“using PyMNE“ crashes Julia

nathanweisz · July 19, 2023, 6:55pm

Hi,

I work with M/EEG data and would like to check out some things in Julia. To load data etc I would need PyMNE:

“using PyMNE“ seems to install some Python packages however crashes Julia at some point. See message below. I would appreciate any pointers.

Thanks & best,
Nathan

Output

…
Linking seaborn-0.12.2-hd8ed1ab_0
Linking pyvista-0.40.1-pyhd8ed1ab_0
Linking pyvistaqt-0.11.0-pyhd8ed1ab_0
Linking mne-1.4.2-h694c41f_0
Transaction finished

[73205] signal (11.1): Segmentation fault: 11
in expression starting at REPL[6]:1
_ZN4llvm17PMTopLevelManager16addImmutablePassEPNS_13ImmutablePassE at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libLLVM-14.dylib (unknown line)
_ZN4llvm17PMTopLevelManager12schedulePassEPNS_4PassE at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libLLVM-14.dylib (unknown line)
_ZN4llvm17PMTopLevelManager12schedulePassEPNS_4PassE at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libLLVM-14.dylib (unknown line)
_ZN4llvm18PassManagerBuilder25populateModulePassManagerERNS_6legacy15PassManagerBaseE at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libLLVM-14.dylib (unknown line)
ffi_call_unix64 at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libffi.8.dylib (unknown line)
ffi_call_int at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libffi.8.dylib (unknown line)
_ctypes_callproc at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/python3.11/lib-dynload/_ctypes.cpython-311-darwin.so (unknown line)
PyCFuncPtr_call at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/python3.11/lib-dynload/_ctypes.cpython-311-darwin.so (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyFunction_Vectorcall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyObject_Call_Prepend at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
slot_tp_call at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyFunction_Vectorcall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyObject_Call_Prepend at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
slot_tp_init at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
type_call at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyFunction_Vectorcall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyFunction_Vectorcall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyObject_Call_Prepend at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
slot_tp_init at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
type_call at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyFunction_Vectorcall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyObject_VectorcallTstate.754 at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
object_vacall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyObject_CallFunctionObjArgs at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyObject_GenericGetAttr at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyFunction_Vectorcall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
property_descr_get at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyObject_GenericGetAttr at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyFunction_Vectorcall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyObject_Call_Prepend at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
slot_tp_init at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
type_call at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_Vector at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyEval_EvalCode at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
builtin_exec at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
cfunction_vectorcall_FASTCALL_KEYWORDS at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyFunction_Vectorcall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyObject_VectorcallTstate.754 at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
object_vacall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyObject_CallMethodObjArgs at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyImport_ImportModuleLevelObject at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_Vector at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyEval_EvalCode at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
builtin_exec at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
cfunction_vectorcall_FASTCALL_KEYWORDS at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyFunction_Vectorcall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyObject_VectorcallTstate.754 at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
object_vacall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyObject_CallMethodObjArgs at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyImport_ImportModuleLevelObject at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_Vector at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyEval_EvalCode at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
builtin_exec at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
cfunction_vectorcall_FASTCALL_KEYWORDS at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyFunction_Vectorcall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyObject_VectorcallTstate.754 at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
object_vacall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyObject_CallMethodObjArgs at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyImport_ImportModuleLevelObject at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_Vector at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyEval_EvalCode at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
builtin_exec at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
cfunction_vectorcall_FASTCALL_KEYWORDS at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyFunction_Vectorcall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyObject_VectorcallTstate.754 at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
object_vacall at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyObject_CallMethodObjArgs at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyImport_ImportModuleLevelObject at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
builtin___import at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
cfunction_vectorcall_FASTCALL_KEYWORDS at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyObject_CallFunction at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyImport_Import at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libpython3.11.dylib (unknown line)
PyImport_Import at /Users/b1019548/.julia/packages/PythonCall/1f5yE/src/cpython/pointers.jl:299 [inlined]
macro expansion at /Users/b1019548/.julia/packages/PythonCall/1f5yE/src/Py.jl:131 [inlined]
pyimport at /Users/b1019548/.julia/packages/PythonCall/1f5yE/src/concrete/import.jl:11
init at /Users/b1019548/.julia/packages/PyMNE/BTa7T/src/PyMNE.jl:20
jfptr___init___1142 at /Users/b1019548/.julia/compiled/v1.9/PyMNE/9TMkg_Y48UT.dylib (unknown line)
ijl_apply_generic at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
jl_module_run_initializer at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
ijl_init_restored_modules at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
register_restored_modules at ./loading.jl:1115
_include_from_serialized at ./loading.jl:1061
_require_search_from_serialized at ./loading.jl:1506
_require at ./loading.jl:1783
_require_prelocked at ./loading.jl:1660
macro expansion at ./loading.jl:1648 [inlined]
macro expansion at ./lock.jl:267 [inlined]
require at ./loading.jl:1611
jfptr_require_55342.clone_1 at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/sys.dylib (unknown line)
ijl_apply_generic at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
eval_import_path at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
jl_toplevel_eval_flex at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
jl_toplevel_eval_flex at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
ijl_toplevel_eval_in at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
eval at ./boot.jl:370 [inlined]
eval_user_input at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/REPL/src/REPL.jl:153
repl_backend_loop at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/REPL/src/REPL.jl:249
#start_repl_backend#46 at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/REPL/src/REPL.jl:234
start_repl_backend at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/REPL/src/REPL.jl:231
ijl_apply_generic at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
#run_repl#59 at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/REPL/src/REPL.jl:379
run_repl at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-9/usr/share/julia/stdlib/v1.9/REPL/src/REPL.jl:365
jfptr_run_repl_60715.clone_1 at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/sys.dylib (unknown line)
ijl_apply_generic at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
#1017 at ./client.jl:421
jfptr_YY.1017_27246.clone_1 at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/sys.dylib (unknown line)
ijl_apply_generic at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
jl_f__call_latest at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
#invokelatest#2 at ./essentials.jl:816 [inlined]
invokelatest at ./essentials.jl:813 [inlined]
run_main_repl at ./client.jl:405
exec_options at ./client.jl:322
_start at ./client.jl:522
jfptr__start_44876.clone_1 at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/sys.dylib (unknown line)
ijl_apply_generic at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
true_main at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
jl_repl_entrypoint at /Users/b1019548/.julia/juliaup/julia-1.9.2+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
Allocations: 6469412 (Pool: 6463536; Big: 5876); GC: 11
zsh: segmentation fault julia

palday · July 19, 2023, 7:46pm

This is a known and tracked issue: Error when loading PyMNE · Issue #17 · beacon-biosignals/PyMNE.jl · GitHub

If you would like to test the proposed fix mentioned at the bottom of the linked issue, that would be helpful!

nathanweisz · July 20, 2023, 9:30am

Thanks. So I did:
pkg> add PyMNE#pa/depup

That took a little longer.

However then I get the crash again:
julia> using PyMNE

[91778] signal (11.1): Segmentation fault: 11
in expression starting at REPL[10]:1
_ZN4llvm17PMTopLevelManager16addImmutablePassEPNS_13ImmutablePassE at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libLLVM-14.dylib (unknown line)
_ZN4llvm17PMTopLevelManager12schedulePassEPNS_4PassE at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libLLVM-14.dylib (unknown line)
_ZN4llvm17PMTopLevelManager12schedulePassEPNS_4PassE at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libLLVM-14.dylib (unknown line)
_ZN4llvm18PassManagerBuilder25populateModulePassManagerERNS_6legacy15PassManagerBaseE at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libLLVM-14.dylib (unknown line)
ffi_call_unix64 at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libffi.8.dylib (unknown line)
ffi_call_int at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libffi.8.dylib (unknown line)
_ctypes_callproc at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/python3.11/lib-dynload/_ctypes.cpython-311-darwin.so (unknown line)
PyCFuncPtr_call at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/python3.11/lib-dynload/_ctypes.cpython-311-darwin.so (unknown line)
… ETCETC …

nathanweisz · July 20, 2023, 9:43am

btw here the versioninfo.

Julia Version 1.9.2
Commit e4ee485e909 (2023-07-05 09:39 UTC)
Platform Info:
OS: macOS (x86_64-apple-darwin22.4.0)
CPU: 8 × Intel(R) Core™ i5-8279U CPU @ 2.40GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-14.0.6 (ORCJIT, skylake)
Threads: 1 on 8 virtual cores

palday · July 20, 2023, 10:01am

Can you also show pkg> status ?

nathanweisz · July 20, 2023, 10:06am

(mnetest) pkg> status
Status ~/Desktop/mnetest/Project.toml
[6c5003b2] PyMNE v0.2.2 https://github.com/beacon-biosignals/PyMNE.jl.git#pa/depup
[6099a3de] PythonCall v0.9.13

palday · July 20, 2023, 10:28am

Hmmm, I’m unable to replicate in a clean environment. Can you try restarting Julia (in your mnetest environment – thanks for using a small environment!) and then re-running using PyMNE? I’m wondering if you were still loading the released version because of the way package updates work on already loaded packages.

nathanweisz · July 20, 2023, 10:53am

It behaves differently now, but in the end still crashed. See below.

Anyhow, thanks a lot. I was just messing around. When doing analysis with MNE I would likely still stick with Python environment. But interested in doing more in Julia in future.

…
inking seaborn-0.12.2-hd8ed1ab_0
Linking pyvista-0.41.0-pyhd8ed1ab_0
Linking pyvistaqt-0.11.0-pyhd8ed1ab_0
Linking mne-1.4.2-h694c41f_0
Transaction finished
CondaPkg Installing Pip packages
│ /Users/b1019548/Desktop/mnetest/.CondaPkg/env/bin/pip
│ install
└ mne >=1.4
Requirement already satisfied: mne>=1.4 in ./.CondaPkg/env/lib/python3.11/site-packages (1.4.2)
Requirement already satisfied: numpy>=1.15.4 in ./.CondaPkg/env/lib/python3.11/site-packages (from mne>=1.4) (1.24.4)
Requirement already satisfied: scipy>=1.6.3 in ./.CondaPkg/env/lib/python3.11/site-packages (from mne>=1.4) (1.11.1)
Requirement already satisfied: matplotlib>=3.4.0 in ./.CondaPkg/env/lib/python3.11/site-packages (from mne>=1.4) (3.7.2)
Requirement already satisfied: tqdm in ./.CondaPkg/env/lib/python3.11/site-packages (from mne>=1.4) (4.65.0)
Requirement already satisfied: pooch>=1.5 in ./.CondaPkg/env/lib/python3.11/site-packages (from mne>=1.4) (1.7.0)
Requirement already satisfied: decorator in ./.CondaPkg/env/lib/python3.11/site-packages (from mne>=1.4) (5.1.1)
Requirement already satisfied: packaging in ./.CondaPkg/env/lib/python3.11/site-packages (from mne>=1.4) (23.1)
Requirement already satisfied: jinja2 in ./.CondaPkg/env/lib/python3.11/site-packages (from mne>=1.4) (3.1.2)
Requirement already satisfied: contourpy>=1.0.1 in ./.CondaPkg/env/lib/python3.11/site-packages (from matplotlib>=3.4.0->mne>=1.4) (1.1.0)
Requirement already satisfied: cycler>=0.10 in ./.CondaPkg/env/lib/python3.11/site-packages (from matplotlib>=3.4.0->mne>=1.4) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in ./.CondaPkg/env/lib/python3.11/site-packages (from matplotlib>=3.4.0->mne>=1.4) (4.41.0)
Requirement already satisfied: kiwisolver>=1.0.1 in ./.CondaPkg/env/lib/python3.11/site-packages (from matplotlib>=3.4.0->mne>=1.4) (1.4.4)
Requirement already satisfied: pillow>=6.2.0 in ./.CondaPkg/env/lib/python3.11/site-packages (from matplotlib>=3.4.0->mne>=1.4) (10.0.0)
Requirement already satisfied: pyparsing<3.1,>=2.3.1 in ./.CondaPkg/env/lib/python3.11/site-packages (from matplotlib>=3.4.0->mne>=1.4) (3.0.9)
Requirement already satisfied: python-dateutil>=2.7 in ./.CondaPkg/env/lib/python3.11/site-packages (from matplotlib>=3.4.0->mne>=1.4) (2.8.2)
Requirement already satisfied: platformdirs>=2.5.0 in ./.CondaPkg/env/lib/python3.11/site-packages (from pooch>=1.5->mne>=1.4) (3.9.1)
Requirement already satisfied: requests>=2.19.0 in ./.CondaPkg/env/lib/python3.11/site-packages (from pooch>=1.5->mne>=1.4) (2.31.0)
Requirement already satisfied: MarkupSafe>=2.0 in ./.CondaPkg/env/lib/python3.11/site-packages (from jinja2->mne>=1.4) (2.1.3)
Requirement already satisfied: six>=1.5 in ./.CondaPkg/env/lib/python3.11/site-packages (from python-dateutil>=2.7->matplotlib>=3.4.0->mne>=1.4) (1.16.0)
Requirement already satisfied: charset-normalizer<4,>=2 in ./.CondaPkg/env/lib/python3.11/site-packages (from requests>=2.19.0->pooch>=1.5->mne>=1.4) (3.2.0)
Requirement already satisfied: idna<4,>=2.5 in ./.CondaPkg/env/lib/python3.11/site-packages (from requests>=2.19.0->pooch>=1.5->mne>=1.4) (3.4)
Requirement already satisfied: urllib3<3,>=1.21.1 in ./.CondaPkg/env/lib/python3.11/site-packages (from requests>=2.19.0->pooch>=1.5->mne>=1.4) (2.0.4)
Requirement already satisfied: certifi>=2017.4.17 in ./.CondaPkg/env/lib/python3.11/site-packages (from requests>=2.19.0->pooch>=1.5->mne>=1.4) (2023.5.7)

[97425] signal (11.1): Segmentation fault: 11
in expression starting at REPL[4]:1
_ZN4llvm17PMTopLevelManager16addImmutablePassEPNS_13ImmutablePassE at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libLLVM-14.dylib (unknown line)
_ZN4llvm17PMTopLevelManager12schedulePassEPNS_4PassE at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libLLVM-14.dylib (unknown line)
_ZN4llvm17PMTopLevelManager12schedulePassEPNS_4PassE at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libLLVM-14.dylib (unknown line)
_ZN4llvm18PassManagerBuilder25populateModulePassManagerERNS_6legacy15PassManagerBaseE at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libLLVM-14.dylib (unknown line)
ffi_call_unix64 at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libffi.8.dylib (unknown line)
ffi_call_int at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/libffi.8.dylib (unknown line)
_ctypes_callproc at /Users/b1019548/Desktop/mnetest/.CondaPkg/env/lib/python3.11/lib-dynload/_ctypes.cpython-311-darwin.so (unknown line)
…

nathanweisz · July 21, 2023, 12:52pm

A more knowledgable colleague had a look today. Turns out that my XCode command line tools were quite outdated. Installing the newest version (from Xcode 15 - Apple Developer) solved the problem.

Now PyMNE installs fine.

Thanks for taking your time!