Package evaluation of BiochemicalAlgorithms on Julia 1.13.0-DEV.955 (13f6b3b5c0*) started at 2025-08-04T01:30:52.155 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.65s ################################################################################ # Installation # Installing BiochemicalAlgorithms... Resolving package versions... Installed Libuuid_jll ───────────────── v2.41.0+0 Installed HarfBuzz_jll ──────────────── v8.5.1+0 Installed Extents ───────────────────── v0.1.6 Installed Calculus ──────────────────── v0.5.2 Installed Bzip2_jll ─────────────────── v1.0.9+0 Installed InlineStrings ─────────────── v1.4.4 Installed Cairo_jll ─────────────────── v1.18.5+0 Installed Graphite2_jll ─────────────── v1.3.15+0 Installed OrderedCollections ────────── v1.8.1 Installed SentinelArrays ────────────── v1.4.8 Installed RDKitMinimalLib ───────────── v1.2.0 Installed RDKit_jll ─────────────────── v2022.9.5+0 Installed FileIO ────────────────────── v1.17.0 Installed Fontconfig_jll ────────────── v2.16.0+0 Installed NaNMath ───────────────────── v1.1.3 Installed UnitfulAtomic ─────────────── v1.0.0 Installed Graphics ──────────────────── v1.1.3 Installed ScopedValues ──────────────── v1.4.0 Installed Xorg_libxcb_jll ───────────── v1.17.1+0 Installed EnumX ─────────────────────── v1.0.5 Installed libinchi_jll ──────────────── v1.6.0+0 Installed Tables ────────────────────── v1.12.1 Installed InverseFunctions ──────────── v0.1.17 Installed Jieko ─────────────────────── v0.2.1 Installed PhysicalConstants ─────────── v0.2.4 Installed Mendeleev ─────────────────── v1.0.1 Installed Reexport ──────────────────── v1.2.2 Installed Missings ──────────────────── v1.2.0 Installed LZO_jll ───────────────────── v2.10.3+0 Installed LLVMOpenMP_jll ────────────── v18.1.8+0 Installed TableTraits ───────────────── v1.0.1 Installed boost_jll ─────────────────── v1.76.0+1 Installed Preferences ───────────────── v1.4.3 Installed LaTeXStrings ──────────────── v1.4.0 Installed SortingAlgorithms ─────────── v1.2.1 Installed Crayons ───────────────────── v4.1.1 Installed UnPack ────────────────────── v1.0.2 Installed Format ────────────────────── v1.3.7 Installed ADTypes ───────────────────── v1.16.0 Installed Inflate ───────────────────── v0.1.5 Installed MacroTools ────────────────── v0.5.16 Installed DataStructures ────────────── v0.18.22 Installed RecursiveArrayTools ───────── v3.36.0 Installed Quaternions ───────────────── v0.7.6 Installed MakieCore ─────────────────── v0.9.5 Installed AbstractTrees ─────────────── v0.4.5 Installed FillArrays ────────────────── v1.13.0 Installed SparseMatrixColorings ─────── v0.4.21 Installed DelimitedFiles ────────────── v1.9.1 Installed ArnoldiMethod ─────────────── v0.4.0 Installed CodecZlib ─────────────────── v0.7.8 Installed Cairo ─────────────────────── v1.1.1 Installed Xorg_libXau_jll ───────────── v1.0.13+0 Installed DataValueInterfaces ───────── v1.0.0 Installed ExprTools ─────────────────── v0.1.10 Installed Observables ───────────────── v0.5.5 Installed LoggingExtras ─────────────── v1.1.0 Installed ArrayInterface ────────────── v7.19.0 Installed Pixman_jll ────────────────── v0.44.2+0 Installed Libffi_jll ────────────────── v3.4.7+0 Installed Expat_jll ─────────────────── v2.6.5+0 Installed RealDot ───────────────────── v0.1.0 Installed GPUArraysCore ─────────────── v0.2.0 Installed ConsoleProgressMonitor ────── v0.1.2 Installed SparseConnectivityTracer ──── v1.0.0 Installed libpng_jll ────────────────── v1.6.50+0 Installed coordgenlibs_jll ──────────── v3.0.2+0 Installed LeftChildRightSiblingTrees ── v0.2.1 Installed SimpleTraits ──────────────── v0.9.4 Installed Setfield ──────────────────── v1.1.2 Installed TerminalLoggers ───────────── v0.1.7 Installed MetaGraphs ────────────────── v0.8.0 Installed PDMats ────────────────────── v0.11.35 Installed PooledArrays ──────────────── v1.4.3 Installed OptimizationBase ──────────── v2.10.0 Installed L_BFGS_B_jll ──────────────── v3.0.1+0 Installed WorkerUtilities ───────────── v1.6.1 Installed DocStringExtensions ───────── v0.9.5 Installed Roots ─────────────────────── v2.2.8 Installed TableOperations ───────────── v1.2.0 Installed Moshi ─────────────────────── v0.3.7 Installed DifferentiationInterface ──── v0.7.4 Installed CompositionsBase ──────────── v0.1.2 Installed HashArrayMappedTries ──────── v0.2.0 Installed CommonSolve ───────────────── v0.2.4 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed FunctionWrappersWrappers ──── v0.1.3 Installed RecipesBase ───────────────── v1.3.4 Installed LBFGSB ────────────────────── v0.4.1 Installed DataAPI ───────────────────── v1.16.0 Installed BiochemicalAlgorithms ─────── v0.5.4 Installed InvertedIndices ───────────── v1.3.1 Installed SciMLOperators ────────────── v1.4.0 Installed SciMLStructures ───────────── v1.7.0 Installed StaticArraysCore ──────────── v1.4.3 Installed StringManipulation ────────── v0.4.1 Installed ColorTypes ────────────────── v0.12.1 Installed Colors ────────────────────── v0.13.1 Installed StaticArrays ──────────────── v1.9.14 Installed Requires ──────────────────── v1.3.1 Installed Glib_jll ──────────────────── v2.84.3+0 Installed FunctionWrappers ──────────── v1.1.3 Installed Parsers ───────────────────── v2.8.3 Installed AutoHashEquals ────────────── v2.2.0 Installed JSON ──────────────────────── v0.21.4 Installed FastClosures ──────────────── v0.3.2 Installed MolecularGraph ────────────── v0.19.1 Installed SciMLBase ─────────────────── v2.107.0 Installed PrettyTables ──────────────── v2.4.0 Installed BioGenerics ───────────────── v0.1.5 Installed Xorg_libXdmcp_jll ─────────── v1.1.6+0 Installed WeakRefStrings ────────────── v1.4.2 Installed Unitful ───────────────────── v1.24.0 Installed JLLWrappers ───────────────── v1.7.1 Installed TestItems ─────────────────── v1.0.0 Installed DataFrames ────────────────── v1.7.0 Installed CSV ───────────────────────── v0.10.15 Installed Pango_jll ─────────────────── v1.56.3+0 Installed GeometryBasics ────────────── v0.5.10 Installed StructTypes ───────────────── v1.11.0 Installed IterTools ─────────────────── v1.10.0 Installed Graphs ────────────────────── v1.13.0 Installed Accessors ─────────────────── v0.1.42 Installed Xorg_xtrans_jll ───────────── v1.6.0+0 Installed FilePathsBase ─────────────── v0.9.24 Installed Measurements ──────────────── v2.14.0 Installed Adapt ─────────────────────── v4.3.0 Installed JLD2 ──────────────────────── v0.5.15 Installed Libmount_jll ──────────────── v2.41.0+0 Installed ConstructionBase ──────────── v1.6.0 Installed RuntimeGeneratedFunctions ─── v0.5.15 Installed ChunkSplitters ────────────── v3.1.2 Installed SymbolicIndexingInterface ─── v0.3.42 Installed CellListMap ───────────────── v0.9.10 Installed BioStructures ─────────────── v4.6.0 Installed Xorg_libX11_jll ───────────── v1.8.12+0 Installed EarCut_jll ────────────────── v2.2.4+0 Installed Compat ────────────────────── v4.18.0 Installed ProgressLogging ───────────── v0.1.5 Installed TranscodingStreams ────────── v0.11.3 Installed Statistics ────────────────── v1.11.1 Installed PrecompileTools ───────────── v1.3.2 Installed Optimization ──────────────── v4.5.0 Installed GettextRuntime_jll ────────── v0.22.4+0 Installed StringEncodings ───────────── v0.3.7 Installed ProgressMeter ─────────────── v1.10.4 Installed FriBidi_jll ───────────────── v1.0.17+0 Installed YAML ──────────────────────── v0.4.14 Installed ExproniconLite ────────────── v0.10.14 Installed JSON3 ─────────────────────── v1.14.3 Installed BioSymbols ────────────────── v5.2.0 Installed Xorg_libXrender_jll ───────── v0.9.12+0 Installed Xorg_libXext_jll ──────────── v1.3.7+0 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed FreeType2_jll ─────────────── v2.13.4+0 Installed FixedPointNumbers ─────────── v0.8.5 Installed Parameters ────────────────── v0.12.3 Installed IntervalSets ──────────────── v0.7.11 Installed Rotations ─────────────────── v1.7.1 Installing 32 artifacts Installed artifact Libffi 44.2 KiB Installed artifact EarCut 80.5 KiB Installed artifact Expat 271.4 KiB Installed artifact Pango 1.1 MiB Installed artifact coordgenlibs 303.6 KiB Installed artifact libpng 328.4 KiB Installed artifact Cairo 2.2 MiB Installed artifact FriBidi 78.9 KiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact Pixman 372.2 KiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact LZO 208.9 KiB Installed artifact HarfBuzz 1.7 MiB Installed artifact L_BFGS_B 45.2 KiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact Libmount 6.4 MiB Installed artifact Graphite2 120.2 KiB Installed artifact Bzip2 503.5 KiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Fontconfig 522.5 KiB Installed artifact FreeType2 1.5 MiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact GettextRuntime 543.0 KiB Installed artifact Libuuid 3.5 MiB Installed artifact libinchi 933.4 KiB Installed artifact Libiconv 1.9 MiB Installed artifact Glib 7.7 MiB Installed artifact boost 22.1 MiB Installed artifact RDKit 56.2 MiB Updating `~/.julia/environments/v1.13/Project.toml` [9d651bdf] + BiochemicalAlgorithms v0.5.4 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.16.0 [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 v0.5.4 [336ed68f] + CSV v0.10.15 [159f3aea] + Cairo v1.1.1 [49dc2e85] + Calculus v0.5.2 [69e1c6dd] + CellListMap v0.9.10 [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 v1.7.0 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [a0c0ee7d] + DifferentiationInterface v0.7.4 [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 v1.13.0 [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 v1.13.0 [076d061b] + HashArrayMappedTries v0.2.0 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.4 [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 v0.5.15 [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 v0.8.0 [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 v4.5.0 [bca83a33] + OptimizationBase v2.10.0 [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 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [33c8b6b6] + ProgressLogging v0.1.5 [92933f4c] + ProgressMeter v1.10.4 [94ee1d12] + Quaternions v0.7.6 [44044271] + RDKitMinimalLib v1.2.0 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [731186ca] + RecursiveArrayTools v3.36.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [f2b01f46] + Roots v2.2.8 [6038ab10] + Rotations v1.7.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.15 [0bca4576] + SciMLBase v2.107.0 [c0aeaf25] + SciMLOperators v1.4.0 [53ae85a6] + SciMLStructures v1.7.0 [7e506255] + ScopedValues v1.4.0 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [699a6c99] + SimpleTraits v0.9.4 [a2af1166] + SortingAlgorithms v1.2.1 [9f842d2f] + SparseConnectivityTracer v1.0.0 [0a514795] + SparseMatrixColorings v0.4.21 [90137ffa] + StaticArrays v1.9.14 [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 v0.3.42 [ab02a1b2] + TableOperations v1.2.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [5d786b92] + TerminalLoggers v0.1.7 [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 v2.6.5+0 [a3f928ae] + Fontconfig_jll v2.16.0+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 v2.84.3+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 v2.41.0+0 [38a345b3] + Libuuid_jll v2.41.0+0 [36c8627f] + Pango_jll v1.56.3+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 v8.15.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.7.15 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 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 29.98s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 5833.6 ms ✓ TestEnv 1 dependency successfully precompiled in 6 seconds. 26 already precompiled. Precompiling package dependencies... Precompilation completed after 947.83s ################################################################################ # Testing # Testing BiochemicalAlgorithms Status `/tmp/jl_dTKt7F/Project.toml` [4c88cf16] Aqua v0.8.13 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.6.0 [3c28c6f8] BioSymbols v5.2.0 [9d651bdf] BiochemicalAlgorithms v0.5.4 [336ed68f] CSV v0.10.15 [69e1c6dd] CellListMap v0.9.10 [a93c6f00] DataFrames v1.7.0 ⌅ [864edb3b] DataStructures v0.18.22 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.5 [86223c79] Graphs v1.13.0 [0f8b85d8] JSON3 v1.14.3 [c116f080] Mendeleev v1.0.1 [626554b9] MetaGraphs v0.8.0 ⌅ [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 [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_dTKt7F/Manifest.toml` [47edcb42] ADTypes v1.16.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [4c88cf16] Aqua v0.8.13 [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 v0.5.4 [336ed68f] CSV v0.10.15 [159f3aea] Cairo v1.1.1 [49dc2e85] Calculus v0.5.2 [69e1c6dd] CellListMap v0.9.10 [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 v1.7.0 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [a0c0ee7d] DifferentiationInterface v0.7.4 [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 v1.13.0 [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 v1.13.0 [076d061b] HashArrayMappedTries v0.2.0 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.4 [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 v0.5.15 [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 v0.8.0 [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 v4.5.0 [bca83a33] OptimizationBase v2.10.0 [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 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [33c8b6b6] ProgressLogging v0.1.5 [92933f4c] ProgressMeter v1.10.4 [94ee1d12] Quaternions v0.7.6 [44044271] RDKitMinimalLib v1.2.0 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [731186ca] RecursiveArrayTools v3.36.0 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [f2b01f46] Roots v2.2.8 [6038ab10] Rotations v1.7.1 [7e49a35a] RuntimeGeneratedFunctions v0.5.15 [0bca4576] SciMLBase v2.107.0 [c0aeaf25] SciMLOperators v1.4.0 [53ae85a6] SciMLStructures v1.7.0 [7e506255] ScopedValues v1.4.0 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield v1.1.2 [699a6c99] SimpleTraits v0.9.4 [a2af1166] SortingAlgorithms v1.2.1 [9f842d2f] SparseConnectivityTracer v1.0.0 [0a514795] SparseMatrixColorings v0.4.21 [90137ffa] StaticArrays v1.9.14 [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 v0.3.42 [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 v2.6.5+0 [a3f928ae] Fontconfig_jll v2.16.0+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 v2.84.3+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 v2.41.0+0 [38a345b3] Libuuid_jll v2.41.0+0 [36c8627f] Pango_jll v1.56.3+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 v8.15.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.7.15 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+0 [efcefdf7] PCRE2_jll v10.45.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Piracy: Error During Test at /home/pkgeval/.julia/packages/Aqua/1UuaV/src/Aqua.jl:103 Got exception outside of a @test FieldError: type Core.TypeName has no field `mt`, available fields: `name`, `module`, `singletonname`, `names`, `atomicfields`, `constfields`, `wrapper`, `Typeofwrapper`, `cache`, `linearcache`, `partial`, `hash`, `max_args`, `n_uninitialized`, `flags`, `cache_entry_count`, `max_methods`, `constprop_heuristic` Stacktrace: [1] getproperty(x::Core.TypeName, f::Symbol) @ Base ./Base_compiler.jl:57 [2] all_methods(mods::Module; skip_deprecated::Bool) @ Aqua.Piracy ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:55 [3] all_methods @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:21 [inlined] [4] #hunt#30 @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:194 [inlined] [5] hunt @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:193 [inlined] [6] test_piracies(m::Module; broken::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:219 [7] test_piracies @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:218 [inlined] [8] macro expansion @ ~/.julia/packages/Aqua/1UuaV/src/Aqua.jl:104 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1929 [inlined] [10] test_all(testtarget::Module; ambiguities::Bool, unbound_args::Bool, undefined_exports::Bool, project_extras::Bool, stale_deps::Bool, deps_compat::Bool, piracies::Bool, persistent_tasks::Bool, undocumented_names::Bool) @ Aqua ~/.julia/packages/Aqua/1UuaV/src/Aqua.jl:104 [11] test_all(testtarget::Module) @ Aqua ~/.julia/packages/Aqua/1UuaV/src/Aqua.jl:59 [12] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/MSDxI/test/aqua.jl:4 [13] eval(m::Module, e::Any) @ Core ./boot.jl:489 [14] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2847 [15] include_string(m::Module, txt::String, fname::String) @ Base ./loading.jl:2857 [16] #run_testitem##6 @ ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:118 [inlined] [17] withpath(f::TestItemRunner.var"#run_testitem##6#run_testitem##7"{String, String, Module}, path::String) @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/vendored_code.jl:7 [18] #run_testitem##4 @ ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:117 [inlined] [19] cd(f::TestItemRunner.var"#run_testitem##4#run_testitem##5"{String, String, Module}, dir::String) @ Base.Filesystem ./file.jl:112 [20] run_testitem(filepath::String, use_default_usings::Bool, setups::Vector{Symbol}, package_name::String, original_code::String, line::Int64, column::Int64, test_setup_module_set::TestItemRunner.TestSetupModuleSet, testsetups::Dict{Symbol, Any}) @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:116 [21] run_tests(path::String; filter::Nothing, verbose::Bool) @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:221 [22] kwcall(::@NamedTuple{verbose::Bool}, ::typeof(TestItemRunner.run_tests), path::String) @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:133 [23] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/MSDxI/test/runtests.jl:3 [24] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:312 [25] top-level scope @ none:6 [26] eval(m::Module, e::Any) @ Core ./boot.jl:489 [27] exec_options(opts::Base.JLOptions) @ Base ./client.jl:286 [28] _start() @ Base ./client.jl:553 ┌ Error: illegal HIN file in line 31: cannot finalize bond (29, 30, BiochemicalAlgorithms.BondOrder.Single)! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/fileformats/hinfile.jl:232 ┌ Error: illegal HIN file in line 31: cannot finalize bond (29, 30, BiochemicalAlgorithms.BondOrder.Single)! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/fileformats/hinfile.jl:232 ┌ Warning: Atom names in HIN files cannot contain spaces! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/fileformats/hinfile.jl:445 ┌ Warning: Atom names in HIN files cannot contain spaces! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/fileformats/hinfile.jl:445 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/mappings/rigid_mapping.jl:176 [ Info: reconstruct_fragments!(): added 1435 atoms. [ Info: build_bonds!(): built 3839 bonds [ Info: reconstruct_fragments!(): added 1435 atoms. [ Info: build_bonds!(): built 3839 bonds [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds ┌ Warning: 2 warnings occurred during setup that were suppressed: │ - Torsion: 2 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/forcefields/common/forcefield.jl:233 [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds ┌ Warning: 2 warnings occurred during setup that were suppressed: │ - Torsion: 2 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/forcefields/common/forcefield.jl:233 [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds ┌ Warning: 2 warnings occurred during setup that were suppressed: │ - Torsion: 2 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/forcefields/common/forcefield.jl:233 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/forcefields/common/forcefield.jl:233 ┌ Warning: 20 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 3 warnings │ - QuadraticAngleBend : 12 warnings │ - Torsion : 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/forcefields/common/forcefield.jl:233 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/forcefields/common/forcefield.jl:233 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/forcefields/common/forcefield.jl:233 ┌ Warning: 20 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 3 warnings │ - QuadraticAngleBend : 12 warnings │ - Torsion : 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/forcefields/common/forcefield.jl:233 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/forcefields/common/forcefield.jl:233 [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: Added 1 atoms. [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: Added 1 atoms. ┌ Warning: write_sdfile: writer only supports 2D data; projecting atoms onto xy-plane... └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/fileformats/sdfile.jl:28 [ Info: 1 records exported. ┌ Warning: write_sdfile: writer only supports 2D data; projecting atoms onto xy-plane... └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/fileformats/sdfile.jl:33 [ Info: 11 records exported. ┌ Warning: write_sdfile: writer only supports 2D data; projecting atoms onto xy-plane... └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/fileformats/sdfile.jl:28 [ Info: 1 records exported. ┌ Warning: write_sdfile: writer only supports 2D data; projecting atoms onto xy-plane... └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/MSDxI/src/fileformats/sdfile.jl:33 [ Info: 11 records exported. Test Summary: | Pass Error Total Time Package | 9921 1 9922 19m47.1s test/substructures/test_sssr.jl | 3 3 1m24.5s Ring Perception | 3 3 1m24.4s test/aqua.jl | 10 1 11 3m38.5s Aqua | 10 1 11 3m38.5s Method ambiguity | 1 1 37.0s Unbound type parameters | 1 1 0.1s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 36.2s Compat bounds | 4 4 0.7s Piracy | 1 1 6.2s Persistent tasks | 1 1 2m01.6s test/core/test_fragment.jl | 1734 1734 1m32.5s FragmentTable | 266 266 31.9s FragmentTable/None | 178 178 2.2s FragmentTable/Nucleotide | 178 178 1.4s FragmentTable/Residue | 178 178 1.4s Fragment | 118 118 11.3s Fragment/None | 272 272 16.8s Fragment/Nucleotide | 272 272 13.8s Fragment/Residue | 272 272 13.5s test/fileformats/test_pdb.jl | 1870 1870 1m22.9s Read PDB | 1824 1824 1m06.1s Write PDB | 14 14 8.1s Read PDBx/mmCIF | 18 18 3.9s Write PDBx/mmCIF | 14 14 4.7s test/substructures/test_smarts.jl | 30 30 56.5s SMARTS | 30 30 56.5s test/core/test_atom.jl | 606 606 30.1s AtomTable | 308 308 9.4s Atom | 298 298 20.7s test/fileformats/test_hinfile.jl | 52 52 17.9s Read HIN | 48 48 6.5s Write HIN | 4 4 11.5s test/mappings/test_mappings.jl | 224 224 48.6s TrivialAtomBijection | 8 8 22.3s RigidTransform | 16 16 0.6s translate! | 88 88 2.6s rigid_transform! | 44 44 4.7s compute_rmsd | 14 14 3.2s compute_rmsd_minimizer | 42 42 12.4s map_rigid! | 12 12 2.9s test/core/test_molecule.jl | 834 834 24.9s MoleculeTable | 238 238 10.2s MoleculeTable/None | 146 146 1.3s MoleculeTable/Protein | 146 146 1.2s Molecule | 68 68 4.1s Molecule/None | 118 118 5.1s Molecule/Protein | 118 118 3.0s test/core/test_amino_acid.jl | 63 63 0.4s AminoAcid | 63 63 0.4s test/fileformats/test_pubchem_json.jl | 106 106 0.8s Read PubChem | 106 106 0.8s test/core/test_bond.jl | 312 312 9.4s BondTable | 176 176 4.3s Bond | 136 136 5.1s test/core/test_system.jl | 618 618 3m25.5s System | 618 618 3m25.5s test/core/test_system_component_table.jl | 78 78 1.5s SystemComponentTableCol | 78 78 1.5s test/core/test_chain.jl | 462 462 11.3s ChainTable | 206 206 7.7s Chain | 256 256 3.5s test/core/test_types.jl | 106 106 2.5s Vector3 | 51 51 1.3s Matrix3 | 51 51 1.2s Properties | 2 2 0.0s Flags | 2 2 0.0s test/optimization/test_optimize_structure.jl | 6 6 2m40.7s Optimize structure | 3 3 2m36.4s Optimize hydrogen positions | 3 3 4.4s test/forcefields/AMBER/test_amberff.jl | 1951 1951 54.5s AmberFF | 1951 1951 54.5s test/preprocessing/test_fragmentdb.jl | 4 4 1.8s FragmentDB | 4 4 1.8s test/core/test_element.jl | 126 126 0.2s Element | 126 126 0.2s test/core/test_moleculargraph_wrapper.jl | 162 162 2.0s Convert to SDFMolGraph | 162 162 2.0s test/substructures/test_substructure.jl | 6 6 1.7s Substructure | 6 6 1.7s test/preprocessing/test_add_hydrogens.jl | 2 2 35.7s FragmentDB | 2 2 35.7s test/core/test_secondary_structure.jl | 514 514 24.9s SecondaryStructureTable | 240 240 7.7s SecondaryStructure | 274 274 17.2s test/fileformats/test_sdfile.jl | 34 34 17.9s Read SDFile | 30 30 3.5s Write SDFile | 4 4 14.4s test/core/test_bond_order.jl | 8 8 0.0s Bond Order | 8 8 0.0s ERROR: LoadError: Some tests did not pass: 9921 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/MSDxI/test/runtests.jl:3 Testing failed after 1239.22s 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:2695 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2544 [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:311 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:320 [14] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 2264.64s: package tests unexpectedly errored