Package evaluation to test BiochemicalAlgorithms on Julia 1.11.8 (29b3528cce*) started at 2026-01-20T16:27:19.479 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.11` Set-up completed after 8.67s ################################################################################ # Installation # Installing BiochemicalAlgorithms... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [9d651bdf] + BiochemicalAlgorithms v0.5.5 Updating `~/.julia/environments/v1.11/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 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 v1.8.1 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [a0c0ee7d] + DifferentiationInterface v0.7.14 [ffbed154] + DocStringExtensions v0.9.5 [4e289a0a] + EnumX v1.0.5 [e2ba6199] + ExprTools v0.1.10 [55351af7] + ExproniconLite v0.10.14 [411431e0] + Extents v0.1.6 [9aa1b823] + FastClosures v0.3.2 [5789e2e9] + FileIO v1.17.1 [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 v0.1.3 [46192b85] + GPUArraysCore v0.2.0 [5c1252a2] + GeometryBasics v0.5.10 [a2bd30eb] + Graphics v1.1.3 [86223c79] + Graphs v1.13.3 [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 [90014a1f] + PDMats v0.11.37 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [5ad8b20f] + PhysicalConstants v0.2.4 [2dfb63ee] + PooledArrays v1.4.3 [d236fae5] + PreallocationTools v1.0.0 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.5.1 ⌅ [08abe8d2] + PrettyTables v2.4.0 [33c8b6b6] + ProgressLogging v0.1.6 [92933f4c] + ProgressMeter v1.11.0 [94ee1d12] + Quaternions v0.7.7 [44044271] + RDKitMinimalLib v1.2.0 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [731186ca] + RecursiveArrayTools v3.44.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [f2b01f46] + Roots v2.2.10 [6038ab10] + Rotations v1.7.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.16 [0bca4576] + SciMLBase v2.134.0 [a6db7da4] + SciMLLogging v1.8.0 [c0aeaf25] + SciMLOperators v1.14.1 [431bcebd] + SciMLPublic v1.0.1 [53ae85a6] + SciMLStructures v1.10.0 [7e506255] + ScopedValues v1.5.0 [91c51154] + SentinelArrays v1.4.9 [efcf1570] + Setfield v1.1.2 [699a6c99] + SimpleTraits v0.9.5 [a2af1166] + SortingAlgorithms v1.2.2 [9f842d2f] + SparseConnectivityTracer v1.1.3 [0a514795] + SparseMatrixColorings v0.4.23 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [69024149] + StringEncodings v0.3.7 [892a3eda] + StringManipulation v0.4.2 [856f2bd8] + StructTypes v1.11.0 ⌃ [2efcf032] + SymbolicIndexingInterface v0.3.44 [ab02a1b2] + TableOperations v1.2.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [5d786b92] + TerminalLoggers v0.1.7 [1c621080] + TestItems v1.0.0 [3bb67fe8] + TranscodingStreams v0.11.3 [3a884ed6] + UnPack v1.0.2 [1986cc42] + Unitful v1.27.0 [a7773ee8] + UnitfulAtomic v1.0.0 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [ddb6d928] + YAML v0.4.16 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.5+0 [5ae413db] + EarCut_jll v2.2.4+0 [2e619515] + Expat_jll v2.7.3+0 [a3f928ae] + Fontconfig_jll v2.17.1+0 [d7e528f0] + FreeType2_jll v2.13.4+0 [559328eb] + FriBidi_jll v1.0.17+0 [b0724c58] + GettextRuntime_jll v0.22.4+0 [7746bdde] + Glib_jll v2.86.2+0 [3b182d85] + Graphite2_jll v1.3.15+0 [2e76f6c2] + HarfBuzz_jll v8.5.1+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [dd4b983a] + LZO_jll v2.10.3+0 [81d17ec3] + L_BFGS_B_jll v3.0.1+0 ⌅ [e9f186c6] + Libffi_jll v3.4.7+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.41.2+0 [38a345b3] + Libuuid_jll v2.41.2+0 [36c8627f] + Pango_jll v1.57.0+0 ⌅ [30392449] + Pixman_jll v0.44.2+0 [03d1d220] + RDKit_jll v2022.9.5+0 [4f6342f7] + Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0 [a3789734] + Xorg_libXdmcp_jll v1.1.6+0 [1082639a] + Xorg_libXext_jll v1.3.7+0 [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [3161d3a3] + Zstd_jll v1.5.7+1 ⌅ [28df3c45] + boost_jll v1.76.0+1 [f6050b86] + coordgenlibs_jll v3.0.2+0 [172afb32] + libinchi_jll v1.6.0+0 [b53b4c65] + libpng_jll v1.6.54+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 v1.6.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [efcefdf7] + PCRE2_jll v10.42.0+1 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 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 8.37s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 38280.2 ms ✓ MolecularGraph 492428.0 ms ✓ BiochemicalAlgorithms 2 dependencies successfully precompiled in 546 seconds. 259 already precompiled. Precompilation completed after 559.28s ################################################################################ # Testing # Testing BiochemicalAlgorithms Status `/tmp/jl_e6W8R4/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 v0.2.4 ⌅ [08abe8d2] PrettyTables v2.4.0 [94ee1d12] Quaternions v0.7.7 [6038ab10] Rotations v1.7.1 [90137ffa] StaticArrays v1.9.16 [10745b16] Statistics v1.11.1 [856f2bd8] StructTypes v1.11.0 [ab02a1b2] TableOperations v1.2.0 [bd369af6] Tables v1.12.1 [f8b46487] TestItemRunner v1.1.4 [1986cc42] Unitful v1.27.0 [a7773ee8] UnitfulAtomic v1.0.0 [37e2e46d] LinearAlgebra v1.11.0 [de0858da] Printf v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_e6W8R4/Manifest.toml` [47edcb42] ADTypes v1.21.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.4.0 [4c88cf16] Aqua v0.8.14 [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 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 v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [a0c0ee7d] DifferentiationInterface v0.7.14 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.5 [e2ba6199] ExprTools v0.1.10 [55351af7] ExproniconLite v0.10.14 [411431e0] Extents v0.1.6 [9aa1b823] FastClosures v0.3.2 [5789e2e9] FileIO v1.17.1 [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 v0.1.3 [46192b85] GPUArraysCore v0.2.0 [5c1252a2] GeometryBasics v0.5.10 [a2bd30eb] Graphics v1.1.3 [86223c79] Graphs v1.13.3 [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 [90014a1f] PDMats v0.11.37 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.3 [5ad8b20f] PhysicalConstants v0.2.4 [2dfb63ee] PooledArrays v1.4.3 [d236fae5] PreallocationTools v1.0.0 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.5.1 ⌅ [08abe8d2] PrettyTables v2.4.0 [33c8b6b6] ProgressLogging v0.1.6 [92933f4c] ProgressMeter v1.11.0 [94ee1d12] Quaternions v0.7.7 [44044271] RDKitMinimalLib v1.2.0 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [731186ca] RecursiveArrayTools v3.44.0 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [f2b01f46] Roots v2.2.10 [6038ab10] Rotations v1.7.1 [7e49a35a] RuntimeGeneratedFunctions v0.5.16 [0bca4576] SciMLBase v2.134.0 [a6db7da4] SciMLLogging v1.8.0 [c0aeaf25] SciMLOperators v1.14.1 [431bcebd] SciMLPublic v1.0.1 [53ae85a6] SciMLStructures v1.10.0 [7e506255] ScopedValues v1.5.0 [91c51154] SentinelArrays v1.4.9 [efcf1570] Setfield v1.1.2 [699a6c99] SimpleTraits v0.9.5 [a2af1166] SortingAlgorithms v1.2.2 [9f842d2f] SparseConnectivityTracer v1.1.3 [0a514795] SparseMatrixColorings v0.4.23 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [69024149] StringEncodings v0.3.7 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available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... ┌ 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. [ 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 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 Optimize structure: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/EdAH5/test/optimization/test_optimize_structure.jl:11 Expression: Int((optimize_structure!(ff)).retcode) == 1 Evaluated: 7 == 1 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:680 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/EdAH5/test/optimization/test_optimize_structure.jl:516 [ 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: 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 [ Info: Added 1 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 22 bonds [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds Test Summary: | Pass Fail Total Time Package | 9921 1 9922 15m55.7s test/aqua.jl | 11 11 2m46.3s Aqua | 11 11 2m46.2s Method ambiguity | 1 1 34.0s Unbound type parameters | 1 1 0.3s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 31.0s Compat bounds | 4 4 0.6s Piracy | 1 1 0.3s Persistent tasks | 1 1 53.2s test/fileformats/test_hinfile.jl | 52 52 48.3s Read HIN | 48 48 35.0s Write HIN | 4 4 13.3s test/core/test_atom.jl | 606 606 36.7s AtomTable | 308 308 17.3s Atom | 298 298 19.4s test/core/test_bond_order.jl | 8 8 0.1s Bond Order | 8 8 0.1s test/fileformats/test_pdb.jl | 1870 1870 1m17.4s Read PDB | 1824 1824 1m06.2s Write PDB | 14 14 5.6s Read PDBx/mmCIF | 18 18 0.6s Write PDBx/mmCIF | 14 14 5.0s test/core/test_chain.jl | 462 462 10.9s ChainTable | 206 206 8.0s Chain | 256 256 2.9s test/substructures/test_substructure.jl | 6 6 17.8s Substructure | 6 6 17.8s test/core/test_bond.jl | 312 312 8.9s BondTable | 176 176 3.3s Bond | 136 136 5.5s test/core/test_secondary_structure.jl | 514 514 23.6s SecondaryStructureTable | 240 240 8.2s SecondaryStructure | 274 274 15.4s test/core/test_types.jl | 106 106 3.4s Vector3 | 51 51 1.9s Matrix3 | 51 51 1.4s Properties | 2 2 0.0s Flags | 2 2 0.0s test/fileformats/test_sdfile.jl | 34 34 49.4s Read SDFile | 30 30 33.0s Write SDFile | 4 4 16.4s test/forcefields/AMBER/test_amberff.jl | 1951 1951 3m33.4s AmberFF | 1951 1951 3m33.4s test/core/test_system_component_table.jl | 78 78 1.8s SystemComponentTableCol | 78 78 1.8s test/core/test_fragment.jl | 1734 1734 48.9s FragmentTable | 266 266 6.9s FragmentTable/None | 178 178 1.0s FragmentTable/Nucleotide | 178 178 1.0s FragmentTable/Residue | 178 178 1.0s Fragment | 118 118 3.2s Fragment/None | 272 272 12.9s Fragment/Nucleotide | 272 272 11.6s Fragment/Residue | 272 272 11.2s test/core/test_system.jl | 618 618 2m24.9s System | 618 618 2m24.9s test/core/test_amino_acid.jl | 63 63 0.3s AminoAcid | 63 63 0.3s test/optimization/test_optimize_structure.jl | 5 1 6 10.2s Optimize structure | 2 1 3 7.1s Optimize hydrogen positions | 3 3 3.0s test/substructures/test_sssr.jl | 3 3 2.4s Ring Perception | 3 3 2.4s test/core/test_element.jl | 126 126 0.2s Element | 126 126 0.2s test/fileformats/test_pubchem_json.jl | 106 106 3.4s Read PubChem | 106 106 3.4s test/mappings/test_mappings.jl | 224 224 17.3s TrivialAtomBijection | 8 8 0.7s RigidTransform | 16 16 0.5s translate! | 88 88 1.2s rigid_transform! | 44 44 2.4s compute_rmsd | 14 14 2.2s compute_rmsd_minimizer | 42 42 8.7s map_rigid! | 12 12 1.6s test/preprocessing/test_add_hydrogens.jl | 2 2 13.8s FragmentDB | 2 2 13.8s test/substructures/test_smarts.jl | 30 30 34.1s SMARTS | 30 30 34.1s test/core/test_moleculargraph_wrapper.jl | 162 162 2.1s Convert to SDFMolGraph | 162 162 2.1s test/core/test_molecule.jl | 834 834 18.6s MoleculeTable | 238 238 7.6s MoleculeTable/None | 146 146 1.1s MoleculeTable/Protein | 146 146 0.9s Molecule | 68 68 1.8s Molecule/None | 118 118 4.1s Molecule/Protein | 118 118 3.0s test/preprocessing/test_fragmentdb.jl | 4 4 1.6s FragmentDB | 4 4 1.6s ERROR: LoadError: Some tests did not pass: 9921 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/EdAH5/test/runtests.jl:3 Testing failed after 1022.84s ERROR: LoadError: Package BiochemicalAlgorithms errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2128 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2011 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1618.24s: package has test failures