Package evaluation to test ElementaryFluxModes on Julia 1.14.0-DEV.2028 (45a2de3f7a*) started at 2026-04-12T20:39:59.647 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 16.03s ################################################################################ # Installation # Installing ElementaryFluxModes... Resolving package versions... Installed Bzip2_jll ───────────────── v1.0.9+0 Installed MacroTools ──────────────── v0.5.16 Installed DiffResults ─────────────── v1.1.0 Installed CodecZlib ───────────────── v0.7.8 Installed ExprTools ───────────────── v0.1.10 Installed RuntimeGeneratedFunctions ─ v0.5.18 Installed DataStructures ──────────── v0.19.4 Installed ForwardDiff ─────────────── v1.3.3 Installed OrderedCollections ──────── v1.8.1 Installed TranscodingStreams ──────── v0.11.3 Installed CommonSubexpressions ────── v0.3.1 Installed Statistics ──────────────── v1.11.1 Installed Compat ──────────────────── v4.18.1 Installed ElementaryFluxModes ─────── v1.0.0 Installed StaticArraysCore ────────── v1.4.4 Installed PrecompileTools ─────────── v1.3.3 Installed StructUtils ─────────────── v2.7.1 Installed NaNMath ─────────────────── v1.1.3 Installed IrrationalConstants ─────── v0.2.6 Installed CodecBzip2 ──────────────── v0.8.5 Installed StaticArrays ────────────── v1.9.18 Installed OpenSpecFun_jll ─────────── v0.5.6+0 Installed Parsers ─────────────────── v2.8.3 Installed DiffRules ───────────────── v1.15.1 Installed LogExpFunctions ─────────── v0.3.29 Installed JSON ────────────────────── v1.5.0 Installed FastDifferentiation ─────── v0.4.5 Installed SpecialFunctions ────────── v2.7.2 Installed MutableArithmetics ──────── v1.7.1 Installed RowEchelon ──────────────── v0.2.1 Installed JLLWrappers ─────────────── v1.7.1 Installed BenchmarkTools ──────────── v1.7.0 Installed JuMP ────────────────────── v1.30.0 Installed Preferences ─────────────── v1.5.2 Installed DocStringExtensions ─────── v0.9.5 Installed MathOptInterface ────────── v1.50.1 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Bzip2 503.5 KiB Updating `~/.julia/environments/v1.14/Project.toml` [89210afb] + ElementaryFluxModes v1.0.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [6e4b80f9] + BenchmarkTools v1.7.0 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.18.1 [864edb3b] + DataStructures v0.19.4 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [ffbed154] + DocStringExtensions v0.9.5 [89210afb] + ElementaryFluxModes v1.0.0 [e2ba6199] + ExprTools v0.1.10 [eb9bf01b] + FastDifferentiation v0.4.5 [f6369f11] + ForwardDiff v1.3.3 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.5.0 [4076af6c] + JuMP v1.30.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.50.1 [d8a4904e] + MutableArithmetics v1.7.1 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.2 [af85af4c] + RowEchelon v0.2.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.18 [276daf66] + SpecialFunctions v2.7.2 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [ec057cc2] + StructUtils v2.7.1 [3bb67fe8] + TranscodingStreams v0.11.3 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf v1.11.0 [9abbd945] + Profile v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 9.93s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 4998.1 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/RUPmD/src/julia-1.13/activate_set.jl:78 Precompiling package dependencies... Precompiling project... 4429.0 ms ✓ MacroTools 1229.4 ms ✓ Reexport 1073.4 ms ✓ MappedArrays 999.5 ms ✓ TensorCore 1247.5 ms ✓ ConstructionBase 2335.7 ms ✓ IrrationalConstants 924.3 ms ✓ DataValueInterfaces 922.6 ms ✓ StatsAPI 2476.0 ms ✓ Format 1086.3 ms ✓ Observables 997.8 ms ✓ RoundingEmulator 897.8 ms ✓ PolygonOps 1421.0 ms ✓ IterTools 1133.4 ms ✓ IntervalSets 946.6 ms ✓ CEnum 1109.4 ms ✓ Inflate 1046.6 ms ✓ Contour 1423.6 ms ✓ TranscodingStreams 906.1 ms ✓ LaTeXStrings 1219.3 ms ✓ Statistics 1068.2 ms ✓ StaticArraysCore 980.2 ms ✓ StableRNGs 3043.8 ms ✓ AdaptivePredicates 880.3 ms ✓ RowEchelon 871.0 ms ✓ PtrArrays 1375.3 ms ✓ Grisu 916.0 ms ✓ DataAPI 1066.3 ms ✓ LazyModules 967.5 ms ✓ InverseFunctions 1207.8 ms ✓ AbstractTrees 886.0 ms ✓ MuladdMacro 1184.8 ms ✓ AbstractFFTs 926.6 ms ✓ EnumX 2431.5 ms ✓ FillArrays 894.0 ms ✓ IntegerMathUtils 958.9 ms ✓ ExprTools 1028.5 ms ✓ TriplotBase 1556.1 ms ✓ IndirectArrays 1062.9 ms ✓ Extents 909.1 ms ✓ RangeArrays 1564.8 ms ✓ 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1201.1 ms ✓ Missings 1400.5 ms ✓ InverseFunctions → InverseFunctionsDatesExt 1909.5 ms ✓ InverseFunctions → InverseFunctionsTestExt 4587.8 ms ✓ AbstractFFTs → AbstractFFTsTestExt 2003.7 ms ✓ FillArrays → FillArraysSparseArraysExt 1112.4 ms ✓ FillArrays → FillArraysStatisticsExt 1254.2 ms ✓ Primes 3575.2 ms ✓ TimerOutputs 1036.9 ms ✓ RuntimeGeneratedFunctions 1508.0 ms ✓ LogExpFunctions 1563.7 ms ✓ PikaParser 4452.8 ms ✓ AbstractFBCModels 1150.3 ms ✓ PaddedViews 975.6 ms ✓ StackViews 852.8 ms ✓ TableTraits 949.8 ms ✓ Ratios 1024.8 ms ✓ Adapt 9345.7 ms ✓ FileIO 1637.0 ms ✓ AxisAlgorithms 2190.1 ms ✓ LDLFactorizations 1741.9 ms ✓ RelocatableFolders 2780.1 ms ✓ Unitful → ConstructionBaseUnitfulExt 2960.8 ms ✓ Unitful → PrintfExt 2576.1 ms ✓ Unitful → InverseFunctionsUnitfulExt 2724.5 ms ✓ Unitful → NaNMathExt 1815.5 ms ✓ FillArrays → FillArraysPDMatsExt 1047.4 ms ✓ Compat → CompatLinearAlgebraExt 1448.7 ms ✓ PrecompileTools 1719.3 ms ✓ JLLWrappers 1894.0 ms ✓ AxisArrays 2339.6 ms ✓ ColorTypes 2395.3 ms ✓ FFTA 4468.7 ms ✓ LinearOperators 845.1 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1026.4 ms ✓ MosaicViews 2063.6 ms ✓ Tables 1005.3 ms ✓ Ratios → RatiosFixedPointNumbersExt 1535.1 ms ✓ Adapt → AdaptSparseArraysExt 874.7 ms ✓ OffsetArrays → OffsetArraysAdaptExt 2868.9 ms ✓ ChainRulesCore 2929.9 ms ✓ FilePathsBase 4500.2 ms ✓ DataStructures 14543.6 ms ✓ SIMD 14979.2 ms ✓ StaticArrays 17671.6 ms ✓ Parsers 2299.3 ms ✓ Libffi_jll 2227.7 ms ✓ EarCut_jll 2320.8 ms ✓ Bzip2_jll 2286.1 ms ✓ isoband_jll 2658.4 ms ✓ OpenBLASConsistentFPCSR_jll 2370.0 ms ✓ XZ_jll 2251.8 ms ✓ Rmath_jll 2329.8 ms ✓ OpenSpecFun_jll 1679.6 ms ✓ Xorg_xtrans_jll 2429.4 ms ✓ Opus_jll 2390.9 ms ✓ x265_jll 2451.7 ms ✓ libpng_jll 2359.4 ms ✓ CRlibm_jll 2518.5 ms ✓ Imath_jll 2389.0 ms ✓ Libmount_jll 2364.2 ms ✓ libfdk_aac_jll 2461.9 ms ✓ Libuuid_jll 2436.7 ms ✓ FriBidi_jll 2370.7 ms ✓ LERC_jll 2300.1 ms ✓ Xorg_libXau_jll 2300.8 ms ✓ Ogg_jll 2517.5 ms ✓ LAME_jll 2881.0 ms ✓ CoreMath_jll 2553.3 ms ✓ Graphite2_jll 2465.1 ms ✓ x264_jll 2497.3 ms ✓ LLVMOpenMP_jll 2246.9 ms ✓ Libiconv_jll 2440.4 ms ✓ libaom_jll 2364.4 ms ✓ Xorg_libXdmcp_jll 2235.6 ms ✓ Giflib_jll 2318.4 ms ✓ Expat_jll 2357.0 ms ✓ JpegTurbo_jll 1462.7 ms ✓ ColorTypes → StyledStringsExt 8600.9 ms ✓ Colors 4257.3 ms ✓ ColorVectorSpace 2579.8 ms ✓ LinearOperators → LinearOperatorsLDLFactorizationsExt 1977.7 ms ✓ StructArrays 1569.6 ms ✓ ChainRulesCore → ChainRulesCoreSparseArraysExt 946.4 ms ✓ AbstractFFTs → AbstractFFTsChainRulesCoreExt 3560.9 ms ✓ LogExpFunctions → LogExpFunctionsChainRulesCoreExt 1683.8 ms ✓ LinearOperators → LinearOperatorsChainRulesCoreExt 3510.8 ms ✓ FilePathsBase → FilePathsBaseTestExt 1332.6 ms ✓ FilePathsBase → FilePathsBaseMmapExt 1770.7 ms ✓ FilePaths 1669.3 ms ✓ SortingAlgorithms 3094.0 ms ✓ QuadGK 4135.4 ms ✓ ConstraintTrees 19767.4 ms ✓ Automa 2079.1 ms ✓ StaticArrays → StaticArraysStatisticsExt 2407.9 ms ✓ StaticArrays → StaticArraysChainRulesCoreExt 1919.4 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 2220.3 ms ✓ FillArrays → FillArraysStaticArraysExt 1898.2 ms ✓ Adapt → AdaptStaticArraysExt 4582.8 ms ✓ JSON 22960.9 ms ✓ GeometryBasics 1486.0 ms ✓ CodecBzip2 2632.8 ms ✓ FreeType2_jll 1415.0 ms ✓ Isoband 2843.5 ms ✓ Rmath 6033.3 ms ✓ SpecialFunctions 1675.5 ms ✓ CRlibm 2380.5 ms ✓ OpenEXR_jll 2438.6 ms ✓ libvorbis_jll 1447.1 ms ✓ CoreMath 2359.3 ms ✓ Pixman_jll 2509.1 ms ✓ GettextRuntime_jll 2534.1 ms ✓ Xorg_libxcb_jll 2757.9 ms ✓ Libtiff_jll 2613.2 ms ✓ libsixel_jll 6339.4 ms ✓ QOI 54960.9 ms ✓ TiffImages 1552.2 ms ✓ Animations 1641.8 ms ✓ Graphics 34281.6 ms ✓ ImageCore 10289.9 ms ✓ ColorSchemes 1793.4 ms ✓ StructArrays → StructArraysSparseArraysExt 1020.7 ms ✓ StructArrays → StructArraysLinearAlgebraExt 994.3 ms ✓ StructArrays → StructArraysAdaptExt 2189.6 ms ✓ StructArrays → StructArraysStaticArraysExt 5586.3 ms ✓ StatsBase 5090.4 ms ✓ Interpolations 3646.1 ms ✓ BenchmarkTools 8283.1 ms ✓ JSONFBCModels 4047.0 ms ✓ ColorBrewer 3980.4 ms ✓ Packing 12856.5 ms ✓ GridLayoutBase 9062.3 ms ✓ MakieCore 4781.6 ms ✓ ShaderAbstractions 2297.7 ms ✓ FreeType 2505.1 ms ✓ Fontconfig_jll 4822.2 ms ✓ SpecialFunctions → SpecialFunctionsChainRulesCoreExt 2730.3 ms ✓ HypergeometricFunctions 1398.9 ms ✓ DiffRules 1930.6 ms ✓ ColorVectorSpace → SpecialFunctionsExt 6491.5 ms ✓ OpenEXR 6285.5 ms ✓ IntervalArithmetic 2494.3 ms ✓ Glib_jll 2515.7 ms ✓ Xorg_libX11_jll 5447.7 ms ✓ ImageBase 8022.0 ms ✓ PNGFiles 13099.3 ms ✓ Sixel 10610.9 ms ✓ JpegTurbo 21432.3 ms ✓ PlotUtils 2326.1 ms ✓ PDMats → StatsBaseExt 4490.2 ms ✓ Interpolations → InterpolationsUnitfulExt 6905.7 ms ✓ FreeTypeAbstraction 3344.5 ms ✓ StatsFuns 8130.4 ms ✓ ForwardDiff 8375.9 ms ✓ FastDifferentiation 2173.0 ms ✓ IntervalArithmetic → IntervalArithmeticSparseArraysExt 1699.9 ms ✓ IntervalArithmetic → IntervalArithmeticIrrationalConstantsExt 1976.5 ms ✓ IntervalArithmetic → IntervalArithmeticLinearAlgebraExt 1467.8 ms ✓ IntervalArithmetic → IntervalArithmeticDiffRulesExt 1416.5 ms ✓ IntervalArithmetic → IntervalArithmeticIntervalSetsExt 2407.0 ms ✓ Xorg_libXrender_jll 2937.8 ms ✓ Xorg_libXext_jll 6783.7 ms ✓ ImageAxes 30087.4 ms ✓ MathTeXEngine 4465.5 ms ✓ StatsFuns → StatsFunsChainRulesCoreExt 1518.7 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 11200.8 ms ✓ Distributions 2403.4 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 2981.7 ms ✓ Unitful → ForwardDiffExt 110504.6 ms ✓ MathOptInterface 1643.6 ms ✓ IntervalArithmetic → IntervalArithmeticForwardDiffExt 8510.7 ms ✓ ExactPredicates 2703.1 ms ✓ Cairo_jll 2641.9 ms ✓ Libglvnd_jll 4854.3 ms ✓ ImageMetadata 4348.2 ms ✓ Distributions → DistributionsTestExt 4431.1 ms ✓ Distributions → DistributionsChainRulesCoreExt 70733.6 ms ✓ JuMP 19170.4 ms ✓ Tulip 12032.7 ms ✓ DelaunayTriangulation 2622.6 ms ✓ HarfBuzz_jll 2689.2 ms ✓ libwebp_jll 9626.9 ms ✓ Netpbm 5210.9 ms ✓ KernelDensity 20212.2 ms ✓ COBREXA 19124.1 ms ✓ ElementaryFluxModes 2452.1 ms ✓ libass_jll 2448.9 ms ✓ Pango_jll 9849.1 ms ✓ WebP ERROR: LoadError: cannot declare DifferentiableMetabolism.differentiate_prepare_kkt public; it is already declared exported Stacktrace:  [1] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:324  [2] top-level scope  @ ~/.julia/packages/DifferentiableMetabolism/yELl2/src/DifferentiableMetabolism.jl:44  [3] include(mod::Module, _path::String)  @ Base ./Base.jl:323  [4] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3294  [5] top-level scope  @ stdin:5  [6] eval(m::Module, e::Any)  @ Core ./boot.jl:517  [7] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3136  [8] include_string  @ ./loading.jl:3146 [inlined]  [9] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:350  [10] _start()  @ Base ./client.jl:593 in expression starting at /home/pkgeval/.julia/packages/DifferentiableMetabolism/yELl2/src/public_api.jl:19 in expression starting at /home/pkgeval/.julia/packages/DifferentiableMetabolism/yELl2/src/DifferentiableMetabolism.jl:19 in expression starting at stdin:5 ✗ DifferentiableMetabolism 2581.2 ms ✓ FFMPEG_jll 3083.0 ms ✓ Cairo 5451.1 ms ✓ ImageIO 296621.8 ms ✓ Makie 251856.3 ms ✓ CairoMakie 268 dependencies successfully precompiled in 1803 seconds. 41 already precompiled. Precompilation completed after 1836.12s ################################################################################ # Testing # Testing ElementaryFluxModes Test Could not use exact versions of packages in manifest, re-resolving. Note: if you do not check your manifest file into source control, then you can probably ignore this message. However, if you do check your manifest file into source control, then you probably want to pass the `allow_reresolve = false` kwarg when calling the `Pkg.test` function. Updating `/tmp/jl_9wB0Lc/Project.toml` [5a4f3dfa] + AbstractFBCModels v1.3.0 [babc4406] + COBREXA v2.9.1 ⌅ [13f3f980] + CairoMakie v0.13.10 [5515826b] + ConstraintTrees v1.11.0 ⌅ [9677e053] + DifferentiableMetabolism v0.2.0 [89210afb] + ElementaryFluxModes v1.0.0 ⌅ [682c06a0] ↓ JSON v1.5.0 ⇒ v0.21.4 [475c1105] + JSONFBCModels v1.0.1 [6dd1b50a] + Tulip v0.9.8 Updating `/tmp/jl_9wB0Lc/Manifest.toml` [14f7f29c] + AMD v0.5.3 [5a4f3dfa] + AbstractFBCModels v1.3.0 [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.5.2 [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 [babc4406] + COBREXA v2.9.1 [96374032] + CRlibm v1.0.2 [159f3aea] + Cairo v1.1.1 ⌅ [13f3f980] + CairoMakie v0.13.10 [d360d2e6] + ChainRulesCore v1.26.1 [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 [5515826b] + ConstraintTrees v1.11.0 [187b0558] + ConstructionBase v1.6.0 [d38c429a] + Contour v0.6.3 [b7a15901] + CoreMath v0.1.0 [9a962f9c] + DataAPI v1.16.0 ⌅ [864edb3b] ↓ DataStructures v0.19.4 ⇒ v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [927a84f5] + DelaunayTriangulation v1.6.6 ⌅ [9677e053] + DifferentiableMetabolism v0.2.0 [31c24e10] + Distributions v0.25.123 [89210afb] + ElementaryFluxModes v1.0.0 [4e289a0a] + EnumX v1.0.7 [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 v0.8.3 [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 [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 v0.15.1 [d1acc4aa] + IntervalArithmetic v1.0.6 [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 v1.5.0 ⇒ v0.21.4 [475c1105] + JSONFBCModels v1.0.1 [b835a17e] + JpegTurbo v0.1.6 [5ab0869b] + KernelDensity v0.6.11 [ba0b0d4f] + Krylov v0.10.6 [40e66cde] + LDLFactorizations v0.10.2 [b964fa9f] + LaTeXStrings v1.4.0 [8cdb02fc] + LazyModules v0.3.1 [5c8ed15e] + LinearOperators v2.13.0 ⌅ [ee78f7c6] + Makie v0.22.10 ⌅ [20f20a25] + MakieCore v0.9.5 [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 v1.4.0 [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 [992d4aef] + Showoff v1.0.3 [73760f76] + SignedDistanceFields v0.4.1 [699a6c99] + SimpleTraits v0.9.5 [45858cf5] + Sixel v0.1.5 [a2af1166] + SortingAlgorithms v1.2.2 [860ef19b] + StableRNGs v1.0.4 [cae243ae] + StackViews v0.1.2 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [09ab397b] + StructArrays v0.7.3 [ec057cc2] - StructUtils v2.7.1 [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 v1.18.6+0 [a38c48d9] + CoreMath_jll v0.1.0+0 [5ae413db] + EarCut_jll v2.2.4+0 [2e619515] + Expat_jll v2.7.3+0 ⌅ [b22a6f82] + FFMPEG_jll v6.1.3+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 v1.3.15+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 v0.3.30+0 [18a262bb] + OpenEXR_jll v3.4.8+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 v5.8.3+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 [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [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 v1.6.57+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 [0dad84c5] + ArgTools v1.1.2 [8bf52ea8] + CRC32c v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [3fa0cd96] + REPL v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [4607b0f0] + SuiteSparse [a4e569a6] + Tar v1.10.0 [deac9b47] + LibCURL_jll v8.19.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2026.3.19 [458c3c95] + OpenSSL_jll v3.5.6+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850ede] + nghttp2_jll v1.68.1+0 [3f19e933] + p7zip_jll v17.8.0+0 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_9wB0Lc/Project.toml` [5a4f3dfa] AbstractFBCModels v1.3.0 [babc4406] COBREXA v2.9.1 ⌅ [13f3f980] CairoMakie v0.13.10 [5515826b] ConstraintTrees v1.11.0 ⌅ [9677e053] DifferentiableMetabolism v0.2.0 [ffbed154] DocStringExtensions v0.9.5 [89210afb] ElementaryFluxModes v1.0.0 [eb9bf01b] FastDifferentiation v0.4.5 ⌅ [682c06a0] JSON v0.21.4 [475c1105] JSONFBCModels v1.0.1 [4076af6c] JuMP v1.30.0 [af85af4c] RowEchelon v0.2.1 [6dd1b50a] Tulip v0.9.8 [37e2e46d] LinearAlgebra v1.13.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_9wB0Lc/Manifest.toml` [14f7f29c] AMD v0.5.3 [5a4f3dfa] AbstractFBCModels v1.3.0 [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.5.2 [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 v1.7.0 [fa961155] CEnum v0.5.0 [babc4406] COBREXA v2.9.1 [96374032] CRlibm v1.0.2 [159f3aea] Cairo v1.1.1 ⌅ [13f3f980] CairoMakie v0.13.10 [d360d2e6] ChainRulesCore v1.26.1 [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 [5515826b] ConstraintTrees v1.11.0 [187b0558] ConstructionBase v1.6.0 [d38c429a] Contour v0.6.3 [b7a15901] CoreMath v0.1.0 [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 v0.2.0 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [89210afb] ElementaryFluxModes v1.0.0 [4e289a0a] EnumX v1.0.7 [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 v0.8.3 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [53c48c17] FixedPointNumbers v0.8.5 [1fa38f19] Format v1.3.7 [f6369f11] ForwardDiff v1.3.3 [b38be410] FreeType v4.1.1 [663a7486] FreeTypeAbstraction v0.10.8 [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 v0.15.1 [d1acc4aa] IntervalArithmetic v1.0.6 [8197267c] IntervalSets v0.7.14 [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 v1.30.0 [5ab0869b] KernelDensity v0.6.11 [ba0b0d4f] Krylov v0.10.6 [40e66cde] LDLFactorizations v0.10.2 [b964fa9f] LaTeXStrings v1.4.0 [8cdb02fc] LazyModules v0.3.1 [5c8ed15e] LinearOperators v2.13.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 ⌅ [ee78f7c6] Makie v0.22.10 ⌅ [20f20a25] MakieCore v0.9.5 [dbb5928d] MappedArrays v0.4.3 [b8f27783] MathOptInterface v1.50.1 [0a4f8689] MathTeXEngine v0.6.7 [e1d29d7a] Missings v1.2.0 [e94cdb99] MosaicViews v0.3.4 [46d2c3a1] MuladdMacro v0.2.4 [d8a4904e] MutableArithmetics v1.7.1 [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 v1.5.2 [27ebfcd6] Primes v0.5.7 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.4.0 [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 [af85af4c] RowEchelon v0.2.1 [7e49a35a] RuntimeGeneratedFunctions v0.5.18 [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 [a2af1166] 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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 v1.3.15+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 v0.3.30+0 [18a262bb] OpenEXR_jll v3.4.8+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 v5.8.3+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 [ea2f1a96] 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compatibility constraints restrict them from upgrading. Testing Running tests... ERROR: LoadError: cannot declare DifferentiableMetabolism.differentiate_prepare_kkt public; it is already declared exported Stacktrace:  [1] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:324  [2] top-level scope  @ ~/.julia/packages/DifferentiableMetabolism/yELl2/src/DifferentiableMetabolism.jl:44  [3] include(mod::Module, _path::String)  @ Base ./Base.jl:323  [4] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3294  [5] top-level scope  @ stdin:5  [6] eval(m::Module, e::Any)  @ Core ./boot.jl:517  [7] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3136  [8] include_string  @ ./loading.jl:3146 [inlined]  [9] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:350  [10] _start()  @ Base ./client.jl:593 in expression starting at /home/pkgeval/.julia/packages/DifferentiableMetabolism/yELl2/src/public_api.jl:19 in expression starting at /home/pkgeval/.julia/packages/DifferentiableMetabolism/yELl2/src/DifferentiableMetabolism.jl:19 in expression starting at stdin:5 1 dependency had output during precompilation: ┌ DifferentiableMetabolism │ [Output was shown above] └ ERROR: LoadError: The following 1 package failed to precompile: DifferentiableMetabolism Failed to precompile DifferentiableMetabolism [9677e053-0fc1-49e6-98a8-2ad3a1525e54] to "/home/pkgeval/.julia/compiled/v1.14/DifferentiableMetabolism/jl_WJXFli" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/ElementaryFluxModes/MPIp7/test/runtests.jl:9 Testing failed after 61.25s ERROR: LoadError: Package ElementaryFluxModes errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/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/v1.14/Pkg/src/Operations.jl:3160 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [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/v1.14/Pkg/src/API.jl:586 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:323 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [14] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 2030.41s: package fails to precompile