Comments (3)
dpryan79
commented on June 10, 2024
It turns out that this is only python 3.5. In version 3.6 everything works fine.
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dpryan79
commented on June 10, 2024
And only the python 3.5.4 in the default channel. The one from conda-forge works correctly. Presumably they're binary incompatible in some edge-case.
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dpryan79
commented on June 10, 2024
For future reference, the backtrace is as follows:
#0 0x00000001012808ef in PyUnicode_InternInPlace () from /Users/ryan/miniconda/lib/libpython3.5m.dylib
#1 0x000000010129066a in PyUnicode_InternFromString () from /Users/ryan/miniconda/lib/libpython3.5m.dylib
#2 0x000000010124b515 in PyType_Ready () from /Users/ryan/miniconda/lib/libpython3.5m.dylib
#3 0x000000010124b45a in PyType_Ready () from /Users/ryan/miniconda/lib/libpython3.5m.dylib
#4 0x000000010111f6d9 in PyInit_pyBigWig () from /Users/ryan/miniconda/lib/python3.5/site-packages/pyBigWig.cpython-35m-darwin.so
#5 0x000000010017f839 in _PyImport_LoadDynamicModuleWithSpec ()
#6 0x000000010017ee7c in _imp_create_dynamic ()
#7 0x000000010008777e in PyCFunction_Call ()
#8 0x000000010015056b in PyEval_EvalFrameEx ()
#9 0x00000001001495df in _PyEval_EvalCodeWithName ()
#10 0x000000010014f86b in PyEval_EvalFrameEx ()
#11 0x000000010014f61e in PyEval_EvalFrameEx ()
#12 0x000000010014f61e in PyEval_EvalFrameEx ()
#13 0x000000010014f61e in PyEval_EvalFrameEx ()
#14 0x000000010014f61e in PyEval_EvalFrameEx ()
#15 0x00000001001495df in _PyEval_EvalCodeWithName ()
#16 0x000000010005488a in function_call ()
#17 0x0000000100013132 in _PyObject_CallMethodIdObjArgs ()
#18 0x00000001001798d5 in PyImport_ImportModuleLevelObject ()
#19 0x00000001001425f5 in builtin___import__ ()
#20 0x00000001000877bf in PyCFunction_Call ()
#21 0x0000000100010d65 in PyObject_Call ()
#22 0x000000010015236a in PyEval_EvalFrameEx ()
#23 0x00000001001495df in _PyEval_EvalCodeWithName ()
#24 0x000000010019e9a5 in PyRun_StringFlags ()
#25 0x000000010019e840 in PyRun_SimpleStringFlags ()
#26 0x00000001001c005f in Py_Main ()
#27 0x0000000100001ac1 in main ()
So something with python's PyUnicode_InternInPlace() function accessing an out of bound area. Further, valgrind reports the following:
==63061== Process terminating with default action of signal 11 (SIGSEGV)
==63061== Access not within mapped region at address 0x25
==63061== at 0x1023258EF: PyUnicode_InternInPlace (in /Users/ryan/miniconda/lib/libpython3.5m.dylib)
==63061== by 0x102335669: PyUnicode_InternFromString (in /Users/ryan/miniconda/lib/libpython3.5m.dylib)
==63061== by 0x1022F0514: PyType_Ready (in /Users/ryan/miniconda/lib/libpython3.5m.dylib)
==63061== by 0x1022F0459: PyType_Ready (in /Users/ryan/miniconda/lib/libpython3.5m.dylib)
==63061== by 0x1021C46D8: PyInit_pyBigWig (in /Users/ryan/miniconda/lib/python3.5/site-packages/pyBigWig.cpython-35m-darwin.so)
==63061== by 0x10017F838: _PyImport_LoadDynamicModuleWithSpec (in /Users/ryan/miniconda/bin/python)
==63061== by 0x10017EE7B: _imp_create_dynamic (in /Users/ryan/miniconda/bin/python)
==63061== by 0x10008777D: PyCFunction_Call (in /Users/ryan/miniconda/bin/python)
==63061== by 0x10015056A: PyEval_EvalFrameEx (in /Users/ryan/miniconda/bin/python)
==63061== by 0x1001495DE: _PyEval_EvalCodeWithName (in /Users/ryan/miniconda/bin/python)
==63061== by 0x10014F86A: PyEval_EvalFrameEx (in /Users/ryan/miniconda/bin/python)
==63061== by 0x10014F61D: PyEval_EvalFrameEx (in /Users/ryan/miniconda/bin/python)
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