Package evaluation to test MicrobeAgents on Julia 1.14.0-DEV.1584 (ac5fadde9b*) started at 2026-01-19T01:04:03.292 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 10.02s ################################################################################ # Installation # Installing MicrobeAgents... Resolving package versions... Installed MKL_jll ───────────────────── v2025.2.0+0 Installed InlineStrings ─────────────── v1.4.5 Installed Extents ───────────────────── v0.1.6 Installed OrderedCollections ────────── v1.8.1 Installed SimpleWeightedGraphs ──────── v1.5.1 Installed SentinelArrays ────────────── v1.4.9 Installed Distances ─────────────────── v0.10.12 Installed SpatialIndexing ───────────── v0.1.6 Installed QuadGK ────────────────────── v2.11.2 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed NearestNeighbors ──────────── v0.4.26 Installed Reexport ──────────────────── v1.2.2 Installed InverseFunctions ──────────── v0.1.17 Installed Tables ────────────────────── v1.12.1 Installed Missings ──────────────────── v1.2.0 Installed FileIO ────────────────────── v1.17.1 Installed TableTraits ───────────────── v1.0.1 Installed Preferences ───────────────── v1.5.1 Installed Polynomials ───────────────── v4.1.0 Installed LaTeXStrings ──────────────── v1.4.0 Installed UnPack ────────────────────── v1.0.2 Installed Crayons ───────────────────── v4.1.1 Installed Inflate ───────────────────── v0.1.5 Installed SortingAlgorithms ─────────── v1.2.2 Installed DataStructures ────────────── v0.18.22 Installed RangeArrays ───────────────── v0.3.2 Installed Autocorrelations ──────────── v0.1.1 Installed MacroTools ────────────────── v0.5.16 Installed Quaternions ───────────────── v0.7.7 Installed URIs ──────────────────────── v1.6.1 Installed oneTBB_jll ────────────────── v2022.0.0+1 Installed FillArrays ────────────────── v1.16.0 Installed AbstractTrees ─────────────── v0.4.5 Installed ArnoldiMethod ─────────────── v0.4.0 Installed IntelOpenMP_jll ───────────── v2025.2.0+0 Installed StatsBase ─────────────────── v0.34.10 Installed CodecZlib ─────────────────── v0.7.8 Installed DataValueInterfaces ───────── v1.0.0 Installed RealDot ───────────────────── v0.1.0 Installed LightSumTypes ─────────────── v5.2.2 Installed LoggingExtras ─────────────── v1.2.0 Installed QuickHeaps ────────────────── v0.1.2 Installed IrrationalConstants ───────── v0.2.6 Installed SimpleTraits ──────────────── v0.9.5 Installed BitFlags ──────────────────── v0.1.9 Installed Setfield ──────────────────── v1.1.2 Installed Scratch ───────────────────── v1.3.0 Installed HTTP ──────────────────────── v1.10.19 Installed MeanSquaredDisplacement ───── v0.3.1 Installed MetaGraphs ────────────────── v0.7.2 Installed Agents ────────────────────── v6.2.10 Installed SimpleBufferStream ────────── v1.2.0 Installed PooledArrays ──────────────── v1.4.3 Installed WorkerUtilities ───────────── v1.6.1 Installed CompositionsBase ──────────── v0.1.2 Installed PDMats ────────────────────── v0.11.37 Installed AxisArrays ────────────────── v0.4.8 Installed CommonSolve ───────────────── v0.2.6 Installed DocStringExtensions ───────── v0.9.5 Installed OnlineStatsBase ───────────── v1.7.1 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed LightXML ──────────────────── v0.9.3 Installed AliasTables ───────────────── v1.1.3 Installed RecipesBase ───────────────── v1.3.4 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed ConcurrentUtilities ───────── v2.5.0 Installed DataAPI ───────────────────── v1.16.0 Installed InvertedIndices ───────────── v1.3.1 Installed StaticArraysCore ──────────── v1.4.4 Installed StringManipulation ────────── v0.4.2 Installed AbstractFFTs ──────────────── v1.5.0 Installed StaticArrays ──────────────── v1.9.16 Installed Requires ──────────────────── v1.3.1 Installed LogExpFunctions ───────────── v0.3.29 Installed LightOSM ──────────────────── v0.3.1 Installed JSON ──────────────────────── v0.21.4 Installed Parsers ───────────────────── v2.8.3 Installed Rmath ─────────────────────── v0.9.0 Installed MicrobeAgents ─────────────── v0.5.3 Installed StatsFuns ─────────────────── v1.5.2 Installed ArrayTools ────────────────── v0.2.7 Installed Distributions ─────────────── v0.25.123 Installed PrettyTables ──────────────── v3.1.2 Installed WeakRefStrings ────────────── v1.4.2 Installed JLLWrappers ───────────────── v1.7.1 Installed GeometryBasics ────────────── v0.5.10 Installed IterTools ─────────────────── v1.10.0 Installed Accessors ─────────────────── v0.1.43 Installed FilePathsBase ─────────────── v0.9.24 Installed StreamSampling ────────────── v0.6.9 Installed DataFrames ────────────────── v1.8.1 Installed ConstructionBase ──────────── v1.6.0 Installed HypergeometricFunctions ───── v0.3.28 Installed JLD2 ──────────────────────── v0.4.55 Installed ExceptionUnwrapping ───────── v0.1.11 Installed EarCut_jll ────────────────── v2.2.4+0 Installed Compat ────────────────────── v4.18.1 Installed TranscodingStreams ────────── v0.11.3 Installed Statistics ────────────────── v1.11.1 Installed Graphs ────────────────────── v1.13.1 Installed PrecompileTools ───────────── v1.3.3 Installed StatsAPI ──────────────────── v1.8.0 Installed ProgressMeter ─────────────── v1.11.0 Installed HybridStructs ─────────────── v0.2.1 Installed StaticGraphs ──────────────── v0.3.1 Installed OffsetArrays ──────────────── v1.17.0 Installed Parameters ────────────────── v0.12.3 Installed OpenSSL ───────────────────── v1.6.1 Installed MbedTLS ───────────────────── v1.1.9 Installed PtrArrays ─────────────────── v1.3.0 Installed XML2_jll ──────────────────── v2.15.1+0 Installed SpecialFunctions ──────────── v2.6.1 Installed IntervalSets ──────────────── v0.7.13 Installed FFTW ──────────────────────── v1.10.0 Installed Rotations ─────────────────── v1.7.1 Installed FFTW_jll ──────────────────── v3.3.11+0 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed Bessels ───────────────────── v0.2.8 Installed MbedTLS_jll ───────────────── v2.28.1010+0 Installed DSP ───────────────────────── v0.8.4 Installed CSV ───────────────────────── v0.10.15 Installing 7 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact EarCut 80.5 KiB Installed artifact Libiconv 1.9 MiB Installed artifact FFTW 2.2 MiB Installed artifact XML2 2.2 MiB Installed artifact MbedTLS 2.2 MiB Updating `~/.julia/environments/v1.14/Project.toml` [b17a4bac] + MicrobeAgents v0.5.3 Updating `~/.julia/environments/v1.14/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.43 [46ada45e] + Agents v6.2.10 [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 ⌅ [1dc0ca97] + ArrayTools v0.2.7 [b9118d5e] + Autocorrelations v0.1.1 [39de3d68] + AxisArrays v0.4.8 [0e736298] + Bessels v0.2.8 [d1d4a3ce] + BitFlags v0.1.9 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [38540f10] + CommonSolve v0.2.6 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [f0e56b4a] + ConcurrentUtilities v2.5.0 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [717857b8] + DSP v0.8.4 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [460bff9d] + ExceptionUnwrapping v0.1.11 [411431e0] + Extents v0.1.6 [7a1cc6ca] + FFTW v1.10.0 [5789e2e9] + FileIO v1.17.1 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [5c1252a2] + GeometryBasics v0.5.10 ⌃ [86223c79] + Graphs v1.13.1 [cd3eb016] + HTTP v1.10.19 [49057fa9] + HybridStructs v0.2.1 [34004b35] + HypergeometricFunctions v0.3.28 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.5 [8197267c] + IntervalSets v0.7.13 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 ⌅ [033835bb] + JLD2 v0.4.55 [692b3bcd] + JLLWrappers v1.7.1 ⌅ [682c06a0] + JSON v0.21.4 [b964fa9f] + LaTeXStrings v1.4.0 [d1922b25] + LightOSM v0.3.1 [f56206fc] + LightSumTypes v5.2.2 [9c8b4983] + LightXML v0.9.3 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.2.0 [1914dd2f] + MacroTools v0.5.16 [739be429] + MbedTLS v1.1.9 [13c93d70] + MeanSquaredDisplacement v0.3.1 ⌅ [626554b9] + MetaGraphs v0.7.2 [b17a4bac] + MicrobeAgents v0.5.3 [e1d29d7a] + Missings v1.2.0 [b8a86587] + NearestNeighbors v0.4.26 [6fe1bfb0] + OffsetArrays v1.17.0 [925886fa] + OnlineStatsBase v1.7.1 [4d8831e6] + OpenSSL v1.6.1 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [f27b6e38] + Polynomials v4.1.0 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [08abe8d2] + PrettyTables v3.1.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [94ee1d12] + Quaternions v0.7.7 ⌅ [30b38841] + QuickHeaps v0.1.2 [b3c3ace0] + RangeArrays v0.3.2 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [6038ab10] + Rotations v1.7.1 [6c6a2e73] + Scratch v1.3.0 [91c51154] + SentinelArrays v1.4.9 [efcf1570] + Setfield v1.1.2 [777ac1f9] + SimpleBufferStream v1.2.0 [699a6c99] + SimpleTraits v0.9.5 [47aef6b3] + SimpleWeightedGraphs v1.5.1 [a2af1166] + SortingAlgorithms v1.2.2 [d4ead438] + SpatialIndexing v0.1.6 [276daf66] + SpecialFunctions v2.6.1 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 ⌅ [4c8beaf5] + StaticGraphs v0.3.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 ⌅ [ff63dad9] + StreamSampling v0.6.9 [892a3eda] + StringManipulation v0.4.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [5c2747f8] + URIs v1.6.1 [3a884ed6] + UnPack v1.0.2 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [5ae413db] + EarCut_jll v2.2.4+0 [f5851436] + FFTW_jll v3.3.11+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [856f044c] + MKL_jll v2025.2.0+0 [c8ffd9c3] + MbedTLS_jll v2.28.1010+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [02c8fc9c] + XML2_jll v2.15.1+0 [1317d2d5] + oneTBB_jll v2022.0.0+1 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [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 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.18.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 12.72s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 5386.6 ms ✓ TestEnv 1 dependency successfully precompiled in 6 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling packages... 4539.0 ms ✓ MacroTools 1858.3 ms ✓ InlineStrings 866.7 ms ✓ Reexport 1386.0 ms ✓ ConstructionBase 2375.9 ms ✓ IrrationalConstants 972.4 ms ✓ DataValueInterfaces 1106.8 ms ✓ StatsAPI 1430.4 ms ✓ IterTools 1091.5 ms ✓ IntervalSets 1055.8 ms ✓ Inflate 895.7 ms ✓ CommonSolve 1487.1 ms ✓ TranscodingStreams 923.1 ms ✓ LaTeXStrings 1791.7 ms ✓ Statistics 967.2 ms ✓ StaticArraysCore 835.5 ms ✓ PtrArrays 806.2 ms ✓ SimpleBufferStream 885.6 ms ✓ DataAPI 828.1 ms ✓ RealDot 1470.2 ms ✓ URIs 858.3 ms ✓ InvertedIndices 1064.9 ms ✓ InverseFunctions 1244.9 ms ✓ ArrayTools 833.0 ms ✓ CompositionsBase 886.6 ms ✓ BitFlags 1134.5 ms ✓ AbstractTrees 1081.7 ms ✓ AbstractFFTs 1022.6 ms ✓ WorkerUtilities 2188.9 ms ✓ FillArrays 794.0 ms ✓ UnPack 2131.1 ms ✓ SpatialIndexing 2518.5 ms ✓ Bessels 1211.3 ms ✓ Extents 850.2 ms ✓ RangeArrays 1289.8 ms ✓ OrderedCollections 1226.8 ms ✓ DocStringExtensions 1596.8 ms ✓ OffsetArrays 750.4 ms ✓ IteratorInterfaceExtensions 1941.4 ms ✓ Crayons 1174.7 ms ✓ Requires 1840.4 ms ✓ ConcurrentUtilities 1920.9 ms ✓ PDMats 925.7 ms ✓ Scratch 2106.1 ms ✓ SentinelArrays 1354.9 ms ✓ LoggingExtras 1886.8 ms ✓ ProgressMeter 1140.9 ms ✓ Compat 1077.2 ms ✓ Preferences 1604.5 ms ✓ ExceptionUnwrapping 3272.4 ms ✓ SimpleTraits 784.5 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 952.2 ms ✓ IntervalSets → IntervalSetsRandomExt 848.0 ms ✓ ConstructionBase → ConstructionBaseIntervalSetsExt 1124.8 ms ✓ CodecZlib 1425.9 ms ✓ Statistics → SparseArraysExt 1503.8 ms ✓ Distances 770.4 ms ✓ IntervalSets → IntervalSetsStatisticsExt 1001.2 ms ✓ AliasTables 1029.0 ms ✓ Missings 1020.0 ms ✓ PooledArrays 1074.0 ms ✓ Quaternions 891.2 ms ✓ InverseFunctions → InverseFunctionsDatesExt 1690.0 ms ✓ InverseFunctions → InverseFunctionsTestExt 819.6 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 3676.8 ms ✓ OpenSSL 3302.8 ms ✓ AbstractFFTs → AbstractFFTsTestExt 1307.8 ms ✓ FillArrays → FillArraysSparseArraysExt 908.4 ms ✓ FillArrays → FillArraysStatisticsExt 936.9 ms ✓ Parameters 1378.5 ms ✓ LogExpFunctions 758.0 ms ✓ TableTraits 8817.1 ms ✓ FileIO 1419.8 ms ✓ FillArrays → FillArraysPDMatsExt 870.1 ms ✓ Compat → CompatLinearAlgebraExt 915.0 ms ✓ PrecompileTools 1206.4 ms ✓ JLLWrappers 2934.8 ms ✓ Setfield 1476.2 ms ✓ AxisArrays 1231.7 ms ✓ Distances → DistancesSparseArraysExt 5117.1 ms ✓ Accessors 976.7 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1752.3 ms ✓ Tables 2106.3 ms ✓ FilePathsBase 3769.8 ms ✓ DataStructures 3155.9 ms ✓ StringManipulation 12533.9 ms ✓ StaticArrays 2260.4 ms ✓ RecipesBase 15374.9 ms ✓ Parsers 3100.3 ms ✓ LightSumTypes 44827.0 ms ✓ JLD2 1481.5 ms ✓ EarCut_jll 1509.2 ms ✓ Rmath_jll 1559.4 ms ✓ OpenSpecFun_jll 4768.3 ms ✓ IntelOpenMP_jll 4788.0 ms ✓ oneTBB_jll 1408.5 ms ✓ FFTW_jll 1616.6 ms ✓ Libiconv_jll 1498.7 ms ✓ MbedTLS_jll 1722.5 ms ✓ Accessors → TestExt 2479.1 ms ✓ Accessors → IntervalSetsExt 2180.7 ms ✓ Accessors → LinearAlgebraExt 2619.2 ms ✓ FilePathsBase → FilePathsBaseTestExt 962.3 ms ✓ FilePathsBase → FilePathsBaseMmapExt 1719.8 ms ✓ SortingAlgorithms 2718.8 ms ✓ QuadGK 1711.6 ms ✓ QuickHeaps 35982.3 ms ✓ PrettyTables 3609.6 ms ✓ ArnoldiMethod 1891.3 ms ✓ StaticArrays → StaticArraysStatisticsExt 1401.2 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 1866.3 ms ✓ FillArrays → FillArraysStaticArraysExt 5027.0 ms ✓ Rotations 1702.7 ms ✓ Accessors → StaticArraysExt 1337.5 ms ✓ IntervalSets → IntervalSetsRecipesBaseExt 37576.8 ms ✓ Polynomials 3727.0 ms ✓ JSON 938.1 ms ✓ InlineStrings → ParsersExt 20721.2 ms ✓ GeometryBasics 1502.0 ms ✓ Rmath 4874.7 ms ✓ SpecialFunctions  Downloading artifact: IntelOpenMP  Downloading artifact: oneTBB 10568.4 ms ✓ MKL_jll 1722.2 ms ✓ XML2_jll 2414.4 ms ✓ MbedTLS 4049.8 ms ✓ HybridStructs 5068.7 ms ✓ StatsBase 79722.3 ms ✓ DataFrames 7964.2 ms ✓ NearestNeighbors 9431.5 ms ✓ Graphs 1875.8 ms ✓ Rotations → RotationsRecipesBaseExt 2392.4 ms ✓ WeakRefStrings 2325.2 ms ✓ HypergeometricFunctions 6757.5 ms ✓ FFTW 1340.8 ms ✓ LightXML 26241.1 ms ✓ HTTP 2760.6 ms ✓ OnlineStatsBase 2158.8 ms ✓ PDMats → StatsBaseExt 10217.3 ms ✓ StaticGraphs 8403.6 ms ✓ MetaGraphs 3926.9 ms ✓ SimpleWeightedGraphs 26112.6 ms ✓ CSV 2877.3 ms ✓ StatsFuns 3213.0 ms ✓ Polynomials → PolynomialsFFTWExt 6292.9 ms ✓ FileIO → HTTPExt 1290.3 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 9389.5 ms ✓ Distributions 6246.5 ms ✓ DSP 14136.9 ms ✓ LightOSM 3596.7 ms ✓ Distributions → DistributionsTestExt 8314.6 ms ✓ StreamSampling 3239.3 ms ✓ DSP → OffsetArraysExt 3878.3 ms ✓ Autocorrelations 29445.3 ms ✓ Agents 4681.4 ms ✓ MeanSquaredDisplacement  Update message: Agents v6  This is a new major version of Agents.jl with lots of cool stuff! However, from this version onwards, we will stop posting update messages to the REPL console!  If you want to be updated, follow this discourse post:  https://discourse.julialang.org/t/agents-jl-v6-releases-announcement-post/111678  (and see the CHANGELOG.md file online for a list of changes!) WARNING: Constructor for type "HyperSphere" was extended in `MicrobeAgents` without explicit qualification or import.  NOTE: Assumed "HyperSphere" refers to `GeometryBasics.HyperSphere`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function HyperSphere end`.  Hint: To silence the warning, qualify `HyperSphere` as `GeometryBasics.HyperSphere` in the method signature or explicitly `import GeometryBasics: HyperSphere`. 36752.2 ms ✓ MicrobeAgents 154 dependencies successfully precompiled in 717 seconds. 41 already precompiled. 2 dependencies had output during precompilation: ┌ MKL_jll │ Downloading artifact: IntelOpenMP │ Downloading artifact: oneTBB └ ┌ MicrobeAgents │ Update message: Agents v6 │ │ This is a new major version of Agents.jl with lots of cool stuff! │ However, from this version onwards, we will stop posting update messages │ to the REPL console! │ │ If you want to be updated, follow this discourse post: │ │ https://discourse.julialang.org/t/agents-jl-v6-releases-announcement-post/111678 │ │ (and see the CHANGELOG.md file online for a list of changes!) │ WARNING: Constructor for type "HyperSphere" was extended in `MicrobeAgents` without explicit qualification or import. │ NOTE: Assumed "HyperSphere" refers to `GeometryBasics.HyperSphere`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function HyperSphere end`. │ Hint: To silence the warning, qualify `HyperSphere` as `GeometryBasics.HyperSphere` in the method signature or explicitly `import GeometryBasics: HyperSphere`. └ Precompilation completed after 722.07s ################################################################################ # Testing # Testing MicrobeAgents Status `/tmp/jl_hFIj0d/Project.toml` [46ada45e] Agents v6.2.10 [b9118d5e] Autocorrelations v0.1.1 [a93c6f00] DataFrames v1.8.1 [31c24e10] Distributions v0.25.123 [5c1252a2] GeometryBasics v0.5.10 [f56206fc] LightSumTypes v5.2.2 [13c93d70] MeanSquaredDisplacement v0.3.1 [b17a4bac] MicrobeAgents v0.5.3 [94ee1d12] Quaternions v0.7.7 [90137ffa] StaticArrays v1.9.16 [2913bbd2] StatsBase v0.34.10 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_hFIj0d/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.43 [46ada45e] Agents v6.2.10 [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 ⌅ [1dc0ca97] ArrayTools v0.2.7 [b9118d5e] Autocorrelations v0.1.1 [39de3d68] AxisArrays v0.4.8 [0e736298] Bessels v0.2.8 [d1d4a3ce] BitFlags v0.1.9 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [38540f10] CommonSolve v0.2.6 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [f0e56b4a] ConcurrentUtilities v2.5.0 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [717857b8] DSP v0.8.4 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [460bff9d] ExceptionUnwrapping v0.1.11 [411431e0] Extents v0.1.6 [7a1cc6ca] FFTW v1.10.0 [5789e2e9] FileIO v1.17.1 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [5c1252a2] GeometryBasics v0.5.10 ⌃ [86223c79] Graphs v1.13.1 [cd3eb016] HTTP v1.10.19 [49057fa9] HybridStructs v0.2.1 [34004b35] HypergeometricFunctions v0.3.28 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.5 [8197267c] IntervalSets v0.7.13 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 ⌅ [033835bb] JLD2 v0.4.55 [692b3bcd] JLLWrappers v1.7.1 ⌅ [682c06a0] JSON v0.21.4 [b964fa9f] LaTeXStrings v1.4.0 [d1922b25] LightOSM v0.3.1 [f56206fc] LightSumTypes v5.2.2 [9c8b4983] LightXML v0.9.3 [2ab3a3ac] LogExpFunctions v0.3.29 [e6f89c97] LoggingExtras v1.2.0 [1914dd2f] MacroTools v0.5.16 [739be429] MbedTLS v1.1.9 [13c93d70] MeanSquaredDisplacement v0.3.1 ⌅ [626554b9] MetaGraphs v0.7.2 [b17a4bac] MicrobeAgents v0.5.3 [e1d29d7a] Missings v1.2.0 [b8a86587] NearestNeighbors v0.4.26 [6fe1bfb0] OffsetArrays v1.17.0 [925886fa] OnlineStatsBase v1.7.1 [4d8831e6] OpenSSL v1.6.1 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.3 [f27b6e38] Polynomials v4.1.0 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [94ee1d12] Quaternions v0.7.7 ⌅ [30b38841] QuickHeaps v0.1.2 [b3c3ace0] RangeArrays v0.3.2 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [6038ab10] Rotations v1.7.1 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.9 [efcf1570] Setfield v1.1.2 [777ac1f9] SimpleBufferStream v1.2.0 [699a6c99] SimpleTraits v0.9.5 [47aef6b3] SimpleWeightedGraphs v1.5.1 [a2af1166] SortingAlgorithms v1.2.2 [d4ead438] SpatialIndexing v0.1.6 [276daf66] SpecialFunctions v2.6.1 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 ⌅ [4c8beaf5] StaticGraphs v0.3.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 ⌅ [ff63dad9] StreamSampling v0.6.9 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [5c2747f8] URIs v1.6.1 [3a884ed6] UnPack v1.0.2 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [5ae413db] EarCut_jll v2.2.4+0 [f5851436] FFTW_jll v3.3.11+0 [1d5cc7b8] IntelOpenMP_jll v2025.2.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [856f044c] MKL_jll v2025.2.0+0 [c8ffd9c3] MbedTLS_jll v2.28.1010+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [02c8fc9c] XML2_jll v2.15.1+0 [1317d2d5] oneTBB_jll v2022.0.0+1 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [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 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.18.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... WARNING: Constructor for type "HyperSphere" was extended in `MicrobeAgents` without explicit qualification or import.  NOTE: Assumed "HyperSphere" refers to `GeometryBasics.HyperSphere`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function HyperSphere end`.  Hint: To silence the warning, qualify `HyperSphere` as `GeometryBasics.HyperSphere` in the method signature or explicitly `import GeometryBasics: HyperSphere`. 1 dependency had output during precompilation: ┌ MicrobeAgents │ [Output was shown above] └ ┌ Warning: From version 6.0 it is necessary to pass at least one of agent_step! or model_step! │ as keywords argument when defining the model. The old version is deprecated. │ Passing these functions to methods of the library which required them before │ version 6.0 is also deprecated since they can be retrieved from the model instance. │ In particular this means it is not needed to pass the stepping functions in step!, │ run!, offline_run!, ensemblerun!, abmplot, abmplot!, abmexploration, abmvideo and │ ABMObservable. └ @ Agents ~/.julia/packages/Agents/WuWeG/src/core/model_standard.jl:145 ┌ Warning: Agent type is not concrete. If your agent is parametrically typed, you're probably │ seeing this warning because you gave `Agent` instead of `Agent{Float64}` │ (for example) to this function. You can also create an instance of your agent │ and pass it to this function. If you want to use `Union` types for mixed agent │ models, you can silence this warning. │ If you are using `ContinuousAgent{D}` as agent type in version 6+, update │ to the new two-parameter version `ContinuousAgent{D,Float64}` to obtain │ the same behavior as previous Agents.jl versions. └ @ Agents ~/.julia/packages/Agents/WuWeG/src/core/model_validation.jl:15 Test Summary: | Pass Total Time MicrobeAgents.jl | 385 385 2m23.7s Testing MicrobeAgents tests passed Testing completed after 761.97s PkgEval succeeded after 1563.32s