Package evaluation of BiochemicalAlgorithms on Julia 1.13.0-DEV.1234 (bbaa34b41d*) started at 2025-10-02T04:05:32.788 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.49s ################################################################################ # Installation # Installing BiochemicalAlgorithms... Resolving package versions... Installed HarfBuzz_jll ──────────────── v8.5.1+0 Installed ChunkCodecLibZstd ─────────── v1.0.0 Installed Bzip2_jll ─────────────────── v1.0.9+0 Installed Libuuid_jll ───────────────── v2.41.2+0 Installed InlineStrings ─────────────── v1.4.5 Installed Extents ───────────────────── v0.1.6 Installed Calculus ──────────────────── v0.5.2 Installed RDKitMinimalLib ───────────── v1.2.0 Installed Cairo_jll ─────────────────── v1.18.5+0 Installed Graphite2_jll ─────────────── v1.3.15+0 Installed UnitfulAtomic ─────────────── v1.0.0 Installed SentinelArrays ────────────── v1.4.8 Installed OrderedCollections ────────── v1.8.1 Installed PreallocationTools ────────── v0.4.34 Installed FileIO ────────────────────── v1.17.0 Installed Fontconfig_jll ────────────── v2.17.1+0 Installed NaNMath ───────────────────── v1.1.3 Installed Graphics ──────────────────── v1.1.3 Installed RDKit_jll ─────────────────── v2022.9.5+0 Installed ScopedValues ──────────────── v1.5.0 Installed libinchi_jll ──────────────── v1.6.0+0 Installed Xorg_libxcb_jll ───────────── v1.17.1+0 Installed EnumX ─────────────────────── v1.0.5 Installed Tables ────────────────────── v1.12.1 Installed InverseFunctions ──────────── v0.1.17 Installed Jieko ─────────────────────── v0.2.1 Installed PhysicalConstants ─────────── v0.2.4 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 Mendeleev ─────────────────── v1.0.1 Installed TableTraits ───────────────── v1.0.1 Installed Preferences ───────────────── v1.5.0 Installed LaTeXStrings ──────────────── v1.4.0 Installed Crayons ───────────────────── v4.1.1 Installed SortingAlgorithms ─────────── v1.2.2 Installed Format ────────────────────── v1.3.7 Installed UnPack ────────────────────── v1.0.2 Installed ADTypes ───────────────────── v1.18.0 Installed RecursiveArrayTools ───────── v3.37.1 Installed boost_jll ─────────────────── v1.76.0+1 Installed Inflate ───────────────────── v0.1.5 Installed DataStructures ────────────── v0.19.1 Installed MacroTools ────────────────── v0.5.16 Installed DelimitedFiles ────────────── v1.9.1 Installed AbstractTrees ─────────────── v0.4.5 Installed Quaternions ───────────────── v0.7.6 Installed SparseMatrixColorings ─────── v0.4.21 Installed FillArrays ────────────────── v1.14.0 Installed MakieCore ─────────────────── v0.9.5 Installed ArnoldiMethod ─────────────── v0.4.0 Installed Xorg_libXau_jll ───────────── v1.0.13+0 Installed ConsoleProgressMonitor ────── v0.1.2 Installed CodecZlib ─────────────────── v0.7.8 Installed Observables ───────────────── v0.5.5 Installed ExprTools ─────────────────── v0.1.10 Installed Cairo ─────────────────────── v1.1.1 Installed ArrayInterface ────────────── v7.20.0 Installed DataValueInterfaces ───────── v1.0.0 Installed Pixman_jll ────────────────── v0.44.2+0 Installed GPUArraysCore ─────────────── v0.2.0 Installed Libffi_jll ────────────────── v3.4.7+0 Installed LoggingExtras ─────────────── v1.1.0 Installed Expat_jll ─────────────────── v2.7.1+0 Installed RealDot ───────────────────── v0.1.0 Installed libpng_jll ────────────────── v1.6.50+0 Installed SimpleTraits ──────────────── v0.9.5 Installed L_BFGS_B_jll ──────────────── v3.0.1+0 Installed TerminalLoggers ───────────── v0.1.7 Installed LeftChildRightSiblingTrees ── v0.2.1 Installed coordgenlibs_jll ──────────── v3.0.2+0 Installed Roots ─────────────────────── v2.2.10 Installed SparseConnectivityTracer ──── v1.1.0 Installed PooledArrays ──────────────── v1.4.3 Installed WorkerUtilities ───────────── v1.6.1 Installed PDMats ────────────────────── v0.11.35 Installed Setfield ──────────────────── v1.1.2 Installed DocStringExtensions ───────── v0.9.5 Installed OptimizationBase ──────────── v2.11.0 Installed MetaGraphs ────────────────── v0.8.1 Installed TableOperations ───────────── v1.2.0 Installed LBFGSB ────────────────────── v0.4.1 Installed CompositionsBase ──────────── v0.1.2 Installed Moshi ─────────────────────── v0.3.7 Installed DifferentiationInterface ──── v0.7.8 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed HashArrayMappedTries ──────── v0.2.0 Installed CommonSolve ───────────────── v0.2.4 Installed FunctionWrappersWrappers ──── v0.1.3 Installed RecipesBase ───────────────── v1.3.4 Installed DataAPI ───────────────────── v1.16.0 Installed SciMLOperators ────────────── v1.7.2 Installed InvertedIndices ───────────── v1.3.1 Installed Colors ────────────────────── v0.13.1 Installed SciMLStructures ───────────── v1.7.0 Installed StaticArraysCore ──────────── v1.4.3 Installed StaticArrays ──────────────── v1.9.15 Installed ColorTypes ────────────────── v0.12.1 Installed BiochemicalAlgorithms ─────── v0.5.5 Installed StringManipulation ────────── v0.4.1 Installed Glib_jll ──────────────────── v2.86.0+0 Installed Requires ──────────────────── v1.3.1 Installed FunctionWrappers ──────────── v1.1.3 Installed MolecularGraph ────────────── v0.19.1 Installed Parsers ───────────────────── v2.8.3 Installed FastClosures ──────────────── v0.3.2 Installed AutoHashEquals ────────────── v2.2.0 Installed JSON ──────────────────────── v0.21.4 Installed PrettyTables ──────────────── v2.4.0 Installed SciMLBase ─────────────────── v2.120.0 Installed Xorg_libXdmcp_jll ─────────── v1.1.6+0 Installed WeakRefStrings ────────────── v1.4.2 Installed TestItems ─────────────────── v1.0.0 Installed Unitful ───────────────────── v1.25.0 Installed JLLWrappers ───────────────── v1.7.1 Installed BioGenerics ───────────────── v0.1.5 Installed DataFrames ────────────────── v1.8.0 Installed Pango_jll ─────────────────── v1.56.4+0 Installed ChunkCodecCore ────────────── v1.0.0 Installed StructTypes ───────────────── v1.11.0 Installed GeometryBasics ────────────── v0.5.10 Installed CSV ───────────────────────── v0.10.15 Installed IterTools ─────────────────── v1.10.0 Installed Graphs ────────────────────── v1.13.1 Installed Xorg_xtrans_jll ───────────── v1.6.0+0 Installed FilePathsBase ─────────────── v0.9.24 Installed Adapt ─────────────────────── v4.4.0 Installed Accessors ─────────────────── v0.1.42 Installed Measurements ──────────────── v2.14.0 Installed JLD2 ──────────────────────── v0.6.2 Installed RuntimeGeneratedFunctions ─── v0.5.15 Installed Libmount_jll ──────────────── v2.41.2+0 Installed ConstructionBase ──────────── v1.6.0 Installed SymbolicIndexingInterface ─── v0.3.44 Installed ChunkSplitters ────────────── v3.1.2 Installed Xorg_libX11_jll ───────────── v1.8.12+0 Installed Compat ────────────────────── v4.18.1 Installed BioStructures ─────────────── v4.7.0 Installed EarCut_jll ────────────────── v2.2.4+0 Installed TranscodingStreams ────────── v0.11.3 Installed ProgressLogging ───────────── v0.1.5 Installed Optimization ──────────────── v4.7.0 Installed CellListMap ───────────────── v0.9.12 Installed Statistics ────────────────── v1.11.1 Installed StringEncodings ───────────── v0.3.7 Installed ProgressMeter ─────────────── v1.11.0 Installed GettextRuntime_jll ────────── v0.22.4+0 Installed JSON3 ─────────────────────── v1.14.3 Installed ExproniconLite ────────────── v0.10.14 Installed BioSymbols ────────────────── v5.2.0 Installed PrecompileTools ───────────── v1.3.3 Installed FriBidi_jll ───────────────── v1.0.17+0 Installed Xorg_libXrender_jll ───────── v0.9.12+0 Installed ChunkCodecLibZlib ─────────── v1.0.0 Installed YAML ──────────────────────── v0.4.14 Installed Parameters ────────────────── v0.12.3 Installed FixedPointNumbers ─────────── v0.8.5 Installed IntervalSets ──────────────── v0.7.11 Installed Rotations ─────────────────── v1.7.1 Installed FreeType2_jll ─────────────── v2.13.4+0 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed Xorg_libXext_jll ──────────── v1.3.7+0 Installing 32 artifacts Installed artifact L_BFGS_B 45.2 KiB Installed artifact Graphite2 120.2 KiB Installed artifact FriBidi 78.9 KiB Installed artifact Bzip2 503.5 KiB Installed artifact coordgenlibs 303.6 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 HarfBuzz 1.7 MiB Installed artifact Cairo 2.2 MiB Installed artifact Pixman 372.2 KiB Installed artifact Libffi 44.2 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact libpng 328.4 KiB Installed artifact LZO 208.9 KiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact EarCut 80.5 KiB Installed artifact Fontconfig 984.8 KiB Installed artifact Pango 1.1 MiB Installed artifact GettextRuntime 543.0 KiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact FreeType2 1.5 MiB Installed artifact Expat 274.7 KiB Installed artifact Libiconv 1.9 MiB Installed artifact Libuuid 3.7 MiB Installed artifact Libmount 6.5 MiB Installed artifact Glib 7.7 MiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact RDKit 56.2 MiB Installed artifact boost 22.1 MiB Updating `~/.julia/environments/v1.13/Project.toml` [9d651bdf] + BiochemicalAlgorithms v0.5.5 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.18.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.4.0 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.20.0 [15f4f7f2] + AutoHashEquals v2.2.0 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.7.0 [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 v0.9.12 [0b6fb165] + ChunkCodecCore v1.0.0 [4c0bbee4] + ChunkCodecLibZlib v1.0.0 [55437552] + ChunkCodecLibZstd v1.0.0 [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 v4.18.1 [a33af91c] 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Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 30.04s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 5022.1 ms ✓ TestEnv 1 dependency successfully precompiled in 6 seconds. 27 already precompiled. Precompiling package dependencies... Precompilation completed after 960.06s ################################################################################ # Testing # Testing BiochemicalAlgorithms Status `/tmp/jl_wJzN0V/Project.toml` [4c88cf16] Aqua v0.8.14 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.7.0 [3c28c6f8] BioSymbols v5.2.0 [9d651bdf] BiochemicalAlgorithms v0.5.5 [336ed68f] CSV v0.10.15 [69e1c6dd] CellListMap v0.9.12 [a93c6f00] DataFrames v1.8.0 [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 v4.7.0 [5ad8b20f] PhysicalConstants v0.2.4 ⌅ [08abe8d2] PrettyTables v2.4.0 [94ee1d12] Quaternions v0.7.6 [6038ab10] Rotations v1.7.1 [90137ffa] StaticArrays v1.9.15 [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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [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 v1.67.1+0 [3f19e933] p7zip_jll v17.6.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints 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:310 [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:310 [9] _start() @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/EdAH5/test/runtests.jl:3 Testing failed after 60.27s 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: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 1087.6s: package tests unexpectedly errored