Package evaluation to test TMscore on Julia 1.14.0-DEV.1352 (749bc618c5*) started at 2025-12-09T19:41:31.808


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

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

Set-up completed after 9.84s


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

Installing TMscore...
   Resolving package versions...
    Updating `~/.julia/environments/v1.14/Project.toml`
  [6e960f36] + TMscore v0.1.0
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [692b3bcd] + JLLWrappers v1.7.1
  [21216c6a] + Preferences v1.5.0
  [6e960f36] + TMscore v0.1.0
  [1d8dad79] + TMscore_jll v1.0.0+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
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0
  [b27032c2] + LibCURL v1.0.0
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [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
  [f489334b] + StyledStrings v1.13.0
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [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
  [458c3c95] + OpenSSL_jll v3.5.4+0
  [efcefdf7] + PCRE2_jll v10.47.0+0
  [83775a58] + Zlib_jll v1.3.1+2
  [3161d3a3] + Zstd_jll v1.5.7+1
  [8e850ede] + nghttp2_jll v1.68.0+1
  [3f19e933] + p7zip_jll v17.7.0+0

Installation completed after 4.55s


################################################################################
# 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 13.76s



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

     Testing TMscore
      Status `/tmp/jl_so0dZL/Project.toml`
  [de9282ab] BioStructures v4.7.0
  [6e960f36] TMscore v0.1.0
  [1d8dad79] TMscore_jll v1.0.0+0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_so0dZL/Manifest.toml`
  [47718e42] BioGenerics v0.1.5
  [de9282ab] BioStructures v4.7.0
  [3c28c6f8] BioSymbols v5.2.0
  [944b1d66] CodecZlib v0.7.8
  [1fa38f19] Format v1.3.7
  [692b3bcd] JLLWrappers v1.7.1
  [aea7be01] PrecompileTools v1.3.3
  [21216c6a] Preferences v1.5.0
  [3cdcf5f2] RecipesBase v1.3.4
  [10745b16] Statistics v1.11.1
  [6e960f36] TMscore v0.1.0
  [3bb67fe8] TranscodingStreams v0.11.3
  [1d8dad79] TMscore_jll v1.0.0+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 v1.13.0
  [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
  [f489334b] StyledStrings v1.13.0
  [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 v8.17.0+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
  [458c3c95] OpenSSL_jll v3.5.4+0
  [efcefdf7] PCRE2_jll v10.47.0+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
     Testing Running tests...
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for BioStructures [de9282ab-8554-53be-b2d6-f6c222edabfc]
│   exception = Required dependency Base.PkgId(Base.UUID("10745b16-79ce-11e8-11f9-7d13ad32a3b2"), "Statistics") failed to load from a cache file.
└ @ Base loading.jl:2891
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("de9282ab-8554-53be-b2d6-f6c222edabfc"), "BioStructures") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=0, inline=true, opt_level=0)
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2813
  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2665
  [4] macro expansion
    @ ./loading.jl:2593 [inlined]
  [5] macro expansion
    @ ./lock.jl:376 [inlined]
  [6] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2557
  [7] require
    @ ./loading.jl:2533 [inlined]
  [8] eval_import_path
    @ ./module.jl:36 [inlined]
  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base ./module.jl:60
 [10] _eval_using
    @ ./module.jl:137 [inlined]
 [11] _eval_using(to::Module, path::Expr)
    @ Base ./module.jl:137
 [12] top-level scope
    @ ~/.julia/packages/TMscore/dgd6A/ext/BioStructuresExt.jl:4
 [13] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3250
 [15] top-level scope
    @ stdin:5
 [16] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:3092
 [18] include_string
    @ ./loading.jl:3102 [inlined]
 [19] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:342
 [20] _start()
    @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/TMscore/dgd6A/ext/BioStructuresExt.jl:1
in expression starting at stdin:5

  1 dependency had output during precompilation:
┌ TMscore → BioStructuresExt
│  [Output was shown above]
└  
┌ Error: Error during loading of extension BioStructuresExt of TMscore, use `Base.retry_load_extensions()` to retry.
│   exception =
│    1-element ExceptionStack:
│    The following 1 package failed to precompile:
│    
│    BioStructuresExt 
│    Failed to precompile BioStructuresExt [96608207-4586-5386-a26a-868f67dee0d5] to "/home/pkgeval/.julia/compiled/v1.14/BioStructuresExt/jl_cgxuO7" (ProcessExited(1)).
│    
└ @ Base loading.jl:1721
[ Info: Downloading file from PDB: 1CRN
[ Info: Downloading file from PDB: 1EJG
[ Info: Downloading file from PDB: 1CRN
[ Info: Downloading file from PDB: 1EJG

TMscore.jl: Error During Test at /home/pkgeval/.julia/packages/TMscore/dgd6A/test/runtests.jl:13
  Test threw exception
  Expression: allequal([tmscore("$(dir)/1CRN.pdb", "$(dir)/1EJG.pdb"), tmscore("$(dir)/1CRN.cif", "$(dir)/1EJG.cif"), tmscore(struc1, struc2), tmscore(struc1, "$(dir)/1EJG.cif"), (run_tmscore(struc1, struc2)).tmscore])
  MethodError: no method matching write_tempfile(::MolecularStructure, ::String)
  The function `write_tempfile` exists, but no method is defined for this combination of argument types.
  Closest candidates are:
    write_tempfile(!Matched::AbstractString, ::Any)
     @ TMscore ~/.julia/packages/TMscore/dgd6A/src/TMscore.jl:221
  Stacktrace:
   [1] (::TMscore.var"#4#5"{@Kwargs{}, MolecularStructure, MolecularStructure})(tempdir::String)
     @ TMscore ~/.julia/packages/TMscore/dgd6A/src/TMscore.jl:225
   [2] mktempdir(fn::TMscore.var"#4#5"{@Kwargs{}, MolecularStructure, MolecularStructure}, parent::String; prefix::String)
     @ Base.Filesystem ./file.jl:936
   [3] mktempdir(fn::Function, parent::String)
     @ Base.Filesystem ./file.jl:932
   [4] run_tmscore(arg1::MolecularStructure, arg2::MolecularStructure; options::@Kwargs{})
     @ TMscore ~/.julia/packages/TMscore/dgd6A/src/TMscore.jl:224
   [5] run_tmscore(arg1::MolecularStructure, arg2::MolecularStructure)
     @ TMscore ~/.julia/packages/TMscore/dgd6A/src/TMscore.jl:223
   [6] tmscore(arg1::MolecularStructure, arg2::MolecularStructure; options::@Kwargs{})
     @ TMscore ~/.julia/packages/TMscore/dgd6A/src/TMscore.jl:240
   [7] tmscore(arg1::MolecularStructure, arg2::MolecularStructure)
     @ TMscore ~/.julia/packages/TMscore/dgd6A/src/TMscore.jl:239
   [8] macro expansion
     @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined]
   [9] (::var"#2#3")(dir::String)
     @ Main ~/.julia/packages/TMscore/dgd6A/test/runtests.jl:13
Test Summary: | Error  Total   Time
TMscore.jl    |     1      1  18.3s
RNG of the outermost testset: Random.Xoshiro(0x2d506ab3a93fefac, 0x42a1b9889728dd6a, 0x81b5b91cbc62f220, 0xb37257f285eb12c3, 0x65e29c7ec616c5df)
ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/TMscore/dgd6A/test/runtests.jl:6

Testing failed after 78.95s

ERROR: LoadError: Package TMscore errored during testing
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/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/v1.14/Pkg/src/Operations.jl:3053
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2902 [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/v1.14/Pkg/src/API.jl:572
  [5] 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
  [6] 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
  [7] 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
  [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160
  [9] test
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined]
 [10] 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
 [11] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:237
 [12] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [13] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:344
 [14] _start()
    @ Base ./client.jl:577
in expression starting at /PkgEval.jl/scripts/evaluate.jl:228

PkgEval failed after 122.49s: package fails to precompile