Package evaluation of XtalsPyTools on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T15:58:59.952


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.88s


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

Installing XtalsPyTools...
   Resolving package versions...
   Installed Conda ── v1.10.2
   Installed PyCall ─ v1.96.4
    Updating `~/.julia/environments/v1.11/Project.toml`
  [eeb819d4] + XtalsPyTools v0.0.4
    Updating `~/.julia/environments/v1.11/Manifest.toml`
⌅ [4c88cf16] + Aqua v0.5.6
  [ec485272] + ArnoldiMethod v0.4.0
⌅ [a963bdd2] + AtomsBase v0.4.2
  [99c8bb3a] + Bio3DView v1.0.0
  [336ed68f] + CSV v0.10.15
  [944b1d66] + CodecZlib v0.7.8
  [34da2185] + Compat v4.16.0
  [8f4d0f93] + Conda v1.10.2
  [a8cc5b0e] + Crayons v4.1.1
  [9a962f9c] + DataAPI v1.16.0
  [a93c6f00] + DataFrames v1.7.0
  [864edb3b] + DataStructures v0.18.22
  [e2d170a0] + DataValueInterfaces v1.0.0
  [3064a664] + FIGlet v0.2.2
  [5789e2e9] + FileIO v1.17.0
  [48062228] + FilePathsBase v0.9.24
  [86223c79] + Graphs v1.12.1
  [d25df0c9] + Inflate v0.1.5
  [842dd82b] + InlineStrings v1.4.3
  [41ab1584] + InvertedIndices v1.3.1
  [82899510] + IteratorInterfaceExtensions v1.0.0
⌅ [033835bb] + JLD2 v0.4.54
  [682c06a0] + JSON v0.21.4
  [b964fa9f] + LaTeXStrings v1.4.0
  [1914dd2f] + MacroTools v0.5.15
⌅ [626554b9] + MetaGraphs v0.7.2
  [e1d29d7a] + Missings v1.2.0
  [bac558e1] + OrderedCollections v1.8.0
  [69de0a69] + Parsers v2.8.1
  [7b2266bf] + PeriodicTable v1.2.1
  [2dfb63ee] + PooledArrays v1.4.3
  [91cefc8d] + PrecompileSignatures v3.0.3
⌅ [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [08abe8d2] + PrettyTables v2.4.0
  [438e738f] + PyCall v1.96.4
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [91c51154] + SentinelArrays v1.4.8
  [699a6c99] + SimpleTraits v0.9.4
  [a2af1166] + SortingAlgorithms v1.2.1
  [90137ffa] + StaticArrays v1.9.13
  [1e83bf80] + StaticArraysCore v1.4.3
  [10745b16] + Statistics v1.11.1
  [892a3eda] + StringManipulation v0.4.1
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.0
  [3bb67fe8] + TranscodingStreams v0.11.3
  [1986cc42] + Unitful v1.22.0
  [a7773ee8] + UnitfulAtomic v1.0.0
  [81def892] + VersionParsing v1.3.0
  [ea10d353] + WeakRefStrings v1.4.2
  [76eceee3] + WorkerUtilities v1.6.1
  [ede5f01d] + Xtals v0.5.1
  [eeb819d4] + XtalsPyTools v0.0.4
  [0dad84c5] + ArgTools v1.1.2
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [8ba89e20] + Distributed v1.11.0
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching v1.11.0
  [9fa8497b] + Future v1.11.0
  [b77e0a4c] + InteractiveUtils 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 v1.11.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [1a1011a3] + SharedArrays v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [2f01184e] + SparseArrays 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 v1.1.1+0
  [deac9b47] + LibCURL_jll v8.6.0+0
  [e37daf67] + LibGit2_jll v1.7.2+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.6+0
  [14a3606d] + MozillaCACerts_jll v2023.12.12
  [4536629a] + OpenBLAS_jll v0.3.27+1
  [bea87d4a] + SuiteSparse_jll v7.7.0+0
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.11.0+0
  [8e850ede] + nghttp2_jll v1.59.0+0
  [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`
    Building Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/b19db3927f0db4151cb86d073689f2428e524576/build.log`
    Building PyCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/9816a3826b0ebf49ab4926e2b18842ad8b5c8f04/build.log`

Installation completed after 68.64s


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# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 40.6s


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

     Testing XtalsPyTools
      Status `/tmp/jl_atwDwC/Project.toml`
⌅ [4c88cf16] Aqua v0.5.6
  [3064a664] FIGlet v0.2.2
  [86223c79] Graphs v1.12.1
  [91cefc8d] PrecompileSignatures v3.0.3
  [438e738f] PyCall v1.96.4
  [ede5f01d] Xtals v0.5.1
  [eeb819d4] XtalsPyTools v0.0.4
  [de0858da] Printf v1.11.0
  [8dfed614] Test v1.11.0
  [cf7118a7] UUIDs v1.11.0
      Status `/tmp/jl_atwDwC/Manifest.toml`
⌅ [4c88cf16] Aqua v0.5.6
  [ec485272] ArnoldiMethod v0.4.0
⌅ [a963bdd2] AtomsBase v0.4.2
  [99c8bb3a] Bio3DView v1.0.0
  [336ed68f] CSV v0.10.15
  [944b1d66] CodecZlib v0.7.8
  [34da2185] Compat v4.16.0
  [8f4d0f93] Conda v1.10.2
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.7.0
  [864edb3b] DataStructures v0.18.22
  [e2d170a0] DataValueInterfaces v1.0.0
  [3064a664] FIGlet v0.2.2
  [5789e2e9] FileIO v1.17.0
  [48062228] FilePathsBase v0.9.24
  [86223c79] Graphs v1.12.1
  [d25df0c9] Inflate v0.1.5
  [842dd82b] InlineStrings v1.4.3
  [41ab1584] InvertedIndices v1.3.1
  [82899510] IteratorInterfaceExtensions v1.0.0
⌅ [033835bb] JLD2 v0.4.54
  [682c06a0] JSON v0.21.4
  [b964fa9f] LaTeXStrings v1.4.0
  [1914dd2f] MacroTools v0.5.15
⌅ [626554b9] MetaGraphs v0.7.2
  [e1d29d7a] Missings v1.2.0
  [bac558e1] OrderedCollections v1.8.0
  [69de0a69] Parsers v2.8.1
  [7b2266bf] PeriodicTable v1.2.1
  [2dfb63ee] PooledArrays v1.4.3
  [91cefc8d] PrecompileSignatures v3.0.3
⌅ [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [08abe8d2] PrettyTables v2.4.0
  [438e738f] PyCall v1.96.4
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.1
  [91c51154] SentinelArrays v1.4.8
  [699a6c99] SimpleTraits v0.9.4
  [a2af1166] SortingAlgorithms v1.2.1
  [90137ffa] StaticArrays v1.9.13
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [892a3eda] StringManipulation v0.4.1
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [3bb67fe8] TranscodingStreams v0.11.3
  [1986cc42] Unitful v1.22.0
  [a7773ee8] UnitfulAtomic v1.0.0
  [81def892] VersionParsing v1.3.0
  [ea10d353] WeakRefStrings v1.4.2
  [76eceee3] WorkerUtilities v1.6.1
  [ede5f01d] Xtals v0.5.1
  [eeb819d4] XtalsPyTools v0.0.4
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [8ba89e20] Distributed v1.11.0
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching v1.11.0
  [9fa8497b] Future v1.11.0
  [b77e0a4c] InteractiveUtils 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 v1.11.0
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [1a1011a3] SharedArrays v1.11.0
  [6462fe0b] Sockets v1.11.0
  [2f01184e] SparseArrays 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 v1.1.1+0
  [deac9b47] LibCURL_jll v8.6.0+0
  [e37daf67] LibGit2_jll v1.7.2+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.6+0
  [14a3606d] MozillaCACerts_jll v2023.12.12
  [4536629a] OpenBLAS_jll v0.3.27+1
  [bea87d4a] SuiteSparse_jll v7.7.0+0
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.59.0+0
  [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...
┌ Warning: Error loading scipy. Some functionaltiy may be missing.
└ @ XtalsPyTools ~/.julia/packages/XtalsPyTools/HLVFH/src/pydeps.jl:17
┌ Warning: Error loading pymatgen. Some functionaltiy may be missing.
└ @ XtalsPyTools ~/.julia/packages/XtalsPyTools/HLVFH/src/pydeps.jl:17
  _    _____   __    _     __   ___   _    _____  ___   ___   _     __
 \ \_/  | |   / /\  | |   ( (` | |_) \ \_/  | |  / / \ / / \ | |   ( (`
 /_/ \  |_|  /_/--\ |_|__ _)_) |_|    |_|   |_|  \_\_/ \_\_/ |_|__ _)_)

[ Info: Running test/misc.jl
┌ Warning: Error loading bogus_python_package. Some functionaltiy may be missing.
└ @ XtalsPyTools ~/.julia/packages/XtalsPyTools/HLVFH/src/pydeps.jl:17
Test Summary:   | Pass  Total  Time
pydep functions |    2      2  0.3s
[ Info: Running test/infer_geometry_based_bonds!.jl
Test Summary: | Pass  Total   Time
scipy dep     |    1      1  37.9s
NiPyC2 Tests: Error During Test at /home/pkgeval/.julia/packages/XtalsPyTools/HLVFH/test/infer_geometry_based_bonds!.jl:26
  Got exception outside of a @test
  Python dependency scipy not loaded.
  Stacktrace:
    [1] error(s::String)
      @ Base ./error.jl:35
    [2] _shared_voronoi_faces(ids_neighbors::Vector{Int64}, xs::Vector{Vector{Float64}})
      @ XtalsPyTools ~/.julia/packages/XtalsPyTools/HLVFH/src/infer_geometry_based_bonds!.jl:97
    [3] bonded_atoms(crystal::Xtals.Crystal, i::Int64, dm::Matrix{Float64}, r::Float64, pad::Float64, covalent_radii::Dict{Symbol, Float64})
      @ XtalsPyTools ~/.julia/packages/XtalsPyTools/HLVFH/src/infer_geometry_based_bonds!.jl:63
    [4] infer_geometry_based_bonds!(crystal::Xtals.Crystal, include_bonds_across_periodic_boundaries::Bool; r::Float64, pad::Float64, covalent_radii::Dict{Symbol, Float64})
      @ XtalsPyTools ~/.julia/packages/XtalsPyTools/HLVFH/src/infer_geometry_based_bonds!.jl:28
    [5] infer_geometry_based_bonds!(crystal::Xtals.Crystal, include_bonds_across_periodic_boundaries::Bool)
      @ XtalsPyTools ~/.julia/packages/XtalsPyTools/HLVFH/src/infer_geometry_based_bonds!.jl:15
    [6] macro expansion
      @ ~/.julia/packages/XtalsPyTools/HLVFH/test/infer_geometry_based_bonds!.jl:49 [inlined]
    [7] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined]
    [8] top-level scope
      @ ~/.julia/packages/XtalsPyTools/HLVFH/test/infer_geometry_based_bonds!.jl:28
    [9] include(fname::String)
      @ Main ./sysimg.jl:38
   [10] top-level scope
      @ ~/.julia/packages/XtalsPyTools/HLVFH/test/runtests.jl:11
   [11] include(fname::String)
      @ Main ./sysimg.jl:38
   [12] top-level scope
      @ none:6
   [13] eval
      @ ./boot.jl:430 [inlined]
   [14] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:296
   [15] _start()
      @ Base ./client.jl:531
Test Summary: | Pass  Error  Total   Time
NiPyC2 Tests  |    2      1      3  19.6s
ERROR: LoadError: Some tests did not pass: 2 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/XtalsPyTools/HLVFH/test/infer_geometry_based_bonds!.jl:1
in expression starting at /home/pkgeval/.julia/packages/XtalsPyTools/HLVFH/test/runtests.jl:9

Testing failed after 92.73s

ERROR: LoadError: Package XtalsPyTools errored during testing
Stacktrace:
 [1] pkgerror(msg::String)
   @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/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/v1.11/Pkg/src/Operations.jl:2124
 [3] test
   @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [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/v1.11/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/v1.11/Pkg/src/API.jl:159
 [6] test
   @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined]
 [7] #test#74
   @ /opt/julia/share/julia/stdlib/v1.11/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 failed after 227.85s: package tests unexpectedly errored