Package evaluation to test ElementaryFluxModes on Julia 1.14.0-DEV.65 (b05afe0f25*) started at 2025-11-11T18:56:38.671 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.75s ################################################################################ # Installation # Installing ElementaryFluxModes... Resolving package versions... Installed Bzip2_jll ───────────────── v1.0.9+0 Installed DiffResults ─────────────── v1.1.0 Installed CodecZlib ───────────────── v0.7.8 Installed ExprTools ───────────────── v0.1.10 Installed MacroTools ──────────────── v0.5.16 Installed ForwardDiff ─────────────── v1.2.2 Installed RuntimeGeneratedFunctions ─ v0.5.16 Installed Compat ──────────────────── v4.18.1 Installed OrderedCollections ──────── v1.8.1 Installed Statistics ──────────────── v1.11.1 Installed DataStructures ──────────── v0.18.22 Installed ElementaryFluxModes ─────── v1.0.0 Installed TranscodingStreams ──────── v0.11.3 Installed PrecompileTools ─────────── v1.3.3 Installed CommonSubexpressions ────── v0.3.1 Installed StaticArraysCore ────────── v1.4.4 Installed IrrationalConstants ─────── v0.2.6 Installed CodecBzip2 ──────────────── v0.8.5 Installed NaNMath ─────────────────── v1.1.3 Installed StructUtils ─────────────── v2.6.0 Installed StaticArrays ────────────── v1.9.15 Installed OpenSpecFun_jll ─────────── v0.5.6+0 Installed DiffRules ───────────────── v1.15.1 Installed LogExpFunctions ─────────── v0.3.29 Installed Parsers ─────────────────── v2.8.3 Installed JSON3 ───────────────────── v1.14.3 Installed FastDifferentiation ─────── v0.4.4 Installed JSON ────────────────────── v1.2.1 Installed JuMP ────────────────────── v1.29.2 Installed RowEchelon ──────────────── v0.2.1 Installed JLLWrappers ─────────────── v1.7.1 Installed StructTypes ─────────────── v1.11.0 Installed SpecialFunctions ────────── v2.6.1 Installed BenchmarkTools ──────────── v1.6.3 Installed Preferences ─────────────── v1.5.0 Installed MutableArithmetics ──────── v1.6.7 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 v0.18.22 [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 v0.4.4 [f6369f11] + ForwardDiff v1.2.2 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.2.1 [0f8b85d8] + JSON3 v1.14.3 [4076af6c] + JuMP v1.29.2 [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 v1.11.0 [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 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 9.71s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 6154.6 ms ✓ TestEnv 1 dependency successfully precompiled in 6 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/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/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... 4447.7 ms ✓ MacroTools 1149.9 ms ✓ Statistics 2159.4 ms ✓ IrrationalConstants 1093.9 ms ✓ StaticArraysCore 1482.3 ms ✓ OrderedCollections 1113.5 ms ✓ DocStringExtensions 822.6 ms ✓ RowEchelon 913.1 ms ✓ ExprTools 1357.1 ms ✓ TranscodingStreams 1017.3 ms ✓ NaNMath 1658.0 ms ✓ StructTypes 1439.7 ms ✓ StructUtils 1175.9 ms ✓ Compat 1365.3 ms ✓ Preferences 11950.0 ms ✓ MutableArithmetics 1842.7 ms ✓ CommonSubexpressions 1312.5 ms ✓ Statistics → SparseArraysExt 889.1 ms ✓ DiffResults 1868.3 ms ✓ LogExpFunctions 935.7 ms ✓ RuntimeGeneratedFunctions 963.3 ms ✓ CodecZlib 865.0 ms ✓ Compat → CompatLinearAlgebraExt 1216.5 ms ✓ JLLWrappers 902.2 ms ✓ PrecompileTools 4015.3 ms ✓ DataStructures 1430.7 ms ✓ Bzip2_jll 1563.2 ms ✓ OpenSpecFun_jll 15126.8 ms ✓ StaticArrays 18174.9 ms ✓ Parsers 1105.8 ms ✓ CodecBzip2 5608.4 ms ✓ SpecialFunctions 1633.4 ms ✓ StaticArrays → StaticArraysStatisticsExt 15881.3 ms ✓ JSON3 7600.0 ms ✓ JSON 1308.4 ms ✓ DiffRules 3890.5 ms ✓ BenchmarkTools 6778.5 ms ✓ ForwardDiff 9406.2 ms ✓ FastDifferentiation 2020.9 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 80860.8 ms ✓ MathOptInterface 72757.6 ms ✓ JuMP 19945.0 ms ✓ ElementaryFluxModes 42 dependencies successfully precompiled in 313 seconds. 19 already precompiled. Precompilation completed after 332.71s ################################################################################ # 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 Extents ───────────────────── v0.1.6 Installed libass_jll ────────────────── v0.17.4+0 Installed HarfBuzz_jll ──────────────── v8.5.1+0 Installed libaom_jll ────────────────── v3.13.1+0 Installed ImageIO ───────────────────── v0.6.9 Installed Libuuid_jll ───────────────── v2.41.2+0 Installed MosaicViews ───────────────── v0.3.4 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 ConstraintTrees ───────────── v1.11.0 Installed Graphics ──────────────────── v1.1.3 Installed QuadGK ────────────────────── v2.11.2 Installed Opus_jll ──────────────────── v1.5.2+0 Installed WoodburyMatrices ──────────── v1.0.0 Installed Tables ────────────────────── v1.12.1 Installed AdaptivePredicates ────────── v1.2.0 Installed FileIO ────────────────────── v1.17.1 Installed COBREXA ───────────────────── v2.9.1 Installed Xorg_libxcb_jll ───────────── v1.17.1+0 Installed Ogg_jll ───────────────────── v1.3.6+0 Installed EnumX ─────────────────────── v1.0.5 Installed InverseFunctions ──────────── v0.1.17 Installed LZO_jll ───────────────────── v2.10.3+0 Installed Reexport ──────────────────── v1.2.2 Installed Missings ──────────────────── v1.2.0 Installed LERC_jll ──────────────────── v4.0.1+0 Installed TableTraits ───────────────── v1.0.1 Installed LLVMOpenMP_jll ────────────── v18.1.8+0 Installed Imath_jll ─────────────────── v3.1.11+0 Installed MappedArrays ──────────────── v0.4.2 Installed LaTeXStrings ──────────────── v1.4.0 Installed SortingAlgorithms ─────────── v1.2.2 Installed Grisu ─────────────────────── v1.0.2 Installed RangeArrays ───────────────── v0.3.2 Installed Format ────────────────────── v1.3.7 Installed CRlibm ────────────────────── v1.0.2 Installed Inflate ───────────────────── v0.1.5 Installed FillArrays ────────────────── v1.15.0 Installed ColorBrewer ───────────────── v0.4.2 Installed AbstractTrees ─────────────── v0.4.5 Installed Packing ───────────────────── v0.5.1 Installed OpenEXR_jll ───────────────── v3.2.4+0 Installed LazyModules ───────────────── v0.3.1 Installed MakieCore ─────────────────── v0.9.5 Installed oneTBB_jll ────────────────── v2022.0.0+1 Installed UnicodeFun ────────────────── v0.4.1 Installed x264_jll ──────────────────── v10164.0.1+0 Installed StatsBase ─────────────────── v0.34.8 Installed Cairo ─────────────────────── v1.1.1 Installed Observables ───────────────── v0.5.5 Installed Xorg_libXau_jll ───────────── v1.0.13+0 Installed Tulip ─────────────────────── v0.9.8 Installed MathTeXEngine ─────────────── v0.6.7 Installed CairoMakie ────────────────── v0.13.10 Installed IntelOpenMP_jll ───────────── v2025.2.0+0 Installed DataValueInterfaces ───────── v1.0.0 Installed Expat_jll ─────────────────── v2.7.3+0 Installed Libffi_jll ────────────────── v3.4.7+0 Installed Pixman_jll ────────────────── v0.44.2+0 Installed CEnum ─────────────────────── v0.5.0 Installed QPSReader ─────────────────── v0.2.1 Installed Contour ───────────────────── v0.6.3 Installed libpng_jll ────────────────── v1.6.50+0 Installed isoband_jll ───────────────── v0.2.3+0 Installed SimpleTraits ──────────────── v0.9.5 Installed ColorVectorSpace ──────────── v0.11.0 Installed ImageMetadata ─────────────── v0.9.10 Installed RoundingEmulator ──────────── v0.2.1 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 Scratch ───────────────────── v1.3.0 Installed libwebp_jll ───────────────── v1.6.0+0 Installed FFMPEG_jll ────────────────── v6.1.3+0 Installed ShaderAbstractions ────────── v0.5.0 Installed CRlibm_jll ────────────────── v1.0.1+0 Installed PDMats ────────────────────── v0.11.36 Installed JpegTurbo ─────────────────── v0.1.6 Installed ImageCore ─────────────────── v0.10.5 Installed AxisArrays ────────────────── v0.4.8 Installed PNGFiles ──────────────────── v0.4.4 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed FreeType ──────────────────── v4.1.1 Installed OpenBLASConsistentFPCSR_jll ─ v0.3.29+0 Installed PkgVersion ────────────────── v0.3.3 Installed RelocatableFolders ────────── v1.0.1 Installed StackViews ────────────────── v0.1.2 Installed KernelDensity ─────────────── v0.6.10 Installed AliasTables ───────────────── v1.1.3 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed SIMD ──────────────────────── v3.7.2 Installed DataAPI ───────────────────── v1.16.0 Installed LDLFactorizations ─────────── v0.10.1 Installed Netpbm ────────────────────── v1.1.1 Installed ImageAxes ─────────────────── v0.6.12 Installed Krylov ────────────────────── v0.10.2 Installed ColorSchemes ──────────────── v3.31.0 Installed AbstractFFTs ──────────────── v1.5.0 Installed Colors ────────────────────── v0.13.1 Installed Libglvnd_jll ──────────────── v1.7.1+1 Installed QOI ───────────────────────── v1.0.1 Installed ColorTypes ────────────────── v0.12.1 Installed AxisAlgorithms ────────────── v1.1.0 Installed Requires ──────────────────── v1.3.1 Installed Glib_jll ──────────────────── v2.86.0+0 Installed BaseDirs ──────────────────── v1.3.2 Installed JSON ──────────────────────── v0.21.4 Installed Rmath ─────────────────────── v0.9.0 Installed FastClosures ──────────────── v0.3.2 Installed FilePaths ─────────────────── v0.8.3 Installed FreeTypeAbstraction ───────── v0.10.8 Installed StatsFuns ─────────────────── v1.5.2 Installed Unitful ───────────────────── v1.25.1 Installed Distributions ─────────────── v0.25.122 Installed JSONFBCModels ─────────────── v1.0.1 Installed OpenEXR ───────────────────── v0.3.3 Installed GridLayoutBase ────────────── v0.11.2 Installed Xorg_libXdmcp_jll ─────────── v1.1.6+0 Installed SignedDistanceFields ──────── v0.4.0 Installed XZ_jll ────────────────────── v5.8.1+0 Installed x265_jll ──────────────────── v4.1.0+0 Installed GeometryBasics ────────────── v0.5.10 Installed ExactPredicates ───────────── v2.2.9 Installed Pango_jll ─────────────────── v1.56.4+0 Installed IterTools ─────────────────── v1.10.0 Installed Xorg_xtrans_jll ───────────── v1.6.0+0 Installed PaddedViews ───────────────── v0.5.12 Installed JpegTurbo_jll ─────────────── v3.1.3+0 Installed FilePathsBase ─────────────── v0.9.24 Installed Adapt ─────────────────────── v4.4.0 Installed TiffImages ────────────────── v0.11.6 Installed ConstructionBase ──────────── v1.6.0 Installed Libmount_jll ──────────────── v2.41.2+0 Installed HypergeometricFunctions ───── v0.3.28 Installed TriplotBase ───────────────── v0.1.0 Installed Sixel ─────────────────────── v0.1.5 Installed Xorg_libX11_jll ───────────── v1.8.12+0 Installed PlotUtils ─────────────────── v1.4.4 Installed TensorCore ────────────────── v0.1.1 Installed EarCut_jll ────────────────── v2.2.4+0 Installed ImageBase ─────────────────── v0.1.7 Installed StatsAPI ──────────────────── v1.7.1 Installed StructArrays ──────────────── v0.7.2 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 AbstractFBCModels ─────────── v1.3.0 Installed FriBidi_jll ───────────────── v1.0.17+0 Installed Animations ────────────────── v0.4.2 Installed ChainRulesCore ────────────── v1.26.0 Installed LAME_jll ──────────────────── v3.100.3+0 Installed Xorg_libXrender_jll ───────── v0.9.12+0 Installed Isoband ───────────────────── v0.1.1 Installed DifferentiableMetabolism ──── v0.2.0 Installed AMD ───────────────────────── v0.5.3 Installed IntervalArithmetic ────────── v1.0.1 Installed libvorbis_jll ─────────────── v1.3.8+0 Installed PtrArrays ─────────────────── v1.3.0 Installed IntervalSets ──────────────── v0.7.12 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 Libffi 44.2 KiB Installed artifact LERC 272.9 KiB Installed artifact Fontconfig 984.8 KiB Installed artifact Ogg 250.3 KiB Installed artifact FreeType2 1.5 MiB Installed artifact x265 1.4 MiB Installed artifact libfdk_aac 2.8 MiB Installed artifact GettextRuntime 543.0 KiB Installed artifact Libtiff 2.3 MiB Installed artifact XZ 1.5 MiB Installed artifact FriBidi 78.9 KiB Installed artifact CRlibm 169.5 KiB Installed artifact HarfBuzz 1.7 MiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact JpegTurbo 1.4 MiB Installed artifact x264 2.1 MiB Installed artifact Rmath 121.9 KiB Installed artifact libsixel 177.3 KiB Installed artifact libaom 6.4 MiB Installed artifact Expat 283.3 KiB Installed artifact libass 427.8 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact LAME 292.5 KiB Installed artifact Cairo 2.2 MiB Installed artifact Pixman 372.2 KiB Installed artifact Imath 182.8 KiB Installed artifact OpenEXR 1.9 MiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact Libglvnd 833.5 KiB Installed artifact EarCut 80.5 KiB Installed artifact isoband 25.7 KiB Installed artifact libwebp 2.6 MiB Installed artifact Graphite2 120.2 KiB Installed artifact LZO 208.9 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact FFTW 2.2 MiB Installed artifact libvorbis 271.0 KiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact Giflib 154.6 KiB Installed artifact Opus 925.5 KiB Installed artifact libpng 328.4 KiB Installed artifact OpenBLASConsistentFPCSR 9.9 MiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact Libiconv 1.9 MiB Installed artifact Pango 1.1 MiB Installed artifact FFMPEG 11.0 MiB Installed artifact Libmount 6.5 MiB Installed artifact Glib 7.7 MiB Installed artifact Libuuid 3.7 MiB Updating `/tmp/jl_UtroQL/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 v1.2.1 ⇒ v0.21.4 [475c1105] + JSONFBCModels v1.0.1 [6dd1b50a] + Tulip v0.9.8 Updating `/tmp/jl_UtroQL/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 [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 v1.0.1 [8197267c] + IntervalSets v0.7.12 [3587e190] + InverseFunctions v0.1.17 [f1662d9f] + Isoband v0.1.1 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 ⌅ [682c06a0] ↓ JSON v1.2.1 ⇒ v0.21.4 [475c1105] + JSONFBCModels v1.0.1 [b835a17e] + JpegTurbo v0.1.6 [5ab0869b] + KernelDensity v0.6.10 [ba0b0d4f] + Krylov v0.10.2 [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 v1.0.1 [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 v1.56.4+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 v1.6.50+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 v8.16.0+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_UtroQL/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 v0.4.4 ⌅ [682c06a0] JSON v0.21.4 [475c1105] JSONFBCModels v1.0.1 [4076af6c] JuMP v1.29.2 [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_UtroQL/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 v0.4.4 [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 v1.2.2 [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 v1.0.1 [8197267c] IntervalSets v0.7.12 [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 v1.29.2 [5ab0869b] KernelDensity v0.6.10 [ba0b0d4f] Krylov v0.10.2 [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 v1.0.1 [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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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:3151  [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:2997  [8] include_string  @ ./loading.jl:3007 [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_udlW4k" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/ElementaryFluxModes/MPIp7/test/runtests.jl:9 Testing failed after 307.97s 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 720.25s: package fails to precompile