JuliaCall segfault (even in fresh enviroment) with Julia 1.12 #748
Description
Affects: JuliaCall
Describe the bug
I had been using JuliaCall for a while.
and today it just stopped working for me.
Python just crashed out, no error or nothing
So I made the most MWE for it. In a fresh environment.
Running:
conda create -n temp -c conda-forge python pip
conda activate temp
pip install juliapkg juliacall
pythonthen running
import juliacall
in python.
the following was the output:
>>> import juliacall
[juliapkg] Found dependencies: /home/frames/miniconda3/envs/temp/lib/python3.14/site-packages/juliacall/juliapkg.json
[juliapkg] Found dependencies: /home/frames/miniconda3/envs/temp/lib/python3.14/site-packages/juliapkg/juliapkg.json
[juliapkg] Locating Julia ^1.10.3
[juliapkg] Using Julia 1.12.5 at /home/frames/.julia/juliaup/julia-1.12.5+0.x64.linux.gnu/bin/julia
[juliapkg] Using Julia project at /home/frames/miniconda3/envs/temp/julia_env
[juliapkg] Writing Project.toml:
| [deps]
| PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
| OpenSSL_jll = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
|
| [compat]
| PythonCall = "=0.9.31"
| OpenSSL_jll = "3.0.0 - 3.6"
[juliapkg] Installing packages:
| import Pkg
| Pkg.Registry.update()
| Pkg.add([
| Pkg.PackageSpec(name="PythonCall", uuid="6099a3de-0909-46bc-b1f4-468b9a2dfc0d"),
| Pkg.PackageSpec(name="OpenSSL_jll", uuid="458c3c95-2e84-50aa-8efc-19380b2a3a95"),
| ])
| Pkg.resolve()
| Pkg.precompile()
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
Updating `~/miniconda3/envs/temp/julia_env/Project.toml`
[6099a3de] + PythonCall v0.9.31
[458c3c95] ~ OpenSSL_jll ⇒ v3.5.4+0
Updating `~/miniconda3/envs/temp/julia_env/Manifest.toml`
[992eb4ea] + CondaPkg v0.2.33
[9a962f9c] + DataAPI v1.16.0
[e2d170a0] + DataValueInterfaces v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[692b3bcd] + JLLWrappers v1.7.1
[0f8b85d8] + JSON3 v1.14.3
[1914dd2f] + MacroTools v0.5.16
[0b3b1443] + MicroMamba v0.1.14
[bac558e1] + OrderedCollections v1.8.1
[69de0a69] + Parsers v2.8.3
[fa939f87] + Pidfile v1.3.0
[aea7be01] + PrecompileTools v1.3.3
[21216c6a] + Preferences v1.5.1
[6099a3de] + PythonCall v0.9.31
[6c6a2e73] + Scratch v1.3.0
[856f2bd8] + StructTypes v1.11.0
[3783bdb8] + TableTraits v1.0.1
[bd369af6] + Tables v1.12.1
[e17b2a0c] + UnsafePointers v1.0.0
⌅ [f8abcde7] + micromamba_jll v1.5.12+0
[4d7b5844] + pixi_jll v0.41.3+0
[0dad84c5] + ArgTools v1.1.2
[56f22d72] + Artifacts v1.11.0
[2a0f44e3] + Base64 v1.11.0
[ade2ca70] + Dates v1.11.0
[f43a241f] + Downloads v1.7.0
[7b1f6079] + FileWatching v1.11.0
[b77e0a4c] + InteractiveUtils v1.11.0
[ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
[4af54fe1] + LazyArtifacts v1.11.0
[b27032c2] + LibCURL v0.6.4
[76f85450] + LibGit2 v1.11.0
[8f399da3] + Libdl v1.11.0
[56ddb016] + Logging v1.11.0
[d6f4376e] + Markdown v1.11.0
[a63ad114] + Mmap v1.11.0
[ca575930] + NetworkOptions v1.3.0
[44cfe95a] + Pkg v1.12.1
[de0858da] + Printf v1.11.0
[9a3f8284] + Random v1.11.0
[ea8e919c] + SHA v0.7.0
[9e88b42a] + Serialization v1.11.0
[f489334b] + StyledStrings v1.11.0
[fa267f1f] + TOML v1.0.3
[a4e569a6] + Tar v1.10.0
[8dfed614] + Test v1.11.0
[cf7118a7] + UUIDs v1.11.0
[4ec0a83e] + Unicode v1.11.0
[e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
[deac9b47] + LibCURL_jll v8.15.0+0
[e37daf67] + LibGit2_jll v1.9.0+0
[29816b5a] + LibSSH2_jll v1.11.3+1
[14a3606d] + MozillaCACerts_jll v2025.11.4
[458c3c95] ~ OpenSSL_jll ⇒ v3.5.4+0
[83775a58] + Zlib_jll v1.3.1+2
[8e850ede] + nghttp2_jll v1.64.0+1
[3f19e933] + p7zip_jll v17.7.0+0
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
Precompiling packages finished.
1 dependency successfully precompiled in 14 seconds. 51 already precompiled.
Project No packages added to or removed from `~/miniconda3/envs/temp/julia_env/Project.toml`
Manifest No packages added to or removed from `~/miniconda3/envs/temp/julia_env/Manifest.toml`
Segmentation fault (core dumped)
frames@joseki:~/repos/biohaus2$
Your system
Please provide detailed information about your system:
- The operating system
$ lsb_release -a
No LSB modules are available.
Distributor ID: Linuxmint
Description: Linux Mint 22
Release: 22
Codename: wilm
- The version of Julia, Python, PythonCall, JuliaCall and any other affected packages
Julia: 1.12.5 (also saw on 1.12.1)
Python: 3.14.3
JuliaCall: 0.9.31
julipkg: 0.1.22
- If an issue with JuliaCall, the output of
pip listorconda listandjuliapkg.status().
>>> import juliapkg
>>> juliapkg.status()
JuliaPkg Status
/home/frames/miniconda3/envs/temp/julia_env/pyjuliapkg/juliapkg.json (empty project)
Julia 1.12.5 @ /home/frames/.julia/juliaup/julia-1.12.5+0.x64.linux.gnu/bin/julia
$ pip list
Package Version
--------- -------
filelock 3.20.3
juliacall 0.9.31
juliapkg 0.1.22
pip 26.0.1
semver 3.0.4
tomli 2.4.0
tomlkit 0.13.3
$ conda list
# packages in environment at /home/frames/miniconda3/envs/temp:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bzip2 1.0.8 hda65f42_8 conda-forge
ca-certificates 2026.1.4 hbd8a1cb_0 conda-forge
filelock 3.20.3 pypi_0 pypi
icu 78.2 h33c6efd_0 conda-forge
juliacall 0.9.31 pypi_0 pypi
juliapkg 0.1.22 pypi_0 pypi
ld_impl_linux-64 2.45.1 default_hbd61a6d_101 conda-forge
libexpat 2.7.3 hecca717_0 conda-forge
libffi 3.5.2 h3435931_0 conda-forge
libgcc 15.2.0 he0feb66_17 conda-forge
libgomp 15.2.0 he0feb66_17 conda-forge
liblzma 5.8.2 hb03c661_0 conda-forge
libmpdec 4.0.0 hb03c661_1 conda-forge
libsqlite 3.51.2 hf4e2dac_0 conda-forge
libstdcxx 15.2.0 h934c35e_17 conda-forge
libuuid 2.41.3 h5347b49_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
openssl 3.6.1 h35e630c_1 conda-forge
pip 26.0.1 pyh145f28c_0 conda-forge
python 3.14.3 h32b2ec7_101_cp314 conda-forge
python_abi 3.14 8_cp314 conda-forge
readline 8.3 h853b02a_0 conda-forge
semver 3.0.4 pypi_0 pypi
tk 8.6.13 noxft_h366c992_103 conda-forge
tomli 2.4.0 pypi_0 pypi
tomlkit 0.13.3 pypi_0 pypi
tzdata 2025c hc9c84f9_1 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge
frames@joseki:~/repos/biohaus2$