Can't build PythonCall

Hi,

Julia 1.11.6:

julia> import Pkg

julia> Pkg.build("PythonCall")
Precompiling project...
  ✗ PythonPlot
  0 dependencies successfully precompiled in 4 seconds. 482 already precompiled.
  1 dependency errored.
  For a report of the errors see `julia> err`. To retry use `pkg> precompile`

julia> err
PkgPrecompileError: The following 1 direct dependency failed to precompile:

PythonPlot 

Failed to precompile PythonPlot [274fc56d-3b97-40fa-a1cd-1b4a50311bf9] to "/home/jska/.julia/compiled/v1.11/PythonPlot/jl_KInpeI".
Python path configuration:
  PYTHONHOME = (not set)
  PYTHONPATH = (not set)
  program name = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/bin/python'
  isolated = 0
  environment = 1
  user site = 1
  safe_path = 0
  import site = 1
  is in build tree = 0
  stdlib dir = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.12'
  sys._base_executable = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/bin/python'
  sys.base_prefix = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default'
  sys.base_exec_prefix = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default'
  sys.platlibdir = 'lib'
  sys.executable = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/bin/python'
  sys.prefix = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default'
  sys.exec_prefix = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default'
  sys.path = [
    '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python312.zip',
    '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.12',
    '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.12/lib-dynload',
  ]
Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding
Python runtime state: core initialized
LookupError: no codec search functions registered: can't find encoding

Current thread 0x00007f07fcc92740 (most recent call first):
  <no Python frame>
ERROR: LoadError: InitError: failed process: Process(setenv(`/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/bin/python /home/jska/.julia/packages/PythonCall/avYrV/src/C/find_libpython.py --list-all`,["PYTHONIOENCODING=UTF-8", "PATH=/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/bin:/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/condabin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/julia-1.9.0/bin", "QT_ACCESSIBILITY=1", "DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/5077/bus", "XDG_CURRENT_DESKTOP=XFCE", "LANG=en_US.UTF8", "LOGNAME=jska", "XDG_SESSION_DESKTOP=xfce", "SHLVL=1", "XDG_RUNTIME_DIR=/run/user/5077"  …  "XMODIFIERS=@im=ibus", "JULIA_LOAD_PATH=/home/jska/.julia/environments/v1.11/Project.toml:/opt/jska-tmp/julia-1.11.6/share/julia/stdlib/v1.11", "CONDA_SHLVL=1", "HOME=/home/jska", "TERM=xterm-256color", "WINDOWPATH=2", "LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=00:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.avif=01;35:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:*~=00;90:*#=00;90:*.bak=00;90:*.old=00;90:*.orig=00;90:*.part=00;90:*.rej=00;90:*.swp=00;90:*.tmp=00;90:*.dpkg-dist=00;90:*.dpkg-old=00;90:*.ucf-dist=00;90:*.ucf-new=00;90:*.ucf-old=00;90:*.rpmnew=00;90:*.rpmorig=00;90:*.rpmsave=00;90:", "COLORTERM=truecolor", "OPENBLAS_MAIN_FREE=1", "VTE_VERSION=7006"]), ProcessExited(1)) [1]

Stacktrace:
  [1] pipeline_error
    @ ./process.jl:598 [inlined]
  [2] (::Base.var"#890#891"{Base.Process})()
    @ Base ./process.jl:356
  [3] iterate (repeats 2 times)
    @ ./io.jl:1235
  [4] _collect
    @ ./array.jl:727
  [5] collect
    @ ./array.jl:716 [inlined]
  [6] readlines
    @ ./io.jl:708 [inlined]
  [7] init_context()
    @ PythonCall.C ~/.julia/packages/PythonCall/avYrV/src/C/context.jl:117
  [8] __init__()
    @ PythonCall.C ~/.julia/packages/PythonCall/avYrV/src/C/C.jl:23
  [9] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1378
 [10] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1366
 [11] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any}, ignore_native::Nothing; register::Bool)
    @ Base ./loading.jl:1254
 [12] _include_from_serialized (repeats 2 times)
    @ ./loading.jl:1210 [inlined]
 [13] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String})
    @ Base ./loading.jl:2057
 [14] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2527
 [15] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2388
 [16] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [17] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [18] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2375
 [19] macro expansion
    @ ./loading.jl:2314 [inlined]
 [20] macro expansion
    @ ./lock.jl:273 [inlined]
 [21] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2271
 [22] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [23] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [24] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2260
 [25] include
    @ ./Base.jl:562 [inlined]
 [26] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2881
 [27] top-level scope
    @ stdin:6
during initialization of module C
in expression starting at /home/jska/.julia/packages/PythonPlot/oS8x4/src/PythonPlot.jl:2
in expression starting at stdin:

that seems to be something else, can you try in an environment without PythonPlot?

1 Like

How can I do that ?

Looks like I was able to:

(@v1.11) pkg> rm PythonPlot
    Updating `~/.julia/environments/v1.11/Project.toml`
  [274fc56d] - PythonPlot v1.0.6
    Updating `~/.julia/environments/v1.11/Manifest.toml`
  [274fc56d] - PythonPlot v1.0.6

(@v1.11) pkg> rm PythonPlot
ERROR: The following package names could not be resolved:
 * PythonPlot (not found in project or manifest)
   Suggestions: PyPlot PythonCall

(@v1.11) pkg> add PythonCall
   Resolving package versions...
  No Changes to `~/.julia/environments/v1.11/Project.toml`
  No Changes to `~/.julia/environments/v1.11/Manifest.toml`

But I still have an error:

julia> using PythonCall
Python path configuration:
  PYTHONHOME = (not set)
  PYTHONPATH = (not set)
  program name = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/bin/python'
  isolated = 0
  environment = 1
  user site = 1
  safe_path = 0
  import site = 1
  is in build tree = 0
  stdlib dir = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.12'
  sys._base_executable = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/bin/python'
  sys.base_prefix = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default'
  sys.base_exec_prefix = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default'
  sys.platlibdir = 'lib'
  sys.executable = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/bin/python'
  sys.prefix = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default'
  sys.exec_prefix = '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default'
  sys.path = [
    '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python312.zip',
    '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.12',
    '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.12/lib-dynload',
  ]
Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding
Python runtime state: core initialized
LookupError: no codec search functions registered: can't find encoding

Current thread 0x00007fd308fff740 (most recent call first):
  <no Python frame>
ERROR: InitError: failed process: Process(setenv(`/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/bin/python /home/jska/.julia/packages/PythonCall/avYrV/src/C/find_libpython.py --list-all`,["PYTHONIOENCODING=UTF-8", "PATH=/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/bin:/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/condabin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/julia-1.9.0/bin", "QT_ACCESSIBILITY=1", "DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/5077/bus", "XDG_CURRENT_DESKTOP=XFCE", "LANG=en_US.UTF8", "LOGNAME=jska", "XDG_SESSION_DESKTOP=xfce", "SHLVL=1", "XDG_RUNTIME_DIR=/run/user/5077"  …  "SESSION_MANAGER=local/sirius:@/tmp/.ICE-unix/1676,unix/sirius:/tmp/.ICE-unix/1676", "XMODIFIERS=@im=ibus", "CONDA_SHLVL=1", "HOME=/home/jska", "TERM=xterm-256color", "WINDOWPATH=2", "LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=00:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.avif=01;35:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:*~=00;90:*#=00;90:*.bak=00;90:*.old=00;90:*.orig=00;90:*.part=00;90:*.rej=00;90:*.swp=00;90:*.tmp=00;90:*.dpkg-dist=00;90:*.dpkg-old=00;90:*.ucf-dist=00;90:*.ucf-new=00;90:*.ucf-old=00;90:*.rpmnew=00;90:*.rpmorig=00;90:*.rpmsave=00;90:", "COLORTERM=truecolor", "OPENBLAS_MAIN_FREE=1", "VTE_VERSION=7006"]), ProcessExited(1)) [1]

Stacktrace:
  [1] pipeline_error
    @ ./process.jl:598 [inlined]
  [2] (::Base.var"#890#891"{Base.Process})()
    @ Base ./process.jl:356
  [3] iterate (repeats 2 times)
    @ ./io.jl:1235
  [4] _collect
    @ ./array.jl:727
  [5] collect
    @ ./array.jl:716 [inlined]
  [6] readlines
    @ ./io.jl:708 [inlined]
  [7] init_context()
    @ PythonCall.C ~/.julia/packages/PythonCall/avYrV/src/C/context.jl:117
  [8] __init__()
    @ PythonCall.C ~/.julia/packages/PythonCall/avYrV/src/C/C.jl:23
  [9] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1378
 [10] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1366
 [11] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any}, ignore_native::Nothing; register::Bool)
    @ Base ./loading.jl:1254
 [12] _include_from_serialized (repeats 2 times)
    @ ./loading.jl:1210 [inlined]
 [13] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String})
    @ Base ./loading.jl:2057
 [14] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2527
 [15] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2388
 [16] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [17] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [18] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2375
 [19] macro expansion
    @ ./loading.jl:2314 [inlined]
 [20] macro expansion
    @ ./lock.jl:273 [inlined]
 [21] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2271
 [22] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [23] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [24] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2260
during initialization of module C

Ok, I forgot to build, now it seems to work:

julia> import Pkg

julia> Pkg.build("PythonCall")

julia> import Pkg

julia> using PythonCall

julia>

Thanks !

1 Like

I still have a stability problem, and I don’t know how to unmark this thread as solved:

julia> using PythonCall

julia> import Pandas
free(): invalid pointer

[122619] signal 6 (-6): Aborted
in expression starting at REPL[2]:1
unknown function (ip: 0x7f4910cadeec)
gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x7f4910ca242e)
unknown function (ip: 0x7f4910cb7869)
unknown function (ip: 0x7f4910cb95f3)
__libc_free at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_PyMem_RawFree at /usr/local/src/conda/python-3.12.11/Objects/obmalloc.c:73 [inlined]
PyMem_RawFree at /usr/local/src/conda/python-3.12.11/Objects/obmalloc.c:685 [inlined]
_PyObject_Free at /usr/local/src/conda/python-3.12.11/Objects/obmalloc.c:1853 [inlined]
PyObject_Free at /usr/local/src/conda/python-3.12.11/Objects/obmalloc.c:830 [inlined]
object_dealloc at /usr/local/src/conda/python-3.12.11/Objects/typeobject.c:5520
_PyImport_LoadDynamicModuleWithSpec at /usr/local/src/conda/python-3.12.11/Python/importdl.c:249 [inlined]
_imp_create_dynamic_impl at /usr/local/src/conda/python-3.12.11/Python/import.c:3789 [inlined]
_imp_create_dynamic at /usr/local/src/conda/python-3.12.11/Python/clinic/import.c.h:506
cfunction_vectorcall_FASTCALL at /usr/local/src/conda/python-3.12.11/Objects/methodobject.c:422
PyCFunction_Call at /usr/local/src/conda/python-3.12.11/Objects/call.c:387 [inlined]
_PyEval_EvalFrameDefault at /home/conda/feedstock_root/build_artifacts/python-split_1749046816465/work/build-shared/Python/bytecodes.c:3263
_PyObject_VectorcallTstate at /usr/local/src/conda/python-3.12.11/Include/internal/pycore_call.h:92 [inlined]
object_vacall at /usr/local/src/conda/python-3.12.11/Objects/call.c:850
PyObject_CallMethodObjArgs at /usr/local/src/conda/python-3.12.11/Objects/call.c:911
import_find_and_load at /usr/local/src/conda/python-3.12.11/Python/import.c:2793 [inlined]
PyImport_ImportModuleLevelObject at /usr/local/src/conda/python-3.12.11/Python/import.c:2876
import_name at /usr/local/src/conda/python-3.12.11/Python/ceval.c:2510 [inlined]
_PyEval_EvalFrameDefault at /home/conda/feedstock_root/build_artifacts/python-split_1749046816465/work/build-shared/Python/bytecodes.c:2144
PyEval_EvalCode at /usr/local/src/conda/python-3.12.11/Python/ceval.c:580
builtin_exec_impl at /usr/local/src/conda/python-3.12.11/Python/bltinmodule.c:1093 [inlined]
builtin_exec at /usr/local/src/conda/python-3.12.11/Python/clinic/bltinmodule.c.h:543
cfunction_vectorcall_FASTCALL_KEYWORDS at /usr/local/src/conda/python-3.12.11/Objects/methodobject.c:438
PyCFunction_Call at /usr/local/src/conda/python-3.12.11/Objects/call.c:387 [inlined]
_PyEval_EvalFrameDefault at /home/conda/feedstock_root/build_artifacts/python-split_1749046816465/work/build-shared/Python/bytecodes.c:3263
_PyObject_VectorcallTstate at /usr/local/src/conda/python-3.12.11/Include/internal/pycore_call.h:92 [inlined]
object_vacall at /usr/local/src/conda/python-3.12.11/Objects/call.c:850
PyObject_CallMethodObjArgs at /usr/local/src/conda/python-3.12.11/Objects/call.c:911
import_find_and_load at /usr/local/src/conda/python-3.12.11/Python/import.c:2793 [inlined]
PyImport_ImportModuleLevelObject at /usr/local/src/conda/python-3.12.11/Python/import.c:2876
import_name at /usr/local/src/conda/python-3.12.11/Python/ceval.c:2510 [inlined]
_PyEval_EvalFrameDefault at /home/conda/feedstock_root/build_artifacts/python-split_1749046816465/work/build-shared/Python/bytecodes.c:2144
PyEval_EvalCode at /usr/local/src/conda/python-3.12.11/Python/ceval.c:580
builtin_exec_impl at /usr/local/src/conda/python-3.12.11/Python/bltinmodule.c:1093 [inlined]
builtin_exec at /usr/local/src/conda/python-3.12.11/Python/clinic/bltinmodule.c.h:543
cfunction_vectorcall_FASTCALL_KEYWORDS at /usr/local/src/conda/python-3.12.11/Objects/methodobject.c:438
PyCFunction_Call at /usr/local/src/conda/python-3.12.11/Objects/call.c:387 [inlined]
_PyEval_EvalFrameDefault at /home/conda/feedstock_root/build_artifacts/python-split_1749046816465/work/build-shared/Python/bytecodes.c:3263
_PyObject_VectorcallTstate at /usr/local/src/conda/python-3.12.11/Include/internal/pycore_call.h:92 [inlined]
object_vacall at /usr/local/src/conda/python-3.12.11/Objects/call.c:850
PyObject_CallMethodObjArgs at /usr/local/src/conda/python-3.12.11/Objects/call.c:911
import_find_and_load at /usr/local/src/conda/python-3.12.11/Python/import.c:2793 [inlined]
PyImport_ImportModuleLevelObject at /usr/local/src/conda/python-3.12.11/Python/import.c:2876
import_name at /usr/local/src/conda/python-3.12.11/Python/ceval.c:2510 [inlined]
_PyEval_EvalFrameDefault at /home/conda/feedstock_root/build_artifacts/python-split_1749046816465/work/build-shared/Python/bytecodes.c:2144
PyEval_EvalCode at /usr/local/src/conda/python-3.12.11/Python/ceval.c:580
builtin_exec_impl at /usr/local/src/conda/python-3.12.11/Python/bltinmodule.c:1093 [inlined]
builtin_exec at /usr/local/src/conda/python-3.12.11/Python/clinic/bltinmodule.c.h:543
cfunction_vectorcall_FASTCALL_KEYWORDS at /usr/local/src/conda/python-3.12.11/Objects/methodobject.c:438
PyCFunction_Call at /usr/local/src/conda/python-3.12.11/Objects/call.c:387 [inlined]
_PyEval_EvalFrameDefault at /home/conda/feedstock_root/build_artifacts/python-split_1749046816465/work/build-shared/Python/bytecodes.c:3263
_PyObject_VectorcallTstate at /usr/local/src/conda/python-3.12.11/Include/internal/pycore_call.h:92 [inlined]
object_vacall at /usr/local/src/conda/python-3.12.11/Objects/call.c:850
PyObject_CallMethodObjArgs at /usr/local/src/conda/python-3.12.11/Objects/call.c:911
import_find_and_load at /usr/local/src/conda/python-3.12.11/Python/import.c:2793 [inlined]
PyImport_ImportModuleLevelObject at /usr/local/src/conda/python-3.12.11/Python/import.c:2876
builtin___import___impl at /usr/local/src/conda/python-3.12.11/Python/bltinmodule.c:276 [inlined]
builtin___import__ at /usr/local/src/conda/python-3.12.11/Python/clinic/bltinmodule.c.h:107
cfunction_vectorcall_FASTCALL_KEYWORDS at /usr/local/src/conda/python-3.12.11/Objects/methodobject.c:438
_PyObject_VectorcallTstate at /usr/local/src/conda/python-3.12.11/Include/internal/pycore_call.h:92 [inlined]
_PyObject_CallFunctionVa at /usr/local/src/conda/python-3.12.11/Objects/call.c:562 [inlined]
PyObject_CallFunction at /usr/local/src/conda/python-3.12.11/Objects/call.c:584
PyImport_Import at /usr/local/src/conda/python-3.12.11/Python/import.c:3062
PyImport_ImportModule at /usr/local/src/conda/python-3.12.11/Python/import.c:2486
_pyimport at /home/jska/.julia/packages/PyCall/1gn3u/src/PyCall.jl:483
pyimport at /home/jska/.julia/packages/PyCall/1gn3u/src/PyCall.jl:507
__init__ at /home/jska/.julia/packages/PyCall/1gn3u/src/pyinit.jl:207
jfptr___init___7065 at /home/jska/.julia/compiled/v1.11/PyCall/GkzkC_hBDxc.so (unknown line)
jl_apply at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
jl_module_run_initializer at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/toplevel.c:76
run_module_init at ./loading.jl:1378
register_restored_modules at ./loading.jl:1366
#_include_from_serialized#1082 at ./loading.jl:1254
_include_from_serialized at ./loading.jl:1210 [inlined]
_include_from_serialized at ./loading.jl:1210 [inlined]
#_require_search_from_serialized#1105 at ./loading.jl:2041
_require_search_from_serialized at ./loading.jl:1969
jfptr__require_search_from_serialized_44906.1 at /opt/jska-tmp/julia-1.11.6/lib/julia/sys.so (unknown line)
_require at ./loading.jl:2527
__require_prelocked at ./loading.jl:2388
jfptr___require_prelocked_71260.1 at /opt/jska-tmp/julia-1.11.6/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
jl_f__call_in_world at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/builtins.c:894
#invoke_in_world#3 at ./essentials.jl:1089 [inlined]
invoke_in_world at ./essentials.jl:1086 [inlined]
_require_prelocked at ./loading.jl:2375
macro expansion at ./loading.jl:2314 [inlined]
macro expansion at ./lock.jl:273 [inlined]
__require at ./loading.jl:2271
jfptr___require_71191.1 at /opt/jska-tmp/julia-1.11.6/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
jl_f__call_in_world at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/builtins.c:894
#invoke_in_world#3 at ./essentials.jl:1089 [inlined]
invoke_in_world at ./essentials.jl:1086 [inlined]
require at ./loading.jl:2260
jfptr_require_71188.1 at /opt/jska-tmp/julia-1.11.6/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
call_require at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/toplevel.c:486 [inlined]
eval_import_path at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/toplevel.c:523
jl_toplevel_eval_flex at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/toplevel.c:812
jl_toplevel_eval_flex at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/toplevel.c:886
ijl_toplevel_eval_in at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/toplevel.c:994
eval at ./boot.jl:430 [inlined]
eval_user_input at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:261
repl_backend_loop at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:368
#start_repl_backend#59 at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:343
start_repl_backend at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:340
#run_repl#76 at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:500
run_repl at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:486
jfptr_run_repl_10230.1 at /opt/jska-tmp/julia-1.11.6/share/julia/compiled/v1.11/REPL/u0gqU_QBeOa.so (unknown line)
#1150 at ./client.jl:446
jfptr_YY.1150_14947.1 at /opt/jska-tmp/julia-1.11.6/share/julia/compiled/v1.11/REPL/u0gqU_QBeOa.so (unknown line)
jl_apply at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
jl_f__call_latest at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/builtins.c:875
#invokelatest#2 at ./essentials.jl:1055 [inlined]
invokelatest at ./essentials.jl:1052 [inlined]
run_main_repl at ./client.jl:430
repl_main at ./client.jl:567 [inlined]
_start at ./client.jl:541
jfptr__start_73597.1 at /opt/jska-tmp/julia-1.11.6/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
true_main at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/jlapi.c:900
jl_repl_entrypoint at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/jlapi.c:1059
main at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/cli/loader_exe.c:58
unknown function (ip: 0x7f4910c4a249)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 2305162 (Pool: 2304163; Big: 999); GC: 4
Aborted

Pandas.jl uses PyCall.jl which out of the box is incompatible with PythonCall.jl and you are likely to get nasty errors using them both together.

The docs has some instructions for how to configure them to work together but it’s not pretty: FAQ & Troubleshooting · PythonCall & JuliaCall?

I’d recommend avoiding mixing them if possible. PythonCall has some functionality built-in for handling pandas dataframes.

2 Likes

Ok thanks.