Package evaluation to test ElementaryFluxModes on Julia 1.14.0-DEV.1299 (6d6224db99*) started at 2025-11-27T16:24:25.463 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.9s ################################################################################ # Installation # Installing ElementaryFluxModes... Resolving package versions... Installed Bzip2_jll ───────────────── v1.0.9+0 Installed CodecZlib ───────────────── v0.7.8 Installed DiffResults ─────────────── v1.1.0 Installed MacroTools ──────────────── v0.5.16 Installed RuntimeGeneratedFunctions ─ v0.5.16 Installed ExprTools ───────────────── v0.1.10 Installed ForwardDiff ─────────────── v1.3.0 Installed DataStructures ──────────── v0.19.3 Installed OrderedCollections ──────── v1.8.1 Installed Compat ──────────────────── v4.18.1 Installed CommonSubexpressions ────── v0.3.1 Installed TranscodingStreams ──────── v0.11.3 Installed Statistics ──────────────── v1.11.1 Installed PrecompileTools ─────────── v1.3.3 Installed StaticArraysCore ────────── v1.4.4 Installed IrrationalConstants ─────── v0.2.6 Installed CodecBzip2 ──────────────── v0.8.5 Installed NaNMath ─────────────────── v1.1.3 Installed ElementaryFluxModes ─────── v1.0.0 Installed StructUtils ─────────────── v2.6.0 Installed StaticArrays ────────────── v1.9.15 Installed OpenSpecFun_jll ─────────── v0.5.6+0 Installed JSON3 ───────────────────── v1.14.3 Installed LogExpFunctions ─────────── v0.3.29 Installed DiffRules ───────────────── v1.15.1 Installed Parsers ─────────────────── v2.8.3 Installed JSON ────────────────────── v1.3.0 Installed SpecialFunctions ────────── v2.6.1 Installed FastDifferentiation ─────── v0.4.5 Installed JuMP ────────────────────── v1.29.3 Installed BenchmarkTools ──────────── v1.6.3 Installed MutableArithmetics ──────── v1.6.7 Installed Preferences ─────────────── v1.5.0 Installed RowEchelon ──────────────── v0.2.1 Installed JLLWrappers ─────────────── v1.7.1 Installed StructTypes ─────────────── v1.11.0 Installed DocStringExtensions ─────── v0.9.5 Installed MathOptInterface ────────── v1.46.0 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 v1.6.3 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.18.1 [864edb3b] + DataStructures v0.19.3 [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 v1.3.0 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.3.0 [0f8b85d8] + JSON3 v1.14.3 [4076af6c] + JuMP v1.29.3 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.46.0 [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 v1.5.0 [af85af4c] + RowEchelon v0.2.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.16 [276daf66] + SpecialFunctions v2.6.1 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [856f2bd8] + StructTypes v1.11.0 [ec057cc2] + StructUtils v2.6.0 [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 v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap 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 v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 8.6s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4607.4 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 4106.0 ms ✓ MacroTools 1108.2 ms ✓ Statistics 2118.1 ms ✓ IrrationalConstants 951.0 ms ✓ StaticArraysCore 1255.5 ms ✓ OrderedCollections 1055.0 ms ✓ DocStringExtensions 788.2 ms ✓ RowEchelon 918.8 ms ✓ ExprTools 1194.5 ms ✓ TranscodingStreams 976.3 ms ✓ NaNMath 1598.6 ms ✓ StructTypes 1385.1 ms ✓ StructUtils 1115.7 ms ✓ Compat 1118.6 ms ✓ Preferences 10910.6 ms ✓ MutableArithmetics 1622.5 ms ✓ CommonSubexpressions 1275.3 ms ✓ Statistics → SparseArraysExt 812.4 ms ✓ DiffResults 3501.5 ms ✓ DataStructures 1367.5 ms ✓ LogExpFunctions 857.6 ms ✓ RuntimeGeneratedFunctions 915.1 ms ✓ CodecZlib 801.9 ms ✓ Compat → CompatLinearAlgebraExt 1140.5 ms ✓ JLLWrappers 881.0 ms ✓ PrecompileTools 1325.0 ms ✓ Bzip2_jll 1361.5 ms ✓ OpenSpecFun_jll 12973.6 ms ✓ StaticArrays 16671.7 ms ✓ Parsers 981.6 ms ✓ CodecBzip2 4948.3 ms ✓ SpecialFunctions 1405.9 ms ✓ StaticArrays → StaticArraysStatisticsExt 14102.0 ms ✓ JSON3 6864.3 ms ✓ JSON 1221.7 ms ✓ DiffRules 3406.8 ms ✓ BenchmarkTools 6459.8 ms ✓ ForwardDiff 8376.9 ms ✓ FastDifferentiation 2036.0 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 76524.9 ms ✓ MathOptInterface 49268.6 ms ✓ JuMP 17895.5 ms ✓ ElementaryFluxModes 42 dependencies successfully precompiled in 270 seconds. 19 already precompiled. Precompilation completed after 285.82s ################################################################################ # 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. Installed Libuuid_jll ───────────────── v2.41.2+0 Installed libass_jll ────────────────── v0.17.4+0 Installed libaom_jll ────────────────── v3.13.1+0 Installed ImageIO ───────────────────── v0.6.9 Installed HarfBuzz_jll ──────────────── v8.5.1+0 Installed MosaicViews ───────────────── v0.3.4 Installed Extents ───────────────────── v0.1.6 Installed PolygonOps ────────────────── v0.1.2 Installed MKL_jll ───────────────────── v2025.2.0+0 Installed Libtiff_jll ───────────────── v4.7.2+0 Installed Cairo_jll ─────────────────── v1.18.5+0 Installed Graphite2_jll ─────────────── v1.3.15+0 Installed Fontconfig_jll ────────────── v2.17.1+0 Installed Giflib_jll ────────────────── v5.2.3+0 Installed Graphics ──────────────────── v1.1.3 Installed QuadGK ────────────────────── v2.11.2 Installed Opus_jll ──────────────────── v1.5.2+0 Installed AdaptivePredicates ────────── v1.2.0 Installed ConstraintTrees ───────────── v1.11.0 Installed WoodburyMatrices ──────────── v1.0.0 Installed Ogg_jll ───────────────────── v1.3.6+0 Installed Xorg_libxcb_jll ───────────── v1.17.1+0 Installed EnumX ─────────────────────── v1.0.5 Installed FileIO ────────────────────── v1.17.1 Installed Tables ────────────────────── v1.12.1 Installed Reexport ──────────────────── v1.2.2 Installed InverseFunctions ──────────── v0.1.17 Installed COBREXA ───────────────────── v2.9.1 Installed LZO_jll ───────────────────── v2.10.3+0 Installed LLVMOpenMP_jll ────────────── v18.1.8+0 Installed TableTraits ───────────────── v1.0.1 Installed Missings ──────────────────── v1.2.0 Installed Imath_jll ─────────────────── v3.1.11+0 Installed LERC_jll ──────────────────── v4.0.1+0 Installed LaTeXStrings ──────────────── v1.4.0 Installed SortingAlgorithms ─────────── v1.2.2 Installed MappedArrays ──────────────── v0.4.2 Installed Grisu ─────────────────────── v1.0.2 Installed RangeArrays ───────────────── v0.3.2 Installed CRlibm ────────────────────── v1.0.2 Installed Inflate ───────────────────── v0.1.5 Installed Format ────────────────────── v1.3.7 Installed ColorBrewer ───────────────── v0.4.2 Installed AbstractTrees ─────────────── v0.4.5 Installed OpenEXR_jll ───────────────── v3.2.4+0 Installed Packing ───────────────────── v0.5.1 Installed DataStructures ────────────── v0.18.22 Installed FillArrays ────────────────── v1.15.0 Installed LazyModules ───────────────── v0.3.1 Installed Tulip ─────────────────────── v0.9.8 Installed oneTBB_jll ────────────────── v2022.0.0+1 Installed Cairo ─────────────────────── v1.1.1 Installed x264_jll ──────────────────── v10164.0.1+0 Installed UnicodeFun ────────────────── v0.4.1 Installed MakieCore ─────────────────── v0.9.5 Installed Observables ───────────────── v0.5.5 Installed Xorg_libXau_jll ───────────── v1.0.13+0 Installed StatsBase ─────────────────── v0.34.8 Installed MathTeXEngine ─────────────── v0.6.7 Installed DataValueInterfaces ───────── v1.0.0 Installed IntelOpenMP_jll ───────────── v2025.2.0+0 Installed CairoMakie ────────────────── v0.13.10 Installed CEnum ─────────────────────── v0.5.0 Installed Libffi_jll ────────────────── v3.4.7+0 Installed Pixman_jll ────────────────── v0.44.2+0 Installed Expat_jll ─────────────────── v2.7.3+0 Installed libpng_jll ────────────────── v1.6.51+0 Installed isoband_jll ───────────────── v0.2.3+0 Installed ColorVectorSpace ──────────── v0.11.0 Installed QPSReader ─────────────────── v0.2.1 Installed Contour ───────────────────── v0.6.3 Installed SimpleTraits ──────────────── v0.9.5 Installed RoundingEmulator ──────────── v0.2.1 Installed ImageMetadata ─────────────── v0.9.10 Installed libfdk_aac_jll ────────────── v2.0.4+0 Installed StableRNGs ────────────────── v1.0.4 Installed libsixel_jll ──────────────── v1.10.5+0 Installed Interpolations ────────────── v0.15.1 Installed PikaParser ────────────────── v0.6.1 Installed libwebp_jll ───────────────── v1.6.0+0 Installed FFMPEG_jll ────────────────── v6.1.3+0 Installed Scratch ───────────────────── v1.3.0 Installed ShaderAbstractions ────────── v0.5.0 Installed CRlibm_jll ────────────────── v1.0.1+0 Installed PDMats ────────────────────── v0.11.36 Installed AxisArrays ────────────────── v0.4.8 Installed PNGFiles ──────────────────── v0.4.4 Installed FreeType ──────────────────── v4.1.1 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed ImageCore ─────────────────── v0.10.5 Installed JpegTurbo ─────────────────── v0.1.6 Installed OpenBLASConsistentFPCSR_jll ─ v0.3.29+0 Installed PkgVersion ────────────────── v0.3.3 Installed RelocatableFolders ────────── v1.0.1 Installed KernelDensity ─────────────── v0.6.10 Installed StackViews ────────────────── v0.1.2 Installed AliasTables ───────────────── v1.1.3 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed LDLFactorizations ─────────── v0.10.1 Installed DataAPI ───────────────────── v1.16.0 Installed SIMD ──────────────────────── v3.7.2 Installed Netpbm ────────────────────── v1.1.1 Installed ImageAxes ─────────────────── v0.6.12 Installed Krylov ────────────────────── v0.10.3 Installed Libglvnd_jll ──────────────── v1.7.1+1 Installed AbstractFFTs ──────────────── v1.5.0 Installed ColorSchemes ──────────────── v3.31.0 Installed Colors ────────────────────── v0.13.1 Installed ColorTypes ────────────────── v0.12.1 Installed AxisAlgorithms ────────────── v1.1.0 Installed QOI ───────────────────────── v1.0.2 Installed Requires ──────────────────── v1.3.1 Installed Glib_jll ──────────────────── v2.86.0+0 Installed BaseDirs ──────────────────── v1.3.2 Installed Rmath ─────────────────────── v0.9.0 Installed JSON ──────────────────────── v0.21.4 Installed FreeTypeAbstraction ───────── v0.10.8 Installed FastClosures ──────────────── v0.3.2 Installed FilePaths ─────────────────── v0.8.3 Installed Distributions ─────────────── v0.25.122 Installed StatsFuns ─────────────────── v1.5.2 Installed Unitful ───────────────────── v1.25.1 Installed Xorg_libXdmcp_jll ─────────── v1.1.6+0 Installed OpenEXR ───────────────────── v0.3.3 Installed GridLayoutBase ────────────── v0.11.2 Installed SignedDistanceFields ──────── v0.4.0 Installed XZ_jll ────────────────────── v5.8.1+0 Installed JSONFBCModels ─────────────── v1.0.1 Installed x265_jll ──────────────────── v4.1.0+0 Installed ExactPredicates ───────────── v2.2.9 Installed Pango_jll ─────────────────── v1.57.0+0 Installed GeometryBasics ────────────── v0.5.10 Installed IterTools ─────────────────── v1.10.0 Installed Xorg_xtrans_jll ───────────── v1.6.0+0 Installed FilePathsBase ─────────────── v0.9.24 Installed TiffImages ────────────────── v0.11.6 Installed JpegTurbo_jll ─────────────── v3.1.3+0 Installed Adapt ─────────────────────── v4.4.0 Installed PaddedViews ───────────────── v0.5.12 Installed ConstructionBase ──────────── v1.6.0 Installed HypergeometricFunctions ───── v0.3.28 Installed Libmount_jll ──────────────── v2.41.2+0 Installed TriplotBase ───────────────── v0.1.0 Installed Xorg_libX11_jll ───────────── v1.8.12+0 Installed Sixel ─────────────────────── v0.1.5 Installed PlotUtils ─────────────────── v1.4.4 Installed StatsAPI ──────────────────── v1.7.1 Installed ImageBase ─────────────────── v0.1.7 Installed TensorCore ────────────────── v0.1.1 Installed StructArrays ──────────────── v0.7.2 Installed EarCut_jll ────────────────── v2.2.4+0 Installed TimerOutputs ──────────────── v0.5.29 Installed OffsetArrays ──────────────── v1.17.0 Installed ProgressMeter ─────────────── v1.11.0 Installed WebP ──────────────────────── v0.1.3 Installed LinearOperators ───────────── v2.11.0 Installed GettextRuntime_jll ────────── v0.22.4+0 Installed Ratios ────────────────────── v0.4.5 Installed FriBidi_jll ───────────────── v1.0.17+0 Installed ChainRulesCore ────────────── v1.26.0 Installed AbstractFBCModels ─────────── v1.3.0 Installed Animations ────────────────── v0.4.2 Installed LAME_jll ──────────────────── v3.100.3+0 Installed Xorg_libXrender_jll ───────── v0.9.12+0 Installed AMD ───────────────────────── v0.5.3 Installed Isoband ───────────────────── v0.1.1 Installed libvorbis_jll ─────────────── v1.3.8+0 Installed IntervalArithmetic ────────── v1.0.2 Installed PtrArrays ─────────────────── v1.3.0 Installed IntervalSets ──────────────── v0.7.13 Installed DifferentiableMetabolism ──── v0.2.0 Installed FixedPointNumbers ─────────── v0.8.5 Installed Showoff ───────────────────── v1.0.3 Installed FreeType2_jll ─────────────── v2.13.4+0 Installed FFTW_jll ──────────────────── v3.3.11+0 Installed FFTW ──────────────────────── v1.10.0 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed Xorg_libXext_jll ──────────── v1.3.7+0 Installed IndirectArrays ────────────── v1.0.0 Installed Automa ────────────────────── v1.1.0 Installed Makie ─────────────────────── v0.22.10 Installed DelaunayTriangulation ─────── v1.6.5 Installing 51 artifacts Installed artifact Xorg_libXau 36.6 KiB Installed artifact LAME 292.5 KiB Installed artifact Pixman 372.2 KiB Installed artifact Expat 283.3 KiB Installed artifact libpng 328.9 KiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact libass 427.8 KiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact Giflib 154.6 KiB Installed artifact Libtiff 2.3 MiB Installed artifact x264 2.1 MiB Installed artifact Libiconv 1.9 MiB Installed artifact EarCut 80.5 KiB Installed artifact Pango 2.0 MiB Installed artifact CRlibm 169.5 KiB Installed artifact Imath 182.8 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact libwebp 2.6 MiB Installed artifact x265 1.4 MiB Installed artifact libfdk_aac 2.8 MiB Installed artifact Graphite2 120.2 KiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact Rmath 121.9 KiB Installed artifact Libuuid 3.7 MiB Installed artifact FFTW 2.2 MiB Installed artifact JpegTurbo 1.4 MiB Installed artifact Cairo 2.2 MiB Installed artifact isoband 25.7 KiB Installed artifact FriBidi 78.9 KiB Installed artifact Fontconfig 984.8 KiB Installed artifact FFMPEG 11.0 MiB Installed artifact XZ 1.5 MiB Installed artifact libvorbis 271.0 KiB Installed artifact GettextRuntime 543.0 KiB Installed artifact OpenEXR 1.9 MiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact libsixel 177.3 KiB Installed artifact HarfBuzz 1.7 MiB Installed artifact LZO 208.9 KiB Installed artifact LERC 272.9 KiB Installed artifact Libmount 6.5 MiB Installed artifact OpenBLASConsistentFPCSR 9.9 MiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact Libffi 44.2 KiB Installed artifact FreeType2 1.5 MiB Installed artifact Opus 925.5 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact Ogg 250.3 KiB Installed artifact Glib 7.7 MiB Installed artifact Libglvnd 833.5 KiB Installed artifact libaom 6.4 MiB Updating `/tmp/jl_TOtz8I/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 v1.3.0 ⇒ v0.21.4 [475c1105] + JSONFBCModels v1.0.1 [6dd1b50a] + Tulip v0.9.8 Updating `/tmp/jl_TOtz8I/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 [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 v1.26.0 [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 [5515826b] + ConstraintTrees v1.11.0 [187b0558] + ConstructionBase v1.6.0 [d38c429a] + Contour v0.6.3 [9a962f9c] + DataAPI v1.16.0 ⌅ [864edb3b] ↓ DataStructures v0.19.3 ⇒ v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [927a84f5] + DelaunayTriangulation v1.6.5 ⌅ [9677e053] + DifferentiableMetabolism v0.2.0 [31c24e10] + Distributions v0.25.122 [89210afb] + ElementaryFluxModes v1.0.0 [4e289a0a] + EnumX v1.0.5 [429591f6] + ExactPredicates v2.2.9 [411431e0] + Extents v0.1.6 [7a1cc6ca] + FFTW v1.10.0 [9aa1b823] + FastClosures v0.3.2 [5789e2e9] + FileIO v1.17.1 ⌅ [8fc22ac5] + FilePaths v0.8.3 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.15.0 [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 ⌅ [a98d9a8b] + Interpolations v0.15.1 [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 v1.3.0 ⇒ v0.21.4 [475c1105] + JSONFBCModels v1.0.1 [b835a17e] + JpegTurbo v0.1.6 [5ab0869b] + KernelDensity v0.6.10 [ba0b0d4f] + Krylov v0.10.3 [40e66cde] + LDLFactorizations v0.10.1 [b964fa9f] + LaTeXStrings v1.4.0 [8cdb02fc] + LazyModules v0.3.1 [5c8ed15e] + LinearOperators v2.11.0 ⌅ [ee78f7c6] + Makie v0.22.10 ⌅ [20f20a25] + MakieCore v0.9.5 [dbb5928d] + MappedArrays v0.4.2 [0a4f8689] + MathTeXEngine v0.6.7 [e1d29d7a] + Missings v1.2.0 [e94cdb99] + MosaicViews v0.3.4 [f09324ee] + Netpbm v1.1.1 [510215fc] + Observables v0.5.5 [6fe1bfb0] + OffsetArrays v1.17.0 [52e1d378] + OpenEXR v0.3.3 [90014a1f] + PDMats v0.11.36 [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 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [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 v0.4.0 [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 v1.7.1 [2913bbd2] + StatsBase v0.34.8 [4c63d2b9] + StatsFuns v1.5.2 [09ab397b] + StructArrays v0.7.2 [ec057cc2] - StructUtils v2.6.0 [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 v1.25.1 [e3aaa7dc] + WebP v0.1.3 [efce3f68] + WoodburyMatrices v1.0.0 [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 v6.1.3+0 [f5851436] + FFTW_jll v3.3.11+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 v2.86.0+0 [3b182d85] + Graphite2_jll v1.3.15+0 [2e76f6c2] + HarfBuzz_jll v8.5.1+0 [905a6f67] + Imath_jll v3.1.11+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [aacddb02] + JpegTurbo_jll v3.1.3+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 [856f044c] + MKL_jll v2025.2.0+0 [e7412a2a] + Ogg_jll v1.3.6+0 [6cdc7f73] + OpenBLASConsistentFPCSR_jll v0.3.29+0 [18a262bb] + OpenEXR_jll v3.2.4+0 [91d4177d] + Opus_jll v1.5.2+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 v5.8.1+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 [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 v1.6.51+0 [075b6546] + libsixel_jll v1.10.5+0 [f27f6e37] + libvorbis_jll v1.3.8+0 [c5f90fcd] + libwebp_jll v1.6.0+0 [1317d2d5] + oneTBB_jll v2022.0.0+1 [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 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [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 v8.17.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850ede] + nghttp2_jll v1.68.0+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` Test Successfully re-resolved Status `/tmp/jl_TOtz8I/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 v1.29.3 [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_TOtz8I/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 v0.13.10 [d360d2e6] ChainRulesCore v1.26.0 [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 [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 v1.6.5 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 ⌅ [9677e053] DifferentiableMetabolism v0.2.0 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [89210afb] ElementaryFluxModes v1.0.0 [4e289a0a] EnumX v1.0.5 [429591f6] ExactPredicates v2.2.9 [e2ba6199] ExprTools v0.1.10 [411431e0] Extents v0.1.6 [7a1cc6ca] FFTW v1.10.0 [9aa1b823] FastClosures v0.3.2 [eb9bf01b] FastDifferentiation v0.4.5 [5789e2e9] FileIO v1.17.1 ⌅ [8fc22ac5] FilePaths v0.8.3 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [53c48c17] FixedPointNumbers v0.8.5 [1fa38f19] Format v1.3.7 [f6369f11] ForwardDiff v1.3.0 [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 ⌅ [a98d9a8b] Interpolations v0.15.1 [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 [0f8b85d8] JSON3 v1.14.3 [475c1105] JSONFBCModels v1.0.1 [b835a17e] JpegTurbo v0.1.6 [4076af6c] JuMP v1.29.3 [5ab0869b] KernelDensity v0.6.10 [ba0b0d4f] Krylov v0.10.3 [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 v0.22.10 ⌅ [20f20a25] MakieCore v0.9.5 [dbb5928d] MappedArrays v0.4.2 [b8f27783] MathOptInterface v1.46.0 [0a4f8689] MathTeXEngine v0.6.7 [e1d29d7a] Missings v1.2.0 [e94cdb99] MosaicViews v0.3.4 [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 v0.11.36 [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 v1.5.0 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [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 [af85af4c] RowEchelon 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 v0.4.0 [699a6c99] SimpleTraits v0.9.5 [45858cf5] Sixel v0.1.5 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [860ef19b] StableRNGs v1.0.4 [cae243ae] StackViews 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p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but 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:310  [2] top-level scope  @ ~/.julia/packages/DifferentiableMetabolism/yELl2/src/DifferentiableMetabolism.jl:44  [3] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [4] include_package_for_output(pkg::Base.PkgId, input::String, 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:3157  [5] top-level scope  @ stdin:5  [6] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [7] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3003  [8] include_string  @ ./loading.jl:3013 [inlined]  [9] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [10] _start()  @ Base ./client.jl:577 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_yUreKh" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/ElementaryFluxModes/MPIp7/test/runtests.jl:9 Testing failed after 292.8s 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:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [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:572 [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:548 [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:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 640.53s: package fails to precompile