Package evaluation to test CellListMap on Julia 1.14.0-DEV.1455 (9d9110fde9*) started at 2026-01-01T14:22:51.706 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.21s ################################################################################ # Installation # Installing CellListMap... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [69e1c6dd] + CellListMap v0.9.15 Updating `~/.julia/environments/v1.14/Manifest.toml` [69e1c6dd] + CellListMap v0.9.15 [ae650224] + ChunkSplitters v3.1.2 [34da2185] + Compat v4.18.1 [187b0558] + ConstructionBase v1.6.0 [ffbed154] + DocStringExtensions v0.9.5 [1914dd2f] + MacroTools v0.5.16 [bac558e1] + OrderedCollections v1.8.1 [d96e819e] + Parameters v0.12.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [92933f4c] + ProgressMeter v1.11.0 [efcf1570] + Setfield v1.1.2 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [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 v1.13.0 [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 [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 v5.15.0+0 Installation completed after 4.09s ################################################################################ # 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:585 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:585 Precompilation failed after 13.17s ################################################################################ # Testing # Testing CellListMap Status `/tmp/jl_ySdRCg/Project.toml` [4c88cf16] Aqua v0.8.14 [6e4b80f9] BenchmarkTools v1.6.3 [69e1c6dd] CellListMap v0.9.15 [46823bd8] Chemfiles v0.10.43 [ae650224] ChunkSplitters v3.1.2 [34da2185] Compat v4.18.1 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.16.1 ⌅ [f6369f11] ForwardDiff v0.10.39 [eff96d63] Measurements v2.14.1 [b8a86587] NearestNeighbors v0.4.26 [e29189f1] PDBTools v3.18.0 [d96e819e] Parameters v0.12.3 [aea7be01] PrecompileTools v1.3.3 [92933f4c] ProgressMeter v1.11.0 [efcf1570] Setfield v1.1.2 [90137ffa] StaticArrays v1.9.16 [f8b46487] TestItemRunner v1.1.4 [1c621080] TestItems v1.0.0 [1986cc42] Unitful v1.27.0 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_ySdRCg/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [4c88cf16] Aqua v0.8.14 [a963bdd2] AtomsBase v0.5.2 [6e4b80f9] BenchmarkTools v1.6.3 [49dc2e85] Calculus v0.5.2 [69e1c6dd] CellListMap v0.9.15 [46823bd8] Chemfiles v0.10.43 [ae650224] ChunkSplitters v3.1.2 [944b1d66] CodecZlib v0.7.8 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [187b0558] ConstructionBase v1.6.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [b4f34e82] Distances v0.10.12 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.16.1 [1fa38f19] Format v1.3.7 ⌅ [f6369f11] ForwardDiff v0.10.39 [d7ba0133] Git v1.5.0 [b5f81e59] IOCapture v1.0.0 [842dd82b] InlineStrings v1.4.5 [92d709cd] IrrationalConstants v0.2.6 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.3.0 [0e77f7df] LazilyInitializedFields v1.3.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [d0879d2d] MarkdownAST v0.1.2 [eff96d63] Measurements v2.14.1 [aea21201] MolSimToolkitShared v1.2.1 [77ba4419] NaNMath v1.1.3 [b8a86587] NearestNeighbors v0.4.26 [bac558e1] OrderedCollections v1.8.1 [e29189f1] PDBTools v3.18.0 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.3 [7b2266bf] PeriodicTable v1.2.1 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [92933f4c] ProgressMeter v1.11.0 [c298f58b] ProteinSecondaryStructures v2.0.3 [2792f1a3] RegistryInstances v0.1.0 [ae029012] Requires v1.3.1 [fdea26ae] SIMD v3.7.2 [efcf1570] Setfield v1.1.2 [276daf66] SpecialFunctions v2.6.1 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [ec057cc2] StructUtils v2.6.0 [f8b46487] TestItemRunner v1.1.4 [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 [78a364fa] Chemfiles_jll v0.10.4+0 [74334e00] DSSP_jll v4.4.0+1 [2e619515] Expat_jll v2.7.3+0 [020c3dae] Git_LFS_jll v3.7.0+0 [f8c6e375] Git_jll v2.52.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [9bd350c2] OpenSSH_jll v10.2.1+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [850473c1] STRIDE_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 [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 [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 [9abbd945] Profile v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets 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 v1.9.2+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 [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 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: The call to compilecache failed to create a usable precompiled cache file for CellListMap [69e1c6dd-3888-40e6-b3c8-31ac5f578864] │ exception = Required dependency Base.PkgId(Base.UUID("34da2185-b29b-5c13-b0c7-acf172513d20"), "Compat") failed to load from a cache file. └ @ Base loading.jl:2950 ┌ Warning: The call to compilecache failed to create a usable precompiled cache file for CellListMap [69e1c6dd-3888-40e6-b3c8-31ac5f578864] │ exception = Required dependency Base.PkgId(Base.UUID("34da2185-b29b-5c13-b0c7-acf172513d20"), "Compat") failed to load from a cache file. └ @ Base loading.jl:2950 ┌ Warning: The call to compilecache failed to create a usable precompiled cache file for CellListMap [69e1c6dd-3888-40e6-b3c8-31ac5f578864] │ exception = Required dependency Base.PkgId(Base.UUID("34da2185-b29b-5c13-b0c7-acf172513d20"), "Compat") failed to load from a cache file. └ @ Base loading.jl:2950 Persistent tasks: Test Failed at /home/pkgeval/.julia/packages/Aqua/MCcFg/src/persistent_tasks.jl:38 Expression: !(has_persistent_tasks(package; kwargs...)) Evaluated: !(has_persistent_tasks(Base.PkgId(Base.UUID("69e1c6dd-3888-40e6-b3c8-31ac5f578864"), "CellListMap"))) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:773 [inlined] [2] test_persistent_tasks(package::Base.PkgId; broken::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/persistent_tasks.jl:38 [3] test_persistent_tasks @ ~/.julia/packages/Aqua/MCcFg/src/persistent_tasks.jl:34 [inlined] [4] #test_persistent_tasks#57 @ ~/.julia/packages/Aqua/MCcFg/src/persistent_tasks.jl:43 [inlined] [5] test_persistent_tasks @ ~/.julia/packages/Aqua/MCcFg/src/persistent_tasks.jl:42 [inlined] [6] macro expansion @ ~/.julia/packages/Aqua/MCcFg/src/Aqua.jl:109 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [8] test_all(testtarget::Module; ambiguities::Bool, unbound_args::Bool, undefined_exports::Bool, project_extras::Bool, stale_deps::Bool, deps_compat::Bool, piracies::Bool, persistent_tasks::Bool, undocumented_names::Bool) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/Aqua.jl:109 WARNING: Ideally, run a multi-threaded test to check the parallel versions. ┌ Warning: attempting to remove probably stale pidfile │ path = "/home/pkgeval/.julia/compiled/v1.14/CellListMap/glLks_FHeQ4.ji.pidfile" └ @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.14/FileWatching/src/pidfile.jl:248 ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("69e1c6dd-3888-40e6-b3c8-31ac5f578864"), "CellListMap") 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:2873  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2725  [4] macro expansion  @ ./loading.jl:2653 [inlined]  [5] macro expansion  @ ./lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2617  [7] require  @ ./loading.jl:2593 [inlined]  [8] eval_import_path  @ ./module.jl:36 [inlined]  [9] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)  @ Base ./module.jl:111  [10] top-level scope  @ ~/.julia/packages/PDBTools/vFeVF/src/tools/sasa.jl:1  [11] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:310  [12] top-level scope  @ ~/.julia/packages/PDBTools/vFeVF/src/PDBTools.jl:116  [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:3309  [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:3151  [18] include_string  @ ./loading.jl:3161 [inlined]  [19] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [20] _start()  @ Base ./client.jl:585 in expression starting at /home/pkgeval/.julia/packages/PDBTools/vFeVF/src/tools/sasa.jl:1 in expression starting at /home/pkgeval/.julia/packages/PDBTools/vFeVF/src/PDBTools.jl:1 in expression starting at stdin:5 1 dependency had output during precompilation: ┌ PDBTools │ [Output was shown above] └ update_cutoff!: Error During Test at /home/pkgeval/.julia/packages/CellListMap/3eL3L/src/ParticleSystem.jl:853 Got exception outside of a @test LoadError: The following 1 package failed to precompile: PDBTools Failed to precompile PDBTools [e29189f1-7114-4dbd-93d0-c5673a921a58] to "/home/pkgeval/.julia/compiled/v1.14/PDBTools/jl_P46pdk" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/CellListMap/3eL3L/src/ParticleSystem.jl:856 WARNING: Ideally, run a multi-threaded test to check the parallel versions. Test Summary: | Pass Fail Error Total Time Package | 1607 1 1 1609 12m48.7s test/namd/ParticleSystem_vs_NAMD.jl | 20 20 1m28.9s test/namd/compare_with_namd.jl | 22 22 11.6s test/gromacs/compare_with_gromacs.jl | 12 12 1.5s test/runtests.jl | 114 1 115 6m58.9s Aqua.test_all | 10 1 11 2m40.5s Method ambiguity | 1 1 44.0s Unbound type parameters | 1 1 0.1s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 42.8s Compat bounds | 4 4 1.0s Piracy | 1 1 15.0s Persistent tasks | 1 1 41.1s disjoint sets | 18 18 33.3s matrix inputs | 2 2 1.5s parallelization | 10 10 19.3s updating lists | 20 20 26.0s applications | 26 26 2m54.8s pathological cells | 28 28 3.5s src/neighborlists.jl | 1146 1146 1m08.5s src/testing.jl | 3 3 14.5s src/CellOperations.jl | 81 81 29.0s src/Box.jl | 38 38 15.0s src/ParticleSystem.jl | 62 1 63 1m05.2s ParticleSystem properties | 30 30 2.2s reducer method basics and errors | 6 6 0.1s update_unitcell! | 6 6 6.1s update_cutoff! | 1 1 33.2s get_computing_box | 1 1 0.0s UpdateParticleSystem! | 8 8 21.3s ParticleSystem - validate coordinates | 11 11 2.3s src/CellLists.jl | 12 12 0.2s test/BasicForParticleSystem.jl | 97 97 55.5s ERROR: LoadError: Some tests did not pass: 1607 passed, 1 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/CellListMap/3eL3L/test/runtests.jl:472 Testing failed after 786.04s ERROR: LoadError: Package CellListMap 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:3067 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2916 [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:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:228 PkgEval failed after 858.8s: package fails to precompile