Package evaluation to test DifferentiableMetabolism on Julia 1.12.4 (f5754389fd*) started at 2026-02-02T12:12:39.780 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 5.13s ################################################################################ # Installation # Installing DifferentiableMetabolism... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [9677e053] + DifferentiableMetabolism v0.5.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [5a4f3dfa] + AbstractFBCModels v1.3.0 [6e4b80f9] + BenchmarkTools v1.6.3 [babc4406] + COBREXA v2.9.1 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.18.1 [5515826b] + ConstraintTrees v1.11.0 [187b0558] + ConstructionBase v1.6.0 ⌅ [864edb3b] + DataStructures v0.18.22 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [9677e053] + DifferentiableMetabolism v0.5.0 [ffbed154] + DocStringExtensions v0.9.5 [e2ba6199] + ExprTools v0.1.10 [eb9bf01b] + FastDifferentiation v0.4.5 [f6369f11] + ForwardDiff v1.3.2 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.4.0 [4076af6c] + JuMP v1.29.4 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.49.0 [d8a4904e] + MutableArithmetics v1.6.7 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.16 [276daf66] + SpecialFunctions v2.6.1 [860ef19b] + StableRNGs v1.0.4 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [ec057cc2] + StructUtils v2.6.2 [3bb67fe8] + TranscodingStreams v0.11.3 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+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 [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 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.1 [de0858da] + Printf v1.11.0 [9abbd945] + Profile 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 v1.12.0 [f489334b] + StyledStrings v1.11.0 [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 v8.15.0+0 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.7.0+0 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 3.69s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 2659.6 ms ✓ TestEnv 1 dependency successfully precompiled in 3 seconds. 26 already precompiled. ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/h9a3r/src/julia-1.12/activate_set.jl:78 Precompiling package dependencies... Precompiling packages... 655.0 ms ✓ RangeArrays 594.0 ms ✓ MuladdMacro 5548.5 ms ✓ BaseDirs 732.3 ms ✓ AbstractFFTs 638.4 ms ✓ LaTeXStrings 617.4 ms ✓ IndirectArrays 624.9 ms ✓ PolygonOps 649.6 ms ✓ ExprTools 541.8 ms ✓ IteratorInterfaceExtensions 641.7 ms ✓ TensorCore 633.1 ms ✓ StatsAPI 662.4 ms ✓ Contour 2495.4 ms ✓ CEnum 1166.0 ms ✓ OffsetArrays 659.1 ms ✓ TriplotBase 1718.5 ms ✓ Format 1285.2 ms ✓ FillArrays 635.0 ms ✓ IntegerMathUtils 693.5 ms ✓ InverseFunctions 796.7 ms ✓ Statistics 835.8 ms ✓ IterTools 5100.3 ms ✓ MacroTools 2688.4 ms ✓ Grisu 2843.1 ms ✓ OrderedCollections 2526.9 ms ✓ Observables 885.8 ms ✓ Requires 557.9 ms ✓ DataValueInterfaces 643.0 ms ✓ EnumX 703.2 ms ✓ StableRNGs 568.8 ms ✓ Reexport 812.9 ms ✓ DocStringExtensions 771.4 ms ✓ AbstractTrees 3330.7 ms ✓ IrrationalConstants 742.9 ms ✓ IntervalSets 657.8 ms ✓ RoundingEmulator 720.5 ms ✓ Extents 589.3 ms ✓ PtrArrays 877.4 ms ✓ TranscodingStreams 1919.5 ms ✓ AdaptivePredicates 2480.4 ms ✓ NaNMath 2440.2 ms ✓ LazyModules 706.9 ms ✓ Inflate 2528.6 ms ✓ ConstructionBase 615.2 ms ✓ DataAPI 602.4 ms ✓ FastClosures 717.9 ms ✓ StaticArraysCore 728.4 ms ✓ MappedArrays 1294.3 ms ✓ GenericLinearAlgebra 10429.7 ms ✓ Krylov 1328.3 ms ✓ ProgressMeter 1203.2 ms ✓ AMD 1249.8 ms ✓ PDMats 950.3 ms ✓ WoodburyMatrices 28137.2 ms ✓ Unitful 654.2 ms ✓ Scratch 824.3 ms ✓ Preferences 2750.5 ms ✓ Compat 2018.7 ms ✓ UnicodeFun 7498.0 ms ✓ MutableArithmetics 2521.4 ms ✓ PkgVersion 2856.4 ms ✓ QPSReader 2628.1 ms ✓ AbstractFFTs → AbstractFFTsTestExt 2463.3 ms ✓ RuntimeGeneratedFunctions 4028.9 ms ✓ TimerOutputs 525.0 ms ✓ TableTraits 607.3 ms ✓ StackViews 656.1 ms ✓ PaddedViews 999.6 ms ✓ FillArrays → FillArraysSparseArraysExt 818.9 ms ✓ Primes 1182.3 ms ✓ InverseFunctions → InverseFunctionsTestExt 636.8 ms ✓ InverseFunctions → InverseFunctionsDatesExt 1021.2 ms ✓ SignedDistanceFields 4612.4 ms ✓ FixedPointNumbers 880.9 ms ✓ Statistics → SparseArraysExt 636.8 ms ✓ FillArrays → FillArraysStatisticsExt 1132.6 ms ✓ CommonSubexpressions 2069.3 ms ✓ SimpleTraits 601.5 ms ✓ Showoff 608.5 ms ✓ Ratios 648.0 ms ✓ Adapt 5825.8 ms ✓ FileIO 1016.3 ms ✓ PikaParser 2503.6 ms ✓ AbstractFBCModels 990.8 ms ✓ LogExpFunctions 580.0 ms ✓ IntervalSets → IntervalSetsRandomExt 575.0 ms ✓ IntervalSets → IntervalSetsStatisticsExt 691.5 ms ✓ AliasTables 669.8 ms ✓ CodecZlib 565.6 ms ✓ ConstructionBase → ConstructionBaseIntervalSetsExt 596.0 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 2555.3 ms ✓ Missings 603.0 ms ✓ DiffResults 2825.9 ms ✓ LDLFactorizations 896.4 ms ✓ QDLDL 924.7 ms ✓ FillArrays → FillArraysPDMatsExt 923.9 ms ✓ AxisAlgorithms 1137.9 ms ✓ Unitful → ConstructionBaseUnitfulExt 1133.5 ms ✓ Unitful → NaNMathExt 1154.1 ms ✓ Unitful → InverseFunctionsUnitfulExt 1210.5 ms ✓ Unitful → PrintfExt 766.1 ms ✓ RelocatableFolders 769.7 ms ✓ SnoopPrecompile 819.3 ms ✓ JLLWrappers 616.4 ms ✓ PrecompileTools 2798.0 ms ✓ ComputePipeline 620.1 ms ✓ Compat → CompatLinearAlgebraExt 2742.2 ms ✓ LinearOperators 3024.3 ms ✓ Tables 688.0 ms ✓ MosaicViews 1871.3 ms ✓ FFTA 3353.4 ms ✓ ColorTypes 592.2 ms ✓ Ratios → RatiosFixedPointNumbersExt 841.2 ms ✓ Adapt → AdaptSparseArraysExt 608.1 ms ✓ OffsetArrays → OffsetArraysAdaptExt 559.6 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1080.1 ms ✓ AxisArrays 958.2 ms ✓ Graphite2_jll 972.9 ms ✓ Libmount_jll 986.7 ms ✓ LLVMOpenMP_jll 982.8 ms ✓ Bzip2_jll 966.4 ms ✓ Rmath_jll 986.4 ms ✓ Xorg_libXau_jll 984.1 ms ✓ libpng_jll 968.1 ms ✓ libfdk_aac_jll 964.8 ms ✓ Imath_jll 965.6 ms ✓ Giflib_jll 972.9 ms ✓ LAME_jll 962.2 ms ✓ LERC_jll 959.5 ms ✓ EarCut_jll 973.6 ms ✓ CRlibm_jll 989.6 ms ✓ JpegTurbo_jll 1019.8 ms ✓ XZ_jll 978.0 ms ✓ Ogg_jll 982.6 ms ✓ Xorg_libXdmcp_jll 980.8 ms ✓ x265_jll 998.6 ms ✓ x264_jll 1012.5 ms ✓ libaom_jll 981.0 ms ✓ Zstd_jll 985.8 ms ✓ Expat_jll 976.9 ms ✓ LZO_jll 967.8 ms ✓ Opus_jll 852.0 ms ✓ Xorg_xtrans_jll 980.0 ms ✓ Libiconv_jll 950.1 ms ✓ Libffi_jll 963.6 ms ✓ isoband_jll 993.0 ms ✓ OpenSpecFun_jll 977.9 ms ✓ Libuuid_jll 950.8 ms ✓ FriBidi_jll 964.1 ms ✓ OpenBLASConsistentFPCSR_jll 11799.7 ms ✓ StaticArrays 13030.6 ms ✓ SIMD 14072.6 ms ✓ Parsers 2643.0 ms ✓ DataStructures 1560.8 ms ✓ FilePathsBase 3473.9 ms ✓ ChainRulesCore 1442.7 ms ✓ LinearOperators → LinearOperatorsLDLFactorizationsExt 2818.3 ms ✓ StructArrays 4132.7 ms ✓ ColorVectorSpace 824.6 ms ✓ ColorTypes → StyledStringsExt 6280.9 ms ✓ Colors 979.7 ms ✓ Pixman_jll 985.6 ms ✓ FreeType2_jll 688.1 ms ✓ CodecBzip2 1084.0 ms ✓ Rmath 980.8 ms ✓ OpenEXR_jll 823.3 ms ✓ CRlibm 974.4 ms ✓ libsixel_jll 942.6 ms ✓ libvorbis_jll 1009.3 ms ✓ Xorg_libxcb_jll 985.3 ms ✓ Libtiff_jll 998.1 ms ✓ GettextRuntime_jll 595.8 ms ✓ Isoband 4009.1 ms ✓ SpecialFunctions 920.1 ms ✓ StaticArrays → StaticArraysStatisticsExt 983.4 ms ✓ FillArrays → FillArraysStaticArraysExt 937.2 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 913.9 ms ✓ Adapt → AdaptStaticArraysExt 18006.3 ms ✓ GeometryBasics 16531.0 ms ✓ Automa 2644.5 ms ✓ JSON 1127.8 ms ✓ SortingAlgorithms 3484.5 ms ✓ QuadGK 2408.9 ms ✓ ConstraintTrees 948.4 ms ✓ FilePathsBase → FilePathsBaseMmapExt 2177.2 ms ✓ FilePathsBase → FilePathsBaseTestExt 1096.8 ms ✓ FilePaths 2602.7 ms ✓ ChainRulesCore → ChainRulesCoreSparseArraysExt 635.6 ms ✓ AbstractFFTs → AbstractFFTsChainRulesCoreExt 2426.4 ms ✓ LogExpFunctions → LogExpFunctionsChainRulesCoreExt 991.7 ms ✓ LinearOperators → LinearOperatorsChainRulesCoreExt 2760.4 ms ✓ StaticArrays → StaticArraysChainRulesCoreExt 612.0 ms ✓ StructArrays → StructArraysAdaptExt 913.7 ms ✓ StructArrays → StructArraysSparseArraysExt 2728.0 ms ✓ StructArrays → StructArraysStaticArraysExt 653.0 ms ✓ StructArrays → StructArraysLinearAlgebraExt 3288.6 ms ✓ QOI 39070.9 ms ✓ TiffImages 2585.5 ms ✓ Graphics 874.2 ms ✓ Animations 25438.6 ms ✓ ImageCore 5707.9 ms ✓ ColorSchemes 1282.1 ms ✓ FreeType 1076.9 ms ✓ Fontconfig_jll 3441.1 ms ✓ OpenEXR 4951.1 ms ✓ IntervalArithmetic 969.4 ms ✓ Xorg_libX11_jll 1059.6 ms ✓ Glib_jll 3284.6 ms ✓ SpecialFunctions → SpecialFunctionsChainRulesCoreExt 1436.1 ms ✓ HypergeometricFunctions 914.5 ms ✓ DiffRules 909.4 ms ✓ ColorVectorSpace → SpecialFunctionsExt 9361.5 ms ✓ GridLayoutBase 1792.2 ms ✓ Packing 3663.1 ms ✓ ShaderAbstractions 1944.0 ms ✓ BenchmarkTools 4995.7 ms ✓ JSONFBCModels 2003.4 ms ✓ ColorBrewer 5263.1 ms ✓ StatsBase 4423.2 ms ✓ Interpolations 2813.8 ms ✓ ImageBase 4521.5 ms ✓ PNGFiles 5495.2 ms ✓ Sixel 6091.6 ms ✓ JpegTurbo 12576.4 ms ✓ PlotUtils 5014.3 ms ✓ FreeTypeAbstraction 964.9 ms ✓ IntervalArithmetic → IntervalArithmeticSparseArraysExt 640.6 ms ✓ IntervalArithmetic → IntervalArithmeticIntervalSetsExt 928.5 ms ✓ IntervalArithmetic → IntervalArithmeticLinearAlgebraExt 969.5 ms ✓ Xorg_libXrender_jll 1010.3 ms ✓ Xorg_libXext_jll 3613.7 ms ✓ StatsFuns 6512.3 ms ✓ ForwardDiff 8149.1 ms ✓ FastDifferentiation 726.3 ms ✓ IntervalArithmetic → IntervalArithmeticDiffRulesExt 1318.2 ms ✓ PDMats → StatsBaseExt 2199.9 ms ✓ Interpolations → InterpolationsUnitfulExt 4137.6 ms ✓ ImageAxes 20305.9 ms ✓ MathTeXEngine 5736.8 ms ✓ ExactPredicates 979.0 ms ✓ Libglvnd_jll 1022.3 ms ✓ Cairo_jll 729.0 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 2451.9 ms ✓ StatsFuns → StatsFunsChainRulesCoreExt 1125.3 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 1254.9 ms ✓ Unitful → ForwardDiffExt 2499.5 ms ✓ IntervalArithmetic → IntervalArithmeticForwardDiffExt 57710.1 ms ✓ MathOptInterface 1632.1 ms ✓ Interpolations → InterpolationsForwardDiffExt 6570.1 ms ✓ Distributions 2366.0 ms ✓ ImageMetadata 8504.1 ms ✓ DelaunayTriangulation 1070.1 ms ✓ libwebp_jll 1027.1 ms ✓ HarfBuzz_jll 34525.1 ms ✓ JuMP 9111.8 ms ✓ Tulip 93203.6 ms ✓ Clarabel 2105.7 ms ✓ Distributions → DistributionsTestExt 3931.8 ms ✓ Distributions → DistributionsChainRulesCoreExt 4215.1 ms ✓ Netpbm 4750.4 ms ✓ WebP 1032.0 ms ✓ libass_jll 1008.6 ms ✓ Pango_jll 10200.3 ms ✓ COBREXA 2808.4 ms ✓ KernelDensity 2699.8 ms ✓ ImageIO 1058.2 ms ✓ FFMPEG_jll 3287.3 ms ✓ Cairo 12092.5 ms ✓ DifferentiableMetabolism 278983.7 ms ✓ Makie 252490.8 ms ✓ CairoMakie 270 dependencies successfully precompiled in 1406 seconds. 41 already precompiled. Precompilation completed after 1422.19s ################################################################################ # Testing # Testing DifferentiableMetabolism Test Could not use exact versions of packages in manifest. Re-resolving dependencies Updating `/tmp/jl_XGIDkk/Project.toml` [13f3f980] + CairoMakie v0.15.8 [61c947e1] + Clarabel v0.11.0 [9677e053] + DifferentiableMetabolism v0.5.0 [475c1105] + JSONFBCModels v1.0.1 [6dd1b50a] + Tulip v0.9.8 Updating `/tmp/jl_XGIDkk/Manifest.toml` [14f7f29c] + AMD v0.5.3 [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.4.0 [35492f91] + AdaptivePredicates v1.2.0 [66dad0bd] + AliasTables v1.1.3 [27a7e980] + Animations v0.4.2 [67c07d97] + Automa v1.1.0 [13072b0f] + AxisAlgorithms v1.1.0 [39de3d68] + AxisArrays v0.4.8 [18cc8868] + BaseDirs v1.3.2 [fa961155] + CEnum v0.5.0 [96374032] + CRlibm v1.0.2 [159f3aea] + Cairo v1.1.1 [13f3f980] + CairoMakie v0.15.8 [d360d2e6] + ChainRulesCore v1.26.0 [61c947e1] + Clarabel v0.11.0 [a2cac450] + ColorBrewer v0.4.2 [35d6a980] + ColorSchemes v3.31.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.1 [95dc2771] + ComputePipeline v0.1.6 [d38c429a] + Contour v0.6.3 [9a962f9c] + DataAPI v1.16.0 [e2d170a0] + DataValueInterfaces v1.0.0 [927a84f5] + DelaunayTriangulation v1.6.6 [9677e053] + DifferentiableMetabolism v0.5.0 [31c24e10] + Distributions v0.25.123 [4e289a0a] + EnumX v1.0.6 [429591f6] + ExactPredicates v2.2.9 [411431e0] + Extents v0.1.6 [b86e33f2] + FFTA v0.3.1 [9aa1b823] + FastClosures v0.3.2 [5789e2e9] + FileIO v1.18.0 [8fc22ac5] + FilePaths v0.9.0 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [53c48c17] + FixedPointNumbers v0.8.5 [1fa38f19] + Format v1.3.7 [b38be410] + FreeType v4.1.1 [663a7486] + FreeTypeAbstraction v0.10.8 [14197337] + GenericLinearAlgebra v0.3.19 [5c1252a2] + GeometryBasics v0.5.10 [a2bd30eb] + Graphics v1.1.3 [3955a311] + GridLayoutBase v0.11.2 [42e2da0e] + Grisu v1.0.2 [34004b35] + HypergeometricFunctions v0.3.28 [2803e5a7] + ImageAxes v0.6.12 [c817782e] + ImageBase v0.1.7 [a09fc81d] + ImageCore v0.10.5 [82e4d734] + ImageIO v0.6.9 [bc367c6b] + ImageMetadata v0.9.10 [9b13fd28] + IndirectArrays v1.0.0 [d25df0c9] + Inflate v0.1.5 [18e54dd8] + IntegerMathUtils v0.1.3 [a98d9a8b] + Interpolations v0.16.2 [d1acc4aa] + IntervalArithmetic v1.0.2 [8197267c] + IntervalSets v0.7.13 [3587e190] + InverseFunctions v0.1.17 [f1662d9f] + Isoband v0.1.1 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 ⌅ [682c06a0] ↓ JSON v1.4.0 ⇒ v0.21.4 [475c1105] + JSONFBCModels v1.0.1 [b835a17e] + JpegTurbo v0.1.6 [5ab0869b] + KernelDensity v0.6.11 [ba0b0d4f] + Krylov v0.10.5 [40e66cde] + LDLFactorizations v0.10.1 [b964fa9f] + LaTeXStrings v1.4.0 [8cdb02fc] + LazyModules v0.3.1 [5c8ed15e] + LinearOperators v2.11.0 [ee78f7c6] + Makie v0.24.8 [dbb5928d] + MappedArrays v0.4.3 [0a4f8689] + MathTeXEngine v0.6.7 [e1d29d7a] + Missings v1.2.0 [e94cdb99] + MosaicViews v0.3.4 [46d2c3a1] + MuladdMacro v0.2.4 [f09324ee] + Netpbm v1.1.1 [510215fc] + Observables v0.5.5 [6fe1bfb0] + OffsetArrays v1.17.0 [52e1d378] + OpenEXR v0.3.3 [90014a1f] + PDMats v0.11.37 [f57f5aa1] + PNGFiles v0.4.4 [19eb6ba3] + Packing v0.5.1 [5432bcbf] + PaddedViews v0.5.12 [3bbf5609] + PikaParser v0.6.1 [eebad327] + PkgVersion v0.3.3 [995b91a9] + PlotUtils v1.4.4 [647866c9] + PolygonOps v0.1.2 [27ebfcd6] + Primes v0.5.7 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [bfc457fd] + QDLDL v0.4.1 [4b34888f] + QOI v1.0.2 [10f199a5] + QPSReader v0.2.1 [1fd47b50] + QuadGK v2.11.2 [b3c3ace0] + RangeArrays v0.3.2 [c84ed2f1] + Ratios v0.4.5 [189a3867] + Reexport v1.2.2 [05181044] + RelocatableFolders v1.0.1 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [5eaf0fd0] + RoundingEmulator v0.2.1 [fdea26ae] + SIMD v3.7.2 [6c6a2e73] + Scratch v1.3.0 [65257c39] + ShaderAbstractions v0.5.0 [992d4aef] + Showoff v1.0.3 [73760f76] + SignedDistanceFields v0.4.1 [699a6c99] + SimpleTraits v0.9.5 [45858cf5] + Sixel v0.1.5 [66db9d55] + SnoopPrecompile v1.0.3 [a2af1166] + SortingAlgorithms v1.2.2 [cae243ae] + StackViews v0.1.2 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [09ab397b] + StructArrays v0.7.2 [ec057cc2] - StructUtils v2.6.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [62fd8b95] + TensorCore v0.1.1 [731e570b] + TiffImages v0.11.6 [a759f4b9] + TimerOutputs v0.5.29 [981d1d27] + TriplotBase v0.1.0 [6dd1b50a] + Tulip v0.9.8 [1cfade01] + UnicodeFun v0.4.1 [1986cc42] + Unitful v1.28.0 [e3aaa7dc] + WebP v0.1.3 [efce3f68] + WoodburyMatrices v1.1.0 [4e9b3aee] + CRlibm_jll v1.0.1+0 [83423d85] + Cairo_jll v1.18.5+0 [5ae413db] + EarCut_jll v2.2.4+0 [2e619515] + Expat_jll v2.7.3+0 [b22a6f82] + FFMPEG_jll v8.0.1+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 [59f7168a] + Giflib_jll v5.2.3+0 [7746bdde] + Glib_jll v2.86.2+0 [3b182d85] + Graphite2_jll v1.3.15+0 [2e76f6c2] + HarfBuzz_jll v8.5.1+0 [905a6f67] + Imath_jll v3.2.2+0 [aacddb02] + JpegTurbo_jll v3.1.4+0 [c1c5ebd0] + LAME_jll v3.100.3+0 [88015f11] + LERC_jll v4.0.1+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [dd4b983a] + LZO_jll v2.10.3+0 ⌅ [e9f186c6] + Libffi_jll v3.4.7+0 [7e76a0d4] + Libglvnd_jll v1.7.1+1 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.41.2+0 [89763e89] + Libtiff_jll v4.7.2+0 [38a345b3] + Libuuid_jll v2.41.2+0 [e7412a2a] + Ogg_jll v1.3.6+0 [6cdc7f73] + OpenBLASConsistentFPCSR_jll v0.3.30+0 [18a262bb] + OpenEXR_jll v3.4.4+0 [91d4177d] + Opus_jll v1.6.1+0 [36c8627f] + Pango_jll v1.57.0+0 ⌅ [30392449] + Pixman_jll v0.44.2+0 [f50d1b31] + Rmath_jll v0.5.1+0 [ffd25f8a] + XZ_jll v5.8.2+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 [9a68df92] + isoband_jll v0.2.3+0 [a4ae2306] + libaom_jll v3.13.1+0 [0ac62f75] + libass_jll v0.17.4+0 [f638f0a6] + libfdk_aac_jll v2.0.4+0 [b53b4c65] + libpng_jll v1.6.54+0 [075b6546] + libsixel_jll v1.10.5+0 [f27f6e37] + libvorbis_jll v1.3.8+0 [c5f90fcd] + libwebp_jll v1.6.0+0 ⌅ [1270edf5] + x264_jll v10164.0.1+0 [dfaa095f] + x265_jll v4.1.0+0 [8bf52ea8] + CRC32c v1.11.0 [a63ad114] + Mmap v1.11.0 [3fa0cd96] + REPL v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [4607b0f0] + SuiteSparse [efcefdf7] + PCRE2_jll v10.44.0+1 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Test Successfully re-resolved Status `/tmp/jl_XGIDkk/Project.toml` [5a4f3dfa] AbstractFBCModels v1.3.0 [babc4406] COBREXA v2.9.1 [13f3f980] CairoMakie v0.15.8 [61c947e1] Clarabel v0.11.0 [5515826b] ConstraintTrees v1.11.0 [9677e053] DifferentiableMetabolism v0.5.0 [ffbed154] DocStringExtensions v0.9.5 [eb9bf01b] FastDifferentiation v0.4.5 [475c1105] JSONFBCModels v1.0.1 [4076af6c] JuMP v1.29.4 [6dd1b50a] Tulip v0.9.8 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.12.0 [2f01184e] SparseArrays v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_XGIDkk/Manifest.toml` [14f7f29c] AMD v0.5.3 [5a4f3dfa] AbstractFBCModels v1.3.0 [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.4.0 [35492f91] AdaptivePredicates v1.2.0 [66dad0bd] AliasTables v1.1.3 [27a7e980] Animations v0.4.2 [67c07d97] Automa v1.1.0 [13072b0f] AxisAlgorithms v1.1.0 [39de3d68] AxisArrays v0.4.8 [18cc8868] BaseDirs v1.3.2 [6e4b80f9] BenchmarkTools v1.6.3 [fa961155] CEnum v0.5.0 [babc4406] COBREXA v2.9.1 [96374032] CRlibm v1.0.2 [159f3aea] Cairo v1.1.1 [13f3f980] CairoMakie v0.15.8 [d360d2e6] ChainRulesCore v1.26.0 [61c947e1] Clarabel v0.11.0 [523fee87] CodecBzip2 v0.8.5 [944b1d66] CodecZlib v0.7.8 [a2cac450] ColorBrewer v0.4.2 [35d6a980] ColorSchemes v3.31.0 [3da002f7] ColorTypes v0.12.1 [c3611d14] ColorVectorSpace v0.11.0 [5ae59095] Colors v0.13.1 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [95dc2771] ComputePipeline v0.1.6 [5515826b] ConstraintTrees v1.11.0 [187b0558] ConstructionBase v1.6.0 [d38c429a] Contour v0.6.3 [9a962f9c] DataAPI v1.16.0 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [927a84f5] DelaunayTriangulation v1.6.6 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [9677e053] DifferentiableMetabolism v0.5.0 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.6 [429591f6] ExactPredicates v2.2.9 [e2ba6199] ExprTools v0.1.10 [411431e0] Extents v0.1.6 [b86e33f2] FFTA v0.3.1 [9aa1b823] FastClosures v0.3.2 [eb9bf01b] FastDifferentiation v0.4.5 [5789e2e9] FileIO v1.18.0 [8fc22ac5] FilePaths v0.9.0 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [53c48c17] FixedPointNumbers v0.8.5 [1fa38f19] Format v1.3.7 [f6369f11] ForwardDiff v1.3.2 [b38be410] FreeType v4.1.1 [663a7486] FreeTypeAbstraction v0.10.8 [14197337] GenericLinearAlgebra v0.3.19 [5c1252a2] GeometryBasics v0.5.10 [a2bd30eb] Graphics v1.1.3 [3955a311] GridLayoutBase v0.11.2 [42e2da0e] Grisu v1.0.2 [34004b35] HypergeometricFunctions v0.3.28 [2803e5a7] ImageAxes v0.6.12 [c817782e] ImageBase v0.1.7 [a09fc81d] ImageCore v0.10.5 [82e4d734] ImageIO v0.6.9 [bc367c6b] ImageMetadata v0.9.10 [9b13fd28] IndirectArrays v1.0.0 [d25df0c9] Inflate v0.1.5 [18e54dd8] IntegerMathUtils v0.1.3 [a98d9a8b] Interpolations v0.16.2 [d1acc4aa] IntervalArithmetic v1.0.2 [8197267c] IntervalSets v0.7.13 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.6 [f1662d9f] Isoband v0.1.1 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 ⌅ [682c06a0] JSON v0.21.4 [475c1105] JSONFBCModels v1.0.1 [b835a17e] JpegTurbo v0.1.6 [4076af6c] JuMP v1.29.4 [5ab0869b] KernelDensity v0.6.11 [ba0b0d4f] Krylov v0.10.5 [40e66cde] LDLFactorizations v0.10.1 [b964fa9f] LaTeXStrings v1.4.0 [8cdb02fc] LazyModules v0.3.1 [5c8ed15e] LinearOperators v2.11.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [ee78f7c6] Makie v0.24.8 [dbb5928d] MappedArrays v0.4.3 [b8f27783] MathOptInterface v1.49.0 [0a4f8689] MathTeXEngine v0.6.7 [e1d29d7a] Missings v1.2.0 [e94cdb99] MosaicViews v0.3.4 [46d2c3a1] MuladdMacro v0.2.4 [d8a4904e] MutableArithmetics v1.6.7 [77ba4419] NaNMath v1.1.3 [f09324ee] Netpbm v1.1.1 [510215fc] Observables v0.5.5 [6fe1bfb0] OffsetArrays v1.17.0 [52e1d378] OpenEXR v0.3.3 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [f57f5aa1] PNGFiles v0.4.4 [19eb6ba3] Packing v0.5.1 [5432bcbf] PaddedViews v0.5.12 [69de0a69] Parsers v2.8.3 [3bbf5609] PikaParser v0.6.1 [eebad327] PkgVersion v0.3.3 [995b91a9] PlotUtils v1.4.4 [647866c9] PolygonOps v0.1.2 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [27ebfcd6] Primes v0.5.7 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [bfc457fd] QDLDL v0.4.1 [4b34888f] QOI v1.0.2 [10f199a5] QPSReader v0.2.1 [1fd47b50] QuadGK v2.11.2 [b3c3ace0] RangeArrays v0.3.2 [c84ed2f1] Ratios v0.4.5 [189a3867] Reexport v1.2.2 [05181044] RelocatableFolders v1.0.1 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [5eaf0fd0] RoundingEmulator v0.2.1 [7e49a35a] RuntimeGeneratedFunctions v0.5.16 [fdea26ae] SIMD v3.7.2 [6c6a2e73] Scratch v1.3.0 [65257c39] ShaderAbstractions v0.5.0 [992d4aef] Showoff v1.0.3 [73760f76] SignedDistanceFields v0.4.1 [699a6c99] SimpleTraits v0.9.5 [45858cf5] Sixel v0.1.5 [66db9d55] SnoopPrecompile v1.0.3 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [860ef19b] StableRNGs v1.0.4 [cae243ae] StackViews v0.1.2 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [09ab397b] StructArrays v0.7.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [62fd8b95] TensorCore v0.1.1 [731e570b] TiffImages v0.11.6 [a759f4b9] TimerOutputs v0.5.29 [3bb67fe8] TranscodingStreams v0.11.3 [981d1d27] TriplotBase v0.1.0 [6dd1b50a] Tulip v0.9.8 [1cfade01] UnicodeFun v0.4.1 [1986cc42] Unitful v1.28.0 [e3aaa7dc] WebP v0.1.3 [efce3f68] WoodburyMatrices v1.1.0 [6e34b625] Bzip2_jll v1.0.9+0 [4e9b3aee] CRlibm_jll v1.0.1+0 [83423d85] Cairo_jll v1.18.5+0 [5ae413db] EarCut_jll v2.2.4+0 [2e619515] Expat_jll v2.7.3+0 [b22a6f82] FFMPEG_jll v8.0.1+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 [59f7168a] Giflib_jll v5.2.3+0 [7746bdde] Glib_jll v2.86.2+0 [3b182d85] Graphite2_jll v1.3.15+0 [2e76f6c2] HarfBuzz_jll v8.5.1+0 [905a6f67] Imath_jll v3.2.2+0 [aacddb02] JpegTurbo_jll v3.1.4+0 [c1c5ebd0] LAME_jll v3.100.3+0 [88015f11] LERC_jll v4.0.1+0 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [dd4b983a] LZO_jll v2.10.3+0 ⌅ [e9f186c6] Libffi_jll v3.4.7+0 [7e76a0d4] Libglvnd_jll v1.7.1+1 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.41.2+0 [89763e89] Libtiff_jll v4.7.2+0 [38a345b3] Libuuid_jll v2.41.2+0 [e7412a2a] Ogg_jll v1.3.6+0 [6cdc7f73] OpenBLASConsistentFPCSR_jll v0.3.30+0 [18a262bb] OpenEXR_jll v3.4.4+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [91d4177d] Opus_jll v1.6.1+0 [36c8627f] Pango_jll v1.57.0+0 ⌅ [30392449] Pixman_jll v0.44.2+0 [f50d1b31] Rmath_jll v0.5.1+0 [ffd25f8a] XZ_jll v5.8.2+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] 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upgrading. Testing Running tests... ------------------------------------------------------------- Clarabel.jl v0.11.0 - Clever Acronym (c) Paul Goulart University of Oxford, 2022 ------------------------------------------------------------- problem: variables = 6 constraints = 19 nnz(P) = 6 nnz(A) = 27 cones (total) = 2 : Zero = 1, numel = 5 : Nonnegative = 1, numel = 14 settings: linear algebra: direct / qdldl, precision: 64 bit (1 thread) max iter = 200, time limit = Inf, max step = 0.990 tol_feas = 1.0e-08, tol_gap_abs = 1.0e-08, tol_gap_rel = 1.0e-08, static reg : on, ϵ1 = 1.0e-08, ϵ2 = 4.9e-32 dynamic reg: on, ϵ = 1.0e-13, δ = 2.0e-07 iter refine: on, reltol = 1.0e-13, abstol = 1.0e-12, max iter = 10, stop ratio = 5.0 equilibrate: on, min_scale = 1.0e-04, max_scale = 1.0e+04 max iter = 10 iter pcost dcost gap pres dres k/t μ step --------------------------------------------------------------------------------------------- 0 8.1662e+04 -2.1285e+06 2.71e+01 1.72e-01 1.29e-16 1.00e+00 4.10e+05 ------ 1 9.3859e+01 -2.2566e+05 2.41e+03 7.83e-03 2.99e-16 1.13e+04 2.44e+04 9.90e-01 2 1.7010e+01 -1.8788e+04 1.11e+03 6.26e-04 2.05e-16 1.35e+02 2.42e+03 9.03e-01 3 1.4683e+01 -5.1608e+02 3.61e+01 1.83e-05 3.47e-15 2.33e+01 9.30e+01 9.73e-01 4 1.4253e+01 -1.4370e+01 2.01e+00 9.86e-07 5.56e-15 1.25e+00 5.05e+00 9.46e-01 5 1.1230e+01 5.0752e+00 1.21e+00 9.61e-08 4.89e-16 2.62e-01 9.65e-01 9.90e-01 6 1.1008e+01 1.0644e+01 3.42e-02 1.11e-09 6.40e-17 1.09e-02 5.32e-02 9.90e-01 7 1.1000e+01 1.0982e+01 1.68e-03 1.16e-11 7.68e-17 5.39e-04 2.50e-03 9.90e-01 8 1.1000e+01 1.1000e+01 2.14e-05 1.08e-13 5.50e-12 6.88e-06 3.17e-05 9.90e-01 9 1.1000e+01 1.1000e+01 2.15e-07 1.05e-15 1.14e-13 6.91e-08 3.18e-07 9.90e-01 10 1.1000e+01 1.1000e+01 2.15e-09 5.09e-17 1.87e-15 6.91e-10 3.18e-09 9.90e-01 --------------------------------------------------------------------------------------------- Terminated with status = solved solve time = 14.0s ┌ Warning: Assignment to `sens` in soft scope is ambiguous because a global variable by the same name exists: `sens` will be treated as a new local. Disambiguate by using `local sens` to suppress this warning or `global sens` to assign to the existing global variable. └ @ ~/.julia/packages/DifferentiableMetabolism/DNa5J/docs/src/3-parameter-estimation.jl:138 Test Summary: | Pass Total Time DifferentiableMetabolism tests | 56 56 8m53.3s Testing DifferentiableMetabolism tests passed Testing completed after 551.37s PkgEval succeeded after 1994.2s