Package evaluation of PyBoltz on Julia 1.10.9 (96dc2d8c45*) started at 2025-06-06T14:52:40.366


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 4.99s


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

Installing PyBoltz...
   Resolving package versions...
    Updating `~/.julia/environments/v1.10/Project.toml`
  [0bca4874] + PyBoltz v0.1.1
    Updating `~/.julia/environments/v1.10/Manifest.toml`
  [34da2185] + Compat v4.16.0
  [992eb4ea] + CondaPkg v0.2.29
  [9a962f9c] + DataAPI v1.16.0
  [e2d170a0] + DataValueInterfaces v1.0.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.0
  [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 v1.2.1
  [21216c6a] + Preferences v1.4.3
  [0bca4874] + PyBoltz v0.1.1
  [6099a3de] + PythonCall v0.9.25
  [ae029012] + Requires v1.3.1
  [6c6a2e73] + Scratch v1.2.1
  [69024149] + StringEncodings v0.3.7
  [856f2bd8] + StructTypes v1.11.0
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [e17b2a0c] + UnsafePointers v1.0.0
  [ddb6d928] + YAML v0.4.14
  [94ce4f54] + Libiconv_jll v1.18.0+0
  [f8abcde7] + micromamba_jll v1.5.8+0
  [4d7b5844] + pixi_jll v0.41.3+0
  [0dad84c5] + ArgTools v1.1.1
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching
  [b77e0a4c] + InteractiveUtils
  [4af54fe1] + LazyArtifacts
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2
  [8f399da3] + Libdl
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [ca575930] + NetworkOptions v1.2.0
  [44cfe95a] + Pkg v1.10.0
  [de0858da] + Printf
  [3fa0cd96] + REPL
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [6462fe0b] + Sockets
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [deac9b47] + LibCURL_jll v8.4.0+0
  [e37daf67] + LibGit2_jll v1.6.4+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.2+1
  [14a3606d] + MozillaCACerts_jll v2023.1.10
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850ede] + nghttp2_jll v1.52.0+1
  [3f19e933] + p7zip_jll v17.4.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

Installation completed after 7.96s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 160.54s


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

     Testing PyBoltz
      Status `/tmp/jl_9FNe4y/Project.toml`
  [00701ae9] BioAlignments v3.1.0
  [7e6ae17a] BioSequences v3.4.1
  [de9282ab] BioStructures v4.5.0
  [34da2185] Compat v4.16.0
  [992eb4ea] CondaPkg v0.2.29
  [0bca4874] PyBoltz v0.1.1
  [6099a3de] PythonCall v0.9.25
  [6c6a2e73] Scratch v1.2.1
  [ddb6d928] YAML v0.4.14
  [1d8dad79] TMscore_jll v1.0.0+0
  [8dfed614] Test
      Status `/tmp/jl_9FNe4y/Manifest.toml`
  [00701ae9] BioAlignments v3.1.0
  [47718e42] BioGenerics v0.1.5
  [7e6ae17a] BioSequences v3.4.1
  [de9282ab] BioStructures v4.5.0
  [3c28c6f8] BioSymbols v5.2.0
  [944b1d66] CodecZlib v0.7.8
  [34da2185] Compat v4.16.0
  [992eb4ea] CondaPkg v0.2.29
  [9a962f9c] DataAPI v1.16.0
  [e2d170a0] DataValueInterfaces v1.0.0
  [1fa38f19] Format v1.3.7
  [524e6230] IntervalTrees v1.1.0
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.7.0
  [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 v1.2.1
  [21216c6a] Preferences v1.4.3
  [0bca4874] PyBoltz v0.1.1
  [6099a3de] PythonCall v0.9.25
  [3cdcf5f2] RecipesBase v1.3.4
  [ae029012] Requires v1.3.1
  [6c6a2e73] Scratch v1.2.1
  [69024149] StringEncodings v0.3.7
  [856f2bd8] StructTypes v1.11.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.1
  [3bb67fe8] TranscodingStreams v0.11.3
  [7200193e] Twiddle v1.1.2
  [e17b2a0c] UnsafePointers v1.0.0
  [ddb6d928] YAML v0.4.14
  [94ce4f54] Libiconv_jll v1.18.0+0
  [1d8dad79] TMscore_jll v1.0.0+0
  [f8abcde7] micromamba_jll v1.5.8+0
  [4d7b5844] pixi_jll v0.41.3+0
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching
  [b77e0a4c] InteractiveUtils
  [4af54fe1] LazyArtifacts
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.10.0
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [6462fe0b] Sockets
  [2f01184e] SparseArrays v1.10.0
  [10745b16] Statistics v1.10.0
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] LibCURL_jll v8.4.0+0
  [e37daf67] LibGit2_jll v1.6.4+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.2+1
  [14a3606d] MozillaCACerts_jll v2023.1.10
  [4536629a] OpenBLAS_jll v0.3.23+4
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.52.0+1
  [3f19e933] p7zip_jll v17.4.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
    CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PyBoltz/VJsW0/CondaPkg.toml
    CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/L4cjh/CondaPkg.toml
    CondaPkg Resolving changes
             + boltz (pip)
             + libstdcxx-ng
             + python
             + uv
    CondaPkg Initialising pixi
             │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /tmp/jl_9FNe4y/.CondaPkg
✔ Created /tmp/jl_9FNe4y/.CondaPkg/pixi.toml
    CondaPkg Wrote /tmp/jl_9FNe4y/.CondaPkg/pixi.toml
             │ [dependencies]
             │ uv = ">=0.4"
             │ libstdcxx-ng = ">=3.4,<14.0"
             │ 
             │     [dependencies.python]
             │     channel = "conda-forge"
             │     build = "*cpython*"
             │     version = ">=3.8,<4"
             │ 
             │ [project]
             │ name = ".CondaPkg"
             │ platforms = ["linux-64"]
             │ channels = ["conda-forge"]
             │ channel-priority = "strict"
             │ description = "automatically generated by CondaPkg.jl"
             │ 
             │ [pypi-dependencies]
             └ boltz = "~=1.0.0"
    CondaPkg Installing packages
             │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ install
             └ --manifest-path /tmp/jl_9FNe4y/.CondaPkg/pixi.toml
✔ The default environment has been installed.

[216] signal (11.1): Segmentation fault
in expression starting at /home/pkgeval/.julia/packages/PyBoltz/VJsW0/test/runtests.jl:1
_PyGCHead_SET_PREV at /usr/local/src/conda/python-3.12.11/Include/internal/pycore_gc.h:74 [inlined]
_PyObject_GC_UNTRACK at /usr/local/src/conda/python-3.12.11/Include/internal/pycore_object.h:259 [inlined]
method_dealloc at /usr/local/src/conda/python-3.12.11/Objects/classobject.c:236
_PyEval_EvalFrameDefault at /home/conda/feedstock_root/build_artifacts/python-split_1749046816465/work/build-shared/Python/bytecodes.c:209
_PyObject_VectorcallTstate at /usr/local/src/conda/python-3.12.11/Include/internal/pycore_call.h:92 [inlined]
object_vacall at /usr/local/src/conda/python-3.12.11/Objects/call.c:850
PyObject_CallMethodObjArgs at /usr/local/src/conda/python-3.12.11/Objects/call.c:911
import_find_and_load at /usr/local/src/conda/python-3.12.11/Python/import.c:2793 [inlined]
PyImport_ImportModuleLevelObject at /usr/local/src/conda/python-3.12.11/Python/import.c:2876
builtin___import___impl at /usr/local/src/conda/python-3.12.11/Python/bltinmodule.c:276 [inlined]
builtin___import__ at /usr/local/src/conda/python-3.12.11/Python/clinic/bltinmodule.c.h:107
cfunction_vectorcall_FASTCALL_KEYWORDS at /usr/local/src/conda/python-3.12.11/Objects/methodobject.c:438
_PyObject_VectorcallTstate at /usr/local/src/conda/python-3.12.11/Include/internal/pycore_call.h:92 [inlined]
_PyObject_CallFunctionVa at /usr/local/src/conda/python-3.12.11/Objects/call.c:562 [inlined]
PyObject_CallFunction at /usr/local/src/conda/python-3.12.11/Objects/call.c:584
PyImport_Import at /usr/local/src/conda/python-3.12.11/Python/import.c:3062
PyImport_Import at /home/pkgeval/.julia/packages/PythonCall/L4cjh/src/C/pointers.jl:303
unknown function (ip: 0x75bbe97e97d5)
_jl_invoke at /source/src/gf.c:2876 [inlined]
ijl_invoke at /source/src/gf.c:2902
unknown function (ip: 0x75bbe97e8b39)
unknown function (ip: 0x75bbe97e8906)
macro expansion at /home/pkgeval/.julia/packages/PythonCall/L4cjh/src/Core/Py.jl:132 [inlined]
pyimport at /home/pkgeval/.julia/packages/PythonCall/L4cjh/src/Core/builtins.jl:1561
unknown function (ip: 0x75bbe97e8835)
_jl_invoke at /source/src/gf.c:2876 [inlined]
ijl_invoke at /source/src/gf.c:2902
unknown function (ip: 0x75bbe97e87b9)
unknown function (ip: 0x75bbe97e861a)
pyimport at /home/pkgeval/.julia/packages/PythonCall/L4cjh/src/Core/builtins.jl:1562 [inlined]
init_consts at /home/pkgeval/.julia/packages/PythonCall/L4cjh/src/Core/consts.jl:205
unknown function (ip: 0x75bbe97e85d2)
_jl_invoke at /source/src/gf.c:2876 [inlined]
ijl_invoke at /source/src/gf.c:2902
unknown function (ip: 0x75bbe97e6ee9)
unknown function (ip: 0x75bbe97e6d8d)
__init__ at /home/pkgeval/.julia/packages/PythonCall/L4cjh/src/Core/Core.jl:42
unknown function (ip: 0x75bbe97e6d2f)
_jl_invoke at /source/src/gf.c:2876 [inlined]
ijl_apply_generic at /source/src/gf.c:3077
jl_apply at /source/src/julia.h:1982 [inlined]
jl_module_run_initializer at /source/src/toplevel.c:76
run_module_init at ./loading.jl:1193
register_restored_modules at ./loading.jl:1181
_include_from_serialized at ./loading.jl:1126
_tryrequire_from_serialized at ./loading.jl:1551
_require_search_from_serialized at ./loading.jl:1644
_require at ./loading.jl:2008
__require_prelocked at ./loading.jl:1882
jfptr___require_prelocked_81107.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2876 [inlined]
ijl_apply_generic at /source/src/gf.c:3077
jl_apply at /source/src/julia.h:1982 [inlined]
jl_f__call_in_world at /source/src/builtins.c:831
#invoke_in_world#3 at ./essentials.jl:926 [inlined]
invoke_in_world at ./essentials.jl:923 [inlined]
_require_prelocked at ./loading.jl:1873
macro expansion at ./loading.jl:1860 [inlined]
macro expansion at ./lock.jl:267 [inlined]
__require at ./loading.jl:1823
jfptr___require_81070.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2876 [inlined]
ijl_apply_generic at /source/src/gf.c:3077
jl_apply at /source/src/julia.h:1982 [inlined]
jl_f__call_in_world at /source/src/builtins.c:831
#invoke_in_world#3 at ./essentials.jl:926 [inlined]
invoke_in_world at ./essentials.jl:923 [inlined]
require at ./loading.jl:1816
jfptr_require_81067.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2876 [inlined]
ijl_apply_generic at /source/src/gf.c:3077
jl_apply at /source/src/julia.h:1982 [inlined]
call_require at /source/src/toplevel.c:481 [inlined]
eval_import_path at /source/src/toplevel.c:518
jl_toplevel_eval_flex at /source/src/toplevel.c:752
jl_toplevel_eval_flex at /source/src/toplevel.c:877
ijl_toplevel_eval_in at /source/src/toplevel.c:985
eval at ./boot.jl:385 [inlined]
include_string at ./loading.jl:2146
_jl_invoke at /source/src/gf.c:2876 [inlined]
ijl_apply_generic at /source/src/gf.c:3077
_include at ./loading.jl:2206
include at ./client.jl:494
unknown function (ip: 0x75bbe9755125)
_jl_invoke at /source/src/gf.c:2876 [inlined]
ijl_apply_generic at /source/src/gf.c:3077
jl_apply at /source/src/julia.h:1982 [inlined]
do_call at /source/src/interpreter.c:126
eval_value at /source/src/interpreter.c:223
eval_stmt_value at /source/src/interpreter.c:174 [inlined]
eval_body at /source/src/interpreter.c:635
jl_interpret_toplevel_thunk at /source/src/interpreter.c:775
jl_toplevel_eval_flex at /source/src/toplevel.c:934
jl_toplevel_eval_flex at /source/src/toplevel.c:877
ijl_toplevel_eval_in at /source/src/toplevel.c:985
eval at ./boot.jl:385 [inlined]
exec_options at ./client.jl:296
_start at ./client.jl:557
jfptr__start_83099.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2876 [inlined]
ijl_apply_generic at /source/src/gf.c:3077
jl_apply at /source/src/julia.h:1982 [inlined]
true_main at /source/src/jlapi.c:582
jl_repl_entrypoint at /source/src/jlapi.c:731
main at /source/cli/loader_exe.c:58
unknown function (ip: 0x75bbea59d249)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 4278190 (Pool: 4274410; Big: 3780); GC: 6

Testing failed after 36.39s

ERROR: LoadError: Package PyBoltz errored during testing (received signal: 11)
Stacktrace:
 [1] pkgerror(msg::String)
   @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70
 [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/v1.10/Pkg/src/Operations.jl:2034
 [3] test
   @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [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::Base.PipeEndpoint})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444
 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159
 [6] test
   @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined]
 [7] #test#74
   @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined]
 [8] top-level scope
   @ /PkgEval.jl/scripts/evaluate.jl:219
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval crashed after 248.62s: a segmentation fault happened