Package evaluation to test BiochemicalAlgorithms on Julia 1.14.0-DEV.2071 (559ec66647*) started at 2026-04-27T01:12:25.317 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.94s ################################################################################ # Installation # Installing BiochemicalAlgorithms... Resolving package versions... Installed Calculus ──────────────────── v0.5.2 Installed OrderedCollections ────────── v1.8.1 Installed Extents ───────────────────── v0.1.6 Installed libinchi_jll ──────────────── v1.6.0+0 Installed SentinelArrays ────────────── v1.4.9 Installed UnitfulAtomic ─────────────── v1.0.0 Installed InlineStrings ─────────────── v1.4.5 Installed PreallocationTools ────────── v1.2.0 Installed Reexport ──────────────────── v1.2.2 Installed Tables ────────────────────── v1.12.1 Installed InverseFunctions ──────────── v0.1.17 Installed OptimizationLBFGSB ────────── v1.4.1 Installed EnumX ─────────────────────── v1.0.7 Installed PhysicalConstants ─────────── v0.2.5 Installed Preferences ───────────────── v1.5.2 Installed Mendeleev ─────────────────── v1.0.2 Installed LaTeXStrings ──────────────── v1.4.0 Installed TableTraits ───────────────── v1.0.1 Installed Crayons ───────────────────── v4.1.1 Installed UnPack ────────────────────── v1.0.2 Installed Format ────────────────────── v1.3.7 Installed Missings ──────────────────── v1.2.0 Installed SortingAlgorithms ─────────── v1.2.2 Installed Inflate ───────────────────── v0.1.5 Installed ADTypes ───────────────────── v1.22.0 Installed RecursiveArrayTools ───────── v4.2.0 Installed MacroTools ────────────────── v0.5.16 Installed DataStructures ────────────── v0.19.4 Installed AbstractTrees ─────────────── v0.4.5 Installed Quaternions ───────────────── v0.7.7 Installed FillArrays ────────────────── v1.16.0 Installed MakieCore ─────────────────── v0.10.0 Installed CodecZlib ─────────────────── v0.7.8 Installed ExprTools ─────────────────── v0.1.10 Installed Observables ───────────────── v0.5.5 Installed DelimitedFiles ────────────── v1.9.1 Installed ArnoldiMethod ─────────────── v0.4.0 Installed ConsoleProgressMonitor ────── v0.1.2 Installed SparseMatrixColorings ─────── v0.4.27 Installed ArrayInterface ────────────── v7.24.0 Installed DataValueInterfaces ───────── v1.0.0 Installed GPUArraysCore ─────────────── v0.2.0 Installed RealDot ───────────────────── v0.1.0 Installed SparseConnectivityTracer ──── v1.2.1 Installed TruncatedStacktraces ──────── v1.4.0 Installed coordgenlibs_jll ──────────── v3.0.2+0 Installed StructUtils ───────────────── v2.8.0 Installed SimpleTraits ──────────────── v0.9.5 Installed BufferedStreams ───────────── v1.2.2 Installed LoggingExtras ─────────────── v1.2.0 Installed TerminalLoggers ───────────── v0.1.7 Installed LeftChildRightSiblingTrees ── v0.2.1 Installed Roots ─────────────────────── v3.0.0 Installed PooledArrays ──────────────── v1.4.3 Installed L_BFGS_B_jll ──────────────── v3.0.1+0 Installed WorkerUtilities ───────────── v1.6.1 Installed PDMats ────────────────────── v0.11.37 Installed DocStringExtensions ───────── v0.9.5 Installed Setfield ──────────────────── v1.1.2 Installed MetaGraphs ────────────────── v0.9.0 Installed OptimizationBase ──────────── v5.1.1 Installed TableOperations ───────────── v1.2.0 Installed CompositionsBase ──────────── v0.1.2 Installed CommonSolve ───────────────── v0.2.6 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed DifferentiationInterface ──── v0.7.16 Installed CSV ───────────────────────── v0.10.16 Installed LBFGSB ────────────────────── v0.4.1 Installed RecipesBase ───────────────── v1.3.4 Installed DataAPI ───────────────────── v1.16.0 Installed FunctionWrappersWrappers ──── v1.8.0 Installed SciMLOperators ────────────── v1.17.0 Installed InvertedIndices ───────────── v1.3.1 Installed StaticArraysCore ──────────── v1.4.4 Installed Colors ────────────────────── v0.13.1 Installed SciMLStructures ───────────── v1.10.0 Installed MolecularGraph ────────────── v0.22.0 Installed StaticArrays ──────────────── v1.9.18 Installed ColorTypes ────────────────── v0.12.1 Installed StringManipulation ────────── v0.4.4 Installed BiochemicalAlgorithms ─────── v0.6.8 Installed FunctionWrappers ──────────── v1.1.3 Installed SciMLPublic ───────────────── v1.0.1 Installed Parsers ───────────────────── v2.8.3 Installed Requires ──────────────────── v1.3.1 Installed AutoHashEquals ────────────── v2.2.0 Installed FastClosures ──────────────── v0.3.2 Installed JSON ──────────────────────── v1.5.0 Installed SciMLBase ─────────────────── v3.6.0 Installed BioGenerics ───────────────── v0.1.5 Installed PrettyTables ──────────────── v3.3.2 Installed TestItems ─────────────────── v1.0.0 Installed JLLWrappers ───────────────── v1.7.1 Installed Unitful ───────────────────── v1.28.0 Installed StructTypes ───────────────── v1.11.0 Installed WeakRefStrings ────────────── v1.4.3 Installed GeometryBasics ────────────── v0.5.10 Installed IterTools ─────────────────── v1.10.0 Installed Measurements ──────────────── v2.14.1 Installed Accessors ─────────────────── v0.1.44 Installed FilePathsBase ─────────────── v0.9.24 Installed DataFrames ────────────────── v1.8.2 Installed BioStructures ─────────────── v4.7.1 Installed Adapt ─────────────────────── v4.5.2 Installed ConstructionBase ──────────── v1.6.0 Installed RuntimeGeneratedFunctions ─── v0.5.18 Installed CellListMap ───────────────── v0.9.17 Installed Graphs ────────────────────── v1.14.0 Installed ChunkSplitters ────────────── v3.2.0 Installed EarCut_jll ────────────────── v2.2.4+0 Installed TranscodingStreams ────────── v0.11.3 Installed Statistics ────────────────── v1.11.1 Installed SymbolicIndexingInterface ─── v0.3.46 Installed Compat ────────────────────── v4.18.1 Installed ProgressLogging ───────────── v0.1.6 Installed StringEncodings ───────────── v0.3.7 Installed YAML ──────────────────────── v0.4.16 Installed Parameters ────────────────── v0.12.3 Installed JSON3 ─────────────────────── v1.14.3 Installed ProgressMeter ─────────────── v1.11.0 Installed BioSymbols ────────────────── v5.2.0 Installed PrecompileTools ───────────── v1.3.3 Installed Optimization ──────────────── v5.5.1 Installed FixedPointNumbers ─────────── v0.8.5 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed Rotations ─────────────────── v1.7.1 Installed IntervalSets ──────────────── v0.7.14 Installed SciMLLogging ──────────────── v1.9.1 Installed Scanf ─────────────────────── v0.5.4 Installing 6 artifacts Installed artifact EarCut 80.5 KiB Installed artifact L_BFGS_B 45.2 KiB Installed artifact libinchi 933.4 KiB Installed artifact Libiconv 1.9 MiB Installed artifact coordgenlibs 303.6 KiB Installed artifact testfiles 6.2 MiB Updating `~/.julia/environments/v1.14/Project.toml` [9d651bdf] + BiochemicalAlgorithms v0.6.8 Updating `~/.julia/environments/v1.14/Manifest.toml` [47edcb42] + ADTypes v1.22.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.5.2 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.24.0 [15f4f7f2] + AutoHashEquals v2.2.0 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.7.1 [3c28c6f8] + BioSymbols v5.2.0 [9d651bdf] + BiochemicalAlgorithms v0.6.8 [e1450e63] + BufferedStreams v1.2.2 [336ed68f] + CSV v0.10.16 [49dc2e85] + Calculus v0.5.2 [69e1c6dd] + CellListMap v0.9.17 [ae650224] + ChunkSplitters v3.2.0 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.1 [5ae59095] + Colors v0.13.1 [38540f10] + CommonSolve v0.2.6 [34da2185] + Compat v4.18.1 [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 v1.8.2 [864edb3b] + DataStructures v0.19.4 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [a0c0ee7d] + DifferentiationInterface v0.7.16 [ffbed154] + DocStringExtensions v0.9.5 [4e289a0a] + EnumX v1.0.7 [e2ba6199] + ExprTools v0.1.10 [411431e0] + Extents v0.1.6 [9aa1b823] + FastClosures v0.3.2 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [53c48c17] + FixedPointNumbers v0.8.5 [1fa38f19] + Format v1.3.7 [069b7b12] + FunctionWrappers v1.1.3 [77dc65aa] + FunctionWrappersWrappers v1.8.0 [46192b85] + GPUArraysCore v0.2.0 [5c1252a2] + GeometryBasics v0.5.10 [86223c79] + Graphs v1.14.0 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.5 [8197267c] + IntervalSets v0.7.14 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.5.0 [0f8b85d8] + JSON3 v1.14.3 [5be7bae1] + LBFGSB v0.4.1 [b964fa9f] + LaTeXStrings v1.4.0 [1d6d02ad] + LeftChildRightSiblingTrees v0.2.1 [e6f89c97] + LoggingExtras v1.2.0 [1914dd2f] + MacroTools v0.5.16 [20f20a25] + MakieCore v0.10.0 [eff96d63] + Measurements v2.14.1 [c116f080] + Mendeleev v1.0.2 [626554b9] + MetaGraphs v0.9.0 [e1d29d7a] + Missings v1.2.0 [6c89ec66] + MolecularGraph v0.22.0 [510215fc] + Observables v0.5.5 [7f7a1694] + Optimization v5.5.1 [bca83a33] + OptimizationBase v5.1.1 [22f7324a] + OptimizationLBFGSB v1.4.1 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [5ad8b20f] + PhysicalConstants v0.2.5 [2dfb63ee] + PooledArrays v1.4.3 [d236fae5] + PreallocationTools v1.2.0 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.3.2 [33c8b6b6] + ProgressLogging v0.1.6 [92933f4c] + ProgressMeter v1.11.0 [94ee1d12] + Quaternions v0.7.7 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [731186ca] + RecursiveArrayTools v4.2.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [f2b01f46] + Roots v3.0.0 [6038ab10] + Rotations v1.7.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.18 [6ef1bc8b] + Scanf v0.5.4 [0bca4576] + SciMLBase v3.6.0 [a6db7da4] + SciMLLogging v1.9.1 [c0aeaf25] + SciMLOperators v1.17.0 [431bcebd] + SciMLPublic v1.0.1 [53ae85a6] + SciMLStructures v1.10.0 [91c51154] + SentinelArrays v1.4.9 [efcf1570] + Setfield v1.1.2 [699a6c99] + SimpleTraits v0.9.5 [a2af1166] + SortingAlgorithms v1.2.2 [9f842d2f] + SparseConnectivityTracer v1.2.1 [0a514795] + SparseMatrixColorings v0.4.27 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [69024149] + StringEncodings v0.3.7 [892a3eda] + StringManipulation v0.4.4 [856f2bd8] + StructTypes v1.11.0 [ec057cc2] + StructUtils v2.8.0 [2efcf032] + SymbolicIndexingInterface v0.3.46 [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 [781d530d] + TruncatedStacktraces v1.4.0 [3a884ed6] + UnPack v1.0.2 [1986cc42] + Unitful v1.28.0 [a7773ee8] + UnitfulAtomic v1.0.0 [ea10d353] + WeakRefStrings v1.4.3 [76eceee3] + WorkerUtilities v1.6.1 [ddb6d928] + YAML v0.4.16 [5ae413db] + EarCut_jll v2.2.4+0 [81d17ec3] + L_BFGS_B_jll v3.0.1+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [f6050b86] + coordgenlibs_jll v3.0.2+0 [172afb32] + libinchi_jll v1.6.0+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 v1.13.0 [b27032c2] + LibCURL v1.0.0 [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 v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [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 v8.19.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2026.3.19 [4536629a] + OpenBLAS_jll v0.3.30+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Installation completed after 14.22s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 5.1 s ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 4.2 s ✓ MacroTools 1.7 s ✓ InlineStrings 0.8 s ✓ Reexport 1.3 s ✓ ConstructionBase 0.9 s ✓ DataValueInterfaces 2.4 s ✓ Format 1.2 s ✓ Observables 1.4 s ✓ Calculus 1.3 s ✓ IterTools 1.1 s ✓ IntervalSets 1.1 s ✓ Inflate 0.9 s ✓ CommonSolve 1.4 s ✓ TranscodingStreams 0.9 s ✓ LaTeXStrings 0.8 s ✓ TestItems 1.2 s ✓ Statistics 1.0 s ✓ StaticArraysCore 1.0 s ✓ ChunkSplitters 1.1 s ✓ AutoHashEquals 1.0 s ✓ DataAPI 1.0 s ✓ SciMLPublic 0.9 s ✓ RealDot 1.0 s ✓ InvertedIndices 1.0 s ✓ InverseFunctions 0.9 s ✓ CompositionsBase 1.3 s ✓ AbstractTrees 1.0 s ✓ EnumX 1.1 s ✓ WorkerUtilities 2.5 s ✓ FillArrays 1.1 s ✓ ExprTools 1.1 s ✓ UnPack 1.2 s ✓ Extents 1.5 s ✓ OrderedCollections 1.6 s ✓ FunctionWrappers 1.7 s ✓ ADTypes 1.3 s ✓ DocStringExtensions 0.9 s ✓ FastClosures 1.2 s ✓ BufferedStreams 0.9 s ✓ IteratorInterfaceExtensions 2.1 s ✓ Crayons 1.2 s ✓ ProgressLogging 1.0 s ✓ DelimitedFiles 1.4 s ✓ Requires 2.7 s ✓ ProgressMeter 36.6 s ✓ Unitful 2.6 s ✓ SentinelArrays 2.2 s ✓ StructTypes 1.7 s ✓ LoggingExtras 1.9 s ✓ StructUtils 2.4 s ✓ PDMats 1.3 s ✓ Compat 1.5 s ✓ Preferences 4.2 s ✓ SimpleTraits 0.8 s ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 1.3 s ✓ Measurements 0.8 s ✓ IntervalSets → IntervalSetsRandomExt 0.8 s ✓ ConstructionBase → ConstructionBaseIntervalSetsExt 1.0 s ✓ BioGenerics 1.0 s ✓ CodecZlib 27.8 s ✓ TestItemRunner 1.8 s ✓ Statistics → SparseArraysExt 4.2 s ✓ FixedPointNumbers 1.0 s ✓ IntervalSets → IntervalSetsStatisticsExt 1.1 s ✓ Missings 1.1 s ✓ PooledArrays 1.3 s ✓ Quaternions 1.3 s ✓ InverseFunctions → InverseFunctionsDatesExt 2.0 s ✓ InverseFunctions → InverseFunctionsTestExt 0.9 s ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1.0 s ✓ LeftChildRightSiblingTrees 1.8 s ✓ FillArrays → FillArraysSparseArraysExt 1.2 s ✓ FillArrays → FillArraysStatisticsExt 1.0 s ✓ RuntimeGeneratedFunctions 1.4 s ✓ Parameters 4.0 s ✓ DataStructures 0.8 s ✓ ADTypes → ADTypesConstructionBaseExt 1.9 s ✓ DifferentiationInterface 1.0 s ✓ Scanf 0.9 s ✓ TableTraits 1.0 s ✓ Adapt 1.7 s ✓ ConsoleProgressMonitor 2.9 s ✓ Unitful → ConstructionBaseUnitfulExt 2.8 s ✓ Unitful → PrintfExt 2.7 s ✓ Unitful → InverseFunctionsUnitfulExt 1.3 s ✓ StructUtils → StructUtilsStaticArraysCoreExt 1.7 s ✓ FillArrays → FillArraysPDMatsExt 1.0 s ✓ Compat → CompatLinearAlgebraExt 1.5 s ✓ PrecompileTools 1.9 s ✓ JLLWrappers 2.8 s ✓ TruncatedStacktraces 2.8 s ✓ SciMLLogging 3.8 s ✓ Setfield 2.9 s ✓ Measurements → MeasurementsUnitfulExt 1.4 s ✓ StructUtils → StructUtilsMeasurementsExt 3.1 s ✓ ColorTypes 5.8 s ✓ Accessors 1.9 s ✓ TerminalLoggers 10.3 s ✓ SparseConnectivityTracer 1.3 s ✓ SortingAlgorithms 1.6 s ✓ DifferentiationInterface → DifferentiationInterfaceSparseArraysExt 2.1 s ✓ Tables 1.2 s ✓ ArrayInterface 1.5 s ✓ Adapt → AdaptSparseArraysExt 1.3 s ✓ GPUArraysCore 10.0 s ✓ UnitfulAtomic 2.8 s ✓ FilePathsBase 7.6 s ✓ Aqua 3.7 s ✓ BioSymbols 4.2 s ✓ StringManipulation 15.2 s ✓ StaticArrays 3.9 s ✓ RecipesBase 18.5 s ✓ Parsers 13.8 s ✓ SparseMatrixColorings 2.5 s ✓ EarCut_jll 2.4 s ✓ libinchi_jll 2.4 s ✓ coordgenlibs_jll 2.5 s ✓ L_BFGS_B_jll 2.4 s ✓ Libiconv_jll 3.9 s ✓ FunctionWrappersWrappers 1.4 s ✓ ColorTypes → StyledStringsExt 8.8 s ✓ Colors 2.5 s ✓ Accessors → TestExt 3.2 s ✓ Accessors → IntervalSetsExt 3.1 s ✓ Accessors → LinearAlgebraExt 2.8 s ✓ Accessors → UnitfulExt 2.1 s ✓ DifferentiationInterface → DifferentiationInterfaceSparseConnectivityTracerExt 1.7 s ✓ TableOperations 1.3 s ✓ StructUtils → StructUtilsTablesExt 0.9 s ✓ ArrayInterface → ArrayInterfaceStaticArraysCoreExt 1.6 s ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 2.3 s ✓ SciMLStructures 3.3 s ✓ PreallocationTools 0.9 s ✓ DifferentiationInterface → DifferentiationInterfaceGPUArraysCoreExt 0.9 s ✓ ArrayInterface → ArrayInterfaceGPUArraysCoreExt 24.6 s ✓ Mendeleev 3.7 s ✓ FilePathsBase → FilePathsBaseTestExt 1.5 s ✓ FilePathsBase → FilePathsBaseMmapExt 47.4 s ✓ PrettyTables 4.4 s ✓ ArnoldiMethod 1.9 s ✓ StaticArrays → StaticArraysStatisticsExt 2.0 s ✓ ConstructionBase → ConstructionBaseStaticArraysExt 2.1 s ✓ FillArrays → FillArraysStaticArraysExt 5.9 s ✓ Rotations 2.0 s ✓ DifferentiationInterface → DifferentiationInterfaceStaticArraysExt 1.8 s ✓ Adapt → AdaptStaticArraysExt 2.0 s ✓ Accessors → StaticArraysExt 1.7 s ✓ IntervalSets → IntervalSetsRecipesBaseExt 1.9 s ✓ Measurements → MeasurementsRecipesBaseExt 15.6 s ✓ BioStructures 15.6 s ✓ JSON3 8.4 s ✓ JSON 1.5 s ✓ InlineStrings → ParsersExt 2.3 s ✓ DifferentiationInterface → DifferentiationInterfaceSparseMatrixColoringsExt 23.0 s ✓ GeometryBasics 1.4 s ✓ LBFGSB 1.6 s ✓ StringEncodings 3.2 s ✓ SparseMatrixColorings → SparseMatrixColoringsColorsExt 7.9 s ✓ Roots 5.5 s ✓ SciMLOperators 4.3 s ✓ SymbolicIndexingInterface 2.4 s ✓ PreallocationTools → PreallocationToolsSparseConnectivityTracerExt 87.4 s ✓ DataFrames 11.0 s ✓ Graphs 29.0 s ✓ CellListMap 2.6 s ✓ Rotations → RotationsRecipesBaseExt 3.6 s ✓ WeakRefStrings 8.6 s ✓ MakieCore 3.1 s ✓ YAML 2.9 s ✓ Roots → RootsUnitfulExt 1.4 s ✓ SciMLOperators → SciMLOperatorsStaticArraysCoreExt 2.1 s ✓ SciMLOperators → SciMLOperatorsSparseArraysExt 4.3 s ✓ SymbolicIndexingInterface → SymbolicIndexingInterfacePrettyTablesExt 9.5 s ✓ RecursiveArrayTools 9.3 s ✓ BioStructures → BioStructuresDataFramesExt 4.0 s ✓ MetaGraphs 27.9 s ✓ CSV 24.9 s ✓ MolecularGraph 17.2 s ✓ PhysicalConstants 2.5 s ✓ RecursiveArrayTools → RecursiveArrayToolsSparseArraysExt 1.8 s ✓ RecursiveArrayTools → RecursiveArrayToolsTablesExt 1.8 s ✓ RecursiveArrayTools → RecursiveArrayToolsStatisticsExt 1.7 s ✓ RecursiveArrayTools → RecursiveArrayToolsMeasurementsExt 4.4 s ✓ BioStructures → BioStructuresGraphsExt 22.1 s ✓ SciMLBase 3.8 s ✓ SciMLBase → SciMLBaseMeasurementsExt 3.6 s ✓ SciMLBase → SciMLBaseDifferentiationInterfaceExt 10.2 s ✓ OptimizationBase 5.3 s ✓ Optimization 6.0 s ✓ OptimizationLBFGSB 74.0 s ✓ BiochemicalAlgorithms 190 dependencies successfully precompiled in 952 seconds. 38 already precompiled. Precompilation completed after 974.37s ################################################################################ # Testing # Testing BiochemicalAlgorithms Status `/tmp/jl_8hGBa1/Project.toml` [4c88cf16] Aqua v0.8.14 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.7.1 [3c28c6f8] BioSymbols v5.2.0 [9d651bdf] BiochemicalAlgorithms v0.6.8 [336ed68f] CSV v0.10.16 [69e1c6dd] CellListMap v0.9.17 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.4 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.7 [86223c79] Graphs v1.14.0 [0f8b85d8] JSON3 v1.14.3 [c116f080] Mendeleev v1.0.2 [626554b9] MetaGraphs v0.9.0 [6c89ec66] MolecularGraph v0.22.0 [510215fc] Observables v0.5.5 [7f7a1694] Optimization v5.5.1 [22f7324a] OptimizationLBFGSB v1.4.1 [5ad8b20f] PhysicalConstants v0.2.5 [08abe8d2] PrettyTables v3.3.2 [94ee1d12] Quaternions v0.7.7 [6038ab10] Rotations v1.7.1 [6ef1bc8b] Scanf v0.5.4 [90137ffa] StaticArrays v1.9.18 [10745b16] Statistics v1.11.1 [856f2bd8] 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[692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.5.0 [0f8b85d8] JSON3 v1.14.3 [5be7bae1] LBFGSB v0.4.1 [b964fa9f] LaTeXStrings v1.4.0 [1d6d02ad] LeftChildRightSiblingTrees v0.2.1 [e6f89c97] LoggingExtras v1.2.0 [1914dd2f] MacroTools v0.5.16 [20f20a25] MakieCore v0.10.0 [eff96d63] Measurements v2.14.1 [c116f080] Mendeleev v1.0.2 [626554b9] MetaGraphs v0.9.0 [e1d29d7a] Missings v1.2.0 [6c89ec66] MolecularGraph v0.22.0 [510215fc] Observables v0.5.5 [7f7a1694] Optimization v5.5.1 [bca83a33] OptimizationBase v5.1.1 [22f7324a] OptimizationLBFGSB v1.4.1 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.3 [5ad8b20f] PhysicalConstants v0.2.5 [2dfb63ee] PooledArrays v1.4.3 [d236fae5] PreallocationTools v1.2.0 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.3.2 [33c8b6b6] ProgressLogging v0.1.6 [92933f4c] ProgressMeter v1.11.0 [94ee1d12] Quaternions v0.7.7 [c1ae055f] RealDot v0.1.0 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TerminalLoggers v0.1.7 [f8b46487] TestItemRunner v1.1.5 [1c621080] TestItems v1.0.0 [3bb67fe8] TranscodingStreams v0.11.3 [781d530d] TruncatedStacktraces v1.4.0 [3a884ed6] UnPack v1.0.2 [1986cc42] Unitful v1.28.0 [a7773ee8] UnitfulAtomic v1.0.0 [ea10d353] WeakRefStrings v1.4.3 [76eceee3] WorkerUtilities v1.6.1 [ddb6d928] YAML v0.4.16 [5ae413db] EarCut_jll v2.2.4+0 [81d17ec3] L_BFGS_B_jll v3.0.1+0 [94ce4f54] Libiconv_jll v1.18.0+0 [f6050b86] coordgenlibs_jll v3.0.2+0 [172afb32] libinchi_jll v1.6.0+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 v1.13.0 [b27032c2] LibCURL v1.0.0 [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 v1.14.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [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 v8.19.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2026.3.19 [4536629a] OpenBLAS_jll v0.3.30+0 [458c3c95] OpenSSL_jll v3.5.6+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Testing Running tests... [ Info: build_bonds!(): built 18 bonds ┌ Warning: Cannot calculate psi angle, no previous or next fragment found └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/core/fragment.jl:707 ┌ Warning: Cannot calculate phi angle, no previous or next fragment found └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/core/fragment.jl:752 ┌ Warning: Cannot calculate omega angle, no previous or next fragment found └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/core/fragment.jl:798 [ Info: build_bonds!(): built 18 bonds ┌ Warning: Cannot calculate psi angle, no previous or next fragment found └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/core/fragment.jl:707 ┌ Warning: Cannot calculate phi angle, no previous or next fragment found └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/core/fragment.jl:752 ┌ Warning: Cannot calculate omega angle, no previous or next fragment found └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/core/fragment.jl:798 [ Info: build_bonds!(): built 18 bonds [ Info: build_bonds!(): built 18 bonds [ Info: reconstruct_fragments!(): added 1423 atoms. [ Info: build_bonds!(): built 3839 bonds [ Info: reconstruct_fragments!(): added 1423 atoms. [ Info: build_bonds!(): built 3839 bonds ┌ Warning: load_pdb: alternate locations other than A are currently not supported. Affected records have been ignored! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/fileformats/pdb.jl:242 ┌ Warning: load_pdb: alternate locations other than A are currently not supported. Affected records have been ignored! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/fileformats/pdb.jl:242 [ Info: reconstruct_fragments!(): added 21 atoms. [ Info: reconstruct_fragments!(): added 4 atoms. [ Info: reconstruct_fragments!(): added 14 atoms. [ Info: reconstruct_fragments!(): added 23 atoms. [ Info: reconstruct_fragments!(): added 16 atoms. [ Info: reconstruct_fragments!(): added 20 atoms. [ Info: reconstruct_fragments!(): added 23 atoms. [ Info: reconstruct_fragments!(): added 9 atoms. [ Info: reconstruct_fragments!(): added 18 atoms. [ Info: reconstruct_fragments!(): added 13 atoms. [ Info: reconstruct_fragments!(): added 15 atoms. [ Info: reconstruct_fragments!(): added 21 atoms. [ Info: reconstruct_fragments!(): added 11 atoms. [ Info: reconstruct_fragments!(): added 10 atoms. [ Info: reconstruct_fragments!(): added 10 atoms. [ Info: reconstruct_fragments!(): added 16 atoms. [ Info: reconstruct_fragments!(): added 18 atoms. [ Info: reconstruct_fragments!(): added 17 atoms. [ Info: reconstruct_fragments!(): added 13 atoms. [ Info: reconstruct_fragments!(): added 19 atoms. [ Info: reconstruct_fragments!(): added 13 atoms. [ Info: reconstruct_fragments!(): added 6 atoms. [ Info: reconstruct_fragments!(): added 0 atoms. ┌ Warning: reconstruct_fragments!(): could not find reference fragment for UNKNOWN:1 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: reconstruct_fragments!(): added 21 atoms. [ Info: reconstruct_fragments!(): added 4 atoms. [ Info: reconstruct_fragments!(): added 14 atoms. [ Info: reconstruct_fragments!(): added 23 atoms. [ Info: reconstruct_fragments!(): added 16 atoms. [ Info: reconstruct_fragments!(): added 20 atoms. [ Info: reconstruct_fragments!(): added 23 atoms. [ Info: reconstruct_fragments!(): added 9 atoms. [ Info: reconstruct_fragments!(): added 18 atoms. [ Info: reconstruct_fragments!(): added 13 atoms. [ Info: reconstruct_fragments!(): added 15 atoms. [ Info: reconstruct_fragments!(): added 21 atoms. [ Info: reconstruct_fragments!(): added 11 atoms. [ Info: reconstruct_fragments!(): added 10 atoms. [ Info: reconstruct_fragments!(): added 10 atoms. [ Info: reconstruct_fragments!(): added 16 atoms. [ Info: reconstruct_fragments!(): added 18 atoms. [ Info: reconstruct_fragments!(): added 17 atoms. [ Info: reconstruct_fragments!(): added 13 atoms. [ Info: reconstruct_fragments!(): added 19 atoms. [ Info: reconstruct_fragments!(): added 13 atoms. [ Info: reconstruct_fragments!(): added 6 atoms. [ Info: reconstruct_fragments!(): added 0 atoms. ┌ Warning: reconstruct_fragments!(): could not find reference fragment for UNKNOWN:1 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: reconstruct_fragments!(): added 0 atoms. [ 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 0 bonds [ Info: Added 1 atoms. [ Info: reconstruct_fragments!(): added 438 atoms. [ Info: build_bonds!(): built 903 bonds [ Info: Added 1 atoms. [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: Added 1 atoms. [ Info: Added 0 atoms. [ Info: Added 0 atoms. [ 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 0 bonds [ Info: Added 1 atoms. [ Info: reconstruct_fragments!(): added 438 atoms. [ Info: build_bonds!(): built 903 bonds [ Info: Added 1 atoms. [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: Added 1 atoms. [ Info: Added 0 atoms. [ Info: Added 0 atoms. [ Info: 1 records exported. [ Info: 11 records exported. [ Info: 1 records exported. [ Info: 11 records exported. [ 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/fi1S8/src/forcefields/common/forcefield.jl:231 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/forcefields/common/forcefield.jl:231 ┌ 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/fi1S8/src/forcefields/common/forcefield.jl:231 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/forcefields/common/forcefield.jl:231 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/forcefields/common/forcefield.jl:231 ┌ 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/fi1S8/src/forcefields/common/forcefield.jl:231 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/forcefields/common/forcefield.jl:231 [ Info: build_bonds!(): built 30 bonds [ Info: build_bonds!(): built 906 bonds [ Info: build_bonds!(): built 1660 bonds [ Info: build_bonds!(): built 465 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: build_bonds!(): built 0 bonds [ Info: build_bonds!(): built 0 bonds ┌ Warning: build_bonds!(): could not find reference fragment for ZZZZZ. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 [ Info: build_bonds!(): built 0 bonds [ Info: build_bonds!(): built 30 bonds [ Info: build_bonds!(): built 906 bonds [ Info: build_bonds!(): built 1660 bonds [ Info: build_bonds!(): built 465 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: build_bonds!(): built 0 bonds [ Info: build_bonds!(): built 0 bonds ┌ Warning: build_bonds!(): could not find reference fragment for ZZZZZ. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 [ Info: build_bonds!(): built 0 bonds ┌ Error: illegal HIN file in line 31: cannot finalize bond (29, 30, BiochemicalAlgorithms.BondOrder.Single)! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/fileformats/hinfile.jl:232 ┌ Error: illegal HIN file in line 31: cannot finalize bond (29, 30, BiochemicalAlgorithms.BondOrder.Single)! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/fileformats/hinfile.jl:232 ┌ Warning: Atom names in HIN files cannot contain spaces! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/fileformats/hinfile.jl:446 ┌ Warning: Atom names in HIN files cannot contain spaces! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/fileformats/hinfile.jl:446 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/mappings/rigid_mapping.jl:176 [ 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/fi1S8/src/forcefields/common/forcefield.jl:231 [ 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/fi1S8/src/forcefields/common/forcefield.jl:231 [ 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/fi1S8/src/forcefields/common/forcefield.jl:231 [ 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 897 bonds [ Info: Added 30 hydrogen bonds. ┌ Warning: load_pdb: alternate locations other than A are currently not supported. Affected records have been ignored! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/fileformats/pdb.jl:242 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for PO4:70 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for UNX:324 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:80 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:101 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:102 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:105 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:110 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:111 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:112 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:113 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:116 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:117 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:119 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:121 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:122 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:125 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:126 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:127 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:129 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:133 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:134 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:138 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:140 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:143 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:144 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:145 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:146 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:156 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:157 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:158 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:159 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:160 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:200 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:201 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:202 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:203 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:204 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:205 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:209 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:210 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:211 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:212 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:214 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:216 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:217 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:218 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:219 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:220 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:223 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:225 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:302 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:304 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:310 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:311 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:312 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:313 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:314 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:315 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:316 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:317 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:318 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:319 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:320 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:321 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:322 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 [ Info: reconstruct_fragments!(): added 103 atoms. ┌ Warning: build_bonds!(): could not find reference fragment for PO4. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for UNX. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 [ Info: build_bonds!(): built 903 bonds [ Info: Added 30 hydrogen bonds. [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 897 bonds [ Info: Added 30 hydrogen bonds. ┌ Warning: load_pdb: alternate locations other than A are currently not supported. Affected records have been ignored! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/fileformats/pdb.jl:242 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for PO4:70 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for UNX:324 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:80 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:101 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:102 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:105 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:110 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:111 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:112 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:113 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:116 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:117 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:119 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:121 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:122 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:125 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:126 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:127 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:129 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:133 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:134 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:138 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:140 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:143 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:144 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:145 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:146 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:156 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:157 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:158 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:159 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:160 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:200 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:201 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:202 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:203 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:204 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:205 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:209 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:210 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:211 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:212 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:214 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:216 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:217 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:218 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:219 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:220 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:223 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:225 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:302 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:304 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:310 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:311 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:312 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:313 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:314 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:315 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:316 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:317 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:318 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:319 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:320 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:321 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 ┌ Warning: reconstruct_fragments!(): could not find reference fragment for DOD:322 └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/reconstruct_fragments.jl:178 [ Info: reconstruct_fragments!(): added 103 atoms. ┌ Warning: build_bonds!(): could not find reference fragment for PO4. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for UNX. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 ┌ Warning: build_bonds!(): could not find reference fragment for DOD. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/build_bonds.jl:14 [ Info: build_bonds!(): built 903 bonds [ Info: Added 30 hydrogen bonds. [ Info: reconstruct_fragments!(): added 2346 atoms. [ Info: build_bonds!(): built 4471 bonds [ Info: Added 181 hydrogen bonds. [ Info: reconstruct_fragments!(): added 2346 atoms. [ Info: build_bonds!(): built 4471 bonds ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 727 running 1 of 1 signal (10): User defined signal 1 unknown function (ip: 0x74b33db0858b) at (unknown file) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 hash at ./abstractdict.jl:542:23 union_split at ./multidimensional.jl:2072:3 [inlined] hash_shaped at ./multidimensional.jl:2094:337 hash_shaped at ./multidimensional.jl:2075:2 [inlined] hash at ./multidimensional.jl:2110:5 [inlined] hash at /home/pkgeval/.julia/packages/AutoHashEquals/LcReq/src/impl.jl:295:50 hash at /home/pkgeval/.julia/packages/AutoHashEquals/LcReq/src/impl.jl:295:26 hash at /home/pkgeval/.julia/packages/AutoHashEquals/LcReq/src/impl.jl:295:7 [inlined] hash at /home/pkgeval/.julia/packages/AutoHashEquals/LcReq/src/impl.jl:295:5 [inlined] hash at ./hashing.jl:40:3 [inlined] hashindex at ./dict.jl:129:8 [inlined] ht_keyindex at ./dict.jl:244:32 haskey at ./dict.jl:550:3 [inlined] predict_hbonds_kabsch_sander! at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/predict_hbonds.jl:83:98 predict_hbonds! at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/predict_hbonds.jl:32:5 unknown function (ip: 0x74b3403d6a52) at (unknown file) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 top-level scope at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/fi1S8/test/preprocessing/test_predict_hbonds.jl:31:211 jl_invoke_oneshot at /source/src/gf.c:4148:23 ijl_eval_thunk at /source/src/toplevel.c:760:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:517:3 include_string at ./loading.jl:3113:145 include_string at ./loading.jl:3123:3 _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] jl_f_invokelatest at /source/src/builtins.c:910:23 #run_testitem##6 at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:119:7 [inlined] withpath at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/vendored_code.jl:7:16 #run_testitem##4 at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:118:16 [inlined] cd at ./file.jl:112:19 unknown function (ip: 0x74b375fbdb86) at (unknown file) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 run_testitem at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:117:127 unknown function (ip: 0x74b375fb94de) at (unknown file) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 macro expansion at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:277:2 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.14/Test/src/Test.jl:2415:5 [inlined] macro expansion at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:275:21 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.14/Test/src/Test.jl:2415:24 [inlined] macro expansion at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:253:26 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.14/Test/src/Test.jl:2415:29 [inlined] #run_tests#7 at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:250:687 run_tests at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:134:24 unknown function (ip: 0x74b375f00776) at (unknown file) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:243:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:693:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884:21 ijl_eval_thunk at /source/src/toplevel.c:768:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:517:3 include_string at ./loading.jl:3113:145 _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 _include at ./loading.jl:3173:45 include at ./Base.jl:327:3 IncludeInto at ./Base.jl:328:4 jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:243:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:693:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884:21 ijl_eval_thunk at /source/src/toplevel.c:768:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:517:3 exec_options at ./client.jl:318:410 _start at ./client.jl:593:36 jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] true_main at /source/src/jlapi.c:971:29 jl_repl_entrypoint at /source/src/jlapi.c:1138:15 main at /source/cli/loader_exe.c:58:15 unknown function (ip: 0x74b392501249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== [ Info: Added 175 hydrogen bonds. [ Info: reconstruct_fragments!(): added 438 atoms. ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457:34 [ Info: build_bonds!(): built 903 bonds wait at ./task.jl:1246:50 wait_forever at ./task.jl:1168:5 jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] start_task at /source/src/task.c:1275:19 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000074b377bfc010 Total snapshots: 10. Utilization: 100% ╎10 @Base/client.jl:593 _start() ╎ 10 @Base/client.jl:318 exec_options(opts::Base.JLOptions) ╎ 10 @Base/boot.jl:517 eval(m::Module, e::Any) ╎ 10 @Base/Base.jl:328 (::Base.IncludeInto)(fname::String) ╎ 10 @Base/Base.jl:327 include(mapexpr::Function, mod::Module, _path::Stri… ╎ 10 @Base/loading.jl:3173 _include(mapexpr::Function, mod::Module, _path… ╎ ╎ 10 @Base/loading.jl:3113 include_string(mapexpr::typeof(identity), mod… ╎ ╎ 10 @Base/boot.jl:517 eval(m::Module, e::Any) ╎ ╎ 10 @TestItemRunner/…r.jl:134 kwcall(::@NamedTuple{verbose::Bool}, ::… ╎ ╎ 10 @TestItemRunner/…r.jl:250 run_tests(path::String; filter::Nothin… ╎ ╎ 10 @Test/src/Test.jl:2415 iterate(A::Vector{String}, state::Int64) ╎ ╎ ╎ 10 @TestItemRunner/….jl:253 macro expansion ╎ ╎ ╎ 10 @Test/src/Test.jl:2415 macro expansion ╎ ╎ ╎ 10 @TestItemRunner/…jl:275 macro expansion ╎ ╎ ╎ 10 @Test/src/Test.jl:2415 macro expansion ╎ ╎ ╎ 10 @TestItemRunner/…l:277 macro expansion ╎ ╎ ╎ ╎ 10 @TestItemRunner/…l:117 run_testitem(filepath::String, use… ╎ ╎ ╎ ╎ 10 @Base/file.jl:112 cd(f::TestItemRunner.var"#run_testitem… ╎ ╎ ╎ ╎ 10 @TestItemRunner/…:118 (::TestItemRunner.var"#run_testit… ╎ ╎ ╎ ╎ 10 @TestItemRunner/…l:7 withpath(f::TestItemRunner.var"#r… ╎ ╎ ╎ ╎ 10 @TestItemRunner/…:119 haskey(d::IdDict{Any, Any}, k::… ╎ ╎ ╎ ╎ ╎ 10 @Base/loading.jl:3123 include_string(m::Module, txt:… ╎ ╎ ╎ ╎ ╎ 10 @Base/…ading.jl:3113 include_string(mapexpr::typeof… ╎ ╎ ╎ ╎ ╎ 10 @Base/boot.jl:517 eval(m::Module, e::Any) ╎ ╎ ╎ ╎ ╎ 10 @BiochemicalAlgorithms/…:31 top-level scope ╎ ╎ ╎ ╎ ╎ 10 @BiochemicalAlgorithms/…:32 predict_hbonds!(ac::… ╎ ╎ ╎ ╎ ╎ ╎ 5 @BiochemicalAlgorithms/…:83 predict_hbonds_kabs… ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/dict.jl:550 broadcasted(::typeof(Biochem… ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/dict.jl:244 ht_keyindex(h::Dict{Biochem… ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/dict.jl:129 hashindex ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ing.jl:40 hash ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @AutoHashEquals/…:295 hash ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @AutoHashEquals/…:295 hash ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @AutoHashEquals/…:295 hash(x::Biochemica… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @AutoHashEquals/…:295 hash(x::Biochemic… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…al.jl:2110 hash(A::Vector{Dict{… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…al.jl:2075 hash_shaped 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…al.jl:2094 hash_shaped(A::Vec… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…al.jl:2072 union_split ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ct.jl:541 hash(a::Dict{Symb… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ct.jl:703 iterate(t::Dict{… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +1 2 @Base/…ct.jl:685 skip_deleted(h::… 2╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +2 2 @Base/…er.jl:58 length(t::Memory{… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:542 hash(a::Dict{Symb… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…al.jl:2110 hash(A::StaticAr… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…al.jl:2075 hash_shaped(A::… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +1 1 @Base/…al.jl:2085 hash_shaped(A::… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +2 1 @Base/…al.jl:2072 union_split(f::… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 1 @Base/…ng.jl:183 hash(x::Float32,… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 1 @Base/…ng.jl:169 hash(x::Float64,… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 1 @Base/…rs.jl:184 isequal(x::Int64… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 1 @Base/…rs.jl:180 ==(y::Int64, x::… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 1 @Base/…on.jl:637 == ╎ ╎ ╎ ╎ ╎ ╎ 2 @BiochemicalAlgorithms/…:84 predict_hbonds_kabs… ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/dict.jl:478 broadcasted(::typeof(Biochem… ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/dict.jl:244 ht_keyindex(h::Dict{Biochem… ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/dict.jl:129 hashindex ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ing.jl:40 hash ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @AutoHashEquals/…:295 hash ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @AutoHashEquals/…:295 hash ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @AutoHashEquals/…:295 hash(x::Biochemica… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @AutoHashEquals/…:295 hash(x::Biochemic… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…al.jl:2110 hash(A::Vector{Dict{… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…al.jl:2075 hash_shaped ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…al.jl:2094 hash_shaped(A::Vec… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…al.jl:2072 getindex(A::Vecto… 2╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ct.jl:542 hash(a::Dict{Symb… ╎ ╎ ╎ ╎ ╎ ╎ 3 @BiochemicalAlgorithms/…:94 predict_hbonds_kabs… ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/dict.jl:358 setindex!(h::Dict{Biochemica… ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/dict.jl:276 ht_keyindex2_shorthash!(h::… ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/dict.jl:129 hashindex(key::Biochemical… ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ing.jl:40 hash(data::BiochemicalAlgo… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @AutoHashEquals/…:295 hash(x::BiochemicalA… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @AutoHashEquals/…:295 hash(x::Biochemical… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @AutoHashEquals/…:295 hash(x::Biochemica… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @AutoHashEquals/…:295 hash(x::Biochemic… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…al.jl:2110 hash(A::Vector{Dict{… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…al.jl:2075 hash_shaped ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…al.jl:2094 hash_shaped(A::Vec… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…al.jl:2072 getindex(A::Vecto… 2╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ct.jl:542 hash(a::Dict{Symb… [ Info: Added 31 hydrogen bonds. ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000076b29fe1f0d0 Total snapshots: 418. Utilization: 0% ╎418 @Base/task.jl:1168 wait_forever() 417╎ 418 @Base/task.jl:1246 wait() [ Info: reconstruct_fragments!(): added 438 atoms. [ Info: build_bonds!(): built 903 bonds [ Info: Added 31 hydrogen bonds. [ Info: Added 0 hydrogen bonds. [ Info: reconstruct_fragments!(): added 2346 atoms. [ Info: build_bonds!(): built 4471 bonds [727] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/fi1S8/test/preprocessing/test_predict_hbonds.jl:2 jl_to_typeof at /source/src/julia.h:1040:12 [inlined] sig_match_fast at /source/src/gf.c:4173:13 [inlined] sig_match_fast at /source/src/gf.c:4164:19 [inlined] jl_lookup_generic_ at /source/src/gf.c:4254:5 [inlined] ijl_apply_generic at /source/src/gf.c:4335:35 in at ./abstractdict.jl:24:12 in at ./abstractdict.jl:22:2 [inlined] == at ./abstractdict.jl:525:34 == at ./abstractarray.jl:3054:31 [inlined] == at /home/pkgeval/.julia/packages/AutoHashEquals/LcReq/src/impl.jl:375:170 == at /home/pkgeval/.julia/packages/AutoHashEquals/LcReq/src/impl.jl:375:50 == at /home/pkgeval/.julia/packages/AutoHashEquals/LcReq/src/impl.jl:375:5 [inlined] == at /home/pkgeval/.julia/packages/AutoHashEquals/LcReq/src/impl.jl:375:5 [inlined] is_previous at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/fi1S8/src/core/fragment.jl:1022:10 [inlined] #predict_hbonds_kabsch_sander!##4 at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/predict_hbonds.jl:59:10 filter at ./array.jl:3022:29 predict_hbonds_kabsch_sander! at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/predict_hbonds.jl:59:44 predict_hbonds! at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/predict_hbonds.jl:32:5 predict_hbonds! at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/fi1S8/src/preprocessing/predict_hbonds.jl:31:1 unknown function (ip: 0x74b33dba5c66) at (unknown file) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 top-level scope at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/fi1S8/test/preprocessing/test_predict_hbonds.jl:11:38 jl_invoke_oneshot at /source/src/gf.c:4148:23 ijl_eval_thunk at /source/src/toplevel.c:760:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:517:3 include_string at ./loading.jl:3113:145 include_string at ./loading.jl:3123:3 _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] jl_f_invokelatest at /source/src/builtins.c:910:23 #run_testitem##6 at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:119:7 [inlined] withpath at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/vendored_code.jl:7:16 #run_testitem##4 at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:118:16 [inlined] cd at ./file.jl:112:19 unknown function (ip: 0x74b375fbdb86) at (unknown file) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 run_testitem at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:117:127 unknown function (ip: 0x74b375fb94de) at (unknown file) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 macro expansion at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:277:2 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.14/Test/src/Test.jl:2415:5 [inlined] macro expansion at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:275:21 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.14/Test/src/Test.jl:2415:24 [inlined] macro expansion at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:253:26 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.14/Test/src/Test.jl:2415:29 [inlined] #run_tests#7 at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:250:687 run_tests at /home/pkgeval/.julia/packages/TestItemRunner/GnoVt/src/TestItemRunner.jl:134:24 unknown function (ip: 0x74b375f00776) at (unknown file) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:243:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:693:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884:21 ijl_eval_thunk at /source/src/toplevel.c:768:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:517:3 include_string at ./loading.jl:3113:145 _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 _include at ./loading.jl:3173:45 include at ./Base.jl:327:3 IncludeInto at ./Base.jl:328:4 jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:243:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:693:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884:21 ijl_eval_thunk at /source/src/toplevel.c:768:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:517:3 exec_options at ./client.jl:318:410 _start at ./client.jl:593:36 jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] true_main at /source/src/jlapi.c:971:29 jl_repl_entrypoint at /source/src/jlapi.c:1138:15 main at /source/cli/loader_exe.c:58:15 unknown function (ip: 0x74b392501249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) Allocations: 683842390 (Pool: 683832928; Big: 9462); GC: 444 PkgEval terminated after 2722.29s: test duration exceeded the time limit