Package evaluation of BiochemicalAlgorithms on Julia 1.13.0-DEV.1125 (fd1c6fd302*) started at 2025-09-16T09:58:59.194 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.76s ################################################################################ # Installation # Installing BiochemicalAlgorithms... Resolving package versions... Installed Libuuid_jll ───────────────── v2.41.1+0 Installed ChunkCodecLibZstd ─────────── v1.0.0 Installed Bzip2_jll ─────────────────── v1.0.9+0 Installed HarfBuzz_jll ──────────────── v8.5.1+0 Installed Calculus ──────────────────── v0.5.2 Installed RDKitMinimalLib ───────────── v1.2.0 Installed Extents ───────────────────── v0.1.6 Installed InlineStrings ─────────────── v1.4.5 Installed RDKit_jll ─────────────────── v2022.9.5+0 Installed Graphite2_jll ─────────────── v1.3.15+0 Installed Cairo_jll ─────────────────── v1.18.5+0 Installed UnitfulAtomic ─────────────── v1.0.0 Installed OrderedCollections ────────── v1.8.1 Installed SentinelArrays ────────────── v1.4.8 Installed PreallocationTools ────────── v0.4.34 Installed Fontconfig_jll ────────────── v2.17.1+0 Installed NaNMath ───────────────────── v1.1.3 Installed libinchi_jll ──────────────── v1.6.0+0 Installed Graphics ──────────────────── v1.1.3 Installed ScopedValues ──────────────── v1.5.0 Installed PhysicalConstants ─────────── v0.2.4 Installed FileIO ────────────────────── v1.17.0 Installed Mendeleev ─────────────────── v1.0.1 Installed Xorg_libxcb_jll ───────────── v1.17.1+0 Installed Tables ────────────────────── v1.12.1 Installed EnumX ─────────────────────── v1.0.5 Installed Reexport ──────────────────── v1.2.2 Installed LZO_jll ───────────────────── v2.10.3+0 Installed InverseFunctions ──────────── v0.1.17 Installed Jieko ─────────────────────── v0.2.1 Installed Preferences ───────────────── v1.5.0 Installed boost_jll ─────────────────── v1.76.0+1 Installed LLVMOpenMP_jll ────────────── v18.1.8+0 Installed LaTeXStrings ──────────────── v1.4.0 Installed Missings ──────────────────── v1.2.0 Installed TableTraits ───────────────── v1.0.1 Installed Crayons ───────────────────── v4.1.1 Installed SortingAlgorithms ─────────── v1.2.2 Installed RecursiveArrayTools ───────── v3.37.1 Installed Format ────────────────────── v1.3.7 Installed UnPack ────────────────────── v1.0.2 Installed Inflate ───────────────────── v0.1.5 Installed ADTypes ───────────────────── v1.18.0 Installed DataStructures ────────────── v0.19.1 Installed MacroTools ────────────────── v0.5.16 Installed MakieCore ─────────────────── v0.9.5 Installed FillArrays ────────────────── v1.14.0 Installed AbstractTrees ─────────────── v0.4.5 Installed ArnoldiMethod ─────────────── v0.4.0 Installed DelimitedFiles ────────────── v1.9.1 Installed Quaternions ───────────────── v0.7.6 Installed SparseMatrixColorings ─────── v0.4.21 Installed Xorg_libXau_jll ───────────── v1.0.13+0 Installed CodecZlib ─────────────────── v0.7.8 Installed Cairo ─────────────────────── v1.1.1 Installed ExprTools ─────────────────── v0.1.10 Installed DataValueInterfaces ───────── v1.0.0 Installed ConsoleProgressMonitor ────── v0.1.2 Installed ArrayInterface ────────────── v7.20.0 Installed Observables ───────────────── v0.5.5 Installed Expat_jll ─────────────────── v2.7.1+0 Installed Libffi_jll ────────────────── v3.4.7+0 Installed Pixman_jll ────────────────── v0.44.2+0 Installed LoggingExtras ─────────────── v1.1.0 Installed RealDot ───────────────────── v0.1.0 Installed GPUArraysCore ─────────────── v0.2.0 Installed coordgenlibs_jll ──────────── v3.0.2+0 Installed SparseConnectivityTracer ──── v1.0.2 Installed libpng_jll ────────────────── v1.6.50+0 Installed L_BFGS_B_jll ──────────────── v3.0.1+0 Installed LeftChildRightSiblingTrees ── v0.2.1 Installed SimpleTraits ──────────────── v0.9.5 Installed TerminalLoggers ───────────── v0.1.7 Installed MetaGraphs ────────────────── v0.8.1 Installed Setfield ──────────────────── v1.1.2 Installed Roots ─────────────────────── v2.2.10 Installed PDMats ────────────────────── v0.11.35 Installed PooledArrays ──────────────── v1.4.3 Installed WorkerUtilities ───────────── v1.6.1 Installed OptimizationBase ──────────── v2.11.0 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 IteratorInterfaceExtensions ─ v1.0.0 Installed HashArrayMappedTries ──────── v0.2.0 Installed FunctionWrappersWrappers ──── v0.1.3 Installed RecipesBase ───────────────── v1.3.4 Installed BiochemicalAlgorithms ─────── v0.5.5 Installed DataAPI ───────────────────── v1.16.0 Installed SciMLOperators ────────────── v1.7.2 Installed InvertedIndices ───────────── v1.3.1 Installed MolecularGraph ────────────── v0.19.1 Installed SciMLStructures ───────────── v1.7.0 Installed StaticArraysCore ──────────── v1.4.3 Installed StaticArrays ──────────────── v1.9.15 Installed Requires ──────────────────── v1.3.1 Installed Glib_jll ──────────────────── v2.86.0+0 Installed StringManipulation ────────── v0.4.1 Installed Colors ────────────────────── v0.13.1 Installed ColorTypes ────────────────── v0.12.1 Installed FunctionWrappers ──────────── v1.1.3 Installed FastClosures ──────────────── v0.3.2 Installed AutoHashEquals ────────────── v2.2.0 Installed Parsers ───────────────────── v2.8.3 Installed JSON ──────────────────────── v0.21.4 Installed BioGenerics ───────────────── v0.1.5 Installed SciMLBase ─────────────────── v2.118.1 Installed Xorg_libXdmcp_jll ─────────── v1.1.6+0 Installed PrettyTables ──────────────── v2.4.0 Installed WeakRefStrings ────────────── v1.4.2 Installed Unitful ───────────────────── v1.24.0 Installed TestItems ─────────────────── v1.0.0 Installed JLLWrappers ───────────────── v1.7.1 Installed ChunkCodecCore ────────────── v1.0.0 Installed Pango_jll ─────────────────── v1.56.4+0 Installed GeometryBasics ────────────── v0.5.10 Installed StructTypes ───────────────── v1.11.0 Installed IterTools ─────────────────── v1.10.0 Installed Xorg_xtrans_jll ───────────── v1.6.0+0 Installed Measurements ──────────────── v2.14.0 Installed Accessors ─────────────────── v0.1.42 Installed DataFrames ────────────────── v1.8.0 Installed FilePathsBase ─────────────── v0.9.24 Installed Adapt ─────────────────────── v4.3.0 Installed JLD2 ──────────────────────── v0.6.2 Installed RuntimeGeneratedFunctions ─── v0.5.15 Installed BioStructures ─────────────── v4.6.1 Installed ConstructionBase ──────────── v1.6.0 Installed Graphs ────────────────────── v1.13.1 Installed Libmount_jll ──────────────── v2.41.1+0 Installed CellListMap ───────────────── v0.9.11 Installed ChunkSplitters ────────────── v3.1.2 Installed Compat ────────────────────── v4.18.0 Installed Xorg_libX11_jll ───────────── v1.8.12+0 Installed SymbolicIndexingInterface ─── v0.3.43 Installed ProgressLogging ───────────── v0.1.5 Installed TranscodingStreams ────────── v0.11.3 Installed EarCut_jll ────────────────── v2.2.4+0 Installed Optimization ──────────────── v4.7.0 Installed Statistics ────────────────── v1.11.1 Installed StringEncodings ───────────── v0.3.7 Installed ProgressMeter ─────────────── v1.11.0 Installed GettextRuntime_jll ────────── v0.22.4+0 Installed ExproniconLite ────────────── v0.10.14 Installed BioSymbols ────────────────── v5.2.0 Installed PrecompileTools ───────────── v1.3.3 Installed FriBidi_jll ───────────────── v1.0.17+0 Installed ChunkCodecLibZlib ─────────── v1.0.0 Installed Xorg_libXrender_jll ───────── v0.9.12+0 Installed YAML ──────────────────────── v0.4.14 Installed JSON3 ─────────────────────── v1.14.3 Installed Parameters ────────────────── v0.12.3 Installed IntervalSets ──────────────── v0.7.11 Installed FixedPointNumbers ─────────── v0.8.5 Installed FreeType2_jll ─────────────── v2.13.4+0 Installed Xorg_libXext_jll ──────────── v1.3.7+0 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed Rotations ─────────────────── v1.7.1 Installed CSV ───────────────────────── v0.10.15 Installing 32 artifacts Installed artifact Graphite2 120.2 KiB Installed artifact EarCut 80.5 KiB Installed artifact coordgenlibs 303.6 KiB Installed artifact Expat 274.7 KiB Installed artifact libinchi 933.4 KiB Installed artifact Libffi 44.2 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Pango 1.1 MiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact L_BFGS_B 45.2 KiB Installed artifact FreeType2 1.5 MiB Installed artifact libpng 328.4 KiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact Pixman 372.2 KiB Installed artifact Bzip2 503.5 KiB Installed artifact LZO 208.9 KiB Installed artifact Fontconfig 984.8 KiB Installed artifact FriBidi 78.9 KiB Installed artifact Libuuid 3.6 MiB Installed artifact GettextRuntime 543.0 KiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact Libiconv 1.9 MiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact Cairo 2.2 MiB Installed artifact Libmount 6.5 MiB Installed artifact HarfBuzz 1.7 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 v4.3.0 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.20.0 [15f4f7f2] + AutoHashEquals v2.2.0 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.6.1 [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 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 v4.18.0 [a33af91c] + 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[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 v1.67.0+0 [3f19e933] + p7zip_jll v17.6.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 32.01s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 5018.3 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... ERROR: LoadError: The following 2 direct dependencies failed to precompile: BiochemicalAlgorithms Failed to precompile BiochemicalAlgorithms [9d651bdf-8945-47d1-9188-34e269d8f7b5] to "/home/pkgeval/.julia/compiled/v1.13/BiochemicalAlgorithms/jl_oM9SnW" (ProcessExited(1)). ERROR: LoadError: could not load symbol "pango_version_string": Stacktrace: [1] top-level scope @ ~/.julia/packages/Cairo/FQrbN/src/Cairo.jl:30 [2] include(mod::Module, _path::String) @ Base ./Base.jl:308 [3] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String) @ Base ./loading.jl:3072 [4] top-level scope @ stdin:5 [5] eval(m::Module, e::Any) @ Core ./boot.jl:489 [6] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2918 [7] include_string @ ./loading.jl:2928 [inlined] [8] exec_options(opts::Base.JLOptions) @ Base ./client.jl:328 [9] _start() @ Base ./client.jl:563 in expression starting at /home/pkgeval/.julia/packages/Cairo/FQrbN/src/Cairo.jl:1 in expression starting at stdin:5 ERROR: LoadError: Failed to precompile Cairo [159f3aea-2a34-519c-b102-8c37f9878175] to "/home/pkgeval/.julia/compiled/v1.13/Cairo/jl_4HN8RE" (ProcessExited(1)). Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing) @ Base ./loading.jl:3359 [3] kwcall(::@NamedTuple{reasons::Dict{String, Int64}, loadable_exts::Nothing}, ::typeof(Base.compilecache), pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base ./loading.jl:3237 [4] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})() @ Base ./loading.jl:2701 [5] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:94 [6] #mkpidlock#7 @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:89 [inlined] [7] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:115 [8] #invokelatest_gr#234 @ ./reflection.jl:1335 [inlined] [9] invokelatest_gr @ ./reflection.jl:1327 [inlined] [10] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64) @ Base ./loading.jl:3930 [11] maybe_cachefile_lock @ ./loading.jl:3927 [inlined] [12] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2687 [13] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2515 [14] macro expansion @ ./loading.jl:2443 [inlined] [15] macro expansion @ ./lock.jl:376 [inlined] [16] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2407 [17] require @ ./loading.jl:2383 [inlined] [18] eval_import_path @ ./module.jl:36 [inlined] [19] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr) @ Base ./module.jl:111 [20] top-level scope @ ~/.julia/packages/MolecularGraph/n9TWP/src/MolecularGraph.jl:112 [21] include(mod::Module, _path::String) @ Base ./Base.jl:308 [22] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String) @ Base ./loading.jl:3072 [23] top-level scope @ stdin:5 [24] eval(m::Module, e::Any) @ Core ./boot.jl:489 [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2918 [26] include_string @ ./loading.jl:2928 [inlined] [27] exec_options(opts::Base.JLOptions) @ Base ./client.jl:328 [28] _start() @ Base ./client.jl:563 in expression starting at /home/pkgeval/.julia/packages/MolecularGraph/n9TWP/src/MolecularGraph.jl:6 in expression starting at stdin:5 ERROR: LoadError: Failed to precompile MolecularGraph [6c89ec66-9cd8-5372-9f91-fabc50dd27fd] to "/home/pkgeval/.julia/compiled/v1.13/MolecularGraph/jl_L7Urws" (ProcessExited(1)). Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing) @ Base ./loading.jl:3359 [3] kwcall(::@NamedTuple{reasons::Dict{String, Int64}, loadable_exts::Nothing}, ::typeof(Base.compilecache), pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base ./loading.jl:3237 [4] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})() @ Base ./loading.jl:2701 [5] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:94 [6] #mkpidlock#7 @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:89 [inlined] [7] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:115 [8] #invokelatest_gr#234 @ ./reflection.jl:1335 [inlined] [9] invokelatest_gr @ ./reflection.jl:1327 [inlined] [10] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64) @ Base ./loading.jl:3930 [11] maybe_cachefile_lock @ ./loading.jl:3927 [inlined] [12] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2687 [13] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2515 [14] macro expansion @ ./loading.jl:2443 [inlined] [15] macro expansion @ ./lock.jl:376 [inlined] [16] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2407 [17] require @ ./loading.jl:2383 [inlined] [18] eval_import_path @ ./module.jl:36 [inlined] [19] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr) @ Base ./module.jl:111 [20] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/BiochemicalAlgorithms.jl:19 [21] include(mod::Module, _path::String) @ Base ./Base.jl:308 [22] include_package_for_output(pkg::Base.PkgId, input::String, 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:3072 [23] top-level scope @ stdin:5 [24] eval(m::Module, e::Any) @ Core ./boot.jl:489 [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2918 [26] include_string @ ./loading.jl:2928 [inlined] [27] exec_options(opts::Base.JLOptions) @ Base ./client.jl:328 [28] _start() @ Base ./client.jl:563 in expression starting at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/EdAH5/src/BiochemicalAlgorithms.jl:1 in expression starting at stdin:5 MolecularGraph Failed to precompile MolecularGraph [6c89ec66-9cd8-5372-9f91-fabc50dd27fd] to "/home/pkgeval/.julia/compiled/v1.13/MolecularGraph/jl_k8x5O3" (ProcessExited(1)). ERROR: LoadError: could not load symbol "pango_version_string": Stacktrace: [1] top-level scope @ ~/.julia/packages/Cairo/FQrbN/src/Cairo.jl:30 [2] include(mod::Module, _path::String) @ Base ./Base.jl:308 [3] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String) @ Base ./loading.jl:3072 [4] top-level scope @ stdin:5 [5] eval(m::Module, e::Any) @ Core ./boot.jl:489 [6] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2918 [7] include_string @ ./loading.jl:2928 [inlined] [8] exec_options(opts::Base.JLOptions) @ Base ./client.jl:328 [9] _start() @ Base ./client.jl:563 in expression starting at /home/pkgeval/.julia/packages/Cairo/FQrbN/src/Cairo.jl:1 in expression starting at stdin:5 ERROR: LoadError: Failed to precompile Cairo [159f3aea-2a34-519c-b102-8c37f9878175] to "/home/pkgeval/.julia/compiled/v1.13/Cairo/jl_WIUCHF" (ProcessExited(1)). Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing) @ Base ./loading.jl:3359 [3] kwcall(::@NamedTuple{reasons::Dict{String, Int64}, loadable_exts::Nothing}, ::typeof(Base.compilecache), pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base ./loading.jl:3237 [4] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})() @ Base ./loading.jl:2701 [5] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:94 [6] #mkpidlock#7 @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:89 [inlined] [7] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:115 [8] #invokelatest_gr#234 @ ./reflection.jl:1335 [inlined] [9] invokelatest_gr @ ./reflection.jl:1327 [inlined] [10] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64) @ Base ./loading.jl:3930 [11] maybe_cachefile_lock @ ./loading.jl:3927 [inlined] [12] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2687 [13] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2515 [14] macro expansion @ ./loading.jl:2443 [inlined] [15] macro expansion @ ./lock.jl:376 [inlined] [16] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2407 [17] require @ ./loading.jl:2383 [inlined] [18] eval_import_path @ ./module.jl:36 [inlined] [19] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr) @ Base ./module.jl:111 [20] top-level scope @ ~/.julia/packages/MolecularGraph/n9TWP/src/MolecularGraph.jl:112 [21] include(mod::Module, _path::String) @ Base ./Base.jl:308 [22] include_package_for_output(pkg::Base.PkgId, input::String, 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:3072 [23] top-level scope @ stdin:5 [24] eval(m::Module, e::Any) @ Core ./boot.jl:489 [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2918 [26] include_string @ ./loading.jl:2928 [inlined] [27] exec_options(opts::Base.JLOptions) @ Base ./client.jl:328 [28] _start() @ Base ./client.jl:563 in expression starting at /home/pkgeval/.julia/packages/MolecularGraph/n9TWP/src/MolecularGraph.jl:6 in expression starting at stdin:5 in expression starting at /PkgEval.jl/scripts/precompile.jl:37 Precompilation failed after 957.64s ################################################################################ # Testing # Testing BiochemicalAlgorithms Status `/tmp/jl_dAI3JF/Project.toml` [4c88cf16] Aqua v0.8.14 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.6.1 [3c28c6f8] BioSymbols v5.2.0 [9d651bdf] BiochemicalAlgorithms v0.5.5 [336ed68f] CSV v0.10.15 [69e1c6dd] CellListMap v0.9.11 [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 [bd369af6] Tables v1.12.1 [f8b46487] TestItemRunner v1.1.0 [1986cc42] Unitful v1.24.0 [a7773ee8] UnitfulAtomic v1.0.0 [37e2e46d] LinearAlgebra v1.13.0 [de0858da] Printf v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_dAI3JF/Manifest.toml` [47edcb42] ADTypes v1.18.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [4c88cf16] Aqua v0.8.14 [ec485272] ArnoldiMethod v0.4.0 [4fba245c] ArrayInterface v7.20.0 [15f4f7f2] AutoHashEquals v2.2.0 [47718e42] BioGenerics v0.1.5 [de9282ab] BioStructures v4.6.1 [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 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 v4.18.0 [a33af91c] CompositionsBase v0.1.2 [88cd18e8] ConsoleProgressMonitor v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.0 [864edb3b] DataStructures v0.19.1 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [a0c0ee7d] DifferentiationInterface v0.7.7 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.5 [e2ba6199] ExprTools v0.1.10 [55351af7] ExproniconLite v0.10.14 [411431e0] Extents v0.1.6 [9aa1b823] FastClosures v0.3.2 [5789e2e9] FileIO v1.17.0 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.14.0 [53c48c17] FixedPointNumbers v0.8.5 [1fa38f19] Format v1.3.7 [069b7b12] FunctionWrappers v1.1.3 [77dc65aa] FunctionWrappersWrappers v0.1.3 [46192b85] GPUArraysCore v0.2.0 [5c1252a2] GeometryBasics v0.5.10 [a2bd30eb] Graphics v1.1.3 [86223c79] Graphs v1.13.1 [076d061b] HashArrayMappedTries v0.2.0 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.5 [8197267c] IntervalSets v0.7.11 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [033835bb] JLD2 v0.6.2 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.3 [ae98c720] Jieko v0.2.1 [5be7bae1] LBFGSB v0.4.1 [b964fa9f] LaTeXStrings v1.4.0 [1d6d02ad] LeftChildRightSiblingTrees v0.2.1 [e6f89c97] LoggingExtras v1.1.0 [1914dd2f] MacroTools v0.5.16 ⌅ [20f20a25] MakieCore v0.9.5 [eff96d63] Measurements v2.14.0 [c116f080] Mendeleev v1.0.1 [626554b9] MetaGraphs v0.8.1 [e1d29d7a] Missings v1.2.0 ⌅ [6c89ec66] MolecularGraph v0.19.1 [2e0e35c7] Moshi v0.3.7 [77ba4419] NaNMath v1.1.3 [510215fc] Observables v0.5.5 [7f7a1694] Optimization v4.7.0 [bca83a33] OptimizationBase v2.11.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.3 [5ad8b20f] PhysicalConstants v0.2.4 [2dfb63ee] PooledArrays v1.4.3 [d236fae5] PreallocationTools v0.4.34 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 ⌅ [08abe8d2] PrettyTables v2.4.0 [33c8b6b6] ProgressLogging v0.1.5 [92933f4c] ProgressMeter v1.11.0 [94ee1d12] Quaternions v0.7.6 [44044271] RDKitMinimalLib v1.2.0 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [731186ca] RecursiveArrayTools v3.37.1 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [f2b01f46] Roots v2.2.10 [6038ab10] Rotations v1.7.1 [7e49a35a] RuntimeGeneratedFunctions v0.5.15 [0bca4576] SciMLBase v2.118.1 [c0aeaf25] SciMLOperators v1.7.2 [53ae85a6] SciMLStructures v1.7.0 [7e506255] ScopedValues v1.5.0 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield v1.1.2 [699a6c99] SimpleTraits v0.9.5 [a2af1166] SortingAlgorithms v1.2.2 [9f842d2f] SparseConnectivityTracer v1.0.2 [0a514795] SparseMatrixColorings v0.4.21 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [69024149] StringEncodings v0.3.7 [892a3eda] StringManipulation v0.4.1 [856f2bd8] StructTypes v1.11.0 [2efcf032] SymbolicIndexingInterface v0.3.43 [ab02a1b2] TableOperations v1.2.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [5d786b92] TerminalLoggers v0.1.7 [f8b46487] TestItemRunner v1.1.0 [1c621080] TestItems v1.0.0 [3bb67fe8] TranscodingStreams v0.11.3 [3a884ed6] UnPack v1.0.2 [1986cc42] Unitful v1.24.0 [a7773ee8] UnitfulAtomic v1.0.0 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [ddb6d928] YAML v0.4.14 [6e34b625] Bzip2_jll v1.0.9+0 [83423d85] Cairo_jll v1.18.5+0 [5ae413db] EarCut_jll v2.2.4+0 [2e619515] Expat_jll v2.7.1+0 [a3f928ae] Fontconfig_jll v2.17.1+0 [d7e528f0] FreeType2_jll v2.13.4+0 [559328eb] FriBidi_jll v1.0.17+0 [b0724c58] GettextRuntime_jll v0.22.4+0 [7746bdde] Glib_jll v2.86.0+0 [3b182d85] Graphite2_jll v1.3.15+0 [2e76f6c2] HarfBuzz_jll v8.5.1+0 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [dd4b983a] LZO_jll v2.10.3+0 [81d17ec3] L_BFGS_B_jll v3.0.1+0 [e9f186c6] Libffi_jll v3.4.7+0 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.41.1+0 [38a345b3] Libuuid_jll v2.41.1+0 [36c8627f] Pango_jll v1.56.4+0 ⌅ [30392449] Pixman_jll v0.44.2+0 [03d1d220] RDKit_jll v2022.9.5+0 [4f6342f7] Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] Xorg_libXau_jll v1.0.13+0 [a3789734] Xorg_libXdmcp_jll v1.1.6+0 [1082639a] Xorg_libXext_jll v1.3.7+0 [ea2f1a96] Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] Xorg_libxcb_jll v1.17.1+0 [c5fb5394] Xorg_xtrans_jll v1.6.0+0 ⌅ [28df3c45] boost_jll v1.76.0+1 [f6050b86] coordgenlibs_jll v3.0.2+0 [172afb32] libinchi_jll v1.6.0+0 [b53b4c65] libpng_jll v1.6.50+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 v1.12.0 [b27032c2] LibCURL v0.6.4 [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 [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 v1.67.0+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 61.23s 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 1089.46s: package fails to precompile