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ImportError: undefined symbol: PyUnicodeUCS2_FromStringAndSize #66

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prullens opened this issue Jul 9, 2020 · 1 comment
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ImportError: undefined symbol: PyUnicodeUCS2_FromStringAndSize #66

prullens opened this issue Jul 9, 2020 · 1 comment

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@prullens
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prullens commented Jul 9, 2020

I am trying to >>> import bx.intervals in python 2.7.5 which I have installed on a computing clusters. Only >>> import bx runs without any trouble, but >>> import bx.intervals gives me the following error:
ImportError: /usr/bin/venv/python2.7/site-packages/bx/intervals/intersection.so: undefined symbol: PyUnicodeUCS2_FromStringAndSize

This Stack thread says I have to recompile python: https://stackoverflow.com/questions/2584198/undefined-symbol-pyunicodeucs2-decode-whilst-trying-to-install-psycopg2/2584554#2584554. I tried that, but without any luck!

@prullens
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prullens commented Jul 9, 2020

The issue was solved! Apparently bx-python was built against a python version that was compiled with ucs2. So to fully enable bx utilities I had to recompile the python version I was using from ucs4 to ucs2. I achieved this through: https://stackoverflow.com/questions/2584198/undefined-symbol-pyunicodeucs2-decode-whilst-trying-to-install-psycopg2/62811981#62811981

@prullens prullens closed this as completed Jul 9, 2020
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