Package evaluation to test DifferentiableMetabolism on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-19T20:19:59.811 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 7.95s ################################################################################ # Installation # Installing DifferentiableMetabolism... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [9677e053] + DifferentiableMetabolism v0.6.1 Updating `~/.julia/environments/v1.12/Manifest.toml` [5a4f3dfa] + AbstractFBCModels v1.3.0 [babc4406] + COBREXA v2.9.1 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [bbf7d656] + CommonSubexpressions v0.3.1 [5515826b] + ConstraintTrees v1.11.1 [187b0558] + ConstructionBase v1.6.0 [864edb3b] + DataStructures v0.19.5 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.16.0 [9677e053] + DifferentiableMetabolism v0.6.1 [ffbed154] + DocStringExtensions v0.9.5 [e2ba6199] + ExprTools v0.1.10 [eb9bf01b] + FastDifferentiation v0.4.5 [f6369f11] + ForwardDiff v1.4.1 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.8.0 [682c06a0] + JSON v1.6.1 [4076af6c] + JuMP v1.30.1 [2ab3a3ac] + LogExpFunctions v1.0.1 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.51.1 [d8a4904e] + MutableArithmetics v1.8.0 [77ba4419] + NaNMath v1.1.4 ⌅ [bac558e1] + OrderedCollections v1.8.2 [69de0a69] + Parsers v2.8.6 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [7e49a35a] + RuntimeGeneratedFunctions v0.5.19 [276daf66] + SpecialFunctions v2.8.0 [860ef19b] + StableRNGs v1.0.4 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [ec057cc2] + StructUtils v2.8.2 [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 [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 v3.5.6+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 6.26s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/RUPmD/src/julia-1.12/activate_set.jl:78 Precompiling package dependencies... Precompiling packages... 118502.3 ms ✓ Tulip 262468.8 ms ✓ Clarabel 134781.4 ms ✓ DifferentiableMetabolism 3 dependencies successfully precompiled in 533 seconds. 311 already precompiled. 24 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 189 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompilation completed after 548.54s ################################################################################ # Testing # Testing DifferentiableMetabolism Test Could not use exact versions of packages in manifest. Re-resolving dependencies Updating `/tmp/jl_tcS2Z6/Project.toml` [13f3f980] + CairoMakie v0.15.11 [61c947e1] + Clarabel v0.11.1 [9677e053] + DifferentiableMetabolism v0.6.1 [475c1105] + JSONFBCModels v1.0.1 [6dd1b50a] + Tulip v0.9.8 Updating `/tmp/jl_tcS2Z6/Manifest.toml` [14f7f29c] + AMD v0.5.3 [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.6.1 [35492f91] + AdaptivePredicates v1.2.0 [66dad0bd] + AliasTables v1.1.3 [27a7e980] + Animations v0.4.2 [67c07d97] + Automa v1.2.0 [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 v0.15.11 [d360d2e6] + ChainRulesCore v1.26.1 [61c947e1] + Clarabel v0.11.1 [6b39b394] + CodecZstd v0.8.7 [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 [34da2185] + Compat v4.18.1 [95dc2771] + ComputePipeline v0.1.8 [d38c429a] + Contour v0.6.3 [b7a15901] + CoreMath v0.1.0 [9a962f9c] + DataAPI v1.16.0 [e2d170a0] + DataValueInterfaces v1.0.0 [927a84f5] + DelaunayTriangulation v1.6.6 [9677e053] + DifferentiableMetabolism v0.6.1 [31c24e10] + Distributions v0.25.127 [4e289a0a] + EnumX v1.0.7 [429591f6] + ExactPredicates v2.2.9 [b86e33f2] + FFTA v0.3.1 [9aa1b823] + FastClosures v0.3.2 [5789e2e9] + FileIO v1.19.0 [8fc22ac5] + FilePaths v0.9.0 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 ⌅ [53c48c17] + FixedPointNumbers v0.8.6 [1fa38f19] + Format v1.3.7 [b38be410] + FreeType v4.1.1 [663a7486] + FreeTypeAbstraction v0.10.8 ⌅ [14197337] + GenericLinearAlgebra v0.3.19 [5c1252a2] + GeometryBasics v0.5.11 [a2bd30eb] + Graphics v1.1.3 [3955a311] + GridLayoutBase v0.11.2 [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 v0.16.3 [d1acc4aa] + IntervalArithmetic v1.0.9 [8197267c] + IntervalSets v0.7.14 [3587e190] + InverseFunctions v0.1.17 [f1662d9f] + Isoband v0.1.1 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 ⌅ [682c06a0] ↓ JSON v1.6.1 ⇒ v0.21.4 [475c1105] + JSONFBCModels v1.0.1 [b835a17e] + JpegTurbo v0.1.6 [5ab0869b] + KernelDensity v0.6.12 [ba0b0d4f] + Krylov v0.10.6 [40e66cde] + LDLFactorizations v0.10.2 [b964fa9f] + LaTeXStrings v1.4.0 [8cdb02fc] + LazyModules v0.3.1 [5c8ed15e] + LinearOperators v2.14.1 ⌅ [2ab3a3ac] ↓ LogExpFunctions v1.0.1 ⇒ v0.3.29 [ee78f7c6] + Makie v0.24.11 [dbb5928d] + MappedArrays v0.4.3 [0a4f8689] + MathTeXEngine v0.6.9 [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 v0.4.5 [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 v1.4.0 [bfc457fd] + QDLDL v0.4.1 [4b34888f] + QOI v1.0.2 [10f199a5] + QPSReader v0.2.1 [1fd47b50] + QuadGK v2.11.3 [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 [73760f76] + SignedDistanceFields v0.4.1 [699a6c99] + SimpleTraits v0.9.6 [45858cf5] + Sixel v0.1.5 [66db9d55] + SnoopPrecompile v1.0.3 [a2af1166] + SortingAlgorithms v1.2.2 [cae243ae] + StackViews v0.1.2 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.12 ⌅ [4c63d2b9] + StatsFuns v1.5.2 [09ab397b] + StructArrays v0.7.3 [ec057cc2] - StructUtils v2.8.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [62fd8b95] + TensorCore v0.1.1 [731e570b] + TiffImages v0.11.9 [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 v1.18.7+0 [a38c48d9] + CoreMath_jll v0.1.0+0 [5ae413db] + EarCut_jll v2.2.4+0 [2e619515] + Expat_jll v2.8.1+0 [b22a6f82] + FFMPEG_jll v8.1.0+0 [a3f928ae] + Fontconfig_jll v2.17.1+0 [d7e528f0] + FreeType2_jll v2.14.3+1 [559328eb] + FriBidi_jll v1.0.17+0 ⌅ [b0724c58] + GettextRuntime_jll v0.22.4+0 [59f7168a] + Giflib_jll v5.2.3+0 [7746bdde] + Glib_jll v2.86.3+0 [3b182d85] + Graphite2_jll v1.3.16+0 [2e76f6c2] + HarfBuzz_jll v8.5.1+0 [905a6f67] + Imath_jll v3.2.2+0 [aacddb02] + JpegTurbo_jll v3.1.5+0 [c1c5ebd0] + LAME_jll v3.100.3+0 [88015f11] + LERC_jll v4.1.0+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+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 v2.42.0+0 [89763e89] + Libtiff_jll v4.7.2+0 [38a345b3] + Libuuid_jll v2.42.0+0 [e7412a2a] + Ogg_jll v1.3.6+0 [6cdc7f73] + OpenBLASConsistentFPCSR_jll v0.3.33+0 [18a262bb] + OpenEXR_jll v3.4.12+0 [91d4177d] + Opus_jll v1.6.1+0 [36c8627f] + Pango_jll v1.57.1+0 [30392449] + Pixman_jll v0.46.4+0 [f50d1b31] + Rmath_jll v0.5.1+0 [ffd25f8a] + XZ_jll v5.8.3+0 [4f6342f7] + Xorg_libX11_jll v1.8.13+0 [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0 [a3789734] + Xorg_libXdmcp_jll v1.1.6+0 [1082639a] + Xorg_libXext_jll v1.3.8+0 [d091e8ba] + Xorg_libXfixes_jll v6.0.2+0 [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.19.0+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 v3.13.3+0 [0ac62f75] + libass_jll v0.17.4+0 [8e53e030] + libdrm_jll v2.4.125+1 [f638f0a6] + libfdk_aac_jll v2.0.4+0 [b53b4c65] + libpng_jll v1.6.58+0 [075b6546] + libsixel_jll v1.10.5+0 [9a156e7d] + libva_jll v2.23.0+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_tcS2Z6/Project.toml` [5a4f3dfa] AbstractFBCModels v1.3.0 [babc4406] COBREXA v2.9.1 [13f3f980] CairoMakie v0.15.11 [61c947e1] Clarabel v0.11.1 [5515826b] ConstraintTrees v1.11.1 [9677e053] DifferentiableMetabolism v0.6.1 [ffbed154] DocStringExtensions v0.9.5 [eb9bf01b] FastDifferentiation v0.4.5 [475c1105] JSONFBCModels v1.0.1 [4076af6c] JuMP v1.30.1 [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_tcS2Z6/Manifest.toml` [14f7f29c] AMD v0.5.3 [5a4f3dfa] AbstractFBCModels v1.3.0 [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.6.1 [35492f91] AdaptivePredicates v1.2.0 [66dad0bd] AliasTables v1.1.3 [27a7e980] Animations v0.4.2 [67c07d97] Automa v1.2.0 [13072b0f] AxisAlgorithms v1.1.0 [39de3d68] AxisArrays v0.4.8 [18cc8868] BaseDirs v1.3.2 [fa961155] CEnum v0.5.0 [babc4406] COBREXA v2.9.1 [96374032] CRlibm v1.0.2 [159f3aea] Cairo v1.1.1 [13f3f980] CairoMakie v0.15.11 [d360d2e6] ChainRulesCore v1.26.1 [61c947e1] Clarabel v0.11.1 [523fee87] CodecBzip2 v0.8.5 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.7 [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 v0.1.8 [5515826b] ConstraintTrees v1.11.1 [187b0558] ConstructionBase v1.6.0 [d38c429a] Contour v0.6.3 [b7a15901] CoreMath v0.1.0 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.5 [e2d170a0] DataValueInterfaces v1.0.0 [927a84f5] DelaunayTriangulation v1.6.6 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.16.0 [9677e053] DifferentiableMetabolism v0.6.1 [31c24e10] Distributions v0.25.127 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.7 [429591f6] ExactPredicates v2.2.9 [e2ba6199] ExprTools v0.1.10 [b86e33f2] FFTA v0.3.1 [9aa1b823] FastClosures v0.3.2 [eb9bf01b] FastDifferentiation v0.4.5 [5789e2e9] FileIO v1.19.0 [8fc22ac5] FilePaths v0.9.0 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 ⌅ [53c48c17] FixedPointNumbers v0.8.6 [1fa38f19] Format v1.3.7 [f6369f11] ForwardDiff v1.4.1 [b38be410] FreeType v4.1.1 [663a7486] FreeTypeAbstraction v0.10.8 ⌅ [14197337] GenericLinearAlgebra v0.3.19 [5c1252a2] GeometryBasics v0.5.11 [a2bd30eb] Graphics v1.1.3 [3955a311] GridLayoutBase v0.11.2 [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 v0.16.3 [d1acc4aa] IntervalArithmetic v1.0.9 [8197267c] IntervalSets v0.7.14 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.6 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Xorg_libpciaccess_jll v0.19.0+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 v3.13.3+0 [0ac62f75] libass_jll v0.17.4+0 [8e53e030] libdrm_jll v2.4.125+1 [f638f0a6] libfdk_aac_jll v2.0.4+0 [b53b4c65] libpng_jll v1.6.58+0 [075b6546] libsixel_jll v1.10.5+0 [9a156e7d] libva_jll v2.23.0+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 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [8bf52ea8] CRC32c 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 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.1 [de0858da] Printf v1.11.0 [3fa0cd96] REPL 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 v8.15.0+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 v3.5.6+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 v5.15.0+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. Testing Running tests... Precompiling packages... 17082.2 ms ✓ Tulip 1 dependency successfully precompiled in 18 seconds. 67 already precompiled. 53 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Bzip2_jll, CodecBzip2, CodecZlib, CommonSubexpressions, CompilerSupportLibraries_jll, Dates, DiffResults, DiffRules, DocStringExtensions, Downloads, ExprTools, ForwardDiff, InteractiveUtils, IrrationalConstants, JLLWrappers, JSON, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibSSH2_jll, LogExpFunctions, Logging, MacroTools, Markdown, MathOptInterface, Mmap, MozillaCACerts_jll, MutableArithmetics, NaNMath, NetworkOptions, OpenLibm_jll, OpenSSL_jll, OpenSpecFun_jll, OrderedCollections, Parsers, PrecompileTools, Preferences, Printf, Serialization, SparseArrays, SpecialFunctions, StaticArraysCore, StyledStrings, SuiteSparse_jll, TOML, Test, TranscodingStreams, UUIDs, Unicode, Zlib_jll and nghttp2_jll). Restart julia to access the new versions. Otherwise, 14 dependents of these packages may trigger further precompilation to work with the unexpected versions. ------------------------------------------------------------- Clarabel.jl v0.11.1 - 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 1.13e-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 1.40e-16 1.35e+02 2.42e+03 9.03e-01 3 1.4683e+01 -5.1608e+02 3.61e+01 1.83e-05 1.50e-15 2.33e+01 9.30e+01 9.73e-01 4 1.4253e+01 -1.4370e+01 2.01e+00 9.86e-07 3.34e-15 1.25e+00 5.05e+00 9.46e-01 5 1.1230e+01 5.0752e+00 1.21e+00 9.61e-08 2.77e-16 2.62e-01 9.65e-01 9.90e-01 6 1.1008e+01 1.0644e+01 3.42e-02 1.11e-09 4.90e-17 1.09e-02 5.32e-02 9.90e-01 7 1.1000e+01 1.0982e+01 1.68e-03 1.16e-11 9.59e-17 5.39e-04 2.50e-03 9.90e-01 8 1.1000e+01 1.1000e+01 2.14e-05 1.08e-13 6.88e-12 6.88e-06 3.17e-05 9.90e-01 9 1.1000e+01 1.1000e+01 2.15e-07 1.09e-15 1.33e-13 6.91e-08 3.18e-07 9.90e-01 10 1.1000e+01 1.1000e+01 2.15e-09 5.09e-17 2.27e-15 6.91e-10 3.18e-09 9.90e-01 --------------------------------------------------------------------------------------------- Terminated with status = solved solve time = 20.4s Precompiling packages... 8115.1 ms ✓ JSONFBCModels 1 dependency successfully precompiled in 8 seconds. 33 already precompiled. 32 dependencies precompiled but different versions are currently loaded (AbstractFBCModels, ArgTools, Base64, Dates, DocStringExtensions, Downloads, InteractiveUtils, JSON, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibSSH2_jll, Logging, Markdown, Mmap, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Parsers, PrecompileTools, Preferences, Printf, Serialization, SparseArrays, StyledStrings, SuiteSparse_jll, TOML, Test, UUIDs, Unicode, Zlib_jll and nghttp2_jll). Restart julia to access the new versions. Otherwise, 2 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 3248.6 ms ✓ LLVMOpenMP_jll 1647.4 ms ✓ libsixel_jll 8333.2 ms ✓ IntervalArithmetic 63867.0 ms ✓ TiffImages 8414.1 ms ✓ WebP 4644.2 ms ✓ StructArrays → StructArraysStaticArraysExt 2350.3 ms ✓ ColorBrewer 32434.3 ms ✓ MathTeXEngine 10524.4 ms ✓ Distributions 10333.4 ms ✓ Sixel 1676.6 ms ✓ IntervalArithmetic → IntervalArithmeticSparseArraysExt 1217.3 ms ✓ IntervalArithmetic → IntervalArithmeticIntervalSetsExt 1313.0 ms ✓ IntervalArithmetic → IntervalArithmeticIrrationalConstantsExt 1531.6 ms ✓ IntervalArithmetic → IntervalArithmeticLinearAlgebraExt 7677.6 ms ✓ Distributions → DistributionsChainRulesCoreExt 9564.1 ms ✓ ExactPredicates 13830.6 ms ✓ KernelDensity 13870.3 ms ✓ DelaunayTriangulation 611214.6 ms ✓ Makie 354998.7 ms ✓ CairoMakie 20 dependencies successfully precompiled in 1167 seconds. 252 already precompiled. 56 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Bzip2_jll, CompilerSupportLibraries_jll, ConstructionBase, ConstructionBase → ConstructionBaseLinearAlgebraExt, ConstructionBase → ConstructionBaseStaticArraysExt, DataStructures, Dates, Distributed, DocStringExtensions, Downloads, InteractiveUtils, IrrationalConstants, JLLWrappers, JSON, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, LogExpFunctions, Logging, MacroTools, Markdown, Mmap, MozillaCACerts_jll, NaNMath, NetworkOptions, OpenLibm_jll, OpenSSL_jll, OpenSpecFun_jll, OrderedCollections, Parsers, Pkg, PrecompileTools, Preferences, Printf, Serialization, SparseArrays, SpecialFunctions, StableRNGs, StaticArrays, StaticArraysCore, StyledStrings, SuiteSparse, SuiteSparse_jll, TOML, Tar, TranscodingStreams, UUIDs, Unicode, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 164 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 5186.1 ms ✓ Unitful → ForwardDiffExt 1 dependency successfully precompiled in 6 seconds. 23 already precompiled. 23 dependencies precompiled but different versions are currently loaded (CommonSubexpressions, CompilerSupportLibraries_jll, Dates, DiffResults, DiffRules, DocStringExtensions, ForwardDiff, IrrationalConstants, JLLWrappers, LogExpFunctions, MacroTools, NaNMath, OpenLibm_jll, OpenSpecFun_jll, Preferences, Printf, SpecialFunctions, StaticArraysCore, TOML, Unicode, Unitful, Unitful → NaNMathExt and Unitful → PrintfExt). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 3862.6 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 6 seconds. 48 already precompiled. 48 dependencies precompiled but different versions are currently loaded (AliasTables, Base64, CompilerSupportLibraries_jll, DataAPI, DataStructures, Dates, Distributions, DocStringExtensions, FillArrays, FillArrays → FillArraysPDMatsExt, FillArrays → FillArraysSparseArraysExt, FillArrays → FillArraysStatisticsExt, HypergeometricFunctions, InteractiveUtils, IrrationalConstants, JLLWrappers, JuliaSyntaxHighlighting, LogExpFunctions, Logging, Markdown, Missings, OpenLibm_jll, OpenSpecFun_jll, OrderedCollections, PDMats, PDMats → StatsBaseExt, Preferences, Printf, PtrArrays, QuadGK, Reexport, Rmath, Rmath_jll, Serialization, SortingAlgorithms, SparseArrays, SpecialFunctions, Statistics, Statistics → SparseArraysExt, StatsAPI, StatsBase, StatsFuns, StyledStrings, SuiteSparse, SuiteSparse_jll, TOML, Test and Unicode). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 2386.7 ms ✓ Interpolations → InterpolationsForwardDiffExt 1 dependency successfully precompiled in 3 seconds. 47 already precompiled. 46 dependencies precompiled but different versions are currently loaded (Adapt, Adapt → AdaptSparseArraysExt, Adapt → AdaptStaticArraysExt, AxisAlgorithms, ChainRulesCore, ChainRulesCore → ChainRulesCoreSparseArraysExt, CommonSubexpressions, Compat, Compat → CompatLinearAlgebraExt, CompilerSupportLibraries_jll, Dates, DiffResults, DiffRules, Distributed, DocStringExtensions, ForwardDiff, ForwardDiff → ForwardDiffStaticArraysExt, Interpolations, IrrationalConstants, JLLWrappers, LogExpFunctions, LogExpFunctions → LogExpFunctionsChainRulesCoreExt, MacroTools, Mmap, NaNMath, OffsetArrays, OffsetArrays → OffsetArraysAdaptExt, OpenLibm_jll, OpenSpecFun_jll, PrecompileTools, Preferences, Printf, Ratios, Requires, Serialization, SparseArrays, SpecialFunctions, SpecialFunctions → SpecialFunctionsChainRulesCoreExt, StaticArrays, StaticArrays → StaticArraysChainRulesCoreExt, StaticArraysCore, SuiteSparse_jll, TOML, UUIDs, Unicode and WoodburyMatrices). Restart julia to access the new versions. Otherwise, 2 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 820.6 ms ✓ IntervalArithmetic → IntervalArithmeticDiffRulesExt 3883.4 ms ✓ IntervalArithmetic → IntervalArithmeticForwardDiffExt 2 dependencies successfully precompiled in 5 seconds. 50 already precompiled. 50 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, CRlibm, CRlibm_jll, CommonSubexpressions, CompilerSupportLibraries_jll, CoreMath, CoreMath_jll, Dates, DiffResults, DiffRules, DocStringExtensions, Downloads, ForwardDiff, IntervalArithmetic, IntervalArithmetic → IntervalArithmeticIrrationalConstantsExt, IntervalArithmetic → IntervalArithmeticLinearAlgebraExt, IrrationalConstants, JLLWrappers, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, LogExpFunctions, Logging, MacroTools, Markdown, MozillaCACerts_jll, NaNMath, NetworkOptions, OpenBLASConsistentFPCSR_jll, OpenLibm_jll, OpenSSL_jll, OpenSpecFun_jll, Pkg, Preferences, Printf, RoundingEmulator, SpecialFunctions, StaticArraysCore, StyledStrings, TOML, Tar, UUIDs, Unicode, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 2 dependents of these packages may trigger further precompilation to work with the unexpected versions. ┌ 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/kQtJf/docs/src/3-parameter-estimation.jl:138 ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 55 running 1 of 1 signal (10): User defined signal 1 _ZL18computeForAddCarryRKN4llvm9KnownBitsES2_bb at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm9KnownBits16computeForAddSubEbbRKS0_S0_ at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZNK4llvm12SelectionDAG16computeKnownBitsENS_7SDValueERKNS_5APIntEj at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZNK4llvm12SelectionDAG16computeKnownBitsENS_7SDValueEj at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZNK4llvm17X86TargetLowering29computeKnownBitsForTargetNodeENS_7SDValueERNS_9KnownBitsERKNS_5APIntERKNS_12SelectionDAGEj at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZNK4llvm12SelectionDAG16computeKnownBitsENS_7SDValueERKNS_5APIntEj at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZNK4llvm12SelectionDAG16computeKnownBitsENS_7SDValueERKNS_5APIntEj at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZNK4llvm12SelectionDAG16computeKnownBitsENS_7SDValueERKNS_5APIntEj at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZNK4llvm12SelectionDAG18ComputeNumSignBitsENS_7SDValueERKNS_5APIntEj at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZNK4llvm12SelectionDAG18ComputeNumSignBitsENS_7SDValueERKNS_5APIntEj at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZNK4llvm12SelectionDAG18ComputeNumSignBitsENS_7SDValueEj at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm16SelectionDAGISel22ComputeLiveOutVRegInfoEv at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm16SelectionDAGISel17CodeGenAndEmitDAGEv at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm16SelectionDAGISel20SelectAllBasicBlocksERKNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm16SelectionDAGISel20runOnMachineFunctionERNS_15MachineFunctionE.part.0 at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN12_GLOBAL__N_115X86DAGToDAGISel20runOnMachineFunctionERN4llvm15MachineFunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm19MachineFunctionPass13runOnFunctionERNS_8FunctionE.part.0 at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm13FPPassManager13runOnFunctionERNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm13FPPassManager11runOnModuleERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm6legacy15PassManagerImpl3runERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm3orc14SimpleCompilerclERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) operator() at /source/src/jitlayers.cpp:1561 addModule at /source/src/jitlayers.cpp:2044 jl_compile_codeinst_now at /source/src/jitlayers.cpp:626 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:824 jl_compile_method_internal at /source/src/gf.c:3528 _jl_invoke at /source/src/gf.c:4006 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:689 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 Test Summary: | Pass Total Time DifferentiableMetabolism tests | 56 56 34m51.8s eval at ./boot.jl:489 include_string at ./loading.jl:2873 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 _include at ./loading.jl:2933 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_53184.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:689 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2873 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 _include at ./loading.jl:2933 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_53184.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:689 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 exec_options at ./client.jl:283 _start at ./client.jl:550 jfptr__start_64964.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7effeea18249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== Testing DifferentiableMetabolism tests passed Testing completed after 2118.62s PkgEval terminated after 2708.22s: test duration exceeded the time limit