Comments (3)
It turns out that this is only python 3.5. In version 3.6 everything works fine.
from pybigwig.
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.
from pybigwig.
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)
from pybigwig.
Related Issues (20)
- RuntimeError: Invalid interval bounds
- Document performance considerations? HOT 4
- Cannot add entries of value type int, but only float HOT 2
- support for osx-arm64 HOT 2
- numpy support broken in 0.3.18? HOT 1
- Create a BedGraph file using addEntries() throws segmentation fault HOT 2
- library import error HOT 4
- pyBigWig fails to find numpy installation when installing from PyPI HOT 5
- Writing a nan value should leave a gap HOT 7
- Can't enforce numpy features when pyBigWig is used as a dependency in downstream package HOT 5
- pip installation broken HOT 4
- Installing through pip not working HOT 9
- addHeader does not support multiple calls HOT 1
- Support for python >=3.11 HOT 1
- Issue Downloading pyBigWig HOT 1
- Simple patch to resolve conflict with roundup() macro
- Stats Sum Not Working as Expected
- 'zsh: segmentation fault ' HOT 1
- Out of memory listing entries on one human chromosome on a machine with 300 GB ram and 165 GB BigBed file HOT 1
- pyBigWig.entries() should return empty array, not None when no entries are found
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from pybigwig.