Segfault in REPL when importing a library #707
Description
Affects: PythonCall
Describe the bug
$ julia --project=@temp
julia> import Pkg; Pkg.activate(temp = true); Pkg.add(["CondaPkg", "PythonCall"]);using CondaPkg; CondaPkg.add("python", version="3.13.*");CondaPkg.add("numpy");using PythonCall;
np = pyimport("numpy")
julia> np.
[33140] signal 11 (1): Segmentation fault```Here is the full dump:
Details
[33140] signal 11 (1): Segmentation fault in expression starting at REPL[2]:1 _PyInterpreterState_GET at /usr/local/src/conda/python-3.13.9/Include/internal/pycore_pystate.h:214 [inlined] _PyType_LookupRef at /usr/local/src/conda/python-3.13.9/Objects/typeobject.c:5234 [inlined] _PyObject_LookupSpecial at /usr/local/src/conda/python-3.13.9/Objects/typeobject.c:2506 _dir_object at /usr/local/src/conda/python-3.13.9/Objects/object.c:1977 [inlined] PyObject_Dir at /usr/local/src/conda/python-3.13.9/Objects/object.c:2009 PyObject_Dir at /home/kjwiik/.julia/packages/PythonCall/mkWc2/src/C/pointers.jl:300 [inlined] macro expansion at /home/kjwiik/.julia/packages/PythonCall/mkWc2/src/Core/Py.jl:118 [inlined] pydir at /home/kjwiik/.julia/packages/PythonCall/mkWc2/src/Core/builtins.jl:191 propertynames at /home/kjwiik/.julia/packages/PythonCall/mkWc2/src/Core/Py.jl:270 unknown function (ip: 0x7b8401753beb) at (unknown file) #complete_symbol!#6 at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPLCompletions.jl:230 complete_symbol! at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPLCompletions.jl:184 unknown function (ip: 0x7b840174bfd6) at (unknown file) completions at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPLCompletions.jl:1150 #complete_line#66 at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:809 complete_line at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/REPL.jl:807 unknown function (ip: 0x7b840170e77c) at (unknown file) #complete_line_named#17 at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:401 complete_line_named at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:400 [inlined] macro expansion at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:442 [inlined] macro expansion at ./lock.jl:376 [inlined] #check_show_hint##2 at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/REPL/src/LineEdit.jl:439 jfptr_YY.check_show_hintYY.YY.2_17954.1 at /home/kjwiik/.julia/juliaup/julia-1.12.1+0.x64.linux.gnu/share/julia/compiled/v1.12/REPL/u0gqU_UDl4g.so (unknown line) jl_apply at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined] start_task at /cache/build/tester-amdci4-14/julialang/julia-release-1-dot-12/src/task.c:1249 Allocations: 29426553 (Pool: 29424566; Big: 1987); GC: 22 Segmentation fault (core dumped)
julia> versioninfo()
Julia Version 1.12.1
Commit ba1e628ee49 (2025-10-17 13:02 UTC)
Build Info:
Official https://julialang.org release
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 4 × Intel(R) Core(TM) i5-4310U CPU @ 2.00GHz
WORD_SIZE: 64
LLVM: libLLVM-18.1.7 (ORCJIT, haswell)
GC: Built with stock GC
Threads: 1 default, 1 interactive, 1 GC (on 4 virtual cores)
julia> CondaPkg.status()
CondaPkg Status /tmp/jl_UfA8Vd/CondaPkg.toml
Environment
/tmp/jl_UfA8Vd/.CondaPkg/.pixi/envs/default
Packages
numpy v2.3.4
python v3.13.9 (3.13.*)
julia> PythonCall.C.CTX
IOContext{REPL.LimitIO{Base.TTY}}:
is_embedded = false
is_initialized = true
is_preinitialized = false
lib_ptr = Ptr{Nothing}(0x00000000159f6d10)
exe_path = "/tmp/jl_UfA8Vd/.CondaPkg/.pixi/envs/default/bin/python"
lib_path = "/tmp/jl_UfA8Vd/.CondaPkg/.pixi/envs/default/lib/libpython3.13.so.1.0"
dlopen_flags = 0x00000046
pyprogname = "/tmp/jl_UfA8Vd/.CondaPkg/.pixi/envs/default/bin/python"
pyprogname_w = MemoryRef{Int32}(Ptr{Nothing}(0x000070c8b541d520), Int32[47, 116, 109, 112, 47, 106, 108, 95, 85, 102 … -1441332048, 28872, -599587392, 28872, -514150800, 28872, -514150800, 28872, -444150752, 28872])
pyhome = "/tmp/jl_UfA8Vd/.CondaPkg/.pixi/envs/default:/tmp/jl_UfA8Vd/.CondaPkg/.pixi/envs/default"
pyhome_w = MemoryRef{Int32}(Ptr{Nothing}(0x000070c8a23249e0), Int32[47, 116, 109, 112, 47, 106, 108, 95, 85, 102 … 0, 0, 0, -514153520, 28872, -677031280, 28872, 19, 0, 0])
which = :CondaPkg
version = v"3.13.9"
Occurs with both Python 3.13 and 3.14 and only in REPL. In script, everything works fine:
$ julia --project=@temp pythoncall.jl
Activating new project at `/tmp/jl_RvnsQJ`
Resolving package versions...
Updating `/tmp/jl_RvnsQJ/Project.toml`
[992eb4ea] + CondaPkg v0.2.33
[6099a3de] + PythonCall v0.9.28
Updating `/tmp/jl_RvnsQJ/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 v1.5.0
[6099a3de] + PythonCall v0.9.28
[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 v1.6.0
[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 v1.12.0
[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
[deac9b47] + LibCURL_jll v8.11.1+1
[e37daf67] + LibGit2_jll v1.9.0+0
[29816b5a] + LibSSH2_jll v1.11.3+1
[14a3606d] + MozillaCACerts_jll v2025.5.20
[458c3c95] + OpenSSL_jll v3.5.1+0
[83775a58] + Zlib_jll v1.3.1+2
[8e850ede] + nghttp2_jll v1.64.0+1
[3f19e933] + p7zip_jll v17.5.0+2
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
CondaPkg Found dependencies: /tmp/jl_RvnsQJ/CondaPkg.toml
CondaPkg Found dependencies: /home/kjwiik/.julia/packages/PythonCall/mkWc2/CondaPkg.toml
CondaPkg Found dependencies: /home/kjwiik/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml
CondaPkg Resolving changes
+ libstdcxx
+ libstdcxx-ng
+ openssl
+ python
CondaPkg Initialising pixi
│ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
│ init
│ --format pixi
└ /tmp/jl_RvnsQJ/.CondaPkg
✔ Created /tmp/jl_RvnsQJ/.CondaPkg/pixi.toml
CondaPkg Wrote /tmp/jl_RvnsQJ/.CondaPkg/pixi.toml
│ [dependencies]
│ openssl = ">=3, <3.6"
│ libstdcxx = ">=3.4,<15.0"
│ libstdcxx-ng = ">=3.4,<15.0"
│
│ [dependencies.python]
│ channel = "conda-forge"
│ build = "*cp*"
│ version = "3.13.*, >=3.9,<4"
│
│ [project]
│ name = ".CondaPkg"
│ platforms = ["linux-64"]
│ channels = ["conda-forge"]
│ channel-priority = "strict"
└ description = "automatically generated by CondaPkg.jl"
CondaPkg Installing packages
│ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
│ install
└ --manifest-path /tmp/jl_RvnsQJ/.CondaPkg/pixi.toml
✔ The default environment has been installed.
CondaPkg Found dependencies: /tmp/jl_RvnsQJ/CondaPkg.toml
CondaPkg Found dependencies: /home/kjwiik/.julia/packages/PythonCall/mkWc2/CondaPkg.toml
CondaPkg Found dependencies: /home/kjwiik/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml
CondaPkg Resolving changes
+ numpy
CondaPkg Initialising pixi
│ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
│ init
│ --format pixi
└ /tmp/jl_RvnsQJ/.CondaPkg
✔ Created /tmp/jl_RvnsQJ/.CondaPkg/pixi.toml
CondaPkg Wrote /tmp/jl_RvnsQJ/.CondaPkg/pixi.toml
│ [dependencies]
│ openssl = ">=3, <3.6"
│ libstdcxx = ">=3.4,<15.0"
│ libstdcxx-ng = ">=3.4,<15.0"
│ numpy = "*"
│
│ [dependencies.python]
│ channel = "conda-forge"
│ build = "*cp*"
│ version = "3.13.*, >=3.9,<4"
│
│ [project]
│ name = ".CondaPkg"
│ platforms = ["linux-64"]
│ channels = ["conda-forge"]
│ channel-priority = "strict"
└ description = "automatically generated by CondaPkg.jl"
CondaPkg Installing packages
│ /home/kjwiik/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
│ install
└ --manifest-path /tmp/jl_RvnsQJ/.CondaPkg/pixi.toml
✔ The default environment has been installed.
[1 2 3 4 5]Script:
import Pkg; Pkg.activate(temp = true); Pkg.add(["CondaPkg", "PythonCall"]);using CondaPkg; CondaPkg.add("numpy");using PythonCall;
np = pyimport("numpy")
println( np.array([1, 2, 3, 4, 5]))