Package evaluation to test AssigningSecondaryStructure on Julia 1.14.0-DEV.1299 (6d6224db99*) started at 2025-11-27T13:16:58.667 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.81s ################################################################################ # Installation # Installing AssigningSecondaryStructure... Resolving package versions... Installed Statistics ────────────────── v1.11.1 Installed StatsAPI ──────────────────── v1.7.1 Installed StaticArraysCore ──────────── v1.4.4 Installed Preferences ───────────────── v1.5.0 Installed PrecompileTools ───────────── v1.3.3 Installed NearestNeighbors ──────────── v0.4.24 Installed Distances ─────────────────── v0.10.12 Installed StaticArrays ──────────────── v1.9.15 Installed AssigningSecondaryStructure ─ v0.5.1 Updating `~/.julia/environments/v1.14/Project.toml` [8ed43e74] + AssigningSecondaryStructure v0.5.1 Updating `~/.julia/environments/v1.14/Manifest.toml` [8ed43e74] + AssigningSecondaryStructure v0.5.1 [b4f34e82] + Distances v0.10.12 [b8a86587] + NearestNeighbors v0.4.24 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates 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 [2f01184e] + SparseArrays v1.13.0 [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 4.8s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4590.7 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 810.7 ms ✓ StatsAPI 921.1 ms ✓ StaticArraysCore 1132.8 ms ✓ Statistics 1130.9 ms ✓ Preferences 1319.4 ms ✓ Statistics → SparseArraysExt 1509.2 ms ✓ Distances 939.0 ms ✓ PrecompileTools 1359.3 ms ✓ Distances → DistancesSparseArraysExt 13062.6 ms ✓ StaticArrays 1415.7 ms ✓ StaticArrays → StaticArraysStatisticsExt 4869.0 ms ✓ NearestNeighbors 2248.0 ms ✓ AssigningSecondaryStructure 12 dependencies successfully precompiled in 31 seconds. 7 already precompiled. Precompilation completed after 48.07s ################################################################################ # Testing # Testing AssigningSecondaryStructure Status `/tmp/jl_niXnls/Project.toml` [8ed43e74] AssigningSecondaryStructure v0.5.1 [de9282ab] BioStructures v4.7.0 [b8a86587] NearestNeighbors v0.4.24 [90137ffa] StaticArrays v1.9.15 [37e2e46d] LinearAlgebra v1.13.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_niXnls/Manifest.toml` [8ed43e74] AssigningSecondaryStructure v0.5.1 [47718e42] BioGenerics v0.1.5 [de9282ab] BioStructures v4.7.0 [3c28c6f8] BioSymbols v5.2.0 [944b1d66] CodecZlib v0.7.8 [b4f34e82] Distances v0.10.12 [1fa38f19] Format v1.3.7 [b8a86587] NearestNeighbors v0.4.24 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [3cdcf5f2] RecipesBase v1.3.4 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [3bb67fe8] TranscodingStreams v0.11.3 [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 v1.0.0 [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 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.17.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.4+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 Testing Running tests... 1ZAK: Error During Test at /home/pkgeval/.julia/packages/AssigningSecondaryStructure/rv7vA/test/runtests.jl:18 Got exception outside of a @test ArgumentError: Tree cannot be queried with points containing NaN values Stacktrace: [1] check_for_nan_in_points @ ~/.julia/packages/NearestNeighbors/zqao0/src/utilities.jl:108 [inlined] [2] inrange! @ ~/.julia/packages/NearestNeighbors/zqao0/src/inrange.jl:67 [inlined] [3] inrange! @ ~/.julia/packages/NearestNeighbors/zqao0/src/inrange.jl:66 [inlined] [4] inrange @ ~/.julia/packages/NearestNeighbors/zqao0/src/inrange.jl:75 [inlined] [5] inrange(tree::NearestNeighbors.KDTree{StaticArraysCore.SVector{3, Float64}, Distances.Euclidean, Float64, StaticArraysCore.SVector{3, Float64}}, point::StaticArraysCore.SVector{3, Float64}, radius::Float64) @ NearestNeighbors ~/.julia/packages/NearestNeighbors/zqao0/src/inrange.jl:75 [6] get_hbond_map(coords::Array{Float64, 3}, cutoff::Float64) @ AssigningSecondaryStructure ~/.julia/packages/AssigningSecondaryStructure/rv7vA/src/hydrogen_bonds.jl:56 [7] get_hbond_map @ ~/.julia/packages/AssigningSecondaryStructure/rv7vA/src/hydrogen_bonds.jl:37 [inlined] [8] assign_secondary_structure(coords::Array{Float64, 3}) @ AssigningSecondaryStructure ~/.julia/packages/AssigningSecondaryStructure/rv7vA/src/assign.jl:90 [9] _broadcast_getindex_evalf @ ./broadcast.jl:698 [inlined] [10] _broadcast_getindex @ ./broadcast.jl:671 [inlined] [11] _getindex @ ./broadcast.jl:619 [inlined] [12] getindex @ ./broadcast.jl:615 [inlined] [13] copy(bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Tuple{Base.OneTo{Int64}}, typeof(assign_secondary_structure), Tuple{Vector{Array{Float64, 3}}}}) @ Base.Broadcast ./broadcast.jl:932 [14] materialize @ ./broadcast.jl:893 [inlined] [15] assign_secondary_structure(chain_backbones::Vector{Array{Float64, 3}}) @ AssigningSecondaryStructure ~/.julia/packages/AssigningSecondaryStructure/rv7vA/src/assign.jl:101 [16] top-level scope @ ~/.julia/packages/AssigningSecondaryStructure/rv7vA/test/runtests.jl:16 [17] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [18] macro expansion @ ~/.julia/packages/AssigningSecondaryStructure/rv7vA/test/runtests.jl:19 [inlined] [19] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [20] macro expansion @ ~/.julia/packages/AssigningSecondaryStructure/rv7vA/test/runtests.jl:19 [inlined] [21] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [22] top-level scope @ none:6 [23] eval(m::Module, e::Any) @ Core ./boot.jl:489 [24] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [25] _start() @ Base ./client.jl:577 Test Summary: | Error Total Time AssigningSecondaryStructure.jl | 1 1 40.0s 1ZAK | 1 1 27.7s RNG of the outermost testset: Random.Xoshiro(0x334d8d3d50bdf917, 0xa32a810a0fa7e8c1, 0x82e96d6e2284ec7f, 0x1f94f4d9bb82814a, 0x886ee5764cdfdadb) ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/AssigningSecondaryStructure/rv7vA/test/runtests.jl:14 Testing failed after 80.3s ERROR: LoadError: Package AssigningSecondaryStructure 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:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [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:219 [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:210 PkgEval failed after 157.79s: package tests unexpectedly errored