Package evaluation to test Molly on Julia 1.14.0-DEV.1354 (1806b0bc31*) started at 2025-12-11T19:50:50.880


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

Installing PkgEval dependencies (TestEnv)...
  Activating project at `~/.julia/environments/v1.14`

Set-up completed after 9.67s


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

Installing Molly...
   Resolving package versions...
    Updating `~/.julia/environments/v1.14/Project.toml`
  [aa0f7f06] + Molly v0.23.0
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [621f4979] + AbstractFFTs v1.5.0
  [6a4ca0a5] + AcceleratedKernels v0.4.3
  [79e6a3ab] + Adapt v4.4.0
  [66dad0bd] + AliasTables v1.1.3
  [dce04be8] + ArgCheck v2.5.0
  [ec485272] + ArnoldiMethod v0.4.0
  [a9b6321e] + Atomix v1.1.2
  [a963bdd2] + AtomsBase v0.5.2
  [a3e0e189] + AtomsCalculators v0.2.3
  [47718e42] + BioGenerics v0.1.5
  [de9282ab] + BioStructures v4.7.0
  [3c28c6f8] + BioSymbols v5.2.0
  [fa961155] + CEnum v0.5.0
  [69e1c6dd] + CellListMap v0.9.15
  [46823bd8] + Chemfiles v0.10.43
  [ae650224] + ChunkSplitters v3.1.2
  [944b1d66] + CodecZlib v0.7.8
  [861a8166] + Combinatorics v1.0.3
  [34da2185] + Compat v4.18.1
  [187b0558] + ConstructionBase v1.6.0
  [9a962f9c] + DataAPI v1.16.0
  [864edb3b] + DataStructures v0.19.3
  [e2d170a0] + DataValueInterfaces v1.0.0
  [b4f34e82] + Distances v0.10.12
  [31c24e10] + Distributions v0.25.122
  [ffbed154] + DocStringExtensions v0.9.5
  [8f5d6c58] + EzXML v1.2.3
  [7a1cc6ca] + FFTW v1.10.0
  [1a297f60] + FillArrays v1.15.0
  [1fa38f19] + Format v1.3.7
  [0c68f7d7] + GPUArrays v11.3.1
  [46192b85] + GPUArraysCore v0.2.0
  [86223c79] + Graphs v1.13.2
  [076d061b] + HashArrayMappedTries v0.2.0
  [34004b35] + HypergeometricFunctions v0.3.28
  [d25df0c9] + Inflate v0.1.5
  [92d709cd] + IrrationalConstants v0.2.6
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.1
  [63c18a36] + KernelAbstractions v0.9.39
  [929cbde3] + LLVM v9.4.4
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [1914dd2f] + MacroTools v0.5.16
  [e1d29d7a] + Missings v1.2.0
  [aa0f7f06] + Molly v0.23.0
  [b8a86587] + NearestNeighbors v0.4.25
  [bac558e1] + OrderedCollections v1.8.1
  [90014a1f] + PDMats v0.11.36
  [d96e819e] + Parameters v0.12.3
  [7b2266bf] + PeriodicTable v1.2.1
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [92933f4c] + ProgressMeter v1.11.0
  [43287f4e] + PtrArrays v1.3.0
  [1fd47b50] + QuadGK v2.11.2
  [3cdcf5f2] + RecipesBase v1.3.4
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [79098fc4] + Rmath v0.9.0
  [7e506255] + ScopedValues v1.5.0
  [efcf1570] + Setfield v1.1.2
  [64031d72] + SimpleCrystals v0.4.5
  [699a6c99] + SimpleTraits v0.9.5
  [a2af1166] + SortingAlgorithms v1.2.2
  [276daf66] + SpecialFunctions v2.6.1
  [90137ffa] + StaticArrays v1.9.15
  [1e83bf80] + StaticArraysCore v1.4.4
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.8.0
  [2913bbd2] + StatsBase v0.34.9
  [4c63d2b9] + StatsFuns v1.5.2
  [09ab397b] + StructArrays v0.7.2
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [1c621080] + TestItems v1.0.0
  [3bb67fe8] + TranscodingStreams v0.11.3
  [3a884ed6] + UnPack v1.0.2
  [1986cc42] + Unitful v1.27.0
  [a7773ee8] + UnitfulAtomic v1.0.0
  [013be700] + UnsafeAtomics v0.3.0
  [78a364fa] + Chemfiles_jll v0.10.4+0
  [f5851436] + FFTW_jll v3.3.11+0
  [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0
  [dad2f222] + LLVMExtra_jll v0.0.38+0
  [94ce4f54] + Libiconv_jll v1.18.0+0
  [856f044c] + MKL_jll v2025.2.0+0
  [efe28fd5] + OpenSpecFun_jll v0.5.6+0
  [f50d1b31] + Rmath_jll v0.5.1+0
  [02c8fc9c] + XML2_jll v2.15.1+0
  [1317d2d5] + oneTBB_jll v2022.0.0+1
  [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 v1.7.0
  [7b1f6079] + FileWatching v1.11.0
  [9fa8497b] + Future v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0
  [4af54fe1] + LazyArtifacts v1.11.0
  [b27032c2] + LibCURL v1.0.0
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.13.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [ca575930] + NetworkOptions v1.3.0
  [44cfe95a] + Pkg v1.14.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v1.0.0
  [9e88b42a] + Serialization v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [2f01184e] + SparseArrays v1.13.0
  [f489334b] + StyledStrings v1.13.0
  [4607b0f0] + SuiteSparse
  [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 v8.17.0+0
  [e37daf67] + LibGit2_jll v1.9.1+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.12.2
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [05823500] + OpenLibm_jll v0.8.7+0
  [458c3c95] + OpenSSL_jll v3.5.4+0
  [efcefdf7] + PCRE2_jll v10.47.0+0
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [3161d3a3] + Zstd_jll v1.5.7+1
  [8e850b90] + libblastrampoline_jll v5.15.0+0
  [8e850ede] + nghttp2_jll v1.68.0+1
  [3f19e933] + p7zip_jll v17.7.0+0

Installation completed after 5.89s


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

ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing)
The function `setindex!` exists, but no method is defined for this combination of argument types.
Stacktrace:
 [1] top-level scope
   @ /PkgEval.jl/scripts/precompile.jl:10
 [2] include(mod::Module, _path::String)
   @ Base ./Base.jl:309
 [3] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:344
 [4] _start()
   @ Base ./client.jl:577
in expression starting at /PkgEval.jl/scripts/precompile.jl:6

caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull)
The function `setindex!` exists, but no method is defined for this combination of argument types.
Stacktrace:
 [1] top-level scope
   @ /PkgEval.jl/scripts/precompile.jl:7
 [2] include(mod::Module, _path::String)
   @ Base ./Base.jl:309
 [3] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:344
 [4] _start()
   @ Base ./client.jl:577

Precompilation failed after 13.17s



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

     Testing Molly

Testing failed after 12.45s

ERROR: LoadError: `LLVM_jll=86de99a1-58d6-5da7-8064-bd56ce2e322c` depends on `libLLVM_jll=8f36deef-c2a5-5394-99ed-8e07531fb29a`, but no such entry exists in the manifest.
Stacktrace:
  [1] pkgerror(::String, ::Vararg{String})
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68
  [2] validate_manifest(julia_version::VersionNumber, project_hash::Base.SHA1, manifest_format::VersionNumber, stage1::Dict{String, Vector{Pkg.Types.Stage1}}, other::Dict{String, Any}, registries::Dict{String, Pkg.Types.ManifestRegistryEntry})
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/manifest.jl:198
  [3] Pkg.Types.Manifest(raw::Dict{String, Any}, f_or_io::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/manifest.jl:299
  [4] read_manifest(f_or_io::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/manifest.jl:322
  [5] Pkg.Types.EnvCache(env::Nothing)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:455
  [6] EnvCache
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:422 [inlined]
  [7] #show_update#282
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3602 [inlined]
  [8] kwcall(::@NamedTuple{io::Base.DevNull, hidden_upgrades_info::Bool}, ::typeof(Pkg.Operations.show_update), env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance})
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3601
  [9] up(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}, level::UpgradeLevel; skip_writing_project::Bool, preserve::Nothing)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2484
 [10] up
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2451 [inlined]
 [11] up(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; level::UpgradeLevel, mode::PackageMode, preserve::Nothing, update_registry::Bool, skip_writing_project::Bool, kwargs::@Kwargs{io::Base.DevNull})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:465
 [12] up
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:433 [inlined]
 [13] up
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:177 [inlined]
 [14] #resolve#170
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:471 [inlined]
 [15] resolve
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:470 [inlined]
 [16] (::Pkg.Operations.var"#215#216"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#230#231"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, PackageSpec}, Pkg.Types.Context, PackageSpec})()
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2801
 [17] with_temp_env(fn::Pkg.Operations.var"#215#216"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#230#231"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, PackageSpec}, Pkg.Types.Context, PackageSpec}, temp_env::String)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2671
 [18] (::Pkg.Operations.var"#211#212"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#230#231"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, PackageSpec}, Pkg.Types.Context, PackageSpec, String, String})(tmp::String)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2785
 [19] mktempdir(fn::Pkg.Operations.var"#211#212"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#230#231"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, PackageSpec}, Pkg.Types.Context, PackageSpec, String, String}, parent::String; prefix::String)
    @ Base.Filesystem ./file.jl:936
 [20] mktempdir(fn::Function, parent::String)
    @ Base.Filesystem ./file.jl:932
 [21] sandbox(fn::Function, ctx::Pkg.Types.Context, target::PackageSpec, sandbox_path::String, sandbox_project_override::Nothing; preferences::Dict{String, Any}, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2732
 [22] kwcall(::@NamedTuple{preferences::Dict{String, Any}, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool}, ::typeof(Pkg.Operations.sandbox), fn::Function, ctx::Pkg.Types.Context, target::PackageSpec, sandbox_path::String, sandbox_project_override::Nothing)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2722
 [23] test(ctx::Pkg.Types.Context, pkgs::Vector{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/v1.14/Pkg/src/Operations.jl:2996
 [24] test
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2902 [inlined]
 [25] test(ctx::Pkg.Types.Context, pkgs::Vector{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/v1.14/Pkg/src/API.jl:572
 [26] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548
 [27] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172
 [28] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161
 [29] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160
 [30] test
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined]
 [31] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String)
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159
 [32] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:237
 [33] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [34] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:344
 [35] _start()
    @ Base ./client.jl:577
in expression starting at /PkgEval.jl/scripts/evaluate.jl:228

PkgEval failed after 64.57s: there were unidentified errors