Package evaluation of BiochemicalAlgorithms on Julia 1.13.0-DEV.582 (c0a1728d50*) started at 2025-05-14T18:52:31.436 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.14s ################################################################################ # Installation # Installing BiochemicalAlgorithms... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [9d651bdf] + BiochemicalAlgorithms v0.5.3 Updating `~/.julia/environments/v1.13/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 v0.9.8 [ae650224] + ChunkSplitters v3.1.2 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.1 [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] + 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IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [033835bb] + JLD2 v0.5.13 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.2 [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 v0.5.16 [20f20a25] + MakieCore v0.9.3 [eff96d63] + Measurements v2.12.0 [c116f080] + Mendeleev v1.0.1 [626554b9] + MetaGraphs v0.8.0 [e1d29d7a] + Missings v1.2.0 [6c89ec66] + MolecularGraph v0.18.0 [2e0e35c7] + Moshi v0.3.5 [77ba4419] + NaNMath v1.1.3 [510215fc] + Observables v0.5.5 [7f7a1694] + Optimization v4.2.0 [bca83a33] + OptimizationBase v2.5.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.35 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [5ad8b20f] + PhysicalConstants v0.2.4 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [33c8b6b6] + ProgressLogging v0.1.4 [92933f4c] + ProgressMeter v1.10.4 [94ee1d12] + Quaternions v0.7.6 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [731186ca] + RecursiveArrayTools v3.33.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [f2b01f46] + Roots v2.2.7 [6038ab10] + Rotations v1.7.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.14 [0bca4576] + SciMLBase v2.89.1 [c0aeaf25] + SciMLOperators v0.4.0 [53ae85a6] + SciMLStructures v1.7.0 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [699a6c99] + SimpleTraits v0.9.4 [a2af1166] + SortingAlgorithms v1.2.1 [9f842d2f] + SparseConnectivityTracer v0.6.18 [0a514795] + SparseMatrixColorings v0.4.19 [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 v0.3.40 [ab02a1b2] + TableOperations 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+ Pango_jll v1.56.1+0 [30392449] + Pixman_jll v0.44.2+0 ⌅ [02c8fc9c] + XML2_jll v2.13.6+1 [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 [f6050b86] + coordgenlibs_jll v3.0.2+0 [172afb32] + libinchi_jll v1.6.0+0 [b53b4c65] + libpng_jll v1.6.48+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 v1.13.0 [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 v8.12.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.2.25 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.0+0 [efcefdf7] + PCRE2_jll v10.44.0+1 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+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 5.45s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 149.54s ################################################################################ # Testing # Testing BiochemicalAlgorithms Status `/tmp/jl_Ojwwll/Project.toml` [4c88cf16] Aqua v0.8.12 [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 v0.9.8 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [ffbed154] DocStringExtensions v0.9.4 [4e289a0a] EnumX v1.0.5 [86223c79] Graphs v1.12.1 [0f8b85d8] JSON3 v1.14.2 [c116f080] Mendeleev v1.0.1 [626554b9] MetaGraphs v0.8.0 [6c89ec66] MolecularGraph v0.18.0 [510215fc] Observables v0.5.5 [7f7a1694] Optimization v4.2.0 [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 [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 v1.22.1 [a7773ee8] UnitfulAtomic v1.0.0 [37e2e46d] LinearAlgebra v1.12.0 [de0858da] Printf v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_Ojwwll/Manifest.toml` [47edcb42] ADTypes v1.14.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [4c88cf16] Aqua v0.8.12 [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 v0.9.8 [ae650224] ChunkSplitters v3.1.2 [944b1d66] CodecZlib v0.7.8 [3da002f7] ColorTypes v0.12.1 [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 v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 ⌅ [a0c0ee7d] DifferentiationInterface v0.6.54 [ffbed154] DocStringExtensions v0.9.4 [4e289a0a] EnumX v1.0.5 [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 v0.9.24 [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 v0.5.9 [a2bd30eb] Graphics v1.1.3 [86223c79] Graphs v1.12.1 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.3 [8197267c] IntervalSets v0.7.11 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [c8e1da08] 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[92933f4c] ProgressMeter v1.10.4 [94ee1d12] Quaternions v0.7.6 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [731186ca] RecursiveArrayTools v3.33.0 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [f2b01f46] Roots v2.2.7 [6038ab10] Rotations v1.7.1 [7e49a35a] RuntimeGeneratedFunctions v0.5.14 [0bca4576] SciMLBase v2.89.1 [c0aeaf25] SciMLOperators v0.4.0 [53ae85a6] SciMLStructures v1.7.0 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield v1.1.2 [699a6c99] SimpleTraits v0.9.4 [a2af1166] SortingAlgorithms v1.2.1 [9f842d2f] SparseConnectivityTracer v0.6.18 [0a514795] SparseMatrixColorings v0.4.19 [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 v0.3.40 [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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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 [f6050b86] coordgenlibs_jll v3.0.2+0 [172afb32] libinchi_jll v1.6.0+0 [b53b4c65] libpng_jll v1.6.48+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 v1.13.0 [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 v8.12.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.2.25 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.0+0 [efcefdf7] PCRE2_jll v10.44.0+1 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+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. Testing Running tests... Precompiling packages... 8722.8 ms ✓ BioStructures → BioStructuresGraphsExt 92137.3 ms ✓ BiochemicalAlgorithms 2 dependencies successfully precompiled in 103 seconds. 241 already precompiled. ┌ 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 ┌ 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. [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds ┌ Warning: 64 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 22 warnings │ - QuadraticAngleBend : 39 warnings │ - Torsion : 3 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:14 Expression: compute_energy!(a_ff) ≈ 1425.5979f0 Evaluated: 1418.8357f0 ≈ 1425.5979f0 Stacktrace: [1] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:14 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:16 Expression: a_ff.energy["Bond Stretches"] ≈ 1.3630637f0 Evaluated: 0.0f0 ≈ 1.3630637f0 Stacktrace: [1] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:16 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:17 Expression: a_ff.energy["Angle Bends"] ≈ 5.4076657f0 Evaluated: 0.0f0 ≈ 5.4076657f0 Stacktrace: [1] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:17 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:19 Expression: a_ff.energy["Improper Torsion"] ≈ 3.9901734f-6 Evaluated: 0.0f0 ≈ 3.9901734f-6 Stacktrace: [1] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:19 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:25 Expression: _rms_F(p) ≈ 1703.33f0 Evaluated: 1700.0266f0 ≈ 1703.33f0 Stacktrace: [1] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:25 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] ┌ Warning: 1 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 1 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:42 Expression: compute_energy!(ff) ≈ T(25.552721448) Evaluated: 0.0f0 ≈ 25.552721f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:42 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:43 Expression: ff.energy["Bond Stretches"] ≈ T(25.552721448) Evaluated: 0.0f0 ≈ 25.552721f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:43 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:52 Expression: _rms_F(sys) ≈ T(228.72667607023757) Evaluated: 0.0f0 ≈ 228.72667f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:52 ┌ Warning: 3 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 2 warnings │ - QuadraticAngleBend : 1 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:61 Expression: compute_energy!(ff) ≈ T(7.895900930651099) Evaluated: 0.0f0 ≈ 7.8959007f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:61 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:63 Expression: ff.energy["Angle Bends"] ≈ T(7.895900930651099) Evaluated: 0.0f0 ≈ 7.8959007f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:63 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:71 Expression: _rms_F(sys) ≈ T(51.16440255175596) Evaluated: 0.0f0 ≈ 51.164402f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:71 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 3 warnings │ - QuadraticAngleBend : 2 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:100 Expression: ff.energy["Bond Stretches"] ≈ T(3.498308129219706e-6) Evaluated: 0.0f0 ≈ 3.4983082f-6 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:100 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:101 Expression: ≈(ff.energy["Angle Bends"], T(4.618658784515784e-6), atol = 1.0e-6) Evaluated: 0.0f0 ≈ 4.6186587f-6 (atol=1.0e-6) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:101 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:109 Expression: _rms_F(sys) ≈ T(14.284901061469098) Evaluated: 14.291931f0 ≈ 14.284901f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:109 ┌ Warning: 87 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 30 warnings │ - QuadraticAngleBend : 52 warnings │ - Torsion : 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:118 Expression: compute_energy!(ff) ≈ T(-314.13298677164846) Evaluated: -325.73004f0 ≈ -314.133f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:118 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:119 Expression: ff.energy["Bond Stretches"] ≈ T(3.004505538267881) Evaluated: 0.0f0 ≈ 3.0045056f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:119 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:120 Expression: ff.energy["Angle Bends"] ≈ T(8.592612636552754) Evaluated: 0.0f0 ≈ 8.592612f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:120 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:128 Expression: _rms_F(sys) ≈ T(35.035943894791984) Evaluated: 26.72995f0 ≈ 35.035942f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:128 ┌ Warning: 87 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 30 warnings │ - QuadraticAngleBend : 52 warnings │ - Torsion : 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:137 Expression: compute_energy!(ff) ≈ T(128.93387144346946) Evaluated: 117.78471f0 ≈ 128.93387f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:137 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:138 Expression: ff.energy["Bond Stretches"] ≈ T(3.0037164329529027) Evaluated: 0.0f0 ≈ 3.0037165f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:138 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:139 Expression: ff.energy["Angle Bends"] ≈ T(8.145414549467489) Evaluated: 0.0f0 ≈ 8.145414f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:139 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:147 Expression: _rms_F(sys) ≈ T(40.63998952652902) Evaluated: 33.939445f0 ≈ 40.639988f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:147 ┌ Warning: 87 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 30 warnings │ - QuadraticAngleBend : 52 warnings │ - Torsion : 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:156 Expression: compute_energy!(ff) ≈ T(-91.22395429471445) Evaluated: -104.08794f0 ≈ -91.22395f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:156 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:157 Expression: ff.energy["Bond Stretches"] ≈ T(3.754803527450929) Evaluated: 0.0f0 ≈ 3.7548034f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:157 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:158 Expression: ff.energy["Angle Bends"] ≈ T(9.109164557456147) Evaluated: 0.0f0 ≈ 9.109164f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:158 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:166 Expression: _rms_F(sys) ≈ T(41.758379137558485) Evaluated: 33.875084f0 ≈ 41.75838f0 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:166 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 3 warnings │ - QuadraticAngleBend : 2 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 ┌ Warning: 1 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 1 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:42 Expression: compute_energy!(ff) ≈ T(25.552721448) Evaluated: 0.0 ≈ 25.552721448 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:42 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:43 Expression: ff.energy["Bond Stretches"] ≈ T(25.552721448) Evaluated: 0.0 ≈ 25.552721448 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:43 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:52 Expression: _rms_F(sys) ≈ T(228.72667607023757) Evaluated: 0.0 ≈ 228.72667607023757 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:52 ┌ Warning: 3 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 2 warnings │ - QuadraticAngleBend : 1 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:61 Expression: compute_energy!(ff) ≈ T(7.895900930651099) Evaluated: 0.0 ≈ 7.895900930651099 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:61 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:63 Expression: ff.energy["Angle Bends"] ≈ T(7.895900930651099) Evaluated: 0.0 ≈ 7.895900930651099 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:63 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:71 Expression: _rms_F(sys) ≈ T(51.16440255175596) Evaluated: 0.0 ≈ 51.16440255175596 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:71 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 3 warnings │ - QuadraticAngleBend : 2 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:99 Expression: compute_energy!(ff) ≈ T(16.954878332796728) Evaluated: 16.95487025276985 ≈ 16.954878332796728 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:99 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:100 Expression: ff.energy["Bond Stretches"] ≈ T(3.498308129219706e-6) Evaluated: 0.0 ≈ 3.498308129219706e-6 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:100 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:101 Expression: ≈(ff.energy["Angle Bends"], T(4.618658784515784e-6), atol = 1.0e-6) Evaluated: 0.0 ≈ 4.618658784515784e-6 (atol=1.0e-6) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:101 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:109 Expression: _rms_F(sys) ≈ T(14.284901061469098) Evaluated: 14.291930855546473 ≈ 14.284901061469098 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:109 ┌ Warning: 87 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 30 warnings │ - QuadraticAngleBend : 52 warnings │ - Torsion : 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:118 Expression: compute_energy!(ff) ≈ T(-314.13298677164846) Evaluated: -325.7301049464689 ≈ -314.13298677164846 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:118 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:119 Expression: ff.energy["Bond Stretches"] ≈ T(3.004505538267881) Evaluated: 0.0 ≈ 3.004505538267881 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:119 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:120 Expression: ff.energy["Angle Bends"] ≈ T(8.592612636552754) Evaluated: 0.0 ≈ 8.592612636552754 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:120 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:128 Expression: _rms_F(sys) ≈ T(35.035943894791984) Evaluated: 26.729972047426834 ≈ 35.035943894791984 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:128 ┌ Warning: 87 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 30 warnings │ - QuadraticAngleBend : 52 warnings │ - Torsion : 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:137 Expression: compute_energy!(ff) ≈ T(128.93387144346946) Evaluated: 117.78474046104898 ≈ 128.93387144346946 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:137 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:138 Expression: ff.energy["Bond Stretches"] ≈ T(3.0037164329529027) Evaluated: 0.0 ≈ 3.0037164329529027 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:138 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:139 Expression: ff.energy["Angle Bends"] ≈ T(8.145414549467489) Evaluated: 0.0 ≈ 8.145414549467489 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:139 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:147 Expression: _rms_F(sys) ≈ T(40.63998952652902) Evaluated: 33.939517757236175 ≈ 40.63998952652902 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:147 ┌ Warning: 87 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 30 warnings │ - QuadraticAngleBend : 52 warnings │ - Torsion : 5 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:156 Expression: compute_energy!(ff) ≈ T(-91.22395429471445) Evaluated: -104.08792237962162 ≈ -91.22395429471445 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:156 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:157 Expression: ff.energy["Bond Stretches"] ≈ T(3.754803527450929) Evaluated: 0.0 ≈ 3.754803527450929 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:157 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:158 Expression: ff.energy["Angle Bends"] ≈ T(9.109164557456147) Evaluated: 0.0 ≈ 9.109164557456147 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:158 AmberFF: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:166 Expression: _rms_F(sys) ≈ T(41.758379137558485) Evaluated: 33.875230891899555 ≈ 41.758379137558485 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [2] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/forcefields/AMBER/test_amberff.jl:166 ┌ Warning: 5 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 3 warnings │ - QuadraticAngleBend : 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: 64 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 22 warnings │ - QuadraticAngleBend : 39 warnings │ - Torsion : 3 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 Optimize structure: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/optimization/test_optimize_structure.jl:10 Expression: compute_energy!(ff) ≈ 1425.5979f0 Evaluated: 1418.8357f0 ≈ 1425.5979f0 Stacktrace: [1] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/optimization/test_optimize_structure.jl:518 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] Optimize structure: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/optimization/test_optimize_structure.jl:12 Expression: compute_energy!(ff) ≈ -374.3136f0 Evaluated: -1716.7289f0 ≈ -374.3136f0 Stacktrace: [1] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/optimization/test_optimize_structure.jl:518 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds ┌ Warning: 64 warnings occurred during setup that were suppressed: │ - QuadraticBondStretch: 22 warnings │ - QuadraticAngleBend : 39 warnings │ - Torsion : 3 warnings │ Use print_warnings(ff) to display them. └ @ BiochemicalAlgorithms ~/.julia/packages/BiochemicalAlgorithms/g6ebH/src/forcefields/common/forcefield.jl:233 Optimize hydrogen positions: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/optimization/test_optimize_structure.jl:24 Expression: compute_energy!(ff) ≈ 1425.5979f0 Evaluated: 1418.8357f0 ≈ 1425.5979f0 Stacktrace: [1] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/optimization/test_optimize_structure.jl:518 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] Optimize hydrogen positions: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/optimization/test_optimize_structure.jl:26 Expression: compute_energy!(ff) ≈ 1421.212f0 Evaluated: 1346.8766f0 ≈ 1421.212f0 Stacktrace: [1] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/optimization/test_optimize_structure.jl:518 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] ┌ 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 Ring Perception: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/substructures/test_sssr.jl:14 Expression: [map(length, sssr) for sssr = detected_sssrs] == num_sssr_atoms Evaluated: [[6], [6], [6], [6], [6], [3, 6, 6], Int64[], [6], [3, 3, 3]] == Vector{Any}[[6], [6], [6], [6], [6], [6, 6, 3], [], [6], [3, 3, 3]] Stacktrace: [1] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/substructures/test_sssr.jl:518 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [ 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 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 Convert to SDFMolGraph: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/core/test_moleculargraph_wrapper.jl:27 Expression: length(bds_sys ∩ bds_g) == nbonds(sys) Evaluated: 21 == 22 Stacktrace: [1] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/core/test_moleculargraph_wrapper.jl:27 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [ Info: reconstruct_fragments!(): added 0 atoms. [ Info: build_bonds!(): built 22 bonds Convert to SDFMolGraph: Test Failed at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/core/test_moleculargraph_wrapper.jl:27 Expression: length(bds_sys ∩ bds_g) == nbonds(sys) Evaluated: 21 == 22 Stacktrace: [1] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/g6ebH/test/core/test_moleculargraph_wrapper.jl:27 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] Test Summary: | Pass Fail Total Time Package | 9867 55 9922 20m23.0s test/core/test_types.jl | 106 106 2m28.4s Vector3 | 51 51 2m27.2s Matrix3 | 51 51 1.1s Properties | 2 2 0.0s Flags | 2 2 0.0s test/mappings/test_mappings.jl | 224 224 53.0s TrivialAtomBijection | 8 8 23.6s RigidTransform | 16 16 0.7s translate! | 88 88 3.4s rigid_transform! | 44 44 4.6s compute_rmsd | 14 14 2.9s compute_rmsd_minimizer | 42 42 14.9s map_rigid! | 12 12 2.9s test/core/test_molecule.jl | 834 834 45.9s MoleculeTable | 238 238 22.8s MoleculeTable/None | 146 146 1.3s MoleculeTable/Protein | 146 146 1.1s Molecule | 68 68 12.4s Molecule/None | 118 118 5.6s Molecule/Protein | 118 118 2.6s test/fileformats/test_sdfile.jl | 34 34 54.4s Read SDFile | 30 30 34.7s Write SDFile | 4 4 19.7s test/core/test_fragment.jl | 1734 1734 1m04.2s FragmentTable | 266 266 10.8s FragmentTable/None | 178 178 1.1s FragmentTable/Nucleotide | 178 178 1.3s FragmentTable/Residue | 178 178 1.2s Fragment | 118 118 4.8s Fragment/None | 272 272 16.5s Fragment/Nucleotide | 272 272 14.3s Fragment/Residue | 272 272 14.1s test/core/test_bond.jl | 312 312 10.0s BondTable | 176 176 4.6s Bond | 136 136 5.4s test/forcefields/AMBER/test_amberff.jl | 1903 48 1951 5m16.2s AmberFF | 1903 48 1951 5m16.2s test/fileformats/test_pubchem_json.jl | 106 106 0.6s Read PubChem | 106 106 0.6s test/substructures/test_substructure.jl | 6 6 2.6s Substructure | 6 6 2.6s test/core/test_bond_order.jl | 8 8 0.0s Bond Order | 8 8 0.0s test/optimization/test_optimize_structure.jl | 2 4 6 12.7s Optimize structure | 1 2 3 7.4s Optimize hydrogen positions | 1 2 3 5.4s test/core/test_atom.jl | 606 606 23.6s AtomTable | 308 308 7.6s Atom | 298 298 16.0s test/fileformats/test_hinfile.jl | 52 52 13.3s Read HIN | 48 48 2.0s Write HIN | 4 4 11.3s test/core/test_chain.jl | 462 462 9.4s ChainTable | 206 206 6.6s Chain | 256 256 2.9s test/aqua.jl | 11 11 2m59.0s Aqua | 11 11 2m59.0s Method ambiguity | 1 1 38.1s 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 38.5s Compat bounds | 4 4 0.7s Piracy | 1 1 0.3s Persistent tasks | 1 1 1m26.0s Undocumented names | 0 0.0s test/fileformats/test_pdb.jl | 1870 1870 32.1s Read PDB | 1824 1824 17.3s Write PDB | 14 14 6.9s Read PDBx/mmCIF | 18 18 3.5s Write PDBx/mmCIF | 14 14 4.4s test/core/test_element.jl | 126 126 0.2s Element | 126 126 0.2s test/substructures/test_sssr.jl | 2 1 3 4.1s Ring Perception | 2 1 3 4.1s test/preprocessing/test_add_hydrogens.jl | 2 2 52.0s FragmentDB | 2 2 52.0s test/core/test_amino_acid.jl | 63 63 0.4s AminoAcid | 63 63 0.4s test/preprocessing/test_fragmentdb.jl | 4 4 1.7s FragmentDB | 4 4 1.7s test/core/test_system_component_table.jl | 78 78 1.4s SystemComponentTableCol | 78 78 1.4s test/substructures/test_smarts.jl | 30 30 35.9s SMARTS | 30 30 35.9s test/core/test_system.jl | 618 618 2m17.4s System | 618 618 2m17.4s test/core/test_moleculargraph_wrapper.jl | 160 2 162 2.2s Convert to SDFMolGraph | 160 2 162 2.2s test/core/test_secondary_structure.jl | 514 514 22.4s SecondaryStructureTable | 240 240 6.6s SecondaryStructure | 274 274 15.8s ERROR: LoadError: Some tests did not pass: 9867 passed, 55 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/g6ebH/test/runtests.jl:3 Testing failed after 1279.38s ERROR: LoadError: Package BiochemicalAlgorithms errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{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/v1.13/Pkg/src/Operations.jl:2418 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2273 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{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/v1.13/Pkg/src/API.jl:498 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:309 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:331 [12] _start() @ Base ./client.jl:564 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1462.98s: package has test failures