Created
June 20, 2016 03:46
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Fixing 'ImportError: dlopen(/usr/local/lib/python2.7/site-packages/scipy/fftpack/_fftpack.so, 2): Library not loaded: /usr/local/opt/gcc/lib/gcc/5/libgfortran.3.dylib' with scipy installed via homebrew
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python /Users/admin/rf/gnuradio/gr-dtv/examples/atsc_ctrlport_monitor.py | |
python | |
import scipy | |
import scipy.fftpack | |
Traceback (most recent call last): | |
File "<stdin>", line 1, in <module> | |
File "/usr/local/lib/python2.7/site-packages/scipy/fftpack/__init__.py", line 95, in <module> | |
from .basic import * | |
File "/usr/local/lib/python2.7/site-packages/scipy/fftpack/basic.py", line 12, in <module> | |
from . import _fftpack | |
ImportError: dlopen(/usr/local/lib/python2.7/site-packages/scipy/fftpack/_fftpack.so, 2): Library not loaded: /usr/local/opt/gcc/lib/gcc/5/libgfortran.3.dylib | |
Referenced from: /usr/local/lib/python2.7/site-packages/scipy/fftpack/_fftpack.so | |
Reason: image not found | |
scipy installed from: brew install scipy | |
hint from https://github.com/Homebrew/homebrew-science/issues/3718 - caused by gcc 5 -> 6 | |
library is linking gcc/5, but we have gcc/6 | |
sudo install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libgfortran.3.dylib /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib /usr/local/lib/python2.7/site-packages/scipy/fftpack/_fftpack.so | |
sudo install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libquadmath.0.dylib /usr/local/opt/gcc/lib/gcc/6/libquadmath.0.dylib /usr/local/lib/python2.7/site-packages/scipy/fftpack/_fftpack.so | |
sudo install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libgfortran.3.dylib /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib /usr/local/lib/python2.7/site-packages/scipy/fftpack/convolve.so | |
sudo install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libquadmath.0.dylib /usr/local/opt/gcc/lib/gcc/6/libquadmath.0.dylib /usr/local/lib/python2.7/site-packages/scipy/fftpack/convolve.so | |
repeat for other libraries as needed, after fixing, should be able to load: | |
$ python | |
>>> import scipy | |
>>> import scipy.fftpack | |
and run: | |
$ python /Users/admin/rf/gnuradio/gr-dtv/examples/atsc_ctrlport_monitor.py | |
Traceback (most recent call last): | |
File "/Users/admin/rf/gnuradio/gr-dtv/examples/atsc_ctrlport_monitor.py", line 147, in <module> | |
host = sys.argv[1] | |
IndexError: list index out of range | |
sudo install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libgfortran.3.dylib /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib /usr/local/lib/python2.7/site-packages/scipy/special/_ufuncs.so
sudo install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libgfortran.3.dylib /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib /usr/local/lib/python2.7/site-packages/scipy/special/specfun.so
sudo install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libquadmath.0.dylib /usr/local/opt/gcc/lib/gcc/6/libquadmath.0.dylib /usr/local/lib/python2.7/site-packages/scipy/special/specfun.so
sudo install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libgfortran.3.dylib /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib /usr/local/lib/python2.7/site-packages/scipy/linalg/_fblas.so
sudo install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libquadmath.0.dylib /usr/local/opt/gcc/lib/gcc/6/libquadmath.0.dylib /usr/local/lib/python2.7/site-packages/scipy/linalg/_fblas.so
sudo install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libgfortran.3.dylib /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib /usr/local/lib/python2.7/site-packages/scipy/linalg/_flapack.so
sudo install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libquadmath.0.dylib /usr/local/opt/gcc/lib/gcc/6/libquadmath.0.dylib /usr/local/lib/python2.7/site-packages/scipy/linalg/_flapack.so
many more.. do all, based on https://github.com/Homebrew/homebrew-science/issues/3718#issuecomment-224997438
sudo -s
find /usr/local/lib/python2.7/site-packages/scipy -name '*.so' | xargs -L1 install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libquadmath.0.dylib /usr/local/opt/gcc/lib/gcc/6/libquadmath.0.dylib
find /usr/local/lib/python2.7/site-packages/scipy -name '*.so' | xargs -L1 install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libgfortran.3.dylib /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib
exit
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https://github.com/Homebrew/homebrew-science/issues/3718