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macOS Catalina - error: command 'gcc' failed with exit status 1

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I'm trying to pip install gdal and struggling. Have spent hours trawling through SO, Guthub and other posts to try and resolve this one but nothing I've tried works. I've tried:

  • xcode-select --install
  • brew doctor maintenance
  • adding to .bash_profile, e.g

    • export CPATH=/Library/Developer/CommandLineTools/usr/include/c++/v1
    • export CPATH=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include
    • export CPATH=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/

And various other things. I cannot escape this error.

$ pip install gdal... [4,382 lines] ...    /usr/local/include/pthread.h:540:6: warning: macro expansion producing 'defined' has undefined behavior [-Wexpansion-to-defined]    /usr/local/include/pthread.h:200:34: note: expanded from macro '_PTHREAD_SWIFT_IMPORTER_NULLABILITY_COMPAT'            defined(SWIFT_CLASS_EXTRA) && (!defined(SWIFT_SDK_OVERLAY_PTHREAD_EPOCH) || (SWIFT_SDK_OVERLAY_PTHREAD_EPOCH < 1))                                            ^    extensions/gdal_wrap.cpp:3096:10: fatal error: 'stdexcept' file not found    #include <stdexcept>             ^~~~~~~~~~~    195 warnings and 1 error generated.    error: command 'gcc' failed with exit status 1    ----------------------------------------ERROR: Command errored out with exit status 1: /Users/username/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_3/b8whcf8d1bb8w_lr2rrscb5m0000gp/T/pip-install-utjkt9xt/gdal/setup.py'"'"'; __file__='"'"'/private/var/folders/_3/b8whcf8d1bb8w_lr2rrscb5m0000gp/T/pip-install-utjkt9xt/gdal/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/_3/b8whcf8d1bb8w_lr2rrscb5m0000gp/T/pip-record-u1hcib4k/install-record.txt --single-version-externally-managed --compile --install-headers /Users/username/anaconda3/include/python3.7m/gdal Check the logs for full command output.

Full error log at https://gist.github.com/geotheory/44e66c17e61c80398ab56590c5634703

Has anyone with macOS Cataloina also running Anaconda and Homebrew got past this?


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