Package evaluation of AtomsIOPython on Julia 1.12.0-DEV.1799 (64d37f533b*) started at 2025-03-24T17:04:45.826


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 9.31s


################################################################################
# Installation
#

Installing AtomsIOPython...
   Resolving package versions...
    Updating `~/.julia/environments/v1.12/Project.toml`
  [9e4c859b] + AtomsIOPython v0.1.3
    Updating `~/.julia/environments/v1.12/Manifest.toml`
  [3da9722f] + ASEconvert v0.1.8
  [a963bdd2] + AtomsBase v0.5.1
  [a3e0e189] + AtomsCalculators v0.2.3
  [1692102d] + AtomsIO v0.3.0
  [9e4c859b] + AtomsIOPython v0.1.3
  [46823bd8] + Chemfiles v0.10.42
  [34da2185] + Compat v4.16.0
  [992eb4ea] + CondaPkg v0.2.26
  [9a962f9c] + DataAPI v1.16.0
  [e2d170a0] + DataValueInterfaces v1.0.0
  [ffbed154] + DocStringExtensions v0.9.3
  [352459e4] + ExtXYZ v0.2.2
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.0
  [0f8b85d8] + JSON3 v1.14.1
  [1914dd2f] + MacroTools v0.5.15
  [0b3b1443] + MicroMamba v0.1.14
  [bac558e1] + OrderedCollections v1.8.0
  [69de0a69] + Parsers v2.8.1
  [7b2266bf] + PeriodicTable v1.2.1
  [fa939f87] + Pidfile v1.3.0
  [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [6099a3de] + PythonCall v0.9.24
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [6c6a2e73] + Scratch v1.2.1
  [90137ffa] + StaticArrays v1.9.13
  [1e83bf80] + StaticArraysCore v1.4.3
  [856f2bd8] + StructTypes v1.11.0
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.0
  [1986cc42] + Unitful v1.22.0
  [a7773ee8] + UnitfulAtomic v1.0.0
  [e17b2a0c] + UnsafePointers v1.0.0
  [78a364fa] + Chemfiles_jll v0.10.4+0
  [6ecdc6fc] + extxyz_jll v0.1.3+0
  [cdc7adba] + libcleri_jll v0.12.1+3
  [f8abcde7] + micromamba_jll v1.5.8+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
  [dc6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [4af54fe1] + LazyArtifacts v1.11.0
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.11.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [ca575930] + NetworkOptions v1.2.0
  [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
  [e66e0078] + CompilerSupportLibraries_jll v1.2.0+0
  [deac9b47] + LibCURL_jll v8.6.0+0
  [e37daf67] + LibGit2_jll v1.8.0+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.6+1
  [14a3606d] + MozillaCACerts_jll v2024.11.26
  [4536629a] + OpenBLAS_jll v0.3.28+3
  [efcefdf7] + PCRE2_jll v10.44.0+0
  [83775a58] + Zlib_jll v1.3.1+1
  [8e850b90] + libblastrampoline_jll v5.11.2+0
  [8e850ede] + nghttp2_jll v1.63.0+1
  [3f19e933] + p7zip_jll v17.5.0+1

Installation completed after 2.57s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 147.09s


################################################################################
# Testing
#

     Testing AtomsIOPython
      Status `/tmp/jl_LUJWIK/Project.toml`
  [3da9722f] ASEconvert v0.1.8
  [a963bdd2] AtomsBase v0.5.1
  [ed7c10db] AtomsBaseTesting v0.4.0
  [1692102d] AtomsIO v0.3.0
  [9e4c859b] AtomsIOPython v0.1.3
  [189a3867] Reexport v1.2.2
  [90137ffa] StaticArrays v1.9.13
  [1986cc42] Unitful v1.22.0
  [a7773ee8] UnitfulAtomic v1.0.0
  [37e2e46d] LinearAlgebra v1.11.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_LUJWIK/Manifest.toml`
  [3da9722f] ASEconvert v0.1.8
  [a963bdd2] AtomsBase v0.5.1
  [ed7c10db] AtomsBaseTesting v0.4.0
  [a3e0e189] AtomsCalculators v0.2.3
  [1692102d] AtomsIO v0.3.0
  [9e4c859b] AtomsIOPython v0.1.3
  [46823bd8] Chemfiles v0.10.42
  [34da2185] Compat v4.16.0
  [992eb4ea] CondaPkg v0.2.26
  [9a962f9c] DataAPI v1.16.0
  [e2d170a0] DataValueInterfaces v1.0.0
  [ffbed154] DocStringExtensions v0.9.3
  [352459e4] ExtXYZ v0.2.2
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.7.0
  [0f8b85d8] JSON3 v1.14.1
  [1914dd2f] MacroTools v0.5.15
  [0b3b1443] MicroMamba v0.1.14
  [bac558e1] OrderedCollections v1.8.0
  [69de0a69] Parsers v2.8.1
  [7b2266bf] PeriodicTable v1.2.1
  [fa939f87] Pidfile v1.3.0
  [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [6099a3de] PythonCall v0.9.24
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.1
  [6c6a2e73] Scratch v1.2.1
  [90137ffa] StaticArrays v1.9.13
  [1e83bf80] StaticArraysCore v1.4.3
  [856f2bd8] StructTypes v1.11.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [1986cc42] Unitful v1.22.0
  [a7773ee8] UnitfulAtomic v1.0.0
  [e17b2a0c] UnsafePointers v1.0.0
  [78a364fa] Chemfiles_jll v0.10.4+0
  [6ecdc6fc] extxyz_jll v0.1.3+0
  [cdc7adba] libcleri_jll v0.12.1+3
  [f8abcde7] micromamba_jll v1.5.8+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
  [dc6e5ff7] JuliaSyntaxHighlighting v1.12.0
  [4af54fe1] LazyArtifacts v1.11.0
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.2.0
  [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
  [e66e0078] CompilerSupportLibraries_jll v1.2.0+0
  [deac9b47] LibCURL_jll v8.6.0+0
  [e37daf67] LibGit2_jll v1.8.0+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.6+1
  [14a3606d] MozillaCACerts_jll v2024.11.26
  [4536629a] OpenBLAS_jll v0.3.28+3
  [efcefdf7] PCRE2_jll v10.44.0+0
  [83775a58] Zlib_jll v1.3.1+1
  [8e850b90] libblastrampoline_jll v5.11.2+0
  [8e850ede] nghttp2_jll v1.63.0+1
  [3f19e933] p7zip_jll v17.5.0+1
     Testing Running tests...

[203] signal 11 (128): Segmentation fault
in expression starting at /home/pkgeval/.julia/packages/AtomsIOPython/b26za/test/runtests.jl:3
jl_object_id__cold at /source/src/builtins.c:441
jl_idset_peek_bp at /source/src/idset.c:34
jl_idset_get at /source/src/idset.c:40
jl_as_global_root at /source/src/staticdata.c:2816 [inlined]
jl_as_global_root at /source/src/staticdata.c:2796
inst_datatype_inner at /source/src/jltypes.c:2275
jl_inst_arg_tuple_type at /source/src/jltypes.c:2498
arg_tuple at /source/src/builtins.c:937
jl_method_error at /source/src/gf.c:2437
jl_f_throw_methoderror at /source/src/builtins.c:587 [inlined]
jl_f_throw_methoderror at /source/src/builtins.c:583
convert at ./some.jl:37 [inlined]
StackFrame at ./stacktraces.jl:51 [inlined]
lookup at ./stacktraces.jl:120
#process_backtrace#823 at ./errorshow.jl:957
process_backtrace at ./errorshow.jl:947 [inlined]
process_backtrace at ./errorshow.jl:947 [inlined]
show_backtrace at ./errorshow.jl:821
#showerror#808 at ./errorshow.jl:108
showerror at ./errorshow.jl:104
unknown function (ip: 0x720c13885252) at (unknown file)
_jl_invoke at /source/src/gf.c:3359 [inlined]
ijl_apply_generic at /source/src/gf.c:3547
#showerror#810 at ./errorshow.jl:121
showerror at ./errorshow.jl:119
unknown function (ip: 0x720c1387c7b2) at (unknown file)
_jl_invoke at /source/src/gf.c:3359 [inlined]
ijl_apply_generic at /source/src/gf.c:3547
#showerror#809 at ./errorshow.jl:114
showerror at ./errorshow.jl:112
unknown function (ip: 0x720c1387c738) at (unknown file)
_jl_invoke at /source/src/gf.c:3359 [inlined]
ijl_apply_generic at /source/src/gf.c:3547
show_exception_stack at ./errorshow.jl:1013
jfptr_show_exception_stack_102669.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:3359 [inlined]
ijl_apply_generic at /source/src/gf.c:3547
#sprint#438 at ./strings/io.jl:115
sprint at ./strings/io.jl:110
unknown function (ip: 0x720c1387bfad) at (unknown file)
_jl_invoke at /source/src/gf.c:3359 [inlined]
ijl_apply_generic at /source/src/gf.c:3547
jl_apply at /source/src/julia.h:2244 [inlined]
jl_f__call_latest at /source/src/builtins.c:883
#invokelatest#1 at ./essentials.jl:1058 [inlined]
invokelatest at ./essentials.jl:1052 [inlined]
Error at /source/usr/share/julia/stdlib/v1.12/Test/src/Test.jl:233
jfptr_Error_3264.1 at /opt/julia/share/julia/compiled/v1.12/Test/JfdTE_9HAIE.so (unknown line)
_jl_invoke at /source/src/gf.c:3359 [inlined]
ijl_apply_generic at /source/src/gf.c:3547
jl_apply at /source/src/julia.h:2244 [inlined]
do_call at /source/src/interpreter.c:125
eval_value at /source/src/interpreter.c:243
eval_stmt_value at /source/src/interpreter.c:194 [inlined]
eval_body at /source/src/interpreter.c:687
eval_body at /source/src/interpreter.c:562
jl_interpret_toplevel_thunk at /source/src/interpreter.c:896
jl_toplevel_eval_flex at /source/src/toplevel.c:1070
jl_toplevel_eval_flex at /source/src/toplevel.c:1010
ijl_toplevel_eval at /source/src/toplevel.c:1082
ijl_toplevel_eval_in at /source/src/toplevel.c:1127
eval at ./boot.jl:485
include_string at ./loading.jl:2846
_jl_invoke at /source/src/gf.c:3359 [inlined]
ijl_apply_generic at /source/src/gf.c:3547
_include at ./loading.jl:2906
include at ./Base.jl:301
IncludeInto at ./Base.jl:302
jfptr_IncludeInto_69083.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:3359 [inlined]
ijl_apply_generic at /source/src/gf.c:3547
jl_apply at /source/src/julia.h:2244 [inlined]
do_call at /source/src/interpreter.c:125
eval_value at /source/src/interpreter.c:243
eval_stmt_value at /source/src/interpreter.c:194 [inlined]
eval_body at /source/src/interpreter.c:687
jl_interpret_toplevel_thunk at /source/src/interpreter.c:896
jl_toplevel_eval_flex at /source/src/toplevel.c:1070
jl_toplevel_eval_flex at /source/src/toplevel.c:1010
ijl_toplevel_eval at /source/src/toplevel.c:1082
ijl_toplevel_eval_in at /source/src/toplevel.c:1127
eval at ./boot.jl:485
exec_options at ./client.jl:295
_start at ./client.jl:558
jfptr__start_108439.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:3359 [inlined]
ijl_apply_generic at /source/src/gf.c:3547
jl_apply at /source/src/julia.h:2244 [inlined]
true_main at /source/src/jlapi.c:922
jl_repl_entrypoint at /source/src/jlapi.c:1081
main at /source/cli/loader_exe.c:58
unknown function (ip: 0x720c14d1b249) at /lib/x86_64-linux-gnu/libc.so.6
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S
Allocations: 4242312 (Pool: 4242161; Big: 151); GC: 5

Testing failed after 23.01s

ERROR: LoadError: Package AtomsIOPython errored during testing (received signal: 11)
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Types.jl:68
  [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2359
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2214 [inlined]
  [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:481
  [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:159
  [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147
  [7] test
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147 [inlined]
  [8] #test#81
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:146 [inlined]
  [9] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:300
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:329
 [12] _start()
    @ Base ./client.jl:558
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval crashed after 202.2s: a segmentation fault happened