10.9-x86_64-cpython-38/hdmedians
creating build/lib.macosx-10.9-x86_64-cpython-38/hdmedians/tests
copying hdmedians/tests/init.py -> build/lib.macosx-10.9-x86_64-cpython-38/hdmedians/tests
copying hdmedians/tests/test_geomedian.py -> build/lib.macosx-10.9-x86_64-cpython-38/hdmedians/tests
copying hdmedians/tests/test_medoid.py -> build/lib.macosx-10.9-x86_64-cpython-38/hdmedians/tests
running build_ext
cythoning hdmedians/geomedian.pyx to hdmedians/geomedian.c
/private/var/folders/qk/xrvbjk6x7hv3jgfv89qfl5h80000gq/T/pip-build-env-2hvtwufc/overlay/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /private/var/folders/qk/xrvbjk6x7hv3jgfv89qfl5h80000gq/T/pip-install-xuu1ll3a/hdmedians_2057b0ac733a4a359714220f1ab3e979/hdmedians/geomedian.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
building 'hdmedians.geomedian' extension
creating build/temp.macosx-10.9-x86_64-cpython-38
creating build/temp.macosx-10.9-x86_64-cpython-38/hdmedians
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wno-nullability-completeness -Wno-expansion-to-defined -fPIC -I/var/folders/dd/xb3jz0tj133_hgnvdttctwxc0000gn/T/tmpur2z_3yt/tools/deps/include -I/var/folders/dd/xb3jz0tj133_hgnvdttctwxc0000gn/T/tmpur2z_3yt/tools/deps/include/ncursesw -I/var/folders/dd/xb3jz0tj133_hgnvdttctwxc0000gn/T/tmpur2z_3yt/tools/deps/lib/libffi-3.2.1/include -I/var/folders/dd/xb3jz0tj133_hgnvdttctwxc0000gn/T/tmpur2z_3yt/tools/deps/include/uuid -F/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks -Werror=unguarded-availability-new -I/private/var/folders/qk/xrvbjk6x7hv3jgfv89qfl5h80000gq/T/pip-build-env-2hvtwufc/overlay/lib/python3.8/site-packages/numpy/core/include "-I/Users/leechman/Library/Application Support/mu/mu_venv-38-20210414-201211/include" "-I/Applications/Mu Editor.app/Contents/Resources/Python/include/python3.8" -c hdmedians/geomedian.c -o build/temp.macosx-10.9-x86_64-cpython-38/hdmedians/geomedian.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command '/usr/bin/clang' failed with exit code 1

ERROR: Failed building wheel for hdmedians
Failed to build scikit-bio hdmedians
ERROR: Could not build wheels for scikit-bio, hdmedians which use PEP 517 and cannot be installed directly

FINISHED