Package evaluation of MDLovoFit on Julia 1.13.0-DEV.717 (51214a7524*) started at 2025-06-08T16:18:49.890


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.11s


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

Installing MDLovoFit...
   Resolving package versions...
    Updating `~/.julia/environments/v1.13/Project.toml`
  [55da9f78] + MDLovoFit v0.1.3
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [4c88cf16] + Aqua v0.8.13
  [a963bdd2] + AtomsBase v0.5.1
  [46823bd8] + Chemfiles v0.10.42
  [34da2185] + Compat v4.16.0
  [8bb1440f] + DelimitedFiles v1.9.1
  [ffbed154] + DocStringExtensions v0.9.5
  [1fa38f19] + Format v1.3.7
  [842dd82b] + InlineStrings v1.4.3
  [692b3bcd] + JLLWrappers v1.7.0
  [55da9f78] + MDLovoFit v0.1.3
  [aea21201] + MolSimToolkitShared v1.1.3
  [bac558e1] + OrderedCollections v1.8.1
⌅ [e29189f1] + PDBTools v2.9.0
  [d96e819e] + Parameters v0.12.3
  [7b2266bf] + PeriodicTable v1.2.1
  [aea7be01] + PrecompileTools v1.3.2
  [21216c6a] + Preferences v1.4.3
  [ae029012] + Requires v1.3.1
  [90137ffa] + StaticArrays v1.9.13
  [1e83bf80] + StaticArraysCore v1.4.3
  [10745b16] + Statistics v1.11.1
  [1c621080] + TestItems v1.0.0
  [3a884ed6] + UnPack v1.0.2
  [1986cc42] + Unitful v1.22.1
  [a7773ee8] + UnitfulAtomic v1.0.0
  [78a364fa] + Chemfiles_jll v0.10.4+0
  [d8780812] + MDLovoFit_jll v20.1.1+0
  [0dad84c5] + ArgTools v1.1.2
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [f43a241f] + Downloads v1.7.0
  [7b1f6079] + FileWatching 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
  [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 v1.3.0+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 v2025.5.20
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [458c3c95] + OpenSSL_jll v3.5.0+0
  [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. To see why use `status --outdated -m`

Installation completed after 4.08s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...
ERROR: LoadError: The following 2 direct dependencies failed to precompile:

PDBTools 

Failed to precompile PDBTools [e29189f1-7114-4dbd-93d0-c5673a921a58] to "/home/pkgeval/.julia/compiled/v1.13/PDBTools/jl_Uptntk" (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:3000
 [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:2846
 [15] include_string
    @ ./loading.jl:2856 [inlined]
 [16] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:322
 [17] _start()
    @ Base ./client.jl:557
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
MDLovoFit 

Failed to precompile MDLovoFit [55da9f78-c647-4a46-be5d-0de490449a34] to "/home/pkgeval/.julia/compiled/v1.13/MDLovoFit/jl_hl4ZnO" (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::String)
    @ Base ./loading.jl:3000
 [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:2846
 [15] include_string
    @ ./loading.jl:2856 [inlined]
 [16] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:322
 [17] _start()
    @ Base ./client.jl:557
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
ERROR: LoadError: Failed to precompile PDBTools [e29189f1-7114-4dbd-93d0-c5673a921a58] to "/home/pkgeval/.julia/compiled/v1.13/PDBTools/jl_El1aWw" (ProcessExited(1)).
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3287
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})()
    @ Base ./loading.jl:2652
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:94
  [5] #mkpidlock#7
    @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:89 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:115
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1282 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1274 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3858
 [10] maybe_cachefile_lock
    @ ./loading.jl:3855 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2638
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2466
 [13] macro expansion
    @ ./loading.jl:2394 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2359
 [16] require
    @ ./loading.jl:2335 [inlined]
 [17] eval_import_path
    @ ./module.jl:36 [inlined]
 [18] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base ./module.jl:60
 [19] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})
    @ Base ./module.jl:101
 [20] top-level scope
    @ ~/.julia/packages/MDLovoFit/no3UY/src/MDLovoFit.jl:7
 [21] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [22] 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:3000
 [23] top-level scope
    @ stdin:5
 [24] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2846
 [26] include_string
    @ ./loading.jl:2856 [inlined]
 [27] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:322
 [28] _start()
    @ Base ./client.jl:557
in expression starting at /home/pkgeval/.julia/packages/MDLovoFit/no3UY/src/MDLovoFit.jl:1
in expression starting at stdin:5
in expression starting at /PkgEval.jl/scripts/precompile.jl:37

Precompilation failed after 70.17s



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

     Testing MDLovoFit
      Status `/tmp/jl_CgukSh/Project.toml`
  [4c88cf16] Aqua v0.8.13
  [46823bd8] Chemfiles v0.10.42
  [8bb1440f] DelimitedFiles v1.9.1
  [55da9f78] MDLovoFit v0.1.3
⌅ [e29189f1] PDBTools v2.9.0
  [10745b16] Statistics v1.11.1
  [f8b46487] TestItemRunner v1.1.0
  [1c621080] TestItems v1.0.0
  [d8780812] MDLovoFit_jll v20.1.1+0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_CgukSh/Manifest.toml`
  [4c88cf16] Aqua v0.8.13
  [a963bdd2] AtomsBase v0.5.1
  [46823bd8] Chemfiles v0.10.42
  [34da2185] Compat v4.16.0
  [8bb1440f] DelimitedFiles v1.9.1
  [ffbed154] DocStringExtensions v0.9.5
  [1fa38f19] Format v1.3.7
  [842dd82b] InlineStrings v1.4.3
  [692b3bcd] JLLWrappers v1.7.0
  [55da9f78] MDLovoFit v0.1.3
  [aea21201] MolSimToolkitShared v1.1.3
  [bac558e1] OrderedCollections v1.8.1
⌅ [e29189f1] PDBTools v2.9.0
  [d96e819e] Parameters v0.12.3
  [7b2266bf] PeriodicTable v1.2.1
  [aea7be01] PrecompileTools v1.3.2
  [21216c6a] Preferences v1.4.3
  [ae029012] Requires v1.3.1
  [90137ffa] StaticArrays v1.9.13
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [f8b46487] TestItemRunner v1.1.0
  [1c621080] TestItems v1.0.0
  [3a884ed6] UnPack v1.0.2
  [1986cc42] Unitful v1.22.1
  [a7773ee8] UnitfulAtomic v1.0.0
  [78a364fa] Chemfiles_jll v0.10.4+0
  [d8780812] MDLovoFit_jll v20.1.1+0
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [f43a241f] Downloads v1.7.0
  [7b1f6079] FileWatching 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
  [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 v1.3.0+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 v2025.5.20
  [4536629a] OpenBLAS_jll v0.3.29+0
  [458c3c95] OpenSSL_jll v3.5.0+0
  [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...
ERROR: LoadError: UndefVarError: `@testiem` not defined in `Main`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
 [1] fl_lower(ex::Expr, mod::Module, filename::String, lineno::UInt64, world::UInt64, warn::Bool)
   @ Base ./flfrontend.jl:24
 [2] include(mapexpr::Function, mod::Module, _path::String)
   @ Base ./Base.jl:310
 [3] top-level scope
   @ none:6
 [4] eval(m::Module, e::Any)
   @ Core ./boot.jl:489
 [5] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:290
 [6] _start()
   @ Base ./client.jl:557
in expression starting at /home/pkgeval/.julia/packages/MDLovoFit/no3UY/test/runtests.jl:8
in expression starting at /home/pkgeval/.julia/packages/MDLovoFit/no3UY/test/runtests.jl:8

Testing failed after 16.29s

ERROR: LoadError: Package MDLovoFit 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:2421
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2276 [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:324
 [12] _start()
    @ Base ./client.jl:557
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 116.17s: package fails to precompile