pip install pyBigWig does not work on latest version of Anaconda (5.3, Python 3.7 version)

[daquang]

I am running on Mac OS X Mojave. Here's the error I get:

Collecting pyBigWig
Using cached https://files.pythonhosted.org/packages/d5/0d/8e2a1edb9524790c6a4d0b70bc800a8e4afee1bc7bdd048c54b8d9cf1c32/pyBigWig-0.3.12.tar.gz
Building wheels for collected packages: pyBigWig
Running setup.py bdist_wheel for pyBigWig ... error
Complete output from command /Users/daquang/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-install-yv7gipao/pyBigWig/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/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-wheel-hr537bj0 --python-tag cp37:
/Users/daquang/anaconda3/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'classifier'
warnings.warn(msg)
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.7
creating build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
copying pyBigWigTest/init.py -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
copying pyBigWigTest/test.py -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
running egg_info
writing pyBigWig.egg-info/PKG-INFO
writing dependency_links to pyBigWig.egg-info/dependency_links.txt
writing requirements to pyBigWig.egg-info/requires.txt
writing top-level names to pyBigWig.egg-info/top_level.txt
reading manifest file 'pyBigWig.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
copying pyBigWigTest/test.bigBed -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
copying pyBigWigTest/test.bw -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
running build_ext
building 'pyBigWig' extension
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/daquang/anaconda3/include -arch x86_64 -I/Users/daquang/anaconda3/include -arch x86_64

creating build/temp.macosx-10.7-x86_64-3.7
creating build/temp.macosx-10.7-x86_64-3.7/libBigWig
compile options: '-DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/Users/daquang/anaconda3/include/python3.7m -I/Users/daquang/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/Users/daquang/anaconda3/include/python3.7m -c'
gcc: libBigWig/bwRead.c
gcc: libBigWig/bwValues.cgcc: libBigWig/io.cgcc: libBigWig/bwStats.c
gcc: libBigWig/bwWrite.c
gcc: pyBigWig.c

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrunxcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: Command "gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/daquang/anaconda3/include -arch x86_64 -I/Users/daquang/anaconda3/include -arch x86_64 -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/Users/daquang/anaconda3/include/python3.7m -I/Users/daquang/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/Users/daquang/anaconda3/include/python3.7m -c libBigWig/io.c -o build/temp.macosx-10.7-x86_64-3.7/libBigWig/io.o" failed with exit status 1

---

Failed building wheel for pyBigWig
Running setup.py clean for pyBigWig
Failed to build pyBigWig
Installing collected packages: pyBigWig
Running setup.py install for pyBigWig ... error
Complete output from command /Users/daquang/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-install-yv7gipao/pyBigWig/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/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-record-w1z6lbxd/install-record.txt --single-version-externally-managed --compile:
/Users/daquang/anaconda3/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'classifier'
warnings.warn(msg)
running install
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.7
creating build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
copying pyBigWigTest/init.py -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
copying pyBigWigTest/test.py -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
running egg_info
writing pyBigWig.egg-info/PKG-INFO
writing dependency_links to pyBigWig.egg-info/dependency_links.txt
writing requirements to pyBigWig.egg-info/requires.txt
writing top-level names to pyBigWig.egg-info/top_level.txt
reading manifest file 'pyBigWig.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
copying pyBigWigTest/test.bigBed -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
copying pyBigWigTest/test.bw -> build/lib.macosx-10.7-x86_64-3.7/pyBigWigTest
running build_ext
building 'pyBigWig' extension
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/daquang/anaconda3/include -arch x86_64 -I/Users/daquang/anaconda3/include -arch x86_64

creating build/temp.macosx-10.7-x86_64-3.7
creating build/temp.macosx-10.7-x86_64-3.7/libBigWig
compile options: '-DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/Users/daquang/anaconda3/include/python3.7m -I/Users/daquang/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/Users/daquang/anaconda3/include/python3.7m -c'
gcc: libBigWig/bwRead.c
gcc: libBigWig/bwStats.cgcc: libBigWig/io.c
gcc: libBigWig/bwValues.c
gcc: libBigWig/bwWrite.c

gcc: pyBigWig.c
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrunxcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: Command "gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/daquang/anaconda3/include -arch x86_64 -I/Users/daquang/anaconda3/include -arch x86_64 -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/Users/daquang/anaconda3/include/python3.7m -I/Users/daquang/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/Users/daquang/anaconda3/include/python3.7m -c libBigWig/bwWrite.c -o build/temp.macosx-10.7-x86_64-3.7/libBigWig/bwWrite.o" failed with exit status 1

----------------------------------------

Command "/Users/daquang/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-install-yv7gipao/pyBigWig/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/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-record-w1z6lbxd/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/37/kbrfsr294cl4wq86whp5vn4h0000gn/T/pip-install-yv7gipao/pyBigWig/

[dpryan79]

You appear to have some random issue with your build environment that falls outside the purview of pyBigWig. Since you're already using conda, simply conda install -c conda-forge -c bioconda pybigwig.

[daquang]

good catch! When I upgraded to Mojave, it uninstalled Xcode. I'll reinstall it and tell you what happens.

[daquang]

It works now! Thanks!

[dpryan79]

Thanks for the quick follow-up!