Package evaluation to test DistributedStwdLDA on Julia 1.14.0-DEV.1584 (ac5fadde9b*) started at 2026-01-18T23:16:08.617 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.64s ################################################################################ # Installation # Installing DistributedStwdLDA... Resolving package versions... Installed Formatting ────────────────── v0.4.3 Installed CompositionsBase ──────────── v0.1.2 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed MacroTools ────────────────── v0.5.16 Installed DefineSingletons ──────────── v0.1.2 Installed FilePathsBase ─────────────── v0.9.24 Installed DataStructures ────────────── v0.18.22 Installed MicroCollections ──────────── v0.1.4 Installed AbstractTrees ─────────────── v0.4.5 Installed FillArrays ────────────────── v1.16.0 Installed Adapt ─────────────────────── v4.4.0 Installed InlineStrings ─────────────── v1.4.5 Installed HypergeometricFunctions ───── v0.3.28 Installed ConstructionBase ──────────── v1.6.0 Installed KernelDensity ─────────────── v0.6.10 Installed oneTBB_jll ────────────────── v2022.0.0+1 Installed MKL_jll ───────────────────── v2025.2.0+0 Installed AliasTables ───────────────── v1.1.3 Installed StatsBase ─────────────────── v0.33.21 Installed CodecZlib ─────────────────── v0.7.8 Installed TranscodingStreams ────────── v0.11.3 Installed Compat ────────────────────── v4.18.1 Installed OrderedCollections ────────── v1.8.1 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed RecipesBase ───────────────── v1.3.4 Installed DataAPI ───────────────────── v1.16.0 Installed ProgressLogging ───────────── v0.1.6 Installed InvertedIndices ───────────── v1.3.1 Installed Statistics ────────────────── v1.11.1 Installed ConsoleProgressMonitor ────── v0.1.2 Installed PrecompileTools ───────────── v1.3.3 Installed InitialValues ─────────────── v0.3.1 Installed IntelOpenMP_jll ───────────── v2025.2.0+0 Installed StatsAPI ──────────────────── v1.8.0 Installed DataValueInterfaces ───────── v1.0.0 Installed OffsetArrays ──────────────── v1.17.0 Installed FileIO ────────────────────── v1.17.1 Installed ArgCheck ──────────────────── v2.5.0 Installed SentinelArrays ────────────── v1.4.9 Installed ProgressMeter ─────────────── v1.11.0 Installed MCMCDiagnosticTools ───────── v0.2.6 Installed StaticArrays ──────────────── v1.9.16 Installed StaticArraysCore ──────────── v1.4.4 Installed LoggingExtras ─────────────── v1.2.0 Installed LogDensityProblems ────────── v2.2.0 Installed IrrationalConstants ───────── v0.2.6 Installed DistributedStwdLDA ────────── v0.2.1 Installed ChainRulesCore ────────────── v1.26.0 Installed BangBang ──────────────────── v0.3.40 Installed AbstractFFTs ──────────────── v1.5.0 Installed QuadGK ────────────────────── v2.11.2 Installed AxisAlgorithms ────────────── v1.1.0 Installed StringManipulation ────────── v0.4.2 Installed TerminalLoggers ───────────── v0.1.7 Installed Ratios ────────────────────── v0.4.5 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed Requires ──────────────────── v1.3.1 Installed LogExpFunctions ───────────── v0.3.29 Installed LeftChildRightSiblingTrees ── v0.2.1 Installed CSV ───────────────────────── v0.10.15 Installed Parsers ───────────────────── v2.8.3 Installed Rmath ─────────────────────── v0.9.0 Installed Interpolations ────────────── v0.16.2 Installed PrettyTables ──────────────── v2.4.0 Installed Distributions ─────────────── v0.25.123 Installed SplittablesBase ───────────── v0.1.15 Installed WoodburyMatrices ──────────── v1.1.0 Installed StatsFuns ─────────────────── v1.5.2 Installed PtrArrays ─────────────────── v1.3.0 Installed Tables ────────────────────── v1.12.1 Installed AbstractMCMC ──────────────── v4.4.2 Installed SpecialFunctions ──────────── v2.6.1 Installed Reexport ──────────────────── v1.2.2 Installed IntervalSets ──────────────── v0.7.13 Installed Transducers ───────────────── v0.4.80 Installed DataFrames ────────────────── v1.8.1 Installed Setfield ──────────────────── v1.1.2 Installed Preferences ───────────────── v1.5.1 Installed Missings ──────────────────── v1.2.0 Installed Baselet ───────────────────── v0.1.1 Installed ScientificTypesBase ───────── v3.0.0 Installed FFTW_jll ──────────────────── v3.3.11+0 Installed PooledArrays ──────────────── v1.4.3 Installed WeakRefStrings ────────────── v1.4.2 Installed FFTW ──────────────────────── v1.10.0 Installed JLLWrappers ───────────────── v1.7.1 Installed LaTeXStrings ──────────────── v1.4.0 Installed TableTraits ───────────────── v1.0.1 Installed PDMats ────────────────────── v0.11.35 Installed Crayons ───────────────────── v4.1.1 Installed IterTools ─────────────────── v1.10.0 Installed AxisArrays ────────────────── v0.4.8 Installed MCMCChains ────────────────── v5.7.1 Installed SortingAlgorithms ─────────── v1.2.2 Installed WorkerUtilities ───────────── v1.6.1 Installed StatisticalTraits ─────────── v3.5.0 Installed RangeArrays ───────────────── v0.3.2 Installed DocStringExtensions ───────── v0.9.5 Installed MLJModelInterface ─────────── v1.12.1 Installed NaturalSort ───────────────── v1.0.0 Installing 3 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact FFTW 2.2 MiB Updating `~/.julia/environments/v1.14/Project.toml` [4f7c0122] + DistributedStwdLDA v0.2.1 Updating `~/.julia/environments/v1.14/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 ⌅ [80f14c24] + AbstractMCMC v4.4.2 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [dce04be8] + ArgCheck v2.5.0 [13072b0f] + AxisAlgorithms v1.1.0 [39de3d68] + AxisArrays v0.4.8 ⌅ [198e06fe] + BangBang v0.3.40 [9718e550] + Baselet v0.1.1 [336ed68f] + CSV v0.10.15 [d360d2e6] + ChainRulesCore v1.26.0 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [88cd18e8] + ConsoleProgressMonitor v0.1.2 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [244e2a9f] + DefineSingletons v0.1.2 [4f7c0122] + DistributedStwdLDA v0.2.1 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [7a1cc6ca] + FFTW v1.10.0 [5789e2e9] + FileIO v1.17.1 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [59287772] + Formatting v0.4.3 [34004b35] + HypergeometricFunctions v0.3.28 [22cec73e] + InitialValues v0.3.1 [842dd82b] + InlineStrings v1.4.5 [a98d9a8b] + Interpolations v0.16.2 [8197267c] + IntervalSets v0.7.13 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [5ab0869b] + KernelDensity v0.6.10 [b964fa9f] + LaTeXStrings v1.4.0 [1d6d02ad] + LeftChildRightSiblingTrees v0.2.1 [6fdf6af0] + LogDensityProblems v2.2.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.2.0 ⌅ [c7f686f2] + MCMCChains v5.7.1 ⌅ [be115224] + MCMCDiagnosticTools v0.2.6 [e80e1ace] + MLJModelInterface v1.12.1 [1914dd2f] + MacroTools v0.5.16 ⌅ [128add7d] + MicroCollections v0.1.4 [e1d29d7a] + Missings v1.2.0 [c020b1a1] + NaturalSort v1.0.0 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 ⌃ [90014a1f] + PDMats v0.11.35 [69de0a69] + Parsers v2.8.3 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 ⌅ [08abe8d2] + PrettyTables v2.4.0 [33c8b6b6] + ProgressLogging v0.1.6 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [b3c3ace0] + RangeArrays v0.3.2 [c84ed2f1] + Ratios v0.4.5 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [30f210dd] + ScientificTypesBase v3.0.0 [91c51154] + SentinelArrays v1.4.9 [efcf1570] + Setfield v1.1.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [171d559e] + SplittablesBase v0.1.15 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [64bff920] + StatisticalTraits v3.5.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.2 [892a3eda] + StringManipulation v0.4.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [5d786b92] + TerminalLoggers v0.1.7 [3bb67fe8] + TranscodingStreams v0.11.3 ⌃ [28d57a85] + Transducers v0.4.80 [ea10d353] + WeakRefStrings v1.4.2 [efce3f68] + WoodburyMatrices v1.1.0 [76eceee3] + WorkerUtilities v1.6.1 [f5851436] + FFTW_jll v3.3.11+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [856f044c] + MKL_jll v2025.2.0+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+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 11.67s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4268.0 ms ✓ TestEnv 1 dependency successfully precompiled in 4 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling packages... 4552.4 ms ✓ MacroTools 1540.1 ms ✓ InlineStrings 846.5 ms ✓ Reexport 1218.7 ms ✓ ConstructionBase 2169.8 ms ✓ IrrationalConstants 841.7 ms ✓ DataValueInterfaces 931.3 ms ✓ StatsAPI 1267.9 ms ✓ IterTools 1070.7 ms ✓ IntervalSets 930.5 ms ✓ ArgCheck 1251.7 ms ✓ TranscodingStreams 845.3 ms ✓ LaTeXStrings 1811.5 ms ✓ Baselet 883.2 ms ✓ Statistics 764.2 ms ✓ StaticArraysCore 704.0 ms ✓ PtrArrays 652.1 ms ✓ NaturalSort 799.2 ms ✓ DataAPI 721.1 ms ✓ InvertedIndices 737.5 ms ✓ CompositionsBase 1173.6 ms ✓ AbstractTrees 1481.8 ms ✓ InitialValues 1045.3 ms ✓ AbstractFFTs 1067.6 ms ✓ WorkerUtilities 2220.1 ms ✓ FillArrays 888.0 ms ✓ ScientificTypesBase 904.5 ms ✓ RangeArrays 1332.9 ms ✓ OrderedCollections 1195.5 ms ✓ ProgressLogging 1147.4 ms ✓ DocStringExtensions 879.4 ms ✓ DefineSingletons 1654.5 ms ✓ OffsetArrays 841.8 ms ✓ IteratorInterfaceExtensions 1879.0 ms ✓ Crayons ┌ Warning: DEPRECATION NOTICE │ │ Formatting.jl has been unmaintained for a while, with some serious │ correctness bugs compromising the original purpose of the package. As a result, │ it has been deprecated - consider using an alternative, such as │ `Format.jl` (https://github.com/JuliaString/Format.jl) or the `Printf` stdlib directly. │ │ If you are not using Formatting.jl as a direct dependency, please consider │ opening an issue on any packages you are using that do use it as a dependency. │ From Julia 1.9 onwards, you can query `]why Formatting` to figure out which │ package originally brings it in as a dependency. └ @ Formatting ~/.julia/packages/Formatting/3VxOt/src/Formatting.jl:12 1307.1 ms ✓ Formatting 1194.4 ms ✓ Requires 1718.4 ms ✓ PDMats 1516.2 ms ✓ WoodburyMatrices 2136.2 ms ✓ SentinelArrays 1106.3 ms ✓ LoggingExtras 1744.4 ms ✓ ProgressMeter 1332.7 ms ✓ Compat 1417.1 ms ✓ Preferences 987.3 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 1102.5 ms ✓ IntervalSets → IntervalSetsRandomExt 1028.6 ms ✓ ConstructionBase → ConstructionBaseIntervalSetsExt 1395.8 ms ✓ CodecZlib 1616.8 ms ✓ Statistics → SparseArraysExt 919.9 ms ✓ IntervalSets → IntervalSetsStatisticsExt 1060.1 ms ✓ AliasTables 1016.4 ms ✓ Missings 1088.4 ms ✓ PooledArrays 949.2 ms ✓ LeftChildRightSiblingTrees 4308.3 ms ✓ AbstractFFTs → AbstractFFTsTestExt 1566.6 ms ✓ FillArrays → FillArraysSparseArraysExt 1062.2 ms ✓ FillArrays → FillArraysStatisticsExt 943.1 ms ✓ StatisticalTraits 1415.5 ms ✓ LogExpFunctions 2259.4 ms ✓ LogDensityProblems 836.8 ms ✓ TableTraits 905.5 ms ✓ Ratios 1000.6 ms ✓ Adapt 9269.9 ms ✓ FileIO 1498.8 ms ✓ FillArrays → FillArraysPDMatsExt 1464.5 ms ✓ AxisAlgorithms 1034.2 ms ✓ ConsoleProgressMonitor 957.2 ms ✓ Compat → CompatLinearAlgebraExt 1005.1 ms ✓ PrecompileTools 1238.3 ms ✓ JLLWrappers 3032.5 ms ✓ Setfield 1609.3 ms ✓ AxisArrays 2054.3 ms ✓ TerminalLoggers 3233.3 ms ✓ MLJModelInterface 2119.7 ms ✓ Tables 1844.1 ms ✓ Adapt → AdaptSparseArraysExt 1149.1 ms ✓ OffsetArrays → OffsetArraysAdaptExt 3171.7 ms ✓ ChainRulesCore 2204.8 ms ✓ FilePathsBase 4087.8 ms ✓ DataStructures 3154.0 ms ✓ StringManipulation 13946.9 ms ✓ StaticArrays 2787.8 ms ✓ RecipesBase 16376.3 ms ✓ Parsers 1501.1 ms ✓ Rmath_jll 1481.4 ms ✓ OpenSpecFun_jll 5294.4 ms ✓ IntelOpenMP_jll 5174.0 ms ✓ oneTBB_jll 1515.7 ms ✓ FFTW_jll 4104.7 ms ✓ SplittablesBase 1659.2 ms ✓ BangBang 1384.2 ms ✓ ChainRulesCore → ChainRulesCoreSparseArraysExt 1006.2 ms ✓ AbstractFFTs → AbstractFFTsChainRulesCoreExt 3715.2 ms ✓ LogExpFunctions → LogExpFunctionsChainRulesCoreExt 2849.8 ms ✓ FilePathsBase → FilePathsBaseTestExt 1001.2 ms ✓ FilePathsBase → FilePathsBaseMmapExt 1571.4 ms ✓ SortingAlgorithms 2802.9 ms ✓ QuadGK 28208.2 ms ✓ PrettyTables 1512.9 ms ✓ StaticArrays → StaticArraysStatisticsExt 1597.3 ms ✓ StaticArrays → StaticArraysChainRulesCoreExt 1554.5 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 1698.4 ms ✓ FillArrays → FillArraysStaticArraysExt 1486.8 ms ✓ Adapt → AdaptStaticArraysExt 1397.5 ms ✓ IntervalSets → IntervalSetsRecipesBaseExt 1079.5 ms ✓ InlineStrings → ParsersExt 1716.4 ms ✓ Rmath 5026.5 ms ✓ SpecialFunctions  Downloading artifact: IntelOpenMP  Downloading artifact: oneTBB 10559.0 ms ✓ MKL_jll 2043.6 ms ✓ MicroCollections 1050.0 ms ✓ BangBang → BangBangChainRulesCoreExt 1621.3 ms ✓ BangBang → BangBangStaticArraysExt 4786.3 ms ✓ StatsBase 72577.3 ms ✓ DataFrames 4153.7 ms ✓ Interpolations 2402.4 ms ✓ WeakRefStrings 4095.1 ms ✓ SpecialFunctions → SpecialFunctionsChainRulesCoreExt 2247.5 ms ✓ HypergeometricFunctions 6881.9 ms ✓ FFTW 6807.2 ms ✓ Transducers 5068.6 ms ✓ BangBang → BangBangDataFramesExt 27479.2 ms ✓ CSV 2753.6 ms ✓ StatsFuns 5263.7 ms ✓ Transducers → TransducersDataFramesExt 4726.4 ms ✓ AbstractMCMC 3647.1 ms ✓ StatsFuns → StatsFunsChainRulesCoreExt 10230.1 ms ✓ Distributions 3219.9 ms ✓ Distributions → DistributionsTestExt 3427.1 ms ✓ Distributions → DistributionsChainRulesCoreExt 5391.0 ms ✓ MCMCDiagnosticTools 5336.1 ms ✓ KernelDensity 9969.3 ms ✓ MCMCChains 19016.1 ms ✓ DistributedStwdLDA 132 dependencies successfully precompiled in 464 seconds. 41 already precompiled. 2 dependencies had output during precompilation: ┌ MKL_jll │ Downloading artifact: IntelOpenMP │ Downloading artifact: oneTBB └ ┌ Formatting │ ┌ Warning: DEPRECATION NOTICE │ │ │ │ Formatting.jl has been unmaintained for a while, with some serious │ │ correctness bugs compromising the original purpose of the package. As a result, │ │ it has been deprecated - consider using an alternative, such as │ │ `Format.jl` (https://github.com/JuliaString/Format.jl) or the `Printf` stdlib directly. │ │ │ │ If you are not using Formatting.jl as a direct dependency, please consider │ │ opening an issue on any packages you are using that do use it as a dependency. │ │ From Julia 1.9 onwards, you can query `]why Formatting` to figure out which │ │ package originally brings it in as a dependency. │ └ @ Formatting ~/.julia/packages/Formatting/3VxOt/src/Formatting.jl:12 └ Precompilation completed after 473.65s ################################################################################ # Testing # Testing DistributedStwdLDA Status `/tmp/jl_1eBrUt/Project.toml` [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [4f7c0122] DistributedStwdLDA v0.2.1 [31c24e10] Distributions v0.25.123 [5789e2e9] FileIO v1.17.1 ⌅ [c7f686f2] MCMCChains v5.7.1 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 ⌅ [2913bbd2] StatsBase v0.33.21 [8ba89e20] Distributed v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [1a1011a3] SharedArrays v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_1eBrUt/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 ⌅ [80f14c24] AbstractMCMC v4.4.2 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [dce04be8] ArgCheck v2.5.0 [13072b0f] AxisAlgorithms v1.1.0 [39de3d68] AxisArrays v0.4.8 ⌅ [198e06fe] BangBang v0.3.40 [9718e550] Baselet v0.1.1 [336ed68f] CSV v0.10.15 [d360d2e6] ChainRulesCore v1.26.0 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [88cd18e8] ConsoleProgressMonitor v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [244e2a9f] DefineSingletons v0.1.2 [4f7c0122] DistributedStwdLDA v0.2.1 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [7a1cc6ca] FFTW v1.10.0 [5789e2e9] FileIO v1.17.1 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [59287772] Formatting v0.4.3 [34004b35] HypergeometricFunctions v0.3.28 [22cec73e] InitialValues v0.3.1 [842dd82b] InlineStrings v1.4.5 [a98d9a8b] Interpolations v0.16.2 [8197267c] IntervalSets v0.7.13 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [5ab0869b] KernelDensity v0.6.10 [b964fa9f] LaTeXStrings v1.4.0 [1d6d02ad] LeftChildRightSiblingTrees v0.2.1 [6fdf6af0] LogDensityProblems v2.2.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e6f89c97] LoggingExtras v1.2.0 ⌅ [c7f686f2] MCMCChains v5.7.1 ⌅ [be115224] MCMCDiagnosticTools v0.2.6 [e80e1ace] MLJModelInterface v1.12.1 [1914dd2f] MacroTools v0.5.16 ⌅ [128add7d] MicroCollections v0.1.4 [e1d29d7a] Missings v1.2.0 [c020b1a1] NaturalSort v1.0.0 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 ⌃ [90014a1f] PDMats v0.11.35 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 ⌅ [08abe8d2] PrettyTables v2.4.0 [33c8b6b6] ProgressLogging v0.1.6 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [b3c3ace0] RangeArrays v0.3.2 [c84ed2f1] Ratios v0.4.5 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [30f210dd] ScientificTypesBase v3.0.0 [91c51154] SentinelArrays v1.4.9 [efcf1570] Setfield v1.1.2 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [171d559e] SplittablesBase v0.1.15 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [64bff920] StatisticalTraits v3.5.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [5d786b92] TerminalLoggers v0.1.7 [3bb67fe8] TranscodingStreams v0.11.3 ⌃ [28d57a85] Transducers v0.4.80 [ea10d353] WeakRefStrings v1.4.2 [efce3f68] WoodburyMatrices v1.1.0 [76eceee3] WorkerUtilities v1.6.1 [f5851436] FFTW_jll v3.3.11+0 [1d5cc7b8] IntelOpenMP_jll v2025.2.0+0 [856f044c] MKL_jll v2025.2.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+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 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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: DEPRECATION NOTICE │ │ Formatting.jl has been unmaintained for a while, with some serious │ correctness bugs compromising the original purpose of the package. As a result, │ it has been deprecated - consider using an alternative, such as │ `Format.jl` (https://github.com/JuliaString/Format.jl) or the `Printf` stdlib directly. │ │ If you are not using Formatting.jl as a direct dependency, please consider │ opening an issue on any packages you are using that do use it as a dependency. │ From Julia 1.9 onwards, you can query `]why Formatting` to figure out which │ package originally brings it in as a dependency. └ @ Formatting ~/.julia/packages/Formatting/3VxOt/src/Formatting.jl:12 1 dependency had output during precompilation: ┌ Formatting │ ┌ Warning: DEPRECATION NOTICE │ │ │ │ Formatting.jl has been unmaintained for a while, with some serious │ │ correctness bugs compromising the original purpose of the package. As a result, │ │ it has been deprecated - consider using an alternative, such as │ │ `Format.jl` (https://github.com/JuliaString/Format.jl) or the `Printf` stdlib directly. │ │ │ │ If you are not using Formatting.jl as a direct dependency, please consider │ │ opening an issue on any packages you are using that do use it as a dependency. │ │ From Julia 1.9 onwards, you can query `]why Formatting` to figure out which │ │ package originally brings it in as a dependency. │ └ @ Formatting ~/.julia/packages/Formatting/3VxOt/src/Formatting.jl:12 └ detected 3 partition running dsLDA with nworkers:4 dsLDA: loading bulk data dsLDA: loading sc data dsLDA: loading meta data pre-qc size of sc data= (934, 2019) pre-qc size of bulk data= (3, 2019) ┌ Warning: `delete!(df::DataFrame, inds)` is deprecated, use `deleteat!(df::DataFrame, inds)` instead. │ caller = filterCells(data::DataFrame, param::Symbol, thresh::Float64) at durian.jl:75 └ @ Core ~/.julia/packages/DistributedStwdLDA/EgTLF/src/durian.jl:75 found 1278 genes expressed in remaining cell types after removing cell types with < 1 cells post-qc deconvolution post-cell qc size of sc data= (926, 1278) imputation post-cell qc size of sc data= (926, 375) post-qc size of bulk data= (3, 1278) bulk log1p scaling selected, add pseudocount of 1, then log transform initializing doc 1 initializing doc 2 initializing doc 3 checking env.... set 3 for corpus of length 3 sc ident selected, add betapseudo(0.0),betaeps(0.01) starting MCMC chain 1 with n = 1000 starting chain 1 begin initializing state arrays: T,A,D,Z,J,W initialization complete for: Z{SharedMatrix{Bool}}: 20417 bytes J{SharedMatrix{Bool}}: 15528 bytes W{SharedMatrix{Bool}}: 6249003 bytes T{SharedVector{Int32}}: 20401 bytes A{SharedVector{Int32}}: 20401 bytes D{SharedVector{Int32}}: 20401 bytes nwinc{SharedMatrix{Int64}}: 123549 bytes allocated nw{Matrix{Int64}}: 122688 bytes ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 Running 1000 samples... 0%| | ETA: 3:11:12 Running 1000 samples... 1%|▍ | ETA: 0:34:33 Running 1000 samples... 2%|▌ | ETA: 0:24:07 Running 1000 samples... 2%|▋ | ETA: 0:18:46 Running 1000 samples... 3%|▊ | ETA: 0:16:02 Running 1000 samples... 4%|█ | ETA: 0:13:43 Running 1000 samples... 4%|█▏ | ETA: 0:12:03 Running 1000 samples... 5%|█▍ | ETA: 0:10:51 Running 1000 samples... 5%|█▌ | ETA: 0:09:53 Running 1000 samples... 6%|█▋ | ETA: 0:09:16 Running 1000 samples... 6%|█▊ | ETA: 0:08:37 Running 1000 samples... 7%|██ | ETA: 0:08:04 Running 1000 samples... 8%|██▏ | ETA: 0:07:37 Running 1000 samples... 8%|██▎ | ETA: 0:07:13 Running 1000 samples... 9%|██▌ | ETA: 0:06:46 Running 1000 samples... 10%|██▊ | ETA: 0:06:23 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initializing state arrays: T,A,D,Z,J,W initialization complete for: Z{SharedMatrix{Bool}}: 20417 bytes J{SharedMatrix{Bool}}: 15528 bytes W{SharedMatrix{Bool}}: 6249003 bytes T{SharedVector{Int32}}: 20401 bytes A{SharedVector{Int32}}: 20401 bytes D{SharedVector{Int32}}: 20401 bytes nwinc{SharedMatrix{Int64}}: 123549 bytes allocated nw{Matrix{Int64}}: 122688 bytes Running 1000 samples... 1%|▎ | ETA: 0:02:29 Running 1000 samples... 2%|▍ | ETA: 0:02:22 Running 1000 samples... 2%|▋ | ETA: 0:02:18 Running 1000 samples... 3%|▉ | ETA: 0:02:17 Running 1000 samples... 4%|█▏ | ETA: 0:02:15 Running 1000 samples... 5%|█▍ | ETA: 0:02:13 Running 1000 samples... 6%|█▌ | ETA: 0:02:12 Running 1000 samples... 6%|█▊ | ETA: 0:02:10 Running 1000 samples... 7%|██ | ETA: 0:02:09 Running 1000 samples... 8%|██▎ | ETA: 0:02:07 Running 1000 samples... 9%|██▍ | ETA: 0:02:06 Running 1000 samples... 10%|██▋ | ETA: 0:02:05 Running 1000 samples... 10%|██▉ | ETA: 0:02:03 Running 1000 samples... 11%|███▏ | ETA: 0:02:02 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94%|██████████████████████████▌ | ETA: 0:00:09 Running 1000 samples... 95%|██████████████████████████▋ | ETA: 0:00:08 Running 1000 samples... 96%|██████████████████████████▊ | ETA: 0:00:07 Running 1000 samples... 96%|███████████████████████████ | ETA: 0:00:06 Running 1000 samples... 97%|███████████████████████████▏| ETA: 0:00:05 Running 1000 samples... 98%|███████████████████████████▎| ETA: 0:00:04 Running 1000 samples... 98%|███████████████████████████▍| ETA: 0:00:03 Running 1000 samples... 98%|███████████████████████████▋| ETA: 0:00:02 Running 1000 samples... 99%|███████████████████████████▊| ETA: 0:00:01 Running 1000 samples... 99%|███████████████████████████▉| ETA: 0:00:01 Running 1000 samples... 100%|████████████████████████████| Time: 0:02:38 sampling: chain 2 mcmc has finished analysis: begin convergence diagnostics r-hat < 1.1, deconvolution succeeds 0.1924986613423668Test Summary: | Pass Total Time deconvolution: baron | 1 1 9m12.2s Testing DistributedStwdLDA tests passed Testing completed after 883.39s PkgEval succeeded after 1607.19s