Package evaluation to test OnlinePCA on Julia 1.14.0-DEV.30 (073666df8b*) started at 2025-11-06T23:57:51.132 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.28s ################################################################################ # Installation # Installing OnlinePCA... Resolving package versions... Installed FilePathsBase ─────────────── v0.9.24 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed MacroTools ────────────────── v0.5.16 Installed URIs ──────────────────────── v1.6.1 Installed CodecZstd ─────────────────── v0.8.6 Installed DataStructures ────────────── v0.19.3 Installed GLM ───────────────────────── v1.9.0 Installed InlineStrings ─────────────── v1.4.5 Installed Mux ───────────────────────── v1.0.2 Installed FillArrays ────────────────── v1.15.0 Installed DelimitedFiles ────────────── v1.9.1 Installed HypergeometricFunctions ───── v0.3.28 Installed libaec_jll ────────────────── v1.1.4+0 Installed StatsModels ───────────────── v0.7.7 Installed MPICH_jll ─────────────────── v4.3.2+0 Installed AliasTables ───────────────── v1.1.3 Installed OnlinePCA ─────────────────── v0.3.10 Installed StatsBase ─────────────────── v0.34.7 Installed ConcurrentUtilities ───────── v2.5.0 Installed CodecZlib ─────────────────── v0.7.8 Installed Observables ───────────────── v0.5.5 Installed ExceptionUnwrapping ───────── v0.1.11 Installed OrderedCollections ────────── v1.8.1 Installed MicrosoftMPI_jll ──────────── v10.1.4+3 Installed Compat ────────────────────── v4.18.1 Installed TranscodingStreams ────────── v0.11.3 Installed ShiftedArrays ─────────────── v2.0.0 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed TensorCore ────────────────── v0.1.1 Installed Kaleido_jll ───────────────── v0.2.1+0 Installed InvertedIndices ───────────── v1.3.1 Installed DataAPI ───────────────────── v1.16.0 Installed Statistics ────────────────── v1.11.1 Installed PrecompileTools ───────────── v1.3.3 Installed WebSockets ────────────────── v1.6.0 Installed Xorg_libpciaccess_jll ─────── v0.18.1+0 Installed StatsAPI ──────────────────── v1.7.1 Installed DataValueInterfaces ───────── v1.0.0 Installed Hiccup ────────────────────── v0.2.2 Installed Colors ────────────────────── v0.13.1 Installed FunctionalCollections ─────── v0.5.0 Installed ProgressMeter ─────────────── v1.11.0 Installed MbedTLS ───────────────────── v1.1.9 Installed SentinelArrays ────────────── v1.4.8 Installed LoggingExtras ─────────────── v1.2.0 Installed OpenSSL ───────────────────── v1.6.0 Installed TextWrap ──────────────────── v1.0.2 Installed IrrationalConstants ───────── v0.2.6 Installed AssetRegistry ─────────────── v0.1.0 Installed QuadGK ────────────────────── v2.11.2 Installed StringManipulation ────────── v0.4.1 Installed ColorTypes ────────────────── v0.12.1 Installed ColorVectorSpace ──────────── v0.11.0 Installed Requires ──────────────────── v1.3.1 Installed Widgets ───────────────────── v0.6.7 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed Pidfile ───────────────────── v1.3.0 Installed HTTP ──────────────────────── v1.10.19 Installed ArgParse ──────────────────── v1.2.0 Installed HDF5_jll ──────────────────── v1.14.6+0 Installed LogExpFunctions ───────────── v0.3.29 Installed BitFlags ──────────────────── v0.1.9 Installed OpenMPI_jll ───────────────── v5.0.8+0 Installed JSON ──────────────────────── v0.21.4 Installed Parsers ───────────────────── v2.8.3 Installed PrettyTables ──────────────── v3.1.0 Installed Hwloc_jll ─────────────────── v2.12.2+0 Installed Rmath ─────────────────────── v0.9.0 Installed Distributions ─────────────── v0.25.122 Installed Parameters ────────────────── v0.12.3 Installed StatsFuns ─────────────────── v1.5.2 Installed Tables ────────────────────── v1.12.1 Installed PlotlyKaleido ─────────────── v2.3.0 Installed MatrixMarket ──────────────── v0.5.2 Installed WebIO ─────────────────────── v0.8.21 Installed XML2_jll ──────────────────── v2.13.9+0 Installed PtrArrays ─────────────────── v1.3.0 Installed Reexport ──────────────────── v1.2.2 Installed SpecialFunctions ──────────── v2.6.1 Installed Preferences ───────────────── v1.5.0 Installed FixedPointNumbers ─────────── v0.8.5 Installed Blink ─────────────────────── v0.12.9 Installed PlotlyBase ────────────────── v0.8.21 Installed SimpleBufferStream ────────── v1.2.0 Installed Missings ──────────────────── v1.2.0 Installed DataFrames ────────────────── v1.8.1 Installed MPIPreferences ────────────── v0.1.11 Installed PooledArrays ──────────────── v1.4.3 Installed WeakRefStrings ────────────── v1.4.2 Installed JLLWrappers ───────────────── v1.7.1 Installed TableTraits ───────────────── v1.0.1 Installed JSExpr ────────────────────── v0.5.4 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed LaTeXStrings ──────────────── v1.4.0 Installed Mustache ──────────────────── v1.0.21 Installed MbedTLS_jll ───────────────── v2.28.10+0 Installed PDMats ────────────────────── v0.11.36 Installed SortingAlgorithms ─────────── v1.2.2 Installed Crayons ───────────────────── v4.1.1 Installed Lazy ──────────────────────── v0.15.1 Installed UnPack ────────────────────── v1.0.2 Installed WorkerUtilities ───────────── v1.6.1 Installed MPItrampoline_jll ─────────── v5.5.4+0 Installed ColorSchemes ──────────────── v3.31.0 Installed DocStringExtensions ───────── v0.9.5 Installed PlotlyJS ──────────────────── v0.18.17 Installed HDF5 ──────────────────────── v0.17.2 Installed CSV ───────────────────────── v0.10.15 Installing 17 artifacts Installed artifact Xorg_libpciaccess 24.8 KiB Installed artifact mathjax 18.7 KiB Installed artifact Rmath 121.9 KiB Installed artifact web 215.6 KiB Installed artifact libaec 49.6 KiB Installed artifact Hwloc 3.5 MiB Installed artifact Libiconv 1.9 MiB Installed artifact plotly 2.3 MiB Installed artifact plotly-base-artifacts 430.0 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact XML2 2.5 MiB Installed artifact MbedTLS 2.2 MiB Installed artifact plotly-artifacts 1.7 MiB Installed artifact HDF5 5.7 MiB Installed artifact MPICH 3.3 MiB Installed artifact electronjs_app 79.1 MiB Installed artifact Kaleido 75.3 MiB Updating `~/.julia/environments/v1.14/Project.toml` [975b03d1] + OnlinePCA v0.3.10 Updating `~/.julia/environments/v1.14/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [c7e460c6] + ArgParse v1.2.0 [bf4720bc] + AssetRegistry v0.1.0 [d1d4a3ce] + BitFlags v0.1.9 [ad839575] + Blink v0.12.9 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.6 [35d6a980] + ColorSchemes v3.31.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.1 [34da2185] + Compat v4.18.1 [f0e56b4a] + ConcurrentUtilities v2.5.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [460bff9d] + ExceptionUnwrapping v0.1.11 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.15.0 [53c48c17] + FixedPointNumbers v0.8.5 [de31a74c] + FunctionalCollections v0.5.0 [38e38edf] + GLM v1.9.0 [f67ccb44] + HDF5 v0.17.2 [cd3eb016] + HTTP v1.10.19 [9fb69e20] + Hiccup v0.2.2 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [97c1335a] + JSExpr v0.5.4 ⌅ [682c06a0] + JSON v0.21.4 [b964fa9f] + LaTeXStrings v1.4.0 [50d2b5c4] + Lazy v0.15.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.2.0 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.16 [4d4711f2] + MatrixMarket v0.5.2 [739be429] + MbedTLS v1.1.9 [e1d29d7a] + Missings v1.2.0 [ffc61752] + Mustache v1.0.21 [a975b10e] + Mux v1.0.2 [510215fc] + Observables v0.5.5 [975b03d1] + OnlinePCA v0.3.10 [4d8831e6] + OpenSSL v1.6.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.36 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [fa939f87] + Pidfile v1.3.0 [a03496cd] + PlotlyBase v0.8.21 [f0f68f2c] + PlotlyJS v0.18.17 [f2990250] + PlotlyKaleido v2.3.0 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.0 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [777ac1f9] + SimpleBufferStream v1.2.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.7 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.7 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [62fd8b95] + TensorCore v0.1.1 [b718987f] + TextWrap v1.0.2 [3bb67fe8] + TranscodingStreams v0.11.3 [5c2747f8] + URIs v1.6.1 [3a884ed6] + UnPack v1.0.2 [ea10d353] + WeakRefStrings v1.4.2 [0f1e0344] + WebIO v0.8.21 [104b5d7c] + WebSockets v1.6.0 [cc8bc4a8] + Widgets v0.6.7 [76eceee3] + WorkerUtilities v1.6.1 [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.2+0 [f7e6163d] + Kaleido_jll v0.2.1+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [7cb0a576] + MPICH_jll v4.3.2+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [c8ffd9c3] + MbedTLS_jll v2.28.10+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.8+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] + libaec_jll v1.1.4+0 [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 v1.12.0 [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 v1.13.0 [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 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.11.0 [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 v8.16.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.9.9 [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 v1.67.1+0 [3f19e933] + p7zip_jll v17.6.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Building WebIO ───→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/0eef0765186f7452e52236fa42ca8c9b3c11c6e3/build.log` Building PlotlyJS → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/287e092914da6c91f002aafcf82a2ec065bf94a3/build.log` Installation completed after 88.86s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4049.8 ms ✓ TestEnv 1 dependency successfully precompiled in 4 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... 4361.6 ms ✓ MacroTools 1673.0 ms ✓ InlineStrings 791.5 ms ✓ Reexport 1070.3 ms ✓ TensorCore 2180.5 ms ✓ IrrationalConstants 806.2 ms ✓ DataValueInterfaces 896.0 ms ✓ StatsAPI 1110.1 ms ✓ Observables 1388.3 ms ✓ TranscodingStreams 870.9 ms ✓ TextWrap 849.0 ms ✓ LaTeXStrings 1124.5 ms ✓ Statistics 1589.7 ms ✓ PtrArrays 1182.7 ms ✓ SimpleBufferStream 904.0 ms ✓ DataAPI 1389.1 ms ✓ URIs 1226.0 ms ✓ InvertedIndices 1288.1 ms ✓ BitFlags 1233.5 ms ✓ ShiftedArrays 989.6 ms ✓ WorkerUtilities 1990.4 ms ✓ FillArrays 785.3 ms ✓ UnPack 1326.8 ms ✓ OrderedCollections 1196.0 ms ✓ DocStringExtensions 753.9 ms ✓ IteratorInterfaceExtensions 1907.2 ms ✓ Crayons 1017.6 ms ✓ DelimitedFiles 1184.2 ms ✓ Requires 1758.6 ms ✓ ConcurrentUtilities 1232.8 ms ✓ SuiteSparse 2669.9 ms ✓ SentinelArrays 1069.9 ms ✓ LoggingExtras 1714.0 ms ✓ ProgressMeter 1179.3 ms ✓ Compat 1164.7 ms ✓ Preferences 1411.4 ms ✓ Pidfile 1648.6 ms ✓ ExceptionUnwrapping 1272.2 ms ✓ FunctionalCollections 5445.0 ms ✓ Lazy 1380.3 ms ✓ Hiccup 1710.9 ms ✓ CodecZstd 980.4 ms ✓ CodecZlib 1720.1 ms ✓ ArgParse 1441.7 ms ✓ Statistics → SparseArraysExt 3891.5 ms ✓ FixedPointNumbers 979.8 ms ✓ AliasTables 1019.9 ms ✓ Missings 1073.3 ms ✓ PooledArrays 4087.9 ms ✓ OpenSSL 1535.8 ms ✓ FillArrays → FillArraysSparseArraysExt 955.4 ms ✓ FillArrays → FillArraysStatisticsExt 1085.4 ms ✓ Parameters 3391.4 ms ✓ DataStructures 1446.8 ms ✓ LogExpFunctions 921.3 ms ✓ TableTraits 1830.5 ms ✓ PDMats 1080.5 ms ✓ Compat → CompatLinearAlgebraExt 1605.5 ms ✓ PrecompileTools 1421.3 ms ✓ JLLWrappers 1513.9 ms ✓ MPIPreferences 1453.6 ms ✓ MatrixMarket 2897.3 ms ✓ ColorTypes 1952.5 ms ✓ SortingAlgorithms 2423.7 ms ✓ QuadGK 1987.4 ms ✓ Tables 1385.5 ms ✓ FillArrays → FillArraysPDMatsExt 2222.6 ms ✓ FilePathsBase 2958.1 ms ✓ StringManipulation 16627.9 ms ✓ Parsers 1448.6 ms ✓ Kaleido_jll 1358.8 ms ✓ Rmath_jll 1142.1 ms ✓ MicrosoftMPI_jll 1384.3 ms ✓ OpenSpecFun_jll 1459.4 ms ✓ libaec_jll 1445.2 ms ✓ Xorg_libpciaccess_jll 1472.0 ms ✓ Libiconv_jll 1496.3 ms ✓ MbedTLS_jll 4637.1 ms ✓ MPItrampoline_jll 1373.6 ms ✓ ColorTypes → StyledStringsExt 8313.1 ms ✓ Colors 3919.5 ms ✓ ColorVectorSpace 4611.7 ms ✓ StatsBase 1275.4 ms ✓ Mustache 2928.2 ms ✓ FilePathsBase → FilePathsBaseTestExt 933.9 ms ✓ FilePathsBase → FilePathsBaseMmapExt 40388.3 ms ✓ PrettyTables 3800.8 ms ✓ JSON 957.3 ms ✓ InlineStrings → ParsersExt 1512.3 ms ✓ Rmath 5160.2 ms ✓ SpecialFunctions 1363.0 ms ✓ XML2_jll 2147.1 ms ✓ MbedTLS 1938.0 ms ✓ Widgets 8525.1 ms ✓ ColorSchemes 1428.3 ms ✓ PDMats → StatsBaseExt 92127.2 ms ✓ DataFrames 1296.3 ms ✓ PlotlyKaleido 1046.5 ms ✓ AssetRegistry 2755.2 ms ✓ WeakRefStrings 2555.1 ms ✓ HypergeometricFunctions 1448.9 ms ✓ ColorVectorSpace → SpecialFunctionsExt 1609.6 ms ✓ Hwloc_jll 27534.1 ms ✓ HTTP 13715.4 ms ✓ PlotlyBase 31471.6 ms ✓ CSV 3017.9 ms ✓ StatsFuns 5271.9 ms ✓ MPICH_jll 5249.9 ms ✓ OpenMPI_jll 4721.1 ms ✓ WebSockets 8648.3 ms ✓ Mux 18227.9 ms ✓ PlotlyBase → DataFramesExt 5004.4 ms ✓ StatsModels 9383.7 ms ✓ Distributions 6005.0 ms ✓ HDF5_jll 8388.7 ms ✓ WebIO 5346.5 ms ✓ GLM 3763.4 ms ✓ Distributions → DistributionsTestExt 9192.8 ms ✓ PlotlyBase → DistributionsExt 15455.8 ms ✓ HDF5 8406.6 ms ✓ JSExpr 12445.6 ms ✓ Blink 18962.7 ms ✓ PlotlyJS 14593.5 ms ✓ PlotlyJS → CSVExt 20165.5 ms ✓ PlotlyJS → DataFramesExt 18494.9 ms ✓ OnlinePCA 125 dependencies successfully precompiled in 610 seconds. 39 already precompiled. 2 dependencies had output during precompilation: ┌ WebSockets │ WARNING: Imported binding Logging.termlength was undeclared at import time during import to WebSockets. │ WARNING: Imported binding Logging.showvalue was undeclared at import time during import to WebSockets. └ ┌ PlotlyBase → DistributionsExt │ WARNING: Constructor for type "Plot" was extended in `DistributionsExt` without explicit qualification or import. │ NOTE: Assumed "Plot" refers to `PlotlyBase.Plot`. 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 Plot end`. │ Hint: To silence the warning, qualify `Plot` as `PlotlyBase.Plot` in the method signature or explicitly `import PlotlyBase: Plot`. └ Precompilation completed after 618.41s ################################################################################ # Testing # Testing OnlinePCA Test Could not use exact versions of packages in manifest, re-resolving. Note: if you do not check your manifest file into source control, then you can probably ignore this message. However, if you do check your manifest file into source control, then you probably want to pass the `allow_reresolve = false` kwarg when calling the `Pkg.test` function. Updating `/tmp/jl_nWbG9X/Project.toml` [31c24e10] ↑ Distributions v0.25.111 ⇒ v0.25.122 [1a297f60] ↑ FillArrays v1.12.0 ⇒ v1.15.0 [975b03d1] + OnlinePCA v0.3.10 [10745b16] ↑ Statistics v1.10.0 ⇒ v1.11.1 [37e2e46d] ~ LinearAlgebra ⇒ v1.13.0 [2f01184e] ↑ SparseArrays v1.10.0 ⇒ v1.13.0 [8dfed614] ~ Test ⇒ v1.11.0 Updating `/tmp/jl_nWbG9X/Manifest.toml` [bf4720bc] + AssetRegistry v0.1.0 [d1d4a3ce] + BitFlags v0.1.9 [ad839575] + Blink v0.12.9 [336ed68f] + CSV v0.10.15 [944b1d66] ↑ CodecZlib v0.7.6 ⇒ v0.7.8 [6b39b394] + CodecZstd v0.8.6 [35d6a980] + ColorSchemes v3.31.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.1 [34da2185] ↑ Compat v4.16.0 ⇒ v4.18.1 [f0e56b4a] + ConcurrentUtilities v2.5.0 [a8cc5b0e] + Crayons v4.1.1 [a93c6f00] + DataFrames v1.8.1 [864edb3b] ↑ DataStructures v0.18.20 ⇒ v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [31c24e10] ↑ Distributions v0.25.111 ⇒ v0.25.122 [ffbed154] ↑ DocStringExtensions v0.9.3 ⇒ v0.9.5 [460bff9d] + ExceptionUnwrapping v0.1.11 [48062228] + FilePathsBase v0.9.24 [1a297f60] ↑ FillArrays v1.12.0 ⇒ v1.15.0 [53c48c17] + FixedPointNumbers v0.8.5 [de31a74c] + FunctionalCollections v0.5.0 [38e38edf] + GLM v1.9.0 [f67ccb44] + HDF5 v0.17.2 [cd3eb016] + HTTP v1.10.19 [9fb69e20] + Hiccup v0.2.2 [34004b35] ↑ HypergeometricFunctions v0.3.24 ⇒ v0.3.28 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] ↑ IrrationalConstants v0.2.2 ⇒ v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] ↑ JLLWrappers v1.5.0 ⇒ v1.7.1 [97c1335a] + JSExpr v0.5.4 ⌅ [682c06a0] + JSON v0.21.4 [b964fa9f] + LaTeXStrings v1.4.0 [50d2b5c4] + Lazy v0.15.1 [2ab3a3ac] ↑ LogExpFunctions v0.3.28 ⇒ v0.3.29 [e6f89c97] + LoggingExtras v1.2.0 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.16 [739be429] + MbedTLS v1.1.9 [ffc61752] + Mustache v1.0.21 [a975b10e] + Mux v1.0.2 [510215fc] + Observables v0.5.5 [975b03d1] + OnlinePCA v0.3.10 [4d8831e6] + OpenSSL v1.6.0 [bac558e1] ↑ OrderedCollections v1.6.3 ⇒ v1.8.1 [90014a1f] ↑ PDMats v0.11.31 ⇒ v0.11.36 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [fa939f87] + Pidfile v1.3.0 [a03496cd] + PlotlyBase v0.8.21 [f0f68f2c] + PlotlyJS v0.18.17 [f2990250] + PlotlyKaleido v2.3.0 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] ↑ Preferences v1.4.3 ⇒ v1.5.0 [08abe8d2] + PrettyTables v3.1.0 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] ↑ PtrArrays v1.2.0 ⇒ v1.3.0 [1fd47b50] ↑ QuadGK v2.10.1 ⇒ v2.11.2 [ae029012] + Requires v1.3.1 [79098fc4] ↑ Rmath v0.7.1 ⇒ v0.9.0 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [777ac1f9] + SimpleBufferStream v1.2.0 [a2af1166] ↑ SortingAlgorithms v1.2.1 ⇒ v1.2.2 [276daf66] ↑ SpecialFunctions v2.4.0 ⇒ v2.6.1 [10745b16] ↑ Statistics v1.10.0 ⇒ v1.11.1 [82ae8749] ↑ StatsAPI v1.7.0 ⇒ v1.7.1 [2913bbd2] ↑ StatsBase v0.34.3 ⇒ v0.34.7 [4c63d2b9] ↑ StatsFuns v1.3.1 ⇒ v1.5.2 [3eaba693] + StatsModels v0.7.7 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [62fd8b95] + TensorCore v0.1.1 [3bb67fe8] ↑ TranscodingStreams v0.11.2 ⇒ v0.11.3 [5c2747f8] + URIs v1.6.1 [3a884ed6] + UnPack v1.0.2 [ea10d353] + WeakRefStrings v1.4.2 [0f1e0344] + WebIO v0.8.21 [104b5d7c] + WebSockets v1.6.0 [cc8bc4a8] + Widgets v0.6.7 [76eceee3] + WorkerUtilities v1.6.1 [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.2+0 [f7e6163d] + Kaleido_jll v0.2.1+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [7cb0a576] + MPICH_jll v4.3.2+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [c8ffd9c3] ↑ MbedTLS_jll v2.28.2+1 ⇒ v2.28.10+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.8+0 [efe28fd5] ↑ OpenSpecFun_jll v0.5.5+0 ⇒ v0.5.6+0 [f50d1b31] ↑ Rmath_jll v0.4.3+0 ⇒ v0.5.1+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] + libaec_jll v1.1.4+0 [0dad84c5] ↑ ArgTools v1.1.1 ⇒ 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 v1.6.0 ⇒ v1.7.0 [7b1f6079] ~ FileWatching ⇒ v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] ~ InteractiveUtils ⇒ v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] ↑ LibCURL v0.6.4 ⇒ 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 v1.2.0 ⇒ v1.3.0 [44cfe95a] ↑ Pkg v1.10.0 ⇒ v1.13.0 [de0858da] ~ Printf ⇒ v1.11.0 [3fa0cd96] ~ REPL ⇒ v1.11.0 [9a3f8284] ~ Random ⇒ v1.11.0 [ea8e919c] ↑ SHA v0.7.0 ⇒ v1.0.0 [9e88b42a] ~ Serialization ⇒ v1.11.0 [6462fe0b] ~ Sockets ⇒ v1.11.0 [2f01184e] ↑ SparseArrays v1.10.0 ⇒ v1.13.0 [f489334b] + StyledStrings v1.11.0 [8dfed614] ~ Test ⇒ v1.11.0 [cf7118a7] ~ UUIDs ⇒ v1.11.0 [4ec0a83e] ~ Unicode ⇒ v1.11.0 [e66e0078] ↑ CompilerSupportLibraries_jll v1.1.1+0 ⇒ v1.3.0+1 [deac9b47] ↑ LibCURL_jll v8.4.0+0 ⇒ v8.16.0+0 [e37daf67] ↑ LibGit2_jll v1.6.4+0 ⇒ v1.9.1+0 [29816b5a] ↑ LibSSH2_jll v1.11.0+1 ⇒ v1.11.3+1 [14a3606d] ↑ MozillaCACerts_jll v2023.1.10 ⇒ v2025.9.9 [4536629a] ↑ OpenBLAS_jll v0.3.23+4 ⇒ v0.3.29+0 [05823500] ↑ OpenLibm_jll v0.8.1+2 ⇒ v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] ↑ SuiteSparse_jll v7.2.1+1 ⇒ v7.10.1+0 [83775a58] ↑ Zlib_jll v1.2.13+1 ⇒ v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] ↑ libblastrampoline_jll v5.8.0+1 ⇒ v5.15.0+0 [8e850ede] ↑ nghttp2_jll v1.52.0+1 ⇒ v1.67.1+0 [3f19e933] ↑ p7zip_jll v17.4.0+2 ⇒ v17.6.0+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_nWbG9X/Project.toml` [c7e460c6] ArgParse v1.2.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [1a297f60] FillArrays v1.15.0 [4d4711f2] MatrixMarket v0.5.2 [975b03d1] OnlinePCA v0.3.10 [10745b16] Statistics v1.11.1 [37e2e46d] LinearAlgebra v1.13.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_nWbG9X/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [c7e460c6] ArgParse v1.2.0 [bf4720bc] AssetRegistry v0.1.0 [d1d4a3ce] BitFlags v0.1.9 [ad839575] Blink v0.12.9 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.6 [35d6a980] ColorSchemes v3.31.0 [3da002f7] ColorTypes v0.12.1 [c3611d14] ColorVectorSpace v0.11.0 [5ae59095] Colors v0.13.1 [34da2185] Compat v4.18.1 [f0e56b4a] ConcurrentUtilities v2.5.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [460bff9d] ExceptionUnwrapping v0.1.11 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [53c48c17] FixedPointNumbers v0.8.5 [de31a74c] FunctionalCollections v0.5.0 [38e38edf] GLM v1.9.0 [f67ccb44] HDF5 v0.17.2 [cd3eb016] HTTP v1.10.19 [9fb69e20] Hiccup v0.2.2 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [97c1335a] JSExpr v0.5.4 ⌅ [682c06a0] JSON v0.21.4 [b964fa9f] LaTeXStrings v1.4.0 [50d2b5c4] Lazy v0.15.1 [2ab3a3ac] LogExpFunctions v0.3.29 [e6f89c97] LoggingExtras v1.2.0 [3da0fdf6] MPIPreferences v0.1.11 [1914dd2f] MacroTools v0.5.16 [4d4711f2] MatrixMarket v0.5.2 [739be429] MbedTLS v1.1.9 [e1d29d7a] Missings v1.2.0 [ffc61752] Mustache v1.0.21 [a975b10e] Mux v1.0.2 [510215fc] Observables v0.5.5 [975b03d1] OnlinePCA v0.3.10 [4d8831e6] OpenSSL v1.6.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.36 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.3 [fa939f87] Pidfile v1.3.0 [a03496cd] PlotlyBase v0.8.21 [f0f68f2c] PlotlyJS v0.18.17 [f2990250] PlotlyKaleido v2.3.0 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.0 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [91c51154] SentinelArrays v1.4.8 [1277b4bf] ShiftedArrays v2.0.0 [777ac1f9] SimpleBufferStream v1.2.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.7 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.7 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [62fd8b95] TensorCore v0.1.1 [b718987f] TextWrap v1.0.2 [3bb67fe8] TranscodingStreams v0.11.3 [5c2747f8] URIs v1.6.1 [3a884ed6] UnPack v1.0.2 [ea10d353] WeakRefStrings v1.4.2 [0f1e0344] WebIO v0.8.21 [104b5d7c] WebSockets v1.6.0 [cc8bc4a8] Widgets v0.6.7 [76eceee3] WorkerUtilities v1.6.1 [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.2+0 [f7e6163d] Kaleido_jll v0.2.1+0 [94ce4f54] Libiconv_jll v1.18.0+0 [7cb0a576] MPICH_jll v4.3.2+0 [f1f71cc9] MPItrampoline_jll v5.5.4+0 [c8ffd9c3] MbedTLS_jll v2.28.10+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [fe0851c0] OpenMPI_jll v5.0.8+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 ⌅ [02c8fc9c] XML2_jll v2.13.9+0 [a65dc6b1] Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] libaec_jll v1.1.4+0 [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 v1.12.0 [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 v1.13.0 [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 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [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 v1.67.1+0 [3f19e933] p7zip_jll v17.6.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... /tmp/jl_RhPfaF Running all tests... ####### Binarization of CSV (Julia API) ####### 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 ####### Binarization of CSV (Command line) ####### Parsed args: binfile => /tmp/jl_RhPfaF/Data.zst csvfile => /tmp/jl_RhPfaF/Data.csv 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 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####### Parsed args: binfile => /tmp/jl_RhPfaF/Data.zst outdir => /tmp/jl_axcm6t pseudocount => 1.0 mode => dense 1 / 2 : Column-wise statistics are calculated... 2 / 2 : Row-wise statistics are calculated... ####### Summarization (Julia API) ####### 1 / 2 : Column-wise statistics are calculated... 2 / 2 : Row-wise statistics are calculated... ####### Summarization (Command line) ####### Parsed args: binfile => /tmp/jl_RhPfaF/Data.mtx.zst outdir => /tmp/jl_glslUO pseudocount => 1.0 mode => sparse_mm 1 / 2 : Column-wise statistics are calculated... 2 / 2 : Row-wise statistics are calculated... ####### HVG (Julia API) ####### Highly Variable Genes are calculated... ####### HVG (Command line) ####### Parsed args: rowvarlist => /tmp/jl_axcm6t/Feature_Vars.csv binfile => /tmp/jl_RhPfaF/Data.zst outdir => /tmp/jl_axcm6t rowcv2list => /tmp/jl_axcm6t/Feature_CV2s.csv rowmeanlist => /tmp/jl_axcm6t/Feature_Means.csv Highly Variable Genes are calculated... ####### Filtering (Julia API) ####### ####### Filtering (Command line) ####### Parsed args: input => /tmp/jl_RhPfaF/Data.zst samplelist => /tmp/jl_axcm6t/Sample_NoCounts.csv outdir => /tmp/jl_axcm6t thr2 => 10 direct1 => + direct2 => + featurelist => /tmp/jl_axcm6t/Feature_Means.csv thr1 => 10 Parsed args: input => /tmp/jl_RhPfaF/Data.zst samplelist => outdir => /tmp/jl_axcm6t thr2 => 10 direct1 => + direct2 => + featurelist => /tmp/jl_axcm6t/Feature_Means.csv thr1 => 10 Parsed args: input => /tmp/jl_RhPfaF/Data.zst samplelist => /tmp/jl_axcm6t/Sample_NoCounts.csv outdir => /tmp/jl_axcm6t thr2 => 10 direct1 => + direct2 => + featurelist => thr1 => 10 ####### GD (Julia API) ####### ####### GD (Command line) ####### Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => nothing scheduling => "robbins-monro" epsilon => 1.0f-8 stepsize => "1.0e-15" dim => "3" lower => 0 rowvarlist => "" offsetStoch => 1.0f-6 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" g => 0.9f0 upper => 1.0f38 numepoch => "1" offsetFull => 1.0f-20 initV => nothing Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => "/tmp/jl_axcm6t/Eigen_vectors.csv" scheduling => "momentum" epsilon => 1.0f-8 stepsize => "1.0e-15" dim => "3" lower => 0 rowvarlist => "" offsetStoch => 1.0f-6 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" g => 0.9f0 upper => 1.0f38 numepoch => "1" offsetFull => 1.0f-20 initV => nothing Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => nothing scheduling => "nag" epsilon => 1.0f-8 stepsize => "1.0e-15" dim => "3" lower => 0 rowvarlist => "" offsetStoch => 1.0f-6 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" g => 0.9f0 upper => 1.0f38 numepoch => "1" offsetFull => 1.0f-20 initV => "/tmp/jl_axcm6t/Loadings.csv" Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => nothing scheduling => "adagrad" epsilon => 1.0f-8 stepsize => "1.0e-15" dim => "3" lower => 0 rowvarlist => "" offsetStoch => 1.0f-6 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" g => 0.9f0 upper => 1.0f38 numepoch => "1" offsetFull => 1.0f-20 initV => nothing ####### Oja (Julia API) ####### Progress: 1%|▎ | ETA: 0:02:43 Progress: 1%|▍ | ETA: 0:03:02 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:02:48 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:02:48 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:01:29 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 ####### Oja (Command line) ####### Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => nothing scheduling => "robbins-monro" epsilon => 1.0f-8 stepsize => "1.0e-15" dim => "3" lower => 0 rowvarlist => "" offsetStoch => 1.0f-6 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" g => 0.9f0 upper => 1.0f38 numepoch => "1" offsetFull => 1.0f-20 initV => nothing Progress: 1%|▎ | ETA: 0:06:14 Progress: 1%|▌ | ETA: 0:03:41 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => nothing scheduling => "momentum" epsilon => 1.0f-8 stepsize => "1.0e-15" dim => "3" lower => 0 rowvarlist => "" offsetStoch => 1.0f-6 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" g => 0.9f0 upper => 1.0f38 numepoch => "1" offsetFull => 1.0f-20 initV => nothing Progress: 1%|▎ | ETA: 0:06:39 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => nothing scheduling => "nag" epsilon => 1.0f-8 stepsize => "1.0e-15" dim => "3" lower => 0 rowvarlist => "" offsetStoch => 1.0f-6 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" g => 0.9f0 upper => 1.0f38 numepoch => "1" offsetFull => 1.0f-20 initV => nothing Progress: 1%|▎ | ETA: 0:08:50 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => nothing scheduling => "adagrad" epsilon => 1.0f-8 stepsize => "1.0e-15" dim => "3" lower => 0 rowvarlist => "" offsetStoch => 1.0f-6 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" g => 0.9f0 upper => 1.0f38 numepoch => "1" offsetFull => 1.0f-20 initV => nothing Progress: 1%|▎ | ETA: 0:07:56 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 ####### SGD (Julia API) ####### Progress: 1%|▎ | ETA: 0:03:08 Progress: 1%|▍ | ETA: 0:03:56 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Progress: 1%|▎ | ETA: 0:04:09 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:03:58 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:02:58 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### SGD (Command line) ####### Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => nothing scheduling => "robbins-monro" epsilon => 1.0f-8 stepsize => "1.0e-15" dim => "3" lower => 0 rowvarlist => "" offsetStoch => 1.0f-6 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" numbatch => 100 rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" g => 0.9f0 upper => 1.0f38 numepoch => "1" offsetFull => 1.0f-20 initV => nothing Progress: 1%|▎ | ETA: 0:07:05 Progress: 1%|▍ | ETA: 0:05:45 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => nothing scheduling => "momentum" epsilon => 1.0f-8 stepsize => "1.0e-15" dim => "3" lower => 0 rowvarlist => "" offsetStoch => 1.0f-6 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" numbatch => 100 rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" g => 0.9f0 upper => 1.0f38 numepoch => "1" offsetFull => 1.0f-20 initV => nothing Progress: 1%|▎ | ETA: 0:07:33 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => nothing scheduling => "nag" epsilon => 1.0f-8 stepsize => "1.0e-15" dim => "3" lower => 0 rowvarlist => "" offsetStoch => 1.0f-6 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" numbatch => 100 rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" g => 0.9f0 upper => 1.0f38 numepoch => "1" offsetFull => 1.0f-20 initV => nothing Progress: 1%|▎ | ETA: 0:09:33 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => nothing scheduling => "adagrad" epsilon => 1.0f-8 stepsize => "1.0e-15" dim => "3" lower => 0 rowvarlist => "" offsetStoch => 1.0f-6 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" numbatch => 100 rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" g => 0.9f0 upper => 1.0f38 numepoch => "1" offsetFull => 1.0f-20 initV => nothing Progress: 1%|▎ | ETA: 0:08:37 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 ####### CCIPCA (Julia API) ####### Progress: 1%|▎ | ETA: 0:02:05 Progress: 1%|▍ | ETA: 0:02:33 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### CCIPCA (Command line) ####### Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => nothing lower => 0 stepsize => "1.0e-15" dim => "3" rowvarlist => "" offsetStoch => 1.0f-15 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" upper => 1.0f38 numepoch => "1" initV => nothing Progress: 1%|▎ | ETA: 0:08:57 Progress: 1%|▍ | ETA: 0:07:31 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 ####### RSGD (Julia API) ####### Progress: 1%|▎ | ETA: 0:16:18 Progress: 1%|▍ | ETA: 0:12:42 Progress: 100%|█████████████████████████████████████████| Time: 0:00:07 Progress: 1%|▎ | ETA: 0:04:10 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:05:39 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Progress: 1%|▎ | ETA: 0:03:07 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### RSGD (Command line) ####### Parsed args: scale => "ftt" logdir => "/tmp/jl_axcm6t" initW => nothing scheduling => "robbins-monro" epsilon => 1.0f-8 stepsize => "1.0e-15" dim => "3" lower => 0 rowvarlist => "" offsetStoch => 1.0f-6 expvar => 0.1f0 input => "/tmp/jl_RhPfaF/Data.zst" perm => false pseudocount => 1.0f0 colsumlist => "" numbatch => 100 rowmeanlist => "/tmp/jl_axcm6t/Feature_FTTMeans.csv" evalfreq => 5000 cper => 1.0f0 outdir => "/tmp/jl_axcm6t" g => 0.9f0 upper => 1.0f38 numepoch => "1" offsetFull => 1.0f-20 initV => nothing Progress: 1%|▎ | ETA: 0:12:34 Progress: 1%|▍ | ETA: 0:09:24 Progress: 100%|█████████████████████████████████████████| Time: 0:00:05 ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 1787 running 1 of 1 signal (10): User defined signal 1 unknown function (ip: 0x755482032fac) at /lib/x86_64-linux-gnu/libc.so.6 unknown function (ip: 0x7554820335be) at /lib/x86_64-linux-gnu/libc.so.6 unknown function (ip: 0x755482033c74) at /lib/x86_64-linux-gnu/libc.so.6 posix_memalign at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) jl_malloc_aligned at /source/src/gc-common.h:112 [inlined] ijl_gc_managed_malloc at /source/src/gc-stock.c:3827 jl_alloc_genericmemory_unchecked at /source/src/genericmemory.c:38 ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 816 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1223 wait_forever at ./task.jl:1145 jfptr_wait_forever_22390.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] start_task at /source/src/task.c:1281 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1223 wait_forever at ./task.jl:1145 jfptr_wait_forever_22390.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] start_task at /source/src/task.c:1281 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.14/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000077282c88c010 Total snapshots: 130. Utilization: 0% ╎130 @Base/task.jl:1145 wait_forever() 129╎ 130 @Base/task.jl:1223 wait() [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1223 wait_forever at ./task.jl:1145 jfptr_wait_forever_22390.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] start_task at /source/src/task.c:1281 unknown function (ip: (nil)) at (unknown file) Allocations: 38760421 (Pool: 38759470; Big: 951); GC: 49 [816] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/OnlinePCA/AhPWT/test/test_rsgd.jl:67 _ZNK4llvm6MCExpr25evaluateAsRelocatableImplERNS_7MCValueEPKNS_11MCAssemblerEPKNS_7MCFixupEPKNS_8DenseMapIPKNS_9MCSectionEmNS_12DenseMapInfoISC_vEENS_6detail12DenseMapPairISC_mEEEEb at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) unknown function (ip: (nil)) at (unknown file) unknown function (ip: (nil)) at (unknown file) Allocations: 64209361 (Pool: 64208398; Big: 963); GC: 38 [1791] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/OnlinePCA/AhPWT/bin/rsgd:138 _ZL25CalcNodeSethiUllmanNumberPKN4llvm5SUnitERSt6vectorIjSaIjEE.part.0 at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN12_GLOBAL__N_118RegReductionPQBase9initNodesERSt6vectorIN4llvm5SUnitESaIS3_EE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN12_GLOBAL__N_117ScheduleDAGRRList8ScheduleEv at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm16SelectionDAGISel17CodeGenAndEmitDAGEv at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm16SelectionDAGISel20SelectAllBasicBlocksERKNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm16SelectionDAGISel20runOnMachineFunctionERNS_15MachineFunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm22SelectionDAGISelLegacy20runOnMachineFunctionERNS_15MachineFunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm19MachineFunctionPass13runOnFunctionERNS_8FunctionE.part.0 at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm13FPPassManager13runOnFunctionERNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm13FPPassManager11runOnModuleERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm6legacy15PassManagerImpl3runERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) operator() at /source/src/jitlayers.cpp:1628 addModule at /source/src/jitlayers.cpp:2119 jl_compile_codeinst_now at /source/src/jitlayers.cpp:682 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:876 jl_compile_method_internal at /source/src/gf.c:3648 _jl_invoke at /source/src/gf.c:4108 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:2994 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3054 include at ./Base.jl:309 exec_options at ./client.jl:344 _start at ./client.jl:577 jfptr__start_73709.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x73e5b8bb5249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) Allocations: 8731289 (Pool: 8731074; Big: 215); GC: 7 PkgEval terminated after 2733.25s: test duration exceeded the time limit