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On PythonCall load, UndefRefError: access to undefined reference #765

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On PythonCall load, UndefRefError: access to undefined reference#765
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bugSomething isn't working

Description

@mkitti
mkitti
opened on Apr 22, 2026

Affects: PythonCall

Describe the bug

https://github.com/JuliaIO/PyTensorStore.jl/actions/runs/24747323082/job/72507767012?pr=3

ERROR: LoadError: InitError: UndefRefError: access to undefined reference
Stacktrace:
  [1] _pyjl_new(t::Ptr{PythonCall.C.PyObject}, ::Ptr{PythonCall.C.PyObject}, ::Ptr{PythonCall.C.PyObject})
    @ PythonCall.JlWrap.Cjl ~/.julia/packages/PythonCall/83z4q/src/JlWrap/C.jl:24
  [2] PyObject_CallObject
    @ ~/.julia/packages/PythonCall/83z4q/src/C/pointers.jl:300 [inlined]
  [3] PyJuliaValue_New
    @ ~/.julia/packages/PythonCall/83z4q/src/JlWrap/C.jl:392 [inlined]
  [4] macro expansion
    @ ~/.julia/packages/PythonCall/83z4q/src/Core/Py.jl:118 [inlined]
  [5] pyjl(t::PythonCall.Py, v::Module)
    @ PythonCall.JlWrap ~/.julia/packages/PythonCall/83z4q/src/JlWrap/base.jl:7
  [6] pyjl
    @ ~/.julia/packages/PythonCall/83z4q/src/JlWrap/any.jl:400 [inlined]
  [7] Py
    @ ~/.julia/packages/PythonCall/83z4q/src/JlWrap/base.jl:141 [inlined]
  [8] macro expansion
    @ ~/.julia/packages/PythonCall/83z4q/src/Core/Py.jl:117 [inlined]
  [9] pysetattr
    @ ~/.julia/packages/PythonCall/83z4q/src/Core/builtins.jl:78 [inlined]
 [10] setproperty!(x::PythonCall.Py, k::Symbol, v::Module)
    @ PythonCall.Core ~/.julia/packages/PythonCall/83z4q/src/Core/Py.jl:281
 [11] __init__()
    @ PythonCall.JlWrap ~/.julia/packages/PythonCall/83z4q/src/JlWrap/JlWrap.jl:70
 [12] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1445
 [13] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1433
 [14] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any}; register::Bool)
    @ Base ./loading.jl:1321
 [15] _include_from_serialized
    @ ./loading.jl:1276 [inlined]
 [16] _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:2117
 [17] _require_search_from_serialized
    @ ./loading.jl:2011 [inlined]
 [18] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2629
 [19] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2495
 [20] macro expansion
    @ ./loading.jl:2423 [inlined]
 [21] macro expansion
    @ ./lock.jl:376 [inlined]
 [22] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2388
 [23] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2364
 [24] top-level scope
    @ ~/work/PyTensorStore.jl/PyTensorStore.jl/src/PyTensorStore.jl:3
 [25] include(mod::Module, _path::String)
    @ Base ./Base.jl:306
 [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:3028
 [27] top-level scope
    @ stdin:5
 [28] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [29] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2874
 [30] include_string
    @ ./loading.jl:2884 [inlined]
 [31] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:315
 [32] _start()
    @ Base ./client.jl:550
during initialization of module JlWrap
in expression starting at /home/runner/work/PyTensorStore.jl/PyTensorStore.jl/src/PyTensorStore.jl:1

Your system
Please provide detailed information about your system:

Ubuntu Linux (Github Linux runner)
Julia 1.12.6
Python 3.14.4
PythonCall v0.9.31

Additional context
Add any other context about the problem here.

Activity

  1. mkitti
    added
    bugSomething isn't working
    on Apr 22, 2026

  2. mkitti commented on Apr 22, 2026

    @mkitti
    mkitti
    on Apr 22, 2026
    MemberAuthor
    julia> CondaPkg.status()
CondaPkg Status /groups/scicompsoft/home/kittisopikulm/src/PyTensorStore.jl/CondaPkg.toml
Environment
  /groups/scicompsoft/home/kittisopikulm/src/PyTensorStore.jl/.CondaPkg/.pixi/envs/default
Packages
  tensorstore v0.1.82

julia> versioninfo()
Julia Version 1.12.6
Commit 15346901f00 (2026-04-09 19:20 UTC)
Build Info:
  Official https://julialang.org release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 96 × Intel(R) Xeon(R) Gold 6248R CPU @ 3.00GHz
  WORD_SIZE: 64
  LLVM: libLLVM-18.1.7 (ORCJIT, cascadelake)
  GC: Built with stock GC
Threads: 1 default, 1 interactive, 1 GC (on 96 virtual cores)
Environment:
  LD_LIBRARY_PATH = /misc/lsf/10.1/linux3.10-glibc2.17-x86_64/lib

  3. mkitti commented on Apr 22, 2026

    @mkitti
    mkitti
    on Apr 22, 2026
    MemberAuthor
    julia> pyjl(Base.Core)
ERROR: UndefRefError: access to undefined reference
Stacktrace:
 [1] _pyjl_new(t::Ptr{PythonCall.C.PyObject}, ::Ptr{PythonCall.C.PyObject}, ::Ptr{PythonCall.C.PyObject})
   @ PythonCall.JlWrap.Cjl ~/.julia/packages/PythonCall/83z4q/src/JlWrap/C.jl:24
 [2] PyObject_CallObject
   @ ~/.julia/packages/PythonCall/83z4q/src/C/pointers.jl:300 [inlined]
 [3] PyJuliaValue_New
   @ ~/.julia/packages/PythonCall/83z4q/src/JlWrap/C.jl:392 [inlined]
 [4] macro expansion
   @ ~/.julia/packages/PythonCall/83z4q/src/Core/Py.jl:118 [inlined]
 [5] pyjl(t::Py, v::Module)
   @ PythonCall.JlWrap ~/.julia/packages/PythonCall/83z4q/src/JlWrap/base.jl:7
 [6] pyjl(v::Module)
   @ PythonCall.JlWrap ~/.julia/packages/PythonCall/83z4q/src/JlWrap/any.jl:400
 [7] top-level scope
   @ REPL[35]:1

  4. mkitti commented on Apr 22, 2026

    @mkitti
    mkitti
    on Apr 22, 2026
    MemberAuthor
    julia> t = pyjltype(Base.Core)
Python: <class 'juliacall.ModuleValue'>

julia> v = Base.Core
Core

julia> PythonCall.JlWrap.Cjl.PyJuliaValue_New(t, v)
ERROR: UndefRefError: access to undefined reference
Stacktrace:
 [1] _pyjl_new(t::Ptr{PythonCall.C.PyObject}, ::Ptr{PythonCall.C.PyObject}, ::Ptr{PythonCall.C.PyObject})
   @ PythonCall.JlWrap.Cjl ~/.julia/packages/PythonCall/83z4q/src/JlWrap/C.jl:24
 [2] PyObject_CallObject
   @ ~/.julia/packages/PythonCall/83z4q/src/C/pointers.jl:300 [inlined]
 [3] PyJuliaValue_New(_t::Py, v::Any)
   @ PythonCall.JlWrap.Cjl ~/.julia/packages/PythonCall/83z4q/src/JlWrap/C.jl:392
 [4] top-level scope
   @ REPL[65]:1

  5. mkitti commented on Apr 22, 2026

    @mkitti
    mkitti
    on Apr 22, 2026
    MemberAuthor

    I isolated it to _pyjl_new. This appears fixed on @MilesCranmer 's #746 and master.

    julia> using PythonCall
ERROR: InitError: UndefRefError: access to undefined reference
...
during initialization of module JlWrap

julia> using PythonCall

julia> ccall(PythonCall.C.POINTERS.PyObject_CallObject, Ptr{PythonCall.C.PyObject}, (Ptr{PythonCall.C.PyObject}, Ptr{PythonCall.C.PyObject}), PythonCall.C.asptr(PythonCall.pyjltype(Base.Core)), PythonCall.C.PyNULL)
ERROR: UndefRefError: access to undefined reference
Stacktrace:
 [1] _pyjl_new(t::Ptr{PythonCall.C.PyObject}, ::Ptr{PythonCall.C.PyObject}, ::Ptr{PythonCall.C.PyObject})
   @ PythonCall.JlWrap.Cjl ~/.julia/packages/PythonCall/83z4q/src/JlWrap/C.jl:24
 [2] top-level scope
   @ ./REPL[2]:1

    I propose that we release soon.

  6. mkitti commented on Apr 22, 2026

    @mkitti
    mkitti
    on Apr 22, 2026
    MemberAuthor

    Switching to main at 8f7baa5 resolves this for me.

    using Pkg
Pkg.add(url="https://github.com/JuliaPy/PythonCall.jl")

  7. cjdoris commented on May 14, 2026

    @cjdoris
    cjdoris
    on May 14, 2026
    Member

    I've just made a release (0.9.32) - please try it out and close this issue if fixed.

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