I got the following error when I try to install openbabel. But I got
errros in pip3.
I also installed open-babel with brew. But it is based on python
installed from homebrew?
Could anybody let me know what is the correct way to install
openbabel? (BTW, I want to avoid using conda if possible.)
$ brew install open-babel
Warning: open-babel 3.0.0 is already installed and up-to-date
To reinstall 3.0.0, run `brew reinstall open-babel`
$ which pip3
/Library/Frameworks/Python.framework/Versions/3.7/bin/pip3
$ pip3 install -U openbabel
Collecting openbabel
Using cached openbabel-2.4.1.tar.gz (74 kB)
Building wheels for collected packages: openbabel
Building wheel for openbabel (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7
-u -c 'import sys, setuptools, tokenize; sys.argv[0] =
'"'"'/private/tmp/mktemp/pip-install-4bqaa5k4/openbabel/setup.py'"'"';
__file__='"'"'/private/tmp/mktemp/pip-install-4bqaa5k4/openbabel/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/tmp/mktemp/pip-wheel-1z83twec
cwd: /private/tmp/mktemp/pip-install-4bqaa5k4/openbabel/
Complete output (65 lines):
running bdist_wheel
running build
running build_ext
Warning: package openbabel-2.0 could not be found by pkg-config.
Guessing Open Babel location:
- include_dirs:
['/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m',
'/usr/local/include/openbabel-2.0']
- library_dirs: ['/usr/local/lib']
building '_openbabel' extension
swigging openbabel-python.i to openbabel-python_wrap.cpp
swig -python -c++ -small -O -templatereduce -naturalvar
-I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m
-I/usr/local/include/openbabel-2.0 -o openbabel-python_wrap.cpp
openbabel-python.i
openbabel-python.i:225: Error: Unable to find 'openbabel/babelconfig.h'
openbabel-python.i:227: Error: Unable to find 'openbabel/data.h'
openbabel-python.i:228: Error: Unable to find 'openbabel/rand.h'
openbabel-python.i:229: Error: Unable to find 'openbabel/obutil.h'
openbabel-python.i:230: Error: Unable to find 'openbabel/math/vector3.h'
openbabel-python.i:232: Error: Unable to find 'openbabel/math/matrix3x3.h'
openbabel-python.i:233: Error: Unable to find 'openbabel/math/transform3d.h'
openbabel-python.i:234: Error: Unable to find 'openbabel/math/spacegroup.h'
openbabel-python.i:238: Error: Unable to find 'openbabel/base.h'
openbabel-python.i:240: Error: Unable to find 'openbabel/generic.h'
openbabel-python.i:241: Error: Unable to find 'openbabel/griddata.h'
openbabel-python.i:243: Error: Unable to find 'openbabel/chains.h'
openbabel-python.i:244: Error: Unable to find 'openbabel/typer.h'
openbabel-python.i:252: Error: Unable to find 'openbabel/plugin.h'
openbabel-python.i:257: Error: Unable to find 'openbabel/oberror.h'
openbabel-python.i:258: Error: Unable to find 'openbabel/format.h'
openbabel-python.i:259: Error: Unable to find 'openbabel/obconversion.h'
openbabel-python.i:260: Error: Unable to find 'openbabel/residue.h'
openbabel-python.i:261: Error: Unable to find 'openbabel/internalcoord.h'
openbabel-python.i:262: Error: Unable to find 'openbabel/atom.h'
openbabel-python.i:263: Error: Unable to find 'openbabel/bond.h'
openbabel-python.i:264: Error: Unable to find 'openbabel/reaction.h'
openbabel-python.i:282: Error: Unable to find 'openbabel/mol.h'
openbabel-python.i:289: Error: Unable to find 'openbabel/ring.h'
openbabel-python.i:290: Error: Unable to find 'openbabel/parsmart.h'
openbabel-python.i:291: Error: Unable to find 'openbabel/alias.h'
openbabel-python.i:292: Error: Unable to find 'openbabel/atomclass.h'
openbabel-python.i:294: Error: Unable to find 'openbabel/fingerprint.h'
openbabel-python.i:296: Error: Unable to find 'openbabel/descriptor.h'
openbabel-python.i:301: Error: Unable to find 'openbabel/forcefield.h'
openbabel-python.i:303: Error: Unable to find 'openbabel/builder.h'
openbabel-python.i:304: Error: Unable to find 'openbabel/op.h'
openbabel-python.i:306: Error: Unable to find 'openbabel/chargemodel.h'
openbabel-python.i:309: Error: Unable to find 'openbabel/phmodel.h'
openbabel-python.i:310: Error: Unable to find 'openbabel/graphsym.h'
openbabel-python.i:311: Error: Unable to find 'openbabel/isomorphism.h'
openbabel-python.i:312: Error: Unable to find 'openbabel/query.h'
openbabel-python.i:313: Error: Unable to find 'openbabel/canon.h'
openbabel-python.i:315: Error: Unable to find 'openbabel/stereo/stereo.h'
openbabel-python.i:318: Error: Unable to find 'openbabel/bitvec.h'
openbabel-python.i:321: Error: Unable to find 'openbabel/rotor.h'
openbabel-python.i:323: Error: Unable to find 'openbabel/rotamer.h'
openbabel-python.i:324: Error: Unable to find 'openbabel/spectrophore.h'
openbabel-python.i:374: Error: Unable to find 'openbabel/obiter.h'
stereo.i:1: Error: Unable to find 'openbabel/stereo/tetranonplanar.h'
stereo.i:2: Error: Unable to find 'openbabel/stereo/tetraplanar.h'
stereo.i:3: Error: Unable to find 'openbabel/stereo/tetrahedral.h'
stereo.i:4: Error: Unable to find 'openbabel/stereo/cistrans.h'
stereo.i:5: Error: Unable to find 'openbabel/stereo/squareplanar.h'
stereo.i:6: Error: Unable to find 'openbabel/stereo/bindings.h'
Error: SWIG failed. Is Open Babel installed?
You may need to manually specify the location of Open Babel include
and library directories. For example:
python setup.py build_ext -I/usr/local/include/openbabel-2.0
-L/usr/local/lib
python setup.py install
----------------------------------------
ERROR: Failed building wheel for openbabel
Running setup.py clean for openbabel
Failed to build openbabel
Installing collected packages: openbabel
Running setup.py install for openbabel ... error
ERROR: Command errored out with exit status 1:
command: /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7
-u -c 'import sys, setuptools, tokenize; sys.argv[0] =
'"'"'/private/tmp/mktemp/pip-install-4bqaa5k4/openbabel/setup.py'"'"';
__file__='"'"'/private/tmp/mktemp/pip-install-4bqaa5k4/openbabel/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/tmp/mktemp/pip-record-jzp7g4i1/install-record.txt
--single-version-externally-managed --compile --install-headers
/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m/openbabel
cwd: /private/tmp/mktemp/pip-install-4bqaa5k4/openbabel/
Complete output (64 lines):
running install
running build_ext
Warning: package openbabel-2.0 could not be found by pkg-config.
Guessing Open Babel location:
- include_dirs:
['/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m',
'/usr/local/include/openbabel-2.0']
- library_dirs: ['/usr/local/lib']
building '_openbabel' extension
swigging openbabel-python.i to openbabel-python_wrap.cpp
swig -python -c++ -small -O -templatereduce -naturalvar
-I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m
-I/usr/local/include/openbabel-2.0 -o openbabel-python_wrap.cpp
openbabel-python.i
openbabel-python.i:225: Error: Unable to find 'openbabel/babelconfig.h'
openbabel-python.i:227: Error: Unable to find 'openbabel/data.h'
openbabel-python.i:228: Error: Unable to find 'openbabel/rand.h'
openbabel-python.i:229: Error: Unable to find 'openbabel/obutil.h'
openbabel-python.i:230: Error: Unable to find 'openbabel/math/vector3.h'
openbabel-python.i:232: Error: Unable to find 'openbabel/math/matrix3x3.h'
openbabel-python.i:233: Error: Unable to find 'openbabel/math/transform3d.h'
openbabel-python.i:234: Error: Unable to find 'openbabel/math/spacegroup.h'
openbabel-python.i:238: Error: Unable to find 'openbabel/base.h'
openbabel-python.i:240: Error: Unable to find 'openbabel/generic.h'
openbabel-python.i:241: Error: Unable to find 'openbabel/griddata.h'
openbabel-python.i:243: Error: Unable to find 'openbabel/chains.h'
openbabel-python.i:244: Error: Unable to find 'openbabel/typer.h'
openbabel-python.i:252: Error: Unable to find 'openbabel/plugin.h'
openbabel-python.i:257: Error: Unable to find 'openbabel/oberror.h'
openbabel-python.i:258: Error: Unable to find 'openbabel/format.h'
openbabel-python.i:259: Error: Unable to find 'openbabel/obconversion.h'
openbabel-python.i:260: Error: Unable to find 'openbabel/residue.h'
openbabel-python.i:261: Error: Unable to find 'openbabel/internalcoord.h'
openbabel-python.i:262: Error: Unable to find 'openbabel/atom.h'
openbabel-python.i:263: Error: Unable to find 'openbabel/bond.h'
openbabel-python.i:264: Error: Unable to find 'openbabel/reaction.h'
openbabel-python.i:282: Error: Unable to find 'openbabel/mol.h'
openbabel-python.i:289: Error: Unable to find 'openbabel/ring.h'
openbabel-python.i:290: Error: Unable to find 'openbabel/parsmart.h'
openbabel-python.i:291: Error: Unable to find 'openbabel/alias.h'
openbabel-python.i:292: Error: Unable to find 'openbabel/atomclass.h'
openbabel-python.i:294: Error: Unable to find 'openbabel/fingerprint.h'
openbabel-python.i:296: Error: Unable to find 'openbabel/descriptor.h'
openbabel-python.i:301: Error: Unable to find 'openbabel/forcefield.h'
openbabel-python.i:303: Error: Unable to find 'openbabel/builder.h'
openbabel-python.i:304: Error: Unable to find 'openbabel/op.h'
openbabel-python.i:306: Error: Unable to find 'openbabel/chargemodel.h'
openbabel-python.i:309: Error: Unable to find 'openbabel/phmodel.h'
openbabel-python.i:310: Error: Unable to find 'openbabel/graphsym.h'
openbabel-python.i:311: Error: Unable to find 'openbabel/isomorphism.h'
openbabel-python.i:312: Error: Unable to find 'openbabel/query.h'
openbabel-python.i:313: Error: Unable to find 'openbabel/canon.h'
openbabel-python.i:315: Error: Unable to find 'openbabel/stereo/stereo.h'
openbabel-python.i:318: Error: Unable to find 'openbabel/bitvec.h'
openbabel-python.i:321: Error: Unable to find 'openbabel/rotor.h'
openbabel-python.i:323: Error: Unable to find 'openbabel/rotamer.h'
openbabel-python.i:324: Error: Unable to find 'openbabel/spectrophore.h'
openbabel-python.i:374: Error: Unable to find 'openbabel/obiter.h'
stereo.i:1: Error: Unable to find 'openbabel/stereo/tetranonplanar.h'
stereo.i:2: Error: Unable to find 'openbabel/stereo/tetraplanar.h'
stereo.i:3: Error: Unable to find 'openbabel/stereo/tetrahedral.h'
stereo.i:4: Error: Unable to find 'openbabel/stereo/cistrans.h'
stereo.i:5: Error: Unable to find 'openbabel/stereo/squareplanar.h'
stereo.i:6: Error: Unable to find 'openbabel/stereo/bindings.h'
Error: SWIG failed. Is Open Babel installed?
You may need to manually specify the location of Open Babel
include and library directories. For example:
python setup.py build_ext -I/usr/local/include/openbabel-2.0
-L/usr/local/lib
python setup.py install
----------------------------------------
ERROR: Command errored out with exit status 1:
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7 -u -c
'import sys, setuptools, tokenize; sys.argv[0] =
'"'"'/private/tmp/mktemp/pip-install-4bqaa5k4/openbabel/setup.py'"'"';
__file__='"'"'/private/tmp/mktemp/pip-install-4bqaa5k4/openbabel/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/tmp/mktemp/pip-record-jzp7g4i1/install-record.txt
--single-version-externally-managed --compile --install-headers
/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m/openbabel
Check the logs for full command output.
--
Regards,
Peng
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