Package evaluation of CellListMap on Julia 1.13.0-DEV.582 (c0a1728d50*) started at 2025-05-14T11:15:12.346


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 11.03s


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

Installing CellListMap...
   Resolving package versions...
    Updating `~/.julia/environments/v1.13/Project.toml`
  [69e1c6dd] + CellListMap v0.9.8
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [69e1c6dd] + CellListMap v0.9.8
  [ae650224] + ChunkSplitters v3.1.2
  [34da2185] + Compat v4.16.0
  [187b0558] + ConstructionBase v1.5.8
  [ffbed154] + DocStringExtensions v0.9.4
  [1914dd2f] + MacroTools v0.5.16
  [bac558e1] + OrderedCollections v1.8.0
  [d96e819e] + Parameters v0.12.3
  [aea7be01] + PrecompileTools v1.3.2
  [21216c6a] + Preferences v1.4.3
  [92933f4c] + ProgressMeter v1.10.4
  [efcf1570] + Setfield v1.1.2
  [90137ffa] + StaticArrays v1.9.13
  [1e83bf80] + StaticArraysCore v1.4.3
  [1c621080] + TestItems v1.0.0
  [3a884ed6] + UnPack v1.0.2
  [56f22d72] + Artifacts v1.11.0
  [ade2ca70] + Dates v1.11.0
  [8ba89e20] + Distributed v1.11.0
  [9fa8497b] + Future v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.12.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [fa267f1f] + TOML v1.0.3
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [8e850b90] + libblastrampoline_jll v5.12.0+0

Installation completed after 4.17s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...
ERROR: LoadError: The following 1 direct dependency failed to precompile:

PDBTools 

Failed to precompile PDBTools [e29189f1-7114-4dbd-93d0-c5673a921a58] to "/home/pkgeval/.julia/compiled/v1.13/PDBTools/jl_1hqkwS" (ProcessExited(1)).
ERROR: LoadError: ArgumentError: Atom N does not have a mass defined
Stacktrace:
  [1] mass(atoms::Vector{PDBTools.Atom{Nothing}})
    @ PDBTools ~/.julia/packages/PDBTools/uEbwn/src/struct_and_iterators/Atom.jl:740
  [2] center_of_mass(atoms::Vector{PDBTools.Atom{Nothing}})
    @ PDBTools ~/.julia/packages/PDBTools/uEbwn/src/tools/tools.jl:112
  [3] macro expansion
    @ ~/.julia/packages/PDBTools/uEbwn/src/package_internals/precompile.jl:10 [inlined]
  [4] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]
  [5] macro expansion
    @ ~/.julia/packages/PDBTools/uEbwn/src/package_internals/precompile.jl:4 [inlined]
  [6] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]
  [7] top-level scope
    @ ~/.julia/packages/PDBTools/uEbwn/src/package_internals/precompile.jl:118
  [8] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [9] top-level scope
    @ ~/.julia/packages/PDBTools/uEbwn/src/PDBTools.jl:108
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [11] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2983
 [12] top-level scope
    @ stdin:5
 [13] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [14] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2829
 [15] include_string
    @ ./loading.jl:2839 [inlined]
 [16] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:329
 [17] _start()
    @ Base ./client.jl:564
in expression starting at /home/pkgeval/.julia/packages/PDBTools/uEbwn/src/package_internals/precompile.jl:1
in expression starting at /home/pkgeval/.julia/packages/PDBTools/uEbwn/src/PDBTools.jl:1
in expression starting at stdin:
in expression starting at /PkgEval.jl/scripts/precompile.jl:37

Precompilation failed after 85.01s



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

     Testing CellListMap
      Status `/tmp/jl_vHdeNL/Project.toml`
  [4c88cf16] Aqua v0.8.12
  [6e4b80f9] BenchmarkTools v1.6.0
  [69e1c6dd] CellListMap v0.9.8
  [46823bd8] Chemfiles v0.10.42
  [ae650224] ChunkSplitters v3.1.2
  [34da2185] Compat v4.16.0
  [ffbed154] DocStringExtensions v0.9.4
  [e30172f5] Documenter v1.11.2
⌅ [f6369f11] ForwardDiff v0.10.38
  [eff96d63] Measurements v2.12.0
  [b8a86587] NearestNeighbors v0.4.21
  [e29189f1] PDBTools v2.9.0
  [d96e819e] Parameters v0.12.3
  [aea7be01] PrecompileTools v1.3.2
  [92933f4c] ProgressMeter v1.10.4
  [efcf1570] Setfield v1.1.2
  [90137ffa] StaticArrays v1.9.13
  [f8b46487] TestItemRunner v1.1.0
  [1c621080] TestItems v1.0.0
  [1986cc42] Unitful v1.22.1
  [37e2e46d] LinearAlgebra v1.12.0
  [9a3f8284] Random v1.11.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_vHdeNL/Manifest.toml`
  [a4c015fc] ANSIColoredPrinters v0.0.1
  [1520ce14] AbstractTrees v0.4.5
  [4c88cf16] Aqua v0.8.12
  [a963bdd2] AtomsBase v0.5.1
  [6e4b80f9] BenchmarkTools v1.6.0
  [49dc2e85] Calculus v0.5.2
  [69e1c6dd] CellListMap v0.9.8
  [46823bd8] Chemfiles v0.10.42
  [ae650224] ChunkSplitters v3.1.2
  [944b1d66] CodecZlib v0.7.8
  [bbf7d656] CommonSubexpressions v0.3.1
  [34da2185] Compat v4.16.0
  [187b0558] ConstructionBase v1.5.8
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [b4f34e82] Distances v0.10.12
  [ffbed154] DocStringExtensions v0.9.4
  [e30172f5] Documenter v1.11.2
  [1fa38f19] Format v1.3.7
⌅ [f6369f11] ForwardDiff v0.10.38
  [d7ba0133] Git v1.4.0
  [b5f81e59] IOCapture v0.2.5
  [842dd82b] InlineStrings v1.4.3
  [92d709cd] IrrationalConstants v0.2.4
  [692b3bcd] JLLWrappers v1.7.0
  [682c06a0] JSON v0.21.4
  [0e77f7df] LazilyInitializedFields v1.3.0
  [2ab3a3ac] LogExpFunctions v0.3.29
  [1914dd2f] MacroTools v0.5.16
  [d0879d2d] MarkdownAST v0.1.2
  [eff96d63] Measurements v2.12.0
  [aea21201] MolSimToolkitShared v1.1.3
  [77ba4419] NaNMath v1.1.3
  [b8a86587] NearestNeighbors v0.4.21
  [bac558e1] OrderedCollections v1.8.0
  [e29189f1] PDBTools v2.9.0
  [d96e819e] Parameters v0.12.3
  [69de0a69] Parsers v2.8.3
  [7b2266bf] PeriodicTable v1.2.1
  [aea7be01] PrecompileTools v1.3.2
  [21216c6a] Preferences v1.4.3
  [92933f4c] ProgressMeter v1.10.4
  [2792f1a3] RegistryInstances v0.1.0
  [ae029012] Requires v1.3.1
  [efcf1570] Setfield v1.1.2
  [276daf66] SpecialFunctions v2.5.1
  [90137ffa] StaticArrays v1.9.13
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.0
  [f8b46487] TestItemRunner v1.1.0
  [1c621080] TestItems v1.0.0
  [3bb67fe8] TranscodingStreams v0.11.3
  [3a884ed6] UnPack v1.0.2
  [1986cc42] Unitful v1.22.1
  [a7773ee8] UnitfulAtomic v1.0.0
  [78a364fa] Chemfiles_jll v0.10.4+0
  [2e619515] Expat_jll v2.6.5+0
  [f8c6e375] Git_jll v2.49.0+0
  [94ce4f54] Libiconv_jll v1.18.0+0
  [9bd350c2] OpenSSH_jll v10.0.1+0
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [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 v1.12.0
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.12.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.3.0
  [44cfe95a] Pkg v1.13.0
  [de0858da] Printf v1.11.0
  [9abbd945] Profile v1.11.0
  [3fa0cd96] REPL v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [6462fe0b] Sockets 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 v1.3.0+1
  [deac9b47] LibCURL_jll v8.12.1+1
  [e37daf67] LibGit2_jll v1.9.0+0
  [29816b5a] LibSSH2_jll v1.11.3+1
  [14a3606d] MozillaCACerts_jll v2025.2.25
  [4536629a] OpenBLAS_jll v0.3.29+0
  [05823500] OpenLibm_jll v0.8.5+0
  [458c3c95] OpenSSL_jll v3.5.0+0
  [efcefdf7] PCRE2_jll v10.44.0+1
  [83775a58] Zlib_jll v1.3.1+2
  [8e850b90] libblastrampoline_jll v5.12.0+0
  [8e850ede] nghttp2_jll v1.65.0+0
  [3f19e933] p7zip_jll v17.5.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...

     WARNING: Ideally, run a multi-threaded test to check the parallel versions.


Precompiling packages...
   3449.7 ms  ✓ BenchmarkTools
  1 dependency successfully precompiled in 4 seconds. 16 already precompiled.
Precompiling packages...
Info Given PDBTools was explicitly requested, output will be shown live 
ERROR: LoadError: ArgumentError: Atom N does not have a mass defined
Stacktrace:
  [1] mass(atoms::Vector{PDBTools.Atom{Nothing}})
    @ PDBTools ~/.julia/packages/PDBTools/uEbwn/src/struct_and_iterators/Atom.jl:740
  [2] center_of_mass(atoms::Vector{PDBTools.Atom{Nothing}})
    @ PDBTools ~/.julia/packages/PDBTools/uEbwn/src/tools/tools.jl:112
  [3] macro expansion
    @ ~/.julia/packages/PDBTools/uEbwn/src/package_internals/precompile.jl:10 [inlined]
  [4] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]
  [5] macro expansion
    @ ~/.julia/packages/PDBTools/uEbwn/src/package_internals/precompile.jl:4 [inlined]
  [6] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]
  [7] top-level scope
    @ ~/.julia/packages/PDBTools/uEbwn/src/package_internals/precompile.jl:118
  [8] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [9] top-level scope
    @ ~/.julia/packages/PDBTools/uEbwn/src/PDBTools.jl:108
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [11] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2983
 [12] top-level scope
    @ stdin:5
 [13] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [14] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2829
 [15] include_string
    @ ./loading.jl:2839 [inlined]
 [16] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:329
 [17] _start()
    @ Base ./client.jl:564
in expression starting at /home/pkgeval/.julia/packages/PDBTools/uEbwn/src/package_internals/precompile.jl:1
in expression starting at /home/pkgeval/.julia/packages/PDBTools/uEbwn/src/PDBTools.jl:1
in expression starting at stdin:5
           ✗ PDBTools
  0 dependencies successfully precompiled in 17 seconds. 33 already precompiled.

ERROR: LoadError: The following 1 direct dependency failed to precompile:

PDBTools 

Failed to precompile PDBTools [e29189f1-7114-4dbd-93d0-c5673a921a58] to "/home/pkgeval/.julia/compiled/v1.13/PDBTools/jl_arTsuJ" (ProcessExited(1)).
ERROR: LoadError: ArgumentError: Atom N does not have a mass defined
Stacktrace:
  [1] mass(atoms::Vector{PDBTools.Atom{Nothing}})
    @ PDBTools ~/.julia/packages/PDBTools/uEbwn/src/struct_and_iterators/Atom.jl:740
  [2] center_of_mass(atoms::Vector{PDBTools.Atom{Nothing}})
    @ PDBTools ~/.julia/packages/PDBTools/uEbwn/src/tools/tools.jl:112
  [3] macro expansion
    @ ~/.julia/packages/PDBTools/uEbwn/src/package_internals/precompile.jl:10 [inlined]
  [4] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]
  [5] macro expansion
    @ ~/.julia/packages/PDBTools/uEbwn/src/package_internals/precompile.jl:4 [inlined]
  [6] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]
  [7] top-level scope
    @ ~/.julia/packages/PDBTools/uEbwn/src/package_internals/precompile.jl:118
  [8] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [9] top-level scope
    @ ~/.julia/packages/PDBTools/uEbwn/src/PDBTools.jl:108
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [11] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2983
 [12] top-level scope
    @ stdin:5
 [13] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [14] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2829
 [15] include_string
    @ ./loading.jl:2839 [inlined]
 [16] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:329
 [17] _start()
    @ Base ./client.jl:564
in expression starting at /home/pkgeval/.julia/packages/PDBTools/uEbwn/src/package_internals/precompile.jl:1
in expression starting at /home/pkgeval/.julia/packages/PDBTools/uEbwn/src/PDBTools.jl:1
in expression starting at stdin:
in expression starting at /home/pkgeval/.julia/packages/CellListMap/FFNdX/src/ParticleSystem.jl:846
in expression starting at /home/pkgeval/.julia/packages/CellListMap/FFNdX/test/runtests.jl:472

Testing failed after 399.39s

ERROR: LoadError: Package CellListMap errored during testing
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Types.jl:68
  [2] 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/v1.13/Pkg/src/Operations.jl:2418
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2273 [inlined]
  [4] 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/v1.13/Pkg/src/API.jl:498
  [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:164
  [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152
  [7] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined]
  [8] #test#81
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:151 [inlined]
  [9] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:331
 [12] _start()
    @ Base ./client.jl:564
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 521.54s: package fails to precompile