Package evaluation of BiochemicalAlgorithms on Julia 1.13.0-DEV.1055 (100ef9d641*) started at 2025-08-29T00:16:04.035 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.75s ################################################################################ # Installation # Installing BiochemicalAlgorithms... Resolving package versions... Installed Bzip2_jll ─────────────────── v1.0.9+0 Installed HarfBuzz_jll ──────────────── v8.5.1+0 Installed Extents ───────────────────── v0.1.6 Installed ChunkCodecLibZstd ─────────── v0.2.1 Installed Libuuid_jll ───────────────── v2.41.1+0 Installed Calculus ──────────────────── v0.5.2 Installed RDKitMinimalLib ───────────── v1.2.0 Installed InlineStrings ─────────────── v1.4.5 Installed Cairo_jll ─────────────────── v1.18.5+0 Installed RDKit_jll ─────────────────── v2022.9.5+0 Installed Graphite2_jll ─────────────── v1.3.15+0 Installed SentinelArrays ────────────── v1.4.8 Installed UnitfulAtomic ─────────────── v1.0.0 Installed Fontconfig_jll ────────────── v2.17.1+0 Installed OrderedCollections ────────── v1.8.1 Installed PreallocationTools ────────── v0.4.33 Installed FileIO ────────────────────── v1.17.0 Installed Graphics ──────────────────── v1.1.3 Installed NaNMath ───────────────────── v1.1.3 Installed libinchi_jll ──────────────── v1.6.0+0 Installed ScopedValues ──────────────── v1.5.0 Installed PhysicalConstants ─────────── v0.2.4 Installed Tables ────────────────────── v1.12.1 Installed Xorg_libxcb_jll ───────────── v1.17.1+0 Installed Mendeleev ─────────────────── v1.0.1 Installed EnumX ─────────────────────── v1.0.5 Installed Jieko ─────────────────────── v0.2.1 Installed InverseFunctions ──────────── v0.1.17 Installed LZO_jll ───────────────────── v2.10.3+0 Installed Reexport ──────────────────── v1.2.2 Installed Missings ──────────────────── v1.2.0 Installed LLVMOpenMP_jll ────────────── v18.1.8+0 Installed LaTeXStrings ──────────────── v1.4.0 Installed TableTraits ───────────────── v1.0.1 Installed Preferences ───────────────── v1.5.0 Installed boost_jll ─────────────────── v1.76.0+1 Installed Crayons ───────────────────── v4.1.1 Installed Format ────────────────────── v1.3.7 Installed UnPack ────────────────────── v1.0.2 Installed SortingAlgorithms ─────────── v1.2.2 Installed Inflate ───────────────────── v0.1.5 Installed ADTypes ───────────────────── v1.17.0 Installed RecursiveArrayTools ───────── v3.37.1 Installed MacroTools ────────────────── v0.5.16 Installed AbstractTrees ─────────────── v0.4.5 Installed MakieCore ─────────────────── v0.9.5 Installed DelimitedFiles ────────────── v1.9.1 Installed FillArrays ────────────────── v1.13.0 Installed SparseMatrixColorings ─────── v0.4.21 Installed Quaternions ───────────────── v0.7.6 Installed DataStructures ────────────── v0.19.1 Installed CodecZlib ─────────────────── v0.7.8 Installed ArnoldiMethod ─────────────── v0.4.0 Installed Xorg_libXau_jll ───────────── v1.0.13+0 Installed Observables ───────────────── v0.5.5 Installed ExprTools ─────────────────── v0.1.10 Installed ArrayInterface ────────────── v7.19.0 Installed ConsoleProgressMonitor ────── v0.1.2 Installed DataValueInterfaces ───────── v1.0.0 Installed LoggingExtras ─────────────── v1.1.0 Installed Cairo ─────────────────────── v1.1.1 Installed Pixman_jll ────────────────── v0.44.2+0 Installed Libffi_jll ────────────────── v3.4.7+0 Installed RealDot ───────────────────── v0.1.0 Installed Expat_jll ─────────────────── v2.7.1+0 Installed GPUArraysCore ─────────────── v0.2.0 Installed coordgenlibs_jll ──────────── v3.0.2+0 Installed SparseConnectivityTracer ──── v1.0.1 Installed TerminalLoggers ───────────── v0.1.7 Installed libpng_jll ────────────────── v1.6.50+0 Installed L_BFGS_B_jll ──────────────── v3.0.1+0 Installed SimpleTraits ──────────────── v0.9.5 Installed LeftChildRightSiblingTrees ── v0.2.1 Installed Setfield ──────────────────── v1.1.2 Installed MetaGraphs ────────────────── v0.8.1 Installed Roots ─────────────────────── v2.2.10 Installed PooledArrays ──────────────── v1.4.3 Installed OptimizationBase ──────────── v2.10.0 Installed PDMats ────────────────────── v0.11.35 Installed WorkerUtilities ───────────── v1.6.1 Installed TableOperations ───────────── v1.2.0 Installed DocStringExtensions ───────── v0.9.5 Installed Moshi ─────────────────────── v0.3.7 Installed DifferentiationInterface ──── v0.7.7 Installed CompositionsBase ──────────── v0.1.2 Installed LBFGSB ────────────────────── v0.4.1 Installed CommonSolve ───────────────── v0.2.4 Installed HashArrayMappedTries ──────── v0.2.0 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed FunctionWrappersWrappers ──── v0.1.3 Installed RecipesBase ───────────────── v1.3.4 Installed DataAPI ───────────────────── v1.16.0 Installed InvertedIndices ───────────── v1.3.1 Installed SciMLOperators ────────────── v1.6.0 Installed StaticArraysCore ──────────── v1.4.3 Installed BiochemicalAlgorithms ─────── v0.5.5 Installed ColorTypes ────────────────── v0.12.1 Installed SciMLStructures ───────────── v1.7.0 Installed Colors ────────────────────── v0.13.1 Installed StaticArrays ──────────────── v1.9.14 Installed StringManipulation ────────── v0.4.1 Installed MolecularGraph ────────────── v0.19.1 Installed Requires ──────────────────── v1.3.1 Installed Glib_jll ──────────────────── v2.84.3+0 Installed FunctionWrappers ──────────── v1.1.3 Installed Parsers ───────────────────── v2.8.3 Installed JSON ──────────────────────── v0.21.4 Installed AutoHashEquals ────────────── v2.2.0 Installed FastClosures ──────────────── v0.3.2 Installed BioGenerics ───────────────── v0.1.5 Installed PrettyTables ──────────────── v2.4.0 Installed SciMLBase ─────────────────── v2.113.0 Installed Xorg_libXdmcp_jll ─────────── v1.1.6+0 Installed CSV ───────────────────────── v0.10.15 Installed TestItems ─────────────────── v1.0.0 Installed Unitful ───────────────────── v1.24.0 Installed WeakRefStrings ────────────── v1.4.2 Installed JLLWrappers ───────────────── v1.7.1 Installed GeometryBasics ────────────── v0.5.10 Installed Pango_jll ─────────────────── v1.56.3+0 Installed ChunkCodecCore ────────────── v0.5.3 Installed StructTypes ───────────────── v1.11.0 Installed IterTools ─────────────────── v1.10.0 Installed Measurements ──────────────── v2.14.0 Installed DataFrames ────────────────── v1.7.1 Installed Graphs ────────────────────── v1.13.1 Installed Xorg_xtrans_jll ───────────── v1.6.0+0 Installed Accessors ─────────────────── v0.1.42 Installed Adapt ─────────────────────── v4.3.0 Installed FilePathsBase ─────────────── v0.9.24 Installed RuntimeGeneratedFunctions ─── v0.5.15 Installed ConstructionBase ──────────── v1.6.0 Installed Libmount_jll ──────────────── v2.41.1+0 Installed JLD2 ──────────────────────── v0.6.0 Installed ChunkSplitters ────────────── v3.1.2 Installed Xorg_libX11_jll ───────────── v1.8.12+0 Installed Compat ────────────────────── v4.18.0 Installed SymbolicIndexingInterface ─── v0.3.43 Installed TranscodingStreams ────────── v0.11.3 Installed ProgressLogging ───────────── v0.1.5 Installed BioStructures ─────────────── v4.6.0 Installed EarCut_jll ────────────────── v2.2.4+0 Installed CellListMap ───────────────── v0.9.11 Installed Statistics ────────────────── v1.11.1 Installed StringEncodings ───────────── v0.3.7 Installed ProgressMeter ─────────────── v1.11.0 Installed ExproniconLite ────────────── v0.10.14 Installed PrecompileTools ───────────── v1.3.2 Installed BioSymbols ────────────────── v5.2.0 Installed GettextRuntime_jll ────────── v0.22.4+0 Installed ChunkCodecLibZlib ─────────── v0.2.1 Installed FriBidi_jll ───────────────── v1.0.17+0 Installed Optimization ──────────────── v4.5.0 Installed YAML ──────────────────────── v0.4.14 Installed Xorg_libXrender_jll ───────── v0.9.12+0 Installed JSON3 ─────────────────────── v1.14.3 Installed Parameters ────────────────── v0.12.3 Installed FreeType2_jll ─────────────── v2.13.4+0 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed IntervalSets ──────────────── v0.7.11 Installed FixedPointNumbers ─────────── v0.8.5 Installed Xorg_libXext_jll ──────────── v1.3.7+0 Installed Rotations ─────────────────── v1.7.1 Installing 32 artifacts Installed artifact Xorg_xtrans 48.2 KiB Installed artifact Graphite2 120.2 KiB Installed artifact Pixman 372.2 KiB Installed artifact Pango 1.1 MiB Installed artifact FriBidi 78.9 KiB Installed artifact Cairo 2.2 MiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact HarfBuzz 1.7 MiB Installed artifact Libiconv 1.9 MiB Installed artifact EarCut 80.5 KiB Installed artifact Glib 7.7 MiB Installed artifact LZO 208.9 KiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact libinchi 933.4 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact FreeType2 1.5 MiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact Libffi 44.2 KiB Installed artifact L_BFGS_B 45.2 KiB Installed artifact coordgenlibs 303.6 KiB Installed artifact libpng 328.4 KiB Installed artifact GettextRuntime 543.0 KiB Installed artifact Expat 274.7 KiB Installed artifact Bzip2 503.5 KiB Installed artifact Fontconfig 984.8 KiB Installed artifact Libuuid 3.6 MiB Installed artifact Libmount 6.5 MiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact boost 22.1 MiB Installed artifact RDKit 56.2 MiB Updating `~/.julia/environments/v1.13/Project.toml` [9d651bdf] + BiochemicalAlgorithms v0.5.5 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.17.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.3.0 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.19.0 [15f4f7f2] + AutoHashEquals v2.2.0 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.6.0 [3c28c6f8] + BioSymbols v5.2.0 [9d651bdf] + BiochemicalAlgorithms v0.5.5 [336ed68f] + CSV v0.10.15 [159f3aea] + Cairo v1.1.1 [49dc2e85] + Calculus v0.5.2 [69e1c6dd] + CellListMap v0.9.11 ⌅ [0b6fb165] + ChunkCodecCore v0.5.3 ⌅ [4c0bbee4] + ChunkCodecLibZlib v0.2.1 ⌅ [55437552] + ChunkCodecLibZstd v0.2.1 [ae650224] + ChunkSplitters v3.1.2 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.1 [5ae59095] + Colors v0.13.1 [38540f10] + CommonSolve v0.2.4 [34da2185] + Compat v4.18.0 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To see why use `status --outdated -m` Installation completed after 35.7s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4963.8 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompilation completed after 979.19s ################################################################################ # Testing # Testing BiochemicalAlgorithms Status `/tmp/jl_qKKePp/Project.toml` [4c88cf16] Aqua v0.8.14 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.6.0 [3c28c6f8] BioSymbols v5.2.0 [9d651bdf] BiochemicalAlgorithms v0.5.5 [336ed68f] CSV v0.10.15 [69e1c6dd] CellListMap v0.9.11 [a93c6f00] DataFrames v1.7.1 [864edb3b] DataStructures v0.19.1 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.5 [86223c79] Graphs v1.13.1 [0f8b85d8] JSON3 v1.14.3 [c116f080] Mendeleev v1.0.1 [626554b9] MetaGraphs v0.8.1 ⌅ [6c89ec66] MolecularGraph v0.19.1 [510215fc] Observables v0.5.5 [7f7a1694] Optimization v4.5.0 [5ad8b20f] PhysicalConstants v0.2.4 ⌅ [08abe8d2] PrettyTables v2.4.0 [94ee1d12] Quaternions v0.7.6 [6038ab10] Rotations v1.7.1 [90137ffa] StaticArrays v1.9.14 [10745b16] Statistics v1.11.1 [856f2bd8] StructTypes v1.11.0 [ab02a1b2] TableOperations v1.2.0 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[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 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [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 v8.15.0+1 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.8.12 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.2+0 [efcefdf7] PCRE2_jll v10.46.0+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 v5.13.1+0 [8e850ede] nghttp2_jll v1.66.0+0 [3f19e933] p7zip_jll v17.6.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ERROR: LoadError: UndefVarError: `push_testset` not defined in `Test` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] getproperty @ ./Base_compiler.jl:50 [inlined] [2] run_tests(path::String; filter::Nothing, verbose::Bool) @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:197 [3] kwcall(::@NamedTuple{verbose::Bool}, ::typeof(TestItemRunner.run_tests), path::String) @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:133 [4] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/EdAH5/test/runtests.jl:3 [5] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:309 [6] top-level scope @ none:6 [7] eval(m::Module, e::Any) @ Core ./boot.jl:489 [8] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [9] _start() @ Base ./client.jl:563 in expression starting at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/EdAH5/test/runtests.jl:3 Testing failed after 62.52s ERROR: LoadError: Package BiochemicalAlgorithms 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:2673 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2522 [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:538 [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/v1.13/Pkg/src/API.jl:515 [6] 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:168 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:157 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [9] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:308 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:330 [14] _start() @ Base ./client.jl:563 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1178.66s: package tests unexpectedly errored