Package evaluation to test MolecularDynamicsFiles on Julia 1.14.0-DEV.30 (073666df8b*) started at 2025-11-04T17:11:15.121 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.52s ################################################################################ # Installation # Installing MolecularDynamicsFiles... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [fdf1312e] + MolecularDynamicsFiles v0.2.1 Updating `~/.julia/environments/v1.14/Manifest.toml` [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 [864edb3b] + DataStructures v0.19.2 [e2d170a0] + DataValueInterfaces v1.0.0 [ffbed154] + DocStringExtensions v0.9.5 [4e289a0a] + EnumX v1.0.5 [48062228] + FilePathsBase v0.9.24 [92fee26a] + GZip v0.6.2 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [b964fa9f] + LaTeXStrings v1.4.0 [e1d29d7a] + Missings v1.2.0 [fdf1312e] + MolecularDynamicsFiles v0.2.1 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.0 [189a3867] + Reexport v1.2.2 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.2 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf 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 v1.11.0 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 4.49s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ 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/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/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... 14828.2 ms ✓ MolecularDynamicsFiles 1 dependency successfully precompiled in 16 seconds. 57 already precompiled. Precompilation completed after 28.97s ################################################################################ # Testing # Testing MolecularDynamicsFiles Status `/tmp/jl_afMjoQ/Project.toml` [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.5 [92fee26a] GZip v0.6.2 [fdf1312e] MolecularDynamicsFiles v0.2.1 [90137ffa] StaticArrays v1.9.15 [37e2e46d] LinearAlgebra v1.13.0 [de0858da] Printf v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_afMjoQ/Manifest.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.2 [e2d170a0] DataValueInterfaces v1.0.0 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.5 [48062228] FilePathsBase v0.9.24 [92fee26a] GZip v0.6.2 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [82899510] IteratorInterfaceExtensions v1.0.0 [b964fa9f] LaTeXStrings v1.4.0 [e1d29d7a] Missings v1.2.0 [fdf1312e] MolecularDynamicsFiles v0.2.1 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.0 [189a3867] Reexport v1.2.2 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [de0858da] Printf 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 v1.11.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [4536629a] OpenBLAS_jll v0.3.29+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 Testing Running tests... Test Summary: | Pass Total Time Reading LAMMPS Dump | 692 692 1m01.9s Writing single frame with property computation: Test Failed at /home/pkgeval/.julia/packages/MolecularDynamicsFiles/rCLfj/test/write_lammps_dump.jl:134 Expression: isapprox(frame_cmp, frame_written) Evaluated: isapprox(MDFrame(0, SimulationBox([11.856311014966876 0.0 0.0; 0.0 11.856311014966876 0.0; 0.0 0.0 11.856311014966876], [0.0, 0.0, 0.0], BoundaryConditions(MolecularDynamicsFiles.BoundaryCondition.Periodic, MolecularDynamicsFiles.BoundaryCondition.Periodic, MolecularDynamicsFiles.BoundaryCondition.Periodic, MolecularDynamicsFiles.BoundaryCondition.Periodic, MolecularDynamicsFiles.BoundaryCondition.Periodic, MolecularDynamicsFiles.BoundaryCondition.Periodic, #undef), false, #undef), 1000×16 DataFrame Row │ id x y z xs ys zs ⋯ │ Int64 Float64 Float64 Float64 Float64 Float64 Float64 ⋯ ──────┼───────────────────────────────────────────────────────────────────────── 1 │ 1 11.2734 1.45304 0.386493 0.950838 0.122554 0.032598 ⋯ 2 │ 2 3.21004 10.9274 2.61432 0.270745 0.921652 0.2205 3 │ 3 1.2245 0.952627 10.3762 0.103278 0.0803477 0.875166 4 │ 4 2.90543 11.7475 1.57039 0.245054 0.990823 0.132452 5 │ 5 5.56131 1.51011 0.570076 0.469059 0.127368 0.048082 ⋯ 6 │ 6 7.53747 1.39675 11.8532 0.635735 0.117807 0.999735 7 │ 7 7.74976 1.62321 2.56805 0.65364 0.136907 0.216597 8 │ 8 7.795 0.752622 3.10279 0.657456 0.0634786 0.261699 ⋮ │ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋱ 994 │ 994 4.98863 0.348295 10.2537 0.420757 0.0293763 0.864833 ⋯ 995 │ 995 2.02666 11.602 9.8553 0.170935 0.97855 0.831228 996 │ 996 6.32335 10.5987 11.4031 0.533332 0.893926 0.961778 997 │ 997 7.19841 11.2946 0.751296 0.607137 0.952619 0.063366 998 │ 998 7.70657 0.407275 0.608713 0.649997 0.0343509 0.051340 ⋯ 999 │ 999 11.0643 9.52508 10.0401 0.933196 0.803376 0.846819 1000 │ 1000 0.675084 10.8147 10.8091 0.0569388 0.912146 0.911678 10 columns and 985 rows omitted, Dict{Symbol, Any}(), #undef), MDFrame(0, SimulationBox([11.856311014966876 0.0 0.0; 0.0 11.856311014966876 0.0; 0.0 0.0 11.856311014966876], [0.0, 0.0, 0.0], BoundaryConditions(MolecularDynamicsFiles.BoundaryCondition.Periodic, MolecularDynamicsFiles.BoundaryCondition.Periodic, MolecularDynamicsFiles.BoundaryCondition.Periodic, MolecularDynamicsFiles.BoundaryCondition.Periodic, MolecularDynamicsFiles.BoundaryCondition.Periodic, MolecularDynamicsFiles.BoundaryCondition.Periodic, #undef), false, #undef), 1000×16 DataFrame Row │ id x y z xs ys zs ⋯ │ Int64 Float64 Float64 Float64 Float64 Float64 Float64 ⋯ ──────┼───────────────────────────────────────────────────────────────────────── 1 │ 1 11.2734 1.45304 0.386493 0.950838 0.122554 0.032598 ⋯ 2 │ 2 3.21004 10.9274 2.61432 0.270745 0.921652 0.2205 3 │ 3 1.2245 0.952627 10.3762 0.103278 0.0803477 0.875166 4 │ 4 2.90543 11.7475 1.57039 0.245054 0.990823 0.132452 5 │ 5 5.56131 1.51011 0.570076 0.469059 0.127368 0.048082 ⋯ 6 │ 6 7.53747 1.39675 11.8532 0.635735 0.117807 0.999735 7 │ 7 7.74976 1.62321 2.56805 0.65364 0.136907 0.216597 8 │ 8 7.795 0.752622 3.10279 0.657456 0.0634786 0.261699 ⋮ │ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋱ 994 │ 994 4.98863 0.348295 10.2537 0.420757 0.0293763 0.864833 ⋯ 995 │ 995 2.02666 11.602 9.8553 0.170935 0.97855 0.831228 996 │ 996 6.32335 10.5987 11.4031 0.533332 0.893926 0.961778 997 │ 997 7.19841 11.2946 0.751296 0.607137 0.952619 0.063366 998 │ 998 7.70657 0.407275 0.608713 0.649997 0.0343509 0.051340 ⋯ 999 │ 999 11.0643 9.52508 10.0401 0.933196 0.803376 0.846819 1000 │ 1000 0.675084 10.8147 10.8091 0.0569388 0.912146 0.911678 10 columns and 985 rows omitted, Dict{Symbol, Any}(), #undef)) Stacktrace: [1] top-level scope @ ~/.julia/packages/MolecularDynamicsFiles/rCLfj/test/write_lammps_dump.jl:66 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [3] macro expansion @ ~/.julia/packages/MolecularDynamicsFiles/rCLfj/test/write_lammps_dump.jl:120 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [5] macro expansion @ ~/.julia/packages/MolecularDynamicsFiles/rCLfj/test/write_lammps_dump.jl:134 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:753 [inlined] Test Summary: | Pass Fail Total Time Writing LAMMPS Dump | 61 1 62 40.0s Simple single frame | 1 1 12.5s Writing single frame | 2 2 0.6s Writing single frame in gzip format | 2 2 1.2s Writing single frame with property computation | 1 1 24.4s Writing multiple frames in one file | 14 14 0.4s Writing multiple frames in one file in gzip format | 14 14 0.6s Writing multiple frames in multiple files | 14 14 0.1s Writing multiple frames in multiple files in gzip format | 14 14 0.2s RNG of the outermost testset: Random.Xoshiro(0x91829d84b05a35cb, 0x5ea450f93d053d09, 0x844c9e865f3bda80, 0xf6e5d4c8a3f4bf4e, 0x03377a8cbf466c88) ERROR: LoadError: Some tests did not pass: 61 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MolecularDynamicsFiles/rCLfj/test/write_lammps_dump.jl:64 in expression starting at /home/pkgeval/.julia/packages/MolecularDynamicsFiles/rCLfj/test/runtests.jl:7 Testing failed after 124.71s ERROR: LoadError: Package MolecularDynamicsFiles 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 182.92s: package has test failures