On PythonCall load, UndefRefError: access to undefined reference

[mkitti]

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.

[mkitti]

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

[mkitti]

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

[mkitti]

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

[mkitti]

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.

[mkitti]

Switching to main at 8f7baa5 resolves this for me.

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