Basically I'm trying to run some Python code from savReaderWriter module in order to create a .sav file ready to open in IBM SPSS. As a macOS user I needed to run these two lines in the terminal first for the module to work:
echo 'export DYLD_LIBRARY_PATH=/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/savReaderWriter/spssio/macos' >> ~/.bash_profile
echo 'export LC_ALL=en_US.UTF-8' >> ~/.bash_profile
Below you can see a piece of code I'm trying to run in Python:
import savReaderWriter
savFileName = "someFile.sav"
records = [['Test1', 1, 1], ['Test2', 2, 1]]
varNames = ['var1', 'v2', 'v3']
varTypes = {'var1': 5, 'v2': 0, 'v3': 0}
with savReaderWriter.SavWriter(savFileName, varNames, varTypes, ioUtf8=True) as writer:
for record in records:
writer.writerow(record)
My problem is that while running the code in Python through terminal.app works like a charm and a new .sav file appears, trying to execute the very same code in an IDE (tried PyCharm and Spyder) gives me an error:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2847, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-2-94007b092d47>", line 7, in <module>
with savReaderWriter.SavWriter(savFileName, varNames, varTypes, ioUtf8=True) as writer:
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/savReaderWriter/savWriter.py", line 198, in __init__
super(Header, self).__init__(savFileName, ioUtf8, ioLocale)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/savReaderWriter/generic.py", line 29, in __init__
self.spssio = self.loadLibrary()
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/savReaderWriter/generic.py", line 117, in loadLibrary
spssio = self._loadLibs("macos")
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/savReaderWriter/generic.py", line 89, in _loadLibs
return [load(os.path.join(path, lib)) for lib in libs][-1]
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/savReaderWriter/generic.py", line 89, in <listcomp>
return [load(os.path.join(path, lib)) for lib in libs][-1]
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ctypes/__init__.py", line 348, in __init__
self._handle = _dlopen(self._name, mode)
OSError: dlopen(/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/savReaderWriter/spssio/macos/libicuuc48.1.dylib, 6): Library not loaded: @executable_path/../lib/libicudata48.1.dylib
Referenced from: /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/savReaderWriter/spssio/macos/libicuuc48.1.dylib
Reason: image not found
The module author was unable to help me on this matter, therefore I would be very glad for any suggestions from this community.
EDIT (added sys.path):
From terminal:
['',
'/Library/Frameworks/Python.framework/Versions/3.6/lib/python36.zip',
'/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6',
'/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/lib-dynload',
'/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages',
'/Users/mg/mne-python']
From IDE:
['/Applications/PyCharm.app/Contents/helpers/pydev',
'/Users/mg/Documents/Python/Projects/MD',
'/Applications/PyCharm.app/Contents/helpers/pydev',
'/Library/Frameworks/Python.framework/Versions/3.6/lib/python36.zip',
'/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6',
'/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/lib-dynload',
'/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages',
'/Users/mg/mne-python',
'/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/IPython/extensions',
'/Users/mg/Documents/Python/Projects/MD']
Regards,
MG
Found the solution!
Basically I needed to create symbolic links to every dylib that appeared in the error, examples below:
sudo ln -s /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/savReaderWriter/spssio/macos/libicudata48.1.dylib /usr/local/lib/libicudata48.1.dylib
sudo ln -s /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/savReaderWriter/spssio/macos/libicui18n48.1.dylib /usr/local/lib/libicui18n48.1.dylib
sudo ln -s /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/savReaderWriter/spssio/macos/libspssdio.dylib /usr/local/lib/libspssdio.dylib
sudo ln -s /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/savReaderWriter/spssio/macos/libzlib123spss.dylib /usr/local/lib/libzlib123spss.dylib
So theoretically speaking:
sudo ln -s /path/to/original /path/to/symbolic/link
Regards,
MG