Dear Openbabel team,
Thank you for building such a useful tool for chemists.
I'm a first-year PhD student, trying to transform SMILES into Formula for
my research.
I was trying to install the package into python (jupyter notebook in
Anaconda). using the following code:
import sys
!{sys.executable} -m pip install openbabel
But error shows up. This might be a basic python issue. But as a beginner
in programming, I really don't know how to do it. I was silly enough to
copy the include and library directories into Anaconda route, still not
working.
It would be much appreciated if you could help me out.
Thank you very much.
Li
ERROR: Command errored out with exit status 1:
command: 'C:\Users\lenovo\anaconda3\python.exe' -u -c 'import sys,
setuptools, tokenize; sys.argv[0] =
'"'"'C:\\Users\\lenovo\\AppData\\Local\\Temp\\pip-install-kbjuf0jl\\openbabel\\setup.py'"'"';
__file__='"'"'C:\\Users\\lenovo\\AppData\\Local\\Temp\\pip-install-kbjuf0jl\\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 'C:\Users\lenovo\AppData\Local\Temp\pip-wheel-vyr067gr'
cwd: C:\Users\lenovo\AppData\Local\Temp\pip-install-kbjuf0jl\openbabel\
Complete output (15 lines):
running bdist_wheel
running build
running build_ext
Warning: invalid version number '3.1.1.1'.
Guessing Open Babel location:
- include_dirs: ['C:\\Users\\lenovo\\anaconda3\\include',
'C:\\Users\\lenovo\\anaconda3\\include',
'/usr/local/include/openbabel3']
- library_dirs: ['C:\\Users\\lenovo\\anaconda3\\libs',
'C:\\Users\\lenovo\\anaconda3\\PCbuild\\amd64', '/usr/local/lib']
building 'openbabel._openbabel' extension
swigging openbabel\openbabel-python.i to openbabel\openbabel-python_wrap.cpp
swig.exe -python -c++ -small -O -templatereduce -naturalvar
-IC:\Users\lenovo\anaconda3\include
-IC:\Users\lenovo\anaconda3\include -I/usr/local/include/openbabel3 -o
openbabel\openbabel-python_wrap.cpp openbabel\openbabel-python.i
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/openbabel3 -L/usr/local/lib
python setup.py install
----------------------------------------
ERROR: Failed building wheel for openbabel
ERROR: Command errored out with exit status 1:
command: 'C:\Users\lenovo\anaconda3\python.exe' -u -c 'import
sys, setuptools, tokenize; sys.argv[0] =
'"'"'C:\\Users\\lenovo\\AppData\\Local\\Temp\\pip-install-kbjuf0jl\\openbabel\\setup.py'"'"';
__file__='"'"'C:\\Users\\lenovo\\AppData\\Local\\Temp\\pip-install-kbjuf0jl\\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
'C:\Users\lenovo\AppData\Local\Temp\pip-record-laodsi4w\install-record.txt'
--single-version-externally-managed --compile --install-headers
'C:\Users\lenovo\anaconda3\Include\openbabel'
cwd: C:\Users\lenovo\AppData\Local\Temp\pip-install-kbjuf0jl\openbabel\
Complete output (14 lines):
running install
running build_ext
Warning: invalid version number '3.1.1.1'.
Guessing Open Babel location:
- include_dirs: ['C:\\Users\\lenovo\\anaconda3\\include',
'C:\\Users\\lenovo\\anaconda3\\include',
'/usr/local/include/openbabel3']
- library_dirs: ['C:\\Users\\lenovo\\anaconda3\\libs',
'C:\\Users\\lenovo\\anaconda3\\PCbuild\\amd64', '/usr/local/lib']
building 'openbabel._openbabel' extension
swigging openbabel\openbabel-python.i to openbabel\openbabel-python_wrap.cpp
swig.exe -python -c++ -small -O -templatereduce -naturalvar
-IC:\Users\lenovo\anaconda3\include
-IC:\Users\lenovo\anaconda3\include -I/usr/local/include/openbabel3 -o
openbabel\openbabel-python_wrap.cpp openbabel\openbabel-python.i
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/openbabel3 -L/usr/local/lib
python setup.py install
----------------------------------------
ERROR: Command errored out with exit status 1:
'C:\Users\lenovo\anaconda3\python.exe' -u -c 'import sys, setuptools,
tokenize; sys.argv[0] =
'"'"'C:\\Users\\lenovo\\AppData\\Local\\Temp\\pip-install-kbjuf0jl\\openbabel\\setup.py'"'"';
__file__='"'"'C:\\Users\\lenovo\\AppData\\Local\\Temp\\pip-install-kbjuf0jl\\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
'C:\Users\lenovo\AppData\Local\Temp\pip-record-laodsi4w\install-record.txt'
--single-version-externally-managed --compile --install-headers
'C:\Users\lenovo\anaconda3\Include\openbabel' Check the logs for full
command output.
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