Package evaluation of BiochemicalAlgorithms on Julia 1.10.9 (96dc2d8c45*) started at 2025-06-06T23:35:25.778 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 4.82s ################################################################################ # Installation # Installing BiochemicalAlgorithms... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [9d651bdf] + BiochemicalAlgorithms v0.5.3 Updating `~/.julia/environments/v1.10/Manifest.toml` [47edcb42] + ADTypes v1.14.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.3.0 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.19.0 [15f4f7f2] + AutoHashEquals v2.2.0 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.5.0 [3c28c6f8] + BioSymbols v5.2.0 [9d651bdf] + BiochemicalAlgorithms v0.5.3 [336ed68f] + CSV v0.10.15 [159f3aea] + Cairo v1.1.1 [49dc2e85] + Calculus v0.5.2 [69e1c6dd] + CellListMap v0.9.10 [ae650224] + ChunkSplitters v3.1.2 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.1 [5ae59095] + Colors v0.13.1 [38540f10] + CommonSolve v0.2.4 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [88cd18e8] + ConsoleProgressMonitor v0.1.2 [187b0558] + ConstructionBase v1.5.8 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + 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To see why use `status --outdated -m` Installation completed after 10.69s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 241.5s ################################################################################ # Testing # Testing BiochemicalAlgorithms Status `/tmp/jl_hto6us/Project.toml` [4c88cf16] Aqua v0.8.13 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.5.0 [3c28c6f8] BioSymbols v5.2.0 [9d651bdf] BiochemicalAlgorithms v0.5.3 [336ed68f] CSV v0.10.15 [69e1c6dd] CellListMap v0.9.10 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [ffbed154] DocStringExtensions v0.9.4 [4e289a0a] EnumX v1.0.5 [86223c79] Graphs v1.13.0 [0f8b85d8] JSON3 v1.14.3 [c116f080] Mendeleev v1.0.1 [626554b9] MetaGraphs v0.8.0 ⌅ [6c89ec66] MolecularGraph v0.18.0 [510215fc] Observables v0.5.5 [7f7a1694] Optimization v4.3.0 [5ad8b20f] PhysicalConstants v0.2.4 [08abe8d2] PrettyTables v2.4.0 [94ee1d12] Quaternions v0.7.6 [6038ab10] Rotations v1.7.1 [90137ffa] StaticArrays v1.9.13 [856f2bd8] StructTypes v1.11.0 [ab02a1b2] TableOperations v1.2.0 [bd369af6] Tables v1.12.1 [f8b46487] 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CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.2+1 [14a3606d] MozillaCACerts_jll v2023.1.10 [4536629a] OpenBLAS_jll v0.3.23+4 [05823500] OpenLibm_jll v0.8.5+0 [efcefdf7] PCRE2_jll v10.42.0+1 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them 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 ┌ Warning: write_sdfile: writer only supports 2D data; projecting atoms onto xy-plane... └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/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/g6ebH/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/g6ebH/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/g6ebH/src/fileformats/sdfile.jl:33 [ Info: 11 records exported. ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/mappings/rigid_mapping.jl:176 [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds ┌ Warning: 2 warnings occurred during setup that were suppressed: │ - Torsion: 2 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/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/g6ebH/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/g6ebH/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/g6ebH/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/g6ebH/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/g6ebH/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/g6ebH/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. ┌ Error: illegal HIN file in line 31: cannot finalize bond (29, 30, BiochemicalAlgorithms.BondOrder.Single)! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/fileformats/hinfile.jl:232 ┌ Error: illegal HIN file in line 31: cannot finalize bond (29, 30, BiochemicalAlgorithms.BondOrder.Single)! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/fileformats/hinfile.jl:232 ┌ Warning: Atom names in HIN files cannot contain spaces! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/fileformats/hinfile.jl:445 ┌ Warning: Atom names in HIN files cannot contain spaces! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/fileformats/hinfile.jl:445 [ 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/g6ebH/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/g6ebH/src/forcefields/common/forcefield.jl:233 Test Summary: | Pass Total Time Package | 9922 9922 10m09.4s test/core/test_types.jl | 106 106 24.5s Vector3 | 51 51 23.3s Matrix3 | 51 51 1.0s Properties | 2 2 0.0s Flags | 2 2 0.0s test/core/test_element.jl | 126 126 0.3s Element | 126 126 0.3s test/core/test_bond.jl | 312 312 13.5s BondTable | 176 176 8.9s Bond | 136 136 4.5s test/preprocessing/test_fragmentdb.jl | 4 4 11.1s FragmentDB | 4 4 11.1s test/core/test_system.jl | 618 618 2m27.6s System | 618 618 2m27.6s test/fileformats/test_pubchem_json.jl | 106 106 4.7s Read PubChem | 106 106 4.7s test/fileformats/test_sdfile.jl | 34 34 31.9s Read SDFile | 30 30 19.7s Write SDFile | 4 4 12.2s test/mappings/test_mappings.jl | 224 224 17.6s TrivialAtomBijection | 8 8 0.6s RigidTransform | 16 16 0.5s translate! | 88 88 1.4s rigid_transform! | 44 44 2.2s compute_rmsd | 14 14 1.9s compute_rmsd_minimizer | 42 42 9.5s map_rigid! | 12 12 1.4s test/core/test_moleculargraph_wrapper.jl | 162 162 2.4s Convert to SDFMolGraph | 162 162 2.4s test/fileformats/test_pdb.jl | 1870 1870 12.6s Read PDB | 1824 1824 5.1s Write PDB | 14 14 3.9s Read PDBx/mmCIF | 18 18 0.4s Write PDBx/mmCIF | 14 14 3.2s test/core/test_amino_acid.jl | 63 63 0.3s AminoAcid | 63 63 0.3s test/aqua.jl | 11 11 1m35.2s Aqua | 11 11 1m35.2s Method ambiguity | 1 1 21.5s Unbound type parameters | 1 1 0.2s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 21.9s Compat bounds | 4 4 0.4s Piracy | 1 1 0.3s Persistent tasks | 1 1 38.5s test/core/test_fragment.jl | 1734 1734 38.8s FragmentTable | 266 266 4.5s FragmentTable/None | 178 178 1.0s FragmentTable/Nucleotide | 178 178 0.8s FragmentTable/Residue | 178 178 0.8s Fragment | 118 118 2.8s Fragment/None | 272 272 10.4s Fragment/Nucleotide | 272 272 9.3s Fragment/Residue | 272 272 9.0s test/core/test_bond_order.jl | 8 8 0.0s Bond Order | 8 8 0.0s test/substructures/test_substructure.jl | 6 6 1.3s Substructure | 6 6 1.3s test/core/test_molecule.jl | 834 834 12.5s MoleculeTable | 238 238 4.1s MoleculeTable/None | 146 146 0.8s MoleculeTable/Protein | 146 146 0.7s Molecule | 68 68 1.2s Molecule/None | 118 118 3.2s Molecule/Protein | 118 118 2.5s test/forcefields/AMBER/test_amberff.jl | 1951 1951 1m53.7s AmberFF | 1951 1951 1m53.7s test/core/test_chain.jl | 462 462 4.8s ChainTable | 206 206 3.0s Chain | 256 256 1.7s test/preprocessing/test_add_hydrogens.jl | 2 2 11.6s FragmentDB | 2 2 11.6s test/fileformats/test_hinfile.jl | 52 52 5.4s Read HIN | 48 48 1.5s Write HIN | 4 4 4.0s test/optimization/test_optimize_structure.jl | 6 6 5.9s Optimize structure | 3 3 3.7s Optimize hydrogen positions | 3 3 2.3s test/substructures/test_sssr.jl | 3 3 1.4s Ring Perception | 3 3 1.4s test/core/test_secondary_structure.jl | 514 514 14.6s SecondaryStructureTable | 240 240 3.1s SecondaryStructure | 274 274 11.5s test/core/test_atom.jl | 606 606 15.2s AtomTable | 308 308 3.3s Atom | 298 298 11.9s test/core/test_system_component_table.jl | 78 78 1.2s SystemComponentTableCol | 78 78 1.2s test/substructures/test_smarts.jl | 30 30 21.4s SMARTS | 30 30 21.4s Testing BiochemicalAlgorithms tests passed Testing completed after 634.08s PkgEval succeeded after 907.38s