Package evaluation to test BiochemicalAlgorithms on Julia 1.14.0-DEV.1441 (812f3beb0a*) started at 2026-01-01T22:49:59.524 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 10.0s ################################################################################ # Installation # Installing BiochemicalAlgorithms... Resolving package versions... Installed HarfBuzz_jll ──────────────── v8.5.1+0 Installed Bzip2_jll ─────────────────── v1.0.9+0 Installed ChunkCodecLibZstd ─────────── v1.0.0 Installed Extents ───────────────────── v0.1.6 Installed InlineStrings ─────────────── v1.4.5 Installed Calculus ──────────────────── v0.5.2 Installed Libuuid_jll ───────────────── v2.41.2+0 Installed RDKitMinimalLib ───────────── v1.2.0 Installed Cairo_jll ─────────────────── v1.18.5+0 Installed OrderedCollections ────────── v1.8.1 Installed Graphite2_jll ─────────────── v1.3.15+0 Installed RDKit_jll ─────────────────── v2022.9.5+0 Installed PreallocationTools ────────── v0.4.34 Installed SentinelArrays ────────────── v1.4.9 Installed UnitfulAtomic ─────────────── v1.0.0 Installed FileIO ────────────────────── v1.17.1 Installed Fontconfig_jll ────────────── v2.17.1+0 Installed libinchi_jll ──────────────── v1.6.0+0 Installed NaNMath ───────────────────── v1.1.3 Installed Graphics ──────────────────── v1.1.3 Installed ScopedValues ──────────────── v1.5.0 Installed Tables ────────────────────── v1.12.1 Installed PhysicalConstants ─────────── v0.2.4 Installed Xorg_libxcb_jll ───────────── v1.17.1+0 Installed EnumX ─────────────────────── v1.0.5 Installed Jieko ─────────────────────── v0.2.1 Installed Reexport ──────────────────── v1.2.2 Installed Mendeleev ─────────────────── v1.0.2 Installed InverseFunctions ──────────── v0.1.17 Installed Missings ──────────────────── v1.2.0 Installed LZO_jll ───────────────────── v2.10.3+0 Installed Preferences ───────────────── v1.5.1 Installed TableTraits ───────────────── v1.0.1 Installed LLVMOpenMP_jll ────────────── v18.1.8+0 Installed LaTeXStrings ──────────────── v1.4.0 Installed SortingAlgorithms ─────────── v1.2.2 Installed boost_jll ─────────────────── v1.76.0+1 Installed Crayons ───────────────────── v4.1.1 Installed UnPack ────────────────────── v1.0.2 Installed RecursiveArrayTools ───────── v3.42.1 Installed Format ────────────────────── v1.3.7 Installed ADTypes ───────────────────── v1.21.0 Installed Inflate ───────────────────── v0.1.5 Installed DataStructures ────────────── v0.19.3 Installed MacroTools ────────────────── v0.5.16 Installed FillArrays ────────────────── v1.15.0 Installed AbstractTrees ─────────────── v0.4.5 Installed DelimitedFiles ────────────── v1.9.1 Installed Quaternions ───────────────── v0.7.7 Installed SparseMatrixColorings ─────── v0.4.23 Installed MakieCore ─────────────────── v0.9.5 Installed ArnoldiMethod ─────────────── v0.4.0 Installed CodecZlib ─────────────────── v0.7.8 Installed Xorg_libXau_jll ───────────── v1.0.13+0 Installed ConsoleProgressMonitor ────── v0.1.2 Installed ExprTools ─────────────────── v0.1.10 Installed Observables ───────────────── v0.5.5 Installed DataValueInterfaces ───────── v1.0.0 Installed ArrayInterface ────────────── v7.22.0 Installed GPUArraysCore ─────────────── v0.2.0 Installed Pixman_jll ────────────────── v0.44.2+0 Installed Expat_jll ─────────────────── v2.7.3+0 Installed RealDot ───────────────────── v0.1.0 Installed LoggingExtras ─────────────── v1.2.0 Installed Cairo ─────────────────────── v1.1.1 Installed Libffi_jll ────────────────── v3.4.7+0 Installed SparseConnectivityTracer ──── v1.1.3 Installed libpng_jll ────────────────── v1.6.53+0 Installed coordgenlibs_jll ──────────── v3.0.2+0 Installed TerminalLoggers ───────────── v0.1.7 Installed L_BFGS_B_jll ──────────────── v3.0.1+0 Installed SimpleTraits ──────────────── v0.9.5 Installed LeftChildRightSiblingTrees ── v0.2.1 Installed Setfield ──────────────────── v1.1.2 Installed Roots ─────────────────────── v2.2.10 Installed MetaGraphs ────────────────── v0.8.1 Installed PooledArrays ──────────────── v1.4.3 Installed OptimizationBase ──────────── v2.14.0 Installed WorkerUtilities ───────────── v1.6.1 Installed PDMats ────────────────────── v0.11.37 Installed DocStringExtensions ───────── v0.9.5 Installed TableOperations ───────────── v1.2.0 Installed LBFGSB ────────────────────── v0.4.1 Installed CompositionsBase ──────────── v0.1.2 Installed CommonSolve ───────────────── v0.2.6 Installed Moshi ─────────────────────── v0.3.7 Installed DifferentiationInterface ──── v0.7.13 Installed HashArrayMappedTries ──────── v0.2.0 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed FunctionWrappersWrappers ──── v0.1.3 Installed RecipesBase ───────────────── v1.3.4 Installed SciMLOperators ────────────── v1.14.1 Installed BiochemicalAlgorithms ─────── v0.5.5 Installed DataAPI ───────────────────── v1.16.0 Installed InvertedIndices ───────────── v1.3.1 Installed SciMLStructures ───────────── v1.9.0 Installed Colors ────────────────────── v0.13.1 Installed StaticArraysCore ──────────── v1.4.4 Installed StaticArrays ──────────────── v1.9.16 Installed ColorTypes ────────────────── v0.12.1 Installed StringManipulation ────────── v0.4.2 Installed SciMLPublic ───────────────── v1.0.1 Installed Glib_jll ──────────────────── v2.86.2+0 Installed MolecularGraph ────────────── v0.19.1 Installed Requires ──────────────────── v1.3.1 Installed FunctionWrappers ──────────── v1.1.3 Installed FastClosures ──────────────── v0.3.2 Installed JSON ──────────────────────── v0.21.4 Installed Parsers ───────────────────── v2.8.3 Installed BioGenerics ───────────────── v0.1.5 Installed AutoHashEquals ────────────── v2.2.0 Installed SciMLBase ─────────────────── v2.131.0 Installed PrettyTables ──────────────── v2.4.0 Installed Xorg_libXdmcp_jll ─────────── v1.1.6+0 Installed WeakRefStrings ────────────── v1.4.2 Installed TestItems ─────────────────── v1.0.0 Installed JLLWrappers ───────────────── v1.7.1 Installed Unitful ───────────────────── v1.27.0 Installed GeometryBasics ────────────── v0.5.10 Installed ChunkCodecCore ────────────── v1.0.1 Installed Pango_jll ─────────────────── v1.57.0+0 Installed StructTypes ───────────────── v1.11.0 Installed IterTools ─────────────────── v1.10.0 Installed CSV ───────────────────────── v0.10.15 Installed Xorg_xtrans_jll ───────────── v1.6.0+0 Installed Measurements ──────────────── v2.14.1 Installed Accessors ─────────────────── v0.1.43 Installed FilePathsBase ─────────────── v0.9.24 Installed DataFrames ────────────────── v1.8.1 Installed JLD2 ──────────────────────── v0.6.3 Installed Graphs ────────────────────── v1.13.3 Installed Adapt ─────────────────────── v4.4.0 Installed RuntimeGeneratedFunctions ─── v0.5.16 Installed ConstructionBase ──────────── v1.6.0 Installed Libmount_jll ──────────────── v2.41.2+0 Installed Xorg_libX11_jll ───────────── v1.8.12+0 Installed Compat ────────────────────── v4.18.1 Installed ChunkSplitters ────────────── v3.1.2 Installed TranscodingStreams ────────── v0.11.3 Installed SymbolicIndexingInterface ─── v0.3.44 Installed BioStructures ─────────────── v4.7.0 Installed ProgressLogging ───────────── v0.1.6 Installed EarCut_jll ────────────────── v2.2.4+0 Installed Statistics ────────────────── v1.11.1 Installed StringEncodings ───────────── v0.3.7 Installed ExproniconLite ────────────── v0.10.14 Installed PrecompileTools ───────────── v1.3.3 Installed CellListMap ───────────────── v0.9.15 Installed ProgressMeter ─────────────── v1.11.0 Installed GettextRuntime_jll ────────── v0.22.4+0 Installed Optimization ──────────────── v4.8.0 Installed FriBidi_jll ───────────────── v1.0.17+0 Installed BioSymbols ────────────────── v5.2.0 Installed ChunkCodecLibZlib ─────────── v1.0.0 Installed YAML ──────────────────────── v0.4.16 Installed Xorg_libXrender_jll ───────── v0.9.12+0 Installed JSON3 ─────────────────────── v1.14.3 Installed Parameters ────────────────── v0.12.3 Installed SciMLLogging ──────────────── v1.8.0 Installed IntervalSets ──────────────── v0.7.13 Installed FixedPointNumbers ─────────── v0.8.5 Installed Xorg_libXext_jll ──────────── v1.3.7+0 Installed FreeType2_jll ─────────────── v2.13.4+0 Installed Rotations ─────────────────── v1.7.1 Installed Libiconv_jll ──────────────── v1.18.0+0 Installing 32 artifacts Installed artifact Xorg_libXau 36.6 KiB Installed artifact FriBidi 78.9 KiB Installed artifact coordgenlibs 303.6 KiB Installed artifact libpng 329.0 KiB Installed artifact Fontconfig 984.8 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Expat 283.3 KiB Installed artifact FreeType2 1.5 MiB Installed artifact L_BFGS_B 45.2 KiB Installed artifact Pixman 372.2 KiB Installed artifact Graphite2 120.2 KiB Installed artifact LZO 208.9 KiB Installed artifact HarfBuzz 1.7 MiB Installed artifact Pango 2.0 MiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact GettextRuntime 543.0 KiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact Bzip2 503.5 KiB Installed artifact libinchi 933.4 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact Glib 7.7 MiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact Cairo 2.2 MiB Installed artifact EarCut 80.5 KiB Installed artifact Libffi 44.2 KiB Installed artifact Libiconv 1.9 MiB Installed artifact Libuuid 3.7 MiB Installed artifact Libmount 6.5 MiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact boost 22.1 MiB Installed artifact RDKit 56.2 MiB Updating `~/.julia/environments/v1.14/Project.toml` [9d651bdf] + BiochemicalAlgorithms v0.5.5 Updating `~/.julia/environments/v1.14/Manifest.toml` [47edcb42] + ADTypes v1.21.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.43 [79e6a3ab] + Adapt v4.4.0 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.22.0 [15f4f7f2] + AutoHashEquals v2.2.0 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.7.0 [3c28c6f8] + BioSymbols v5.2.0 [9d651bdf] + BiochemicalAlgorithms v0.5.5 [336ed68f] + CSV v0.10.15 [159f3aea] + Cairo v1.1.1 [49dc2e85] + Calculus v0.5.2 [69e1c6dd] + CellListMap v0.9.15 [0b6fb165] + ChunkCodecCore v1.0.1 [4c0bbee4] + ChunkCodecLibZlib v1.0.0 [55437552] + ChunkCodecLibZstd v1.0.0 [ae650224] + ChunkSplitters v3.1.2 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.1 [5ae59095] + Colors 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[076d061b] + HashArrayMappedTries v0.2.0 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.5 [8197267c] + IntervalSets v0.7.13 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [033835bb] + JLD2 v0.6.3 [692b3bcd] + JLLWrappers v1.7.1 ⌅ [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.3 [ae98c720] + Jieko v0.2.1 [5be7bae1] + LBFGSB v0.4.1 [b964fa9f] + LaTeXStrings v1.4.0 [1d6d02ad] + LeftChildRightSiblingTrees v0.2.1 [e6f89c97] + LoggingExtras v1.2.0 [1914dd2f] + MacroTools v0.5.16 ⌅ [20f20a25] + MakieCore v0.9.5 [eff96d63] + Measurements v2.14.1 [c116f080] + Mendeleev v1.0.2 [626554b9] + MetaGraphs v0.8.1 [e1d29d7a] + Missings v1.2.0 ⌅ [6c89ec66] + MolecularGraph v0.19.1 [2e0e35c7] + Moshi v0.3.7 [77ba4419] + NaNMath v1.1.3 [510215fc] + Observables v0.5.5 ⌅ [7f7a1694] + Optimization v4.8.0 ⌅ [bca83a33] + OptimizationBase v2.14.0 [bac558e1] + OrderedCollections v1.8.1 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LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 31.47s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 Precompilation failed after 13.91s ################################################################################ # Testing # Testing BiochemicalAlgorithms Status `/tmp/jl_JzwZBX/Project.toml` [4c88cf16] Aqua v0.8.14 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.7.0 [3c28c6f8] BioSymbols v5.2.0 [9d651bdf] BiochemicalAlgorithms v0.5.5 [336ed68f] CSV v0.10.15 [69e1c6dd] CellListMap v0.9.15 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.5 [86223c79] Graphs v1.13.3 [0f8b85d8] JSON3 v1.14.3 [c116f080] Mendeleev v1.0.2 [626554b9] MetaGraphs v0.8.1 ⌅ [6c89ec66] MolecularGraph v0.19.1 [510215fc] Observables v0.5.5 ⌅ [7f7a1694] Optimization v4.8.0 [5ad8b20f] PhysicalConstants 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OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... [ Info: reconstruct_fragments!(): added 1435 atoms. [ Info: build_bonds!(): built 3839 bonds [ Info: reconstruct_fragments!(): added 1435 atoms. [ Info: build_bonds!(): built 3839 bonds [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds ┌ Warning: 2 warnings occurred during setup that were suppressed: │ - Torsion: 2 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/forcefields/common/forcefield.jl:233 [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds ┌ Warning: 2 warnings occurred during setup that were suppressed: │ - Torsion: 2 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/forcefields/common/forcefield.jl:233 [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: Added 1 atoms. [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: Added 1 atoms. ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/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/EdAH5/src/forcefields/common/forcefield.jl:233 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/forcefields/common/forcefield.jl:233 ┌ Warning: 20 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 3 warnings │ - QuadraticAngleBend : 12 warnings │ - Torsion : 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/forcefields/common/forcefield.jl:233 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/forcefields/common/forcefield.jl:233 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/forcefields/common/forcefield.jl:233 ┌ Warning: 20 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 3 warnings │ - QuadraticAngleBend : 12 warnings │ - Torsion : 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/forcefields/common/forcefield.jl:233 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - Torsion: 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/forcefields/common/forcefield.jl:233 [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds ┌ Error: illegal HIN file in line 31: cannot finalize bond (29, 30, BiochemicalAlgorithms.BondOrder.Single)! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/fileformats/hinfile.jl:232 ┌ Error: illegal HIN file in line 31: cannot finalize bond (29, 30, BiochemicalAlgorithms.BondOrder.Single)! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/fileformats/hinfile.jl:232 ┌ Warning: Atom names in HIN files cannot contain spaces! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/fileformats/hinfile.jl:445 ┌ Warning: Atom names in HIN files cannot contain spaces! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/fileformats/hinfile.jl:445 ┌ Warning: write_sdfile: writer only supports 2D data; projecting atoms onto xy-plane... └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/fileformats/sdfile.jl:28 [ Info: 1 records exported. ┌ Warning: write_sdfile: writer only supports 2D data; projecting atoms onto xy-plane... └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/fileformats/sdfile.jl:33 [ Info: 11 records exported. ┌ Warning: write_sdfile: writer only supports 2D data; projecting atoms onto xy-plane... └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/fileformats/sdfile.jl:28 [ Info: 1 records exported. ┌ Warning: write_sdfile: writer only supports 2D data; projecting atoms onto xy-plane... └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/EdAH5/src/fileformats/sdfile.jl:33 [ Info: 11 records exported. Test Summary: | Pass Total Time Package | 9922 9922 27m21.0s test/fileformats/test_pubchem_json.jl | 106 106 14m20.3s Read PubChem | 106 106 14m20.2s test/core/test_atom.jl | 606 606 31.7s AtomTable | 308 308 15.2s Atom | 298 298 16.5s test/substructures/test_substructure.jl | 6 6 2.1s Substructure | 6 6 2.1s test/core/test_system.jl | 618 618 2m36.5s System | 618 618 2m36.5s test/core/test_secondary_structure.jl | 514 514 17.9s SecondaryStructureTable | 240 240 6.0s SecondaryStructure | 274 274 12.0s test/optimization/test_optimize_structure.jl | 6 6 1m36.8s Optimize structure | 3 3 1m33.6s Optimize hydrogen positions | 3 3 3.2s test/aqua.jl | 11 11 3m33.3s Aqua | 11 11 3m33.3s Method ambiguity | 1 1 30.7s Unbound type parameters | 1 1 0.1s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 32.5s Compat bounds | 4 4 0.5s Piracy | 1 1 40.0s Persistent tasks | 1 1 1m10.1s test/fileformats/test_pdb.jl | 1870 1870 20.0s Read PDB | 1824 1824 9.8s Write PDB | 14 14 4.9s Read PDBx/mmCIF | 18 18 2.4s Write PDBx/mmCIF | 14 14 2.9s test/preprocessing/test_add_hydrogens.jl | 2 2 31.7s FragmentDB | 2 2 31.7s test/core/test_fragment.jl | 1734 1734 43.8s FragmentTable | 266 266 6.9s FragmentTable/None | 178 178 1.4s FragmentTable/Nucleotide | 178 178 1.3s FragmentTable/Residue | 178 178 1.1s Fragment | 118 118 1.8s Fragment/None | 272 272 10.8s Fragment/Nucleotide | 272 272 10.3s Fragment/Residue | 272 272 10.3s test/mappings/test_mappings.jl | 224 224 19.5s TrivialAtomBijection | 8 8 0.5s RigidTransform | 16 16 0.5s translate! | 88 88 1.9s rigid_transform! | 44 44 2.9s compute_rmsd | 14 14 2.1s compute_rmsd_minimizer | 42 42 9.3s map_rigid! | 12 12 2.4s test/core/test_amino_acid.jl | 63 63 0.3s AminoAcid | 63 63 0.3s test/core/test_system_component_table.jl | 78 78 1.1s SystemComponentTableCol | 78 78 1.1s test/forcefields/AMBER/test_amberff.jl | 1951 1951 47.0s AmberFF | 1951 1951 47.0s test/core/test_bond.jl | 312 312 6.3s BondTable | 176 176 2.8s Bond | 136 136 3.5s test/core/test_molecule.jl | 834 834 14.4s MoleculeTable | 238 238 6.3s MoleculeTable/None | 146 146 1.0s MoleculeTable/Protein | 146 146 0.9s Molecule | 68 68 0.8s Molecule/None | 118 118 3.1s Molecule/Protein | 118 118 2.4s test/core/test_bond_order.jl | 8 8 0.0s Bond Order | 8 8 0.0s test/core/test_moleculargraph_wrapper.jl | 162 162 1.8s Convert to SDFMolGraph | 162 162 1.8s test/fileformats/test_hinfile.jl | 52 52 8.4s Read HIN | 48 48 1.8s Write HIN | 4 4 6.6s test/substructures/test_sssr.jl | 3 3 17.1s Ring Perception | 3 3 17.1s test/core/test_chain.jl | 462 462 7.1s ChainTable | 206 206 4.9s Chain | 256 256 2.2s test/preprocessing/test_fragmentdb.jl | 4 4 1.5s FragmentDB | 4 4 1.5s test/core/test_element.jl | 126 126 0.2s Element | 126 126 0.2s test/substructures/test_smarts.jl | 30 30 27.2s SMARTS | 30 30 27.2s test/core/test_types.jl | 106 106 1.8s Vector3 | 51 51 1.0s Matrix3 | 51 51 0.8s Properties | 2 2 0.0s Flags | 2 2 0.0s test/fileformats/test_sdfile.jl | 34 34 13.0s Read SDFile | 30 30 2.6s Write SDFile | 4 4 10.4s Testing BiochemicalAlgorithms tests passed Testing completed after 1680.17s PkgEval succeeded after 1806.11s