Package evaluation of BiochemicalAlgorithms on Julia 1.13.0-DEV.140 (fac1ce7906*) started at 2025-03-02T17:44:50.486 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 7.43s ################################################################################ # Installation # Installing BiochemicalAlgorithms... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [9d651bdf] + BiochemicalAlgorithms v0.5.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.13.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.2.0 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.18.0 [15f4f7f2] + AutoHashEquals v2.2.0 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.4.0 [3c28c6f8] + BioSymbols v5.1.3 [9d651bdf] + BiochemicalAlgorithms v0.5.0 [336ed68f] + CSV v0.10.15 [159f3aea] + Cairo v1.1.1 [49dc2e85] + Calculus v0.5.2 [69e1c6dd] + CellListMap v0.9.8 [ae650224] + ChunkSplitters v3.1.1 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.0 [5ae59095] + Colors v0.13.0 [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] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.20 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [a0c0ee7d] + DifferentiationInterface v0.6.42 [ffbed154] + DocStringExtensions v0.9.3 [4e289a0a] + EnumX v1.0.4 [e2ba6199] + ExprTools v0.1.10 [55351af7] + ExproniconLite v0.10.14 [411431e0] + Extents v0.1.5 [9aa1b823] + FastClosures v0.3.2 [5789e2e9] + FileIO v1.17.0 [48062228] + FilePathsBase v0.9.23 [1a297f60] + FillArrays v1.13.0 [53c48c17] + FixedPointNumbers v0.8.5 [1fa38f19] + Format v1.3.7 [069b7b12] + FunctionWrappers v1.1.3 [77dc65aa] + FunctionWrappersWrappers v0.1.3 [46192b85] + GPUArraysCore v0.2.0 [68eda718] + GeoFormatTypes v0.4.4 [cf35fbd7] + GeoInterface v1.4.1 [5c1252a2] + GeometryBasics v0.5.5 [a2bd30eb] + Graphics v1.1.3 [86223c79] + Graphs v1.12.0 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.3 [8197267c] + IntervalSets v0.7.10 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [033835bb] + JLD2 v0.5.11 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.1 [ae98c720] + Jieko v0.2.1 [5be7bae1] + LBFGSB v0.4.1 [b964fa9f] + LaTeXStrings v1.4.0 [1d6d02ad] + LeftChildRightSiblingTrees v0.2.0 [e6f89c97] + LoggingExtras v1.1.0 [1914dd2f] + MacroTools v0.5.15 [20f20a25] + MakieCore v0.9.1 [eff96d63] + Measurements v2.12.0 [c116f080] + Mendeleev v1.0.1 [626554b9] + MetaGraphs v0.8.0 [e1d29d7a] + Missings v1.2.0 [6c89ec66] + MolecularGraph v0.17.3 [2e0e35c7] + Moshi v0.3.5 [77ba4419] + NaNMath v1.1.2 [510215fc] + Observables v0.5.5 [7f7a1694] + Optimization v4.1.1 [bca83a33] + OptimizationBase v2.4.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.32 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.1 [5ad8b20f] + PhysicalConstants v0.2.4 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [33c8b6b6] + ProgressLogging v0.1.4 [92933f4c] + ProgressMeter v1.10.2 [94ee1d12] + Quaternions v0.7.6 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [731186ca] + RecursiveArrayTools v3.31.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [f2b01f46] + Roots v2.2.6 [6038ab10] + Rotations v1.7.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.13 [0bca4576] + SciMLBase v2.75.1 [c0aeaf25] + SciMLOperators v0.3.12 [53ae85a6] + SciMLStructures v1.6.1 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [699a6c99] + SimpleTraits v0.9.4 [a2af1166] + SortingAlgorithms v1.2.1 [9f842d2f] + SparseConnectivityTracer v0.6.13 [0a514795] + SparseMatrixColorings v0.4.13 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [69024149] + StringEncodings v0.3.7 [892a3eda] + StringManipulation v0.4.1 [856f2bd8] + StructTypes v1.11.0 [2efcf032] + SymbolicIndexingInterface v0.3.38 [ab02a1b2] + TableOperations v1.2.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [5d786b92] + TerminalLoggers v0.1.7 [1c621080] + TestItems v1.0.0 [3bb67fe8] + TranscodingStreams v0.11.3 [3a884ed6] + UnPack v1.0.2 [1986cc42] + Unitful v1.22.0 [a7773ee8] + UnitfulAtomic v1.0.0 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [ddb6d928] + YAML v0.4.13 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.2+1 [5ae413db] + EarCut_jll v2.2.4+0 [2e619515] + Expat_jll v2.6.5+0 [a3f928ae] + Fontconfig_jll v2.15.0+0 [d7e528f0] + FreeType2_jll v2.13.3+1 [559328eb] + FriBidi_jll v1.0.16+0 [78b55507] + Gettext_jll v0.21.0+0 [7746bdde] + Glib_jll v2.82.4+0 [3b182d85] + Graphite2_jll v1.3.14+1 [2e76f6c2] + HarfBuzz_jll v8.5.0+0 [1d63c593] + LLVMOpenMP_jll v18.1.7+0 [dd4b983a] + LZO_jll v2.10.3+0 [81d17ec3] + L_BFGS_B_jll v3.0.1+0 ⌅ [e9f186c6] + Libffi_jll v3.2.2+2 [d4300ac3] + Libgcrypt_jll v1.11.0+0 [7add5ba3] + Libgpg_error_jll v1.51.1+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.40.3+0 [38a345b3] + Libuuid_jll v2.40.3+0 [36c8627f] + Pango_jll v1.56.1+0 ⌅ [30392449] + Pixman_jll v0.43.4+0 [02c8fc9c] + XML2_jll v2.13.6+1 [aed1982a] + XSLT_jll v1.1.42+0 [4f6342f7] + Xorg_libX11_jll v1.8.6+3 [0c0b7dd1] + Xorg_libXau_jll v1.0.12+0 [a3789734] + Xorg_libXdmcp_jll v1.1.5+0 [1082639a] + Xorg_libXext_jll v1.3.6+3 [ea2f1a96] + Xorg_libXrender_jll v0.9.11+1 [14d82f49] + Xorg_libpthread_stubs_jll v0.1.2+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.0+3 [c5fb5394] + Xorg_xtrans_jll v1.5.1+0 [f6050b86] + coordgenlibs_jll v3.0.2+0 [172afb32] + libinchi_jll v1.6.0+0 [b53b4c65] + libpng_jll v1.6.46+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.11.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2024.12.31 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [efcefdf7] + PCRE2_jll v10.44.0+1 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.99s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 360.71s ################################################################################ # Testing # Testing BiochemicalAlgorithms Status `/tmp/jl_azD1nR/Project.toml` [4c88cf16] Aqua v0.8.11 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.4.0 [3c28c6f8] BioSymbols v5.1.3 [9d651bdf] BiochemicalAlgorithms v0.5.0 [336ed68f] CSV v0.10.15 [69e1c6dd] CellListMap v0.9.8 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.20 [ffbed154] DocStringExtensions v0.9.3 [4e289a0a] EnumX v1.0.4 [86223c79] Graphs v1.12.0 [0f8b85d8] JSON3 v1.14.1 [c116f080] Mendeleev v1.0.1 [626554b9] MetaGraphs v0.8.0 [6c89ec66] MolecularGraph v0.17.3 [510215fc] Observables v0.5.5 [7f7a1694] Optimization v4.1.1 [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 [10745b16] Statistics v1.11.1 [856f2bd8] StructTypes v1.11.0 [ab02a1b2] TableOperations v1.2.0 [bd369af6] Tables v1.12.0 [f8b46487] TestItemRunner v1.1.0 [1986cc42] Unitful v1.22.0 [a7773ee8] UnitfulAtomic v1.0.0 [37e2e46d] LinearAlgebra v1.12.0 [de0858da] Printf v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_azD1nR/Manifest.toml` [47edcb42] ADTypes v1.13.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.2.0 [4c88cf16] Aqua v0.8.11 [ec485272] ArnoldiMethod v0.4.0 [4fba245c] ArrayInterface v7.18.0 [15f4f7f2] AutoHashEquals v2.2.0 [47718e42] BioGenerics v0.1.5 [de9282ab] BioStructures v4.4.0 [3c28c6f8] BioSymbols v5.1.3 [9d651bdf] BiochemicalAlgorithms v0.5.0 [336ed68f] CSV v0.10.15 [159f3aea] Cairo v1.1.1 [49dc2e85] Calculus v0.5.2 [69e1c6dd] CellListMap v0.9.8 [ae650224] ChunkSplitters v3.1.1 [944b1d66] CodecZlib v0.7.8 [3da002f7] ColorTypes v0.12.0 [5ae59095] Colors v0.13.0 [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] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.20 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [a0c0ee7d] DifferentiationInterface v0.6.42 [ffbed154] DocStringExtensions v0.9.3 [4e289a0a] EnumX v1.0.4 [e2ba6199] ExprTools v0.1.10 [55351af7] ExproniconLite v0.10.14 [411431e0] Extents v0.1.5 [9aa1b823] FastClosures v0.3.2 [5789e2e9] FileIO v1.17.0 [48062228] FilePathsBase v0.9.23 [1a297f60] FillArrays v1.13.0 [53c48c17] FixedPointNumbers v0.8.5 [1fa38f19] Format v1.3.7 [069b7b12] FunctionWrappers v1.1.3 [77dc65aa] FunctionWrappersWrappers v0.1.3 [46192b85] GPUArraysCore v0.2.0 [68eda718] GeoFormatTypes v0.4.4 [cf35fbd7] GeoInterface v1.4.1 [5c1252a2] GeometryBasics v0.5.5 [a2bd30eb] Graphics v1.1.3 [86223c79] Graphs v1.12.0 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.3 [8197267c] IntervalSets v0.7.10 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [033835bb] JLD2 v0.5.11 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.1 [ae98c720] Jieko v0.2.1 [5be7bae1] LBFGSB v0.4.1 [b964fa9f] LaTeXStrings v1.4.0 [1d6d02ad] LeftChildRightSiblingTrees v0.2.0 [e6f89c97] LoggingExtras v1.1.0 [1914dd2f] MacroTools v0.5.15 [20f20a25] MakieCore v0.9.1 [eff96d63] Measurements v2.12.0 [c116f080] Mendeleev v1.0.1 [626554b9] MetaGraphs v0.8.0 [e1d29d7a] Missings v1.2.0 [6c89ec66] MolecularGraph v0.17.3 [2e0e35c7] Moshi v0.3.5 [77ba4419] NaNMath v1.1.2 [510215fc] Observables v0.5.5 [7f7a1694] Optimization v4.1.1 [bca83a33] OptimizationBase v2.4.0 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.32 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.1 [5ad8b20f] PhysicalConstants v0.2.4 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [33c8b6b6] ProgressLogging v0.1.4 [92933f4c] ProgressMeter v1.10.2 [94ee1d12] Quaternions v0.7.6 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [731186ca] RecursiveArrayTools v3.31.0 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [f2b01f46] Roots v2.2.6 [6038ab10] Rotations v1.7.1 [7e49a35a] RuntimeGeneratedFunctions v0.5.13 [0bca4576] SciMLBase v2.75.1 [c0aeaf25] SciMLOperators v0.3.12 [53ae85a6] SciMLStructures v1.6.1 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield v1.1.2 [699a6c99] SimpleTraits v0.9.4 [a2af1166] SortingAlgorithms v1.2.1 [9f842d2f] SparseConnectivityTracer v0.6.13 [0a514795] SparseMatrixColorings v0.4.13 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [69024149] StringEncodings v0.3.7 [892a3eda] StringManipulation v0.4.1 [856f2bd8] StructTypes v1.11.0 [2efcf032] SymbolicIndexingInterface v0.3.38 [ab02a1b2] TableOperations v1.2.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [5d786b92] TerminalLoggers v0.1.7 [f8b46487] 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v1.12.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.11.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2024.12.31 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.0.16+0 [efcefdf7] PCRE2_jll v10.44.0+1 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... 25572.4 ms ✓ BioStructures → BioStructuresGraphsExt Info Given BiochemicalAlgorithms was explicitly requested, output will be shown live  WARNING: Detected access to binding `CellListMap.Cell` in a world prior to its definition world.  Julia 1.12 has introduced more strict world age semantics for global bindings.  !!! This code may malfunction under Revise.  !!! This code will error in future versions of Julia. Hint: Add an appropriate `invokelatest` around the access to this binding. 323677.3 ms ✓ BiochemicalAlgorithms 2 dependencies successfully precompiled in 353 seconds. 243 already precompiled. 1 dependency had output during precompilation: ┌ BiochemicalAlgorithms │ [Output was shown above] └ ┌ Warning: write_sdfile: writer only supports 2D data; projecting atoms onto xy-plane... └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/ZwvVk/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/ZwvVk/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/ZwvVk/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/ZwvVk/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/ZwvVk/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/ZwvVk/src/forcefields/common/forcefield.jl:233 ┌ Error: illegal HIN file in line 31: cannot finalize bond (29, 30, BiochemicalAlgorithms.BondOrder.Single)! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/ZwvVk/src/fileformats/hinfile.jl:232 ┌ Error: illegal HIN file in line 31: cannot finalize bond (29, 30, BiochemicalAlgorithms.BondOrder.Single)! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/ZwvVk/src/fileformats/hinfile.jl:232 ┌ Warning: Atom names in HIN files cannot contain spaces! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/ZwvVk/src/fileformats/hinfile.jl:445 ┌ Warning: Atom names in HIN files cannot contain spaces! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/ZwvVk/src/fileformats/hinfile.jl:445 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/ZwvVk/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/ZwvVk/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/ZwvVk/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/ZwvVk/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/ZwvVk/src/mappings/rigid_mapping.jl:176 ┌ Warning: Correlation matrix is not positive definit! Computing rotation through `RMSDMinimizerCoutsias` instead! └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/ZwvVk/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 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/ZwvVk/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/ZwvVk/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/ZwvVk/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/ZwvVk/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/ZwvVk/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/ZwvVk/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/ZwvVk/src/forcefields/common/forcefield.jl:233 Test Summary: | Pass Total Time Package | 9920 9920 25m41.0s test/fileformats/test_sdfile.jl | 34 34 7m59.3s Read SDFile | 30 30 7m27.1s Write SDFile | 4 4 32.1s test/optimization/test_optimize_structure.jl | 6 6 4m23.2s Optimize structure | 3 3 4m18.3s Optimize hydrogen positions | 3 3 4.9s test/substructures/test_smarts.jl | 30 30 1m04.7s SMARTS | 30 30 1m04.7s test/aqua.jl | 11 11 3m46.8s Aqua | 11 11 3m46.8s Method ambiguity | 1 1 57.1s 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 57.3s Compat bounds | 4 4 0.7s Piracy | 1 1 0.5s Persistent tasks | 1 1 1m19.4s test/core/test_chain.jl | 462 462 25.6s ChainTable | 206 206 19.1s Chain | 256 256 6.5s test/core/test_bond.jl | 312 312 10.7s BondTable | 176 176 5.2s Bond | 136 136 5.6s test/fileformats/test_pubchem_json.jl | 106 106 17.1s Read PubChem | 106 106 17.1s test/fileformats/test_hinfile.jl | 52 52 15.9s Read HIN | 48 48 3.8s Write HIN | 4 4 12.1s test/core/test_element.jl | 126 126 0.2s Element | 126 126 0.2s test/fileformats/test_pdb.jl | 1870 1870 35.2s Read PDB | 1824 1824 18.5s Write PDB | 14 14 8.5s Read PDBx/mmCIF | 18 18 3.2s Write PDBx/mmCIF | 14 14 5.0s test/substructures/test_sssr.jl | 3 3 3.3s Ring Perception | 3 3 3.3s test/core/test_molecule.jl | 834 834 23.6s MoleculeTable | 238 238 10.0s MoleculeTable/None | 146 146 1.4s MoleculeTable/Protein | 146 146 1.3s Molecule | 68 68 3.2s Molecule/None | 118 118 4.9s Molecule/Protein | 118 118 2.9s test/substructures/test_substructure.jl | 6 6 1.7s Substructure | 6 6 1.7s test/core/test_amino_acid.jl | 63 63 0.4s AminoAcid | 63 63 0.4s test/core/test_secondary_structure.jl | 514 514 28.7s SecondaryStructureTable | 240 240 10.4s SecondaryStructure | 274 274 18.3s test/core/test_atom.jl | 606 606 25.2s AtomTable | 308 308 8.0s Atom | 298 298 17.2s test/core/test_fragment.jl | 1734 1734 1m01.2s FragmentTable | 266 266 10.1s FragmentTable/None | 178 178 1.2s FragmentTable/Nucleotide | 178 178 1.5s FragmentTable/Residue | 178 178 1.4s Fragment | 118 118 2.5s Fragment/None | 272 272 14.8s Fragment/Nucleotide | 272 272 14.8s Fragment/Residue | 272 272 14.9s test/mappings/test_mappings.jl | 224 224 27.7s TrivialAtomBijection | 8 8 1.9s RigidTransform | 16 16 0.7s translate! | 88 88 2.2s rigid_transform! | 44 44 4.8s compute_rmsd | 14 14 3.2s compute_rmsd_minimizer | 42 42 12.2s map_rigid! | 12 12 2.7s test/preprocessing/test_fragmentdb.jl | 4 4 1.6s FragmentDB | 4 4 1.6s test/core/test_moleculargraph_wrapper.jl | 162 162 22.0s Convert to SDFMolGraph | 162 162 22.0s test/core/test_bond_order.jl | 8 8 0.0s Bond Order | 8 8 0.0s test/core/test_types.jl | 106 106 2.6s Vector3 | 51 51 1.3s Matrix3 | 51 51 1.3s Properties | 2 2 0.0s Flags | 2 2 0.0s test/core/test_system.jl | 618 618 2m24.1s System | 618 618 2m24.1s test/core/test_system_component_table.jl | 78 78 1.3s SystemComponentTableCol | 78 78 1.3s test/forcefields/AMBER/test_amberff.jl | 1951 1951 58.9s AmberFF | 1951 1951 58.9s Testing BiochemicalAlgorithms tests passed Testing completed after 1586.79s PkgEval succeeded after 1981.33s