Package evaluation to test OnlinePCA on Julia 1.10.10 (df86fe4d49*) started at 2026-02-04T05:22:30.988 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.10` Set-up completed after 4.97s ################################################################################ # Installation # Installing OnlinePCA... Resolving package versions... Installed PlotlyJS ─ v0.18.17 Installed WebIO ──── v0.8.21 Updating `~/.julia/environments/v1.10/Project.toml` [975b03d1] + OnlinePCA v0.3.10 Updating `~/.julia/environments/v1.10/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [c7e460c6] + ArgParse v1.2.0 [bf4720bc] + AssetRegistry v0.1.1 [d1d4a3ce] + BitFlags v0.1.9 [ad839575] + Blink v0.12.9 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [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 v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [460bff9d] + ExceptionUnwrapping v0.1.11 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [53c48c17] + FixedPointNumbers v0.8.5 [de31a74c] + FunctionalCollections v0.5.0 [38e38edf] + GLM v1.9.2 [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 v1.6.1 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [fa939f87] + Pidfile v1.3.0 [a03496cd] + PlotlyBase v0.8.23 [f0f68f2c] + PlotlyJS v0.18.17 [f2990250] + PlotlyKaleido v2.3.1 [2dfb63ee] + PooledArrays v1.4.3 ⌅ [aea7be01] + PrecompileTools v1.2.1 [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 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [91c51154] + SentinelArrays v1.4.9 [1277b4bf] + ShiftedArrays v2.0.0 [777ac1f9] + SimpleBufferStream v1.2.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.8 [892a3eda] + StringManipulation v0.4.2 [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 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.9+0 [458c3c95] + OpenSSL_jll v3.5.5+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 [3161d3a3] + Zstd_jll v1.5.7+1 [477f73a3] + libaec_jll v1.1.5+0 [0dad84c5] + ArgTools v1.1.1 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [8ba89e20] + Distributed [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching [9fa8497b] + Future [b77e0a4c] + InteractiveUtils [4af54fe1] + LazyArtifacts [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.10.0 [de0858da] + Printf [3fa0cd96] + REPL [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [6462fe0b] + Sockets [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.4.0+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.1010+0 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.23+5 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.52.0+1 [3f19e933] + p7zip_jll v17.4.0+2 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 51.09s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 853.1 ms ✓ TestEnv 1 dependency successfully precompiled in 3 seconds Precompiling package dependencies... Precompiling packages... 1553.1 ms ✓ SentinelArrays 1303.9 ms ✓ MbedTLS 897.3 ms ✓ Compat 680.7 ms ✓ OrderedCollections 578.3 ms ✓ Observables 496.4 ms ✓ TextWrap 511.4 ms ✓ Requires 488.8 ms ✓ DelimitedFiles 394.5 ms ✓ UnPack 1057.1 ms ✓ FillArrays 379.7 ms ✓ DataValueInterfaces 446.4 ms ✓ LaTeXStrings 450.8 ms ✓ InvertedIndices 407.0 ms ✓ Reexport 582.0 ms ✓ DocStringExtensions 717.6 ms ✓ InlineStrings 1121.8 ms ✓ IrrationalConstants 609.6 ms ✓ URIs 370.7 ms ✓ IteratorInterfaceExtensions 407.0 ms ✓ SimpleBufferStream 470.2 ms ✓ TensorCore 447.9 ms ✓ DataAPI 499.7 ms ✓ WorkerUtilities 442.3 ms ✓ StatsAPI 416.9 ms ✓ CompilerSupportLibraries_jll 952.2 ms ✓ Crayons 428.4 ms ✓ BitFlags 898.8 ms ✓ ProgressMeter 2097.1 ms ✓ MacroTools 592.5 ms ✓ FunctionalCollections 531.1 ms ✓ LoggingExtras 519.6 ms ✓ ExceptionUnwrapping 388.5 ms ✓ PtrArrays 670.8 ms ✓ ConcurrentUtilities 608.3 ms ✓ TranscodingStreams 553.2 ms ✓ Preferences 428.9 ms ✓ ShiftedArrays 454.0 ms ✓ Pidfile 693.4 ms ✓ SuiteSparse 896.9 ms ✓ Statistics 406.5 ms ✓ Compat → CompatLinearAlgebraExt 1846.2 ms ✓ DataStructures 790.9 ms ✓ ArgParse 468.6 ms ✓ Parameters 823.9 ms ✓ FillArrays → FillArraysSparseArraysExt 712.1 ms ✓ LogExpFunctions 376.5 ms ✓ TableTraits 488.0 ms ✓ Missings 535.7 ms ✓ PooledArrays 2566.7 ms ✓ Lazy 719.6 ms ✓ Hiccup 490.3 ms ✓ AliasTables 508.8 ms ✓ CodecZlib 630.4 ms ✓ MPIPreferences 436.0 ms ✓ PrecompileTools 504.5 ms ✓ JLLWrappers 1027.1 ms ✓ PDMats 2410.5 ms ✓ FixedPointNumbers 860.5 ms ✓ FilePathsBase 537.5 ms ✓ SortingAlgorithms 1065.2 ms ✓ QuadGK 807.4 ms ✓ FillArrays → FillArraysStatisticsExt 882.5 ms ✓ Tables 743.2 ms ✓ MatrixMarket 8675.6 ms ✓ Parsers 1492.6 ms ✓ StringManipulation 611.7 ms ✓ OpenSSL_jll 580.0 ms ✓ Kaleido_jll 567.1 ms ✓ Rmath_jll 454.8 ms ✓ MicrosoftMPI_jll 584.5 ms ✓ Zstd_jll 568.7 ms ✓ Libiconv_jll 565.1 ms ✓ Xorg_libpciaccess_jll 565.8 ms ✓ libaec_jll 490.7 ms ✓ MPItrampoline_jll 570.6 ms ✓ OpenSpecFun_jll 806.8 ms ✓ FillArrays → FillArraysPDMatsExt 1763.2 ms ✓ ColorTypes 408.7 ms ✓ FilePathsBase → FilePathsBaseMmapExt 2367.0 ms ✓ StatsBase 556.0 ms ✓ Mustache 1790.9 ms ✓ JSON 540.6 ms ✓ InlineStrings → ParsersExt 18848.3 ms ✓ PrettyTables 1822.1 ms ✓ OpenSSL 756.1 ms ✓ Rmath 915.0 ms ✓ CodecZstd 617.6 ms ✓ XML2_jll 2752.2 ms ✓ SpecialFunctions 4697.1 ms ✓ Colors 2493.3 ms ✓ ColorVectorSpace 1039.4 ms ✓ FilePathsBase → FilePathsBaseTestExt 806.4 ms ✓ PDMats → StatsBaseExt 554.4 ms ✓ PlotlyKaleido 518.5 ms ✓ AssetRegistry 828.1 ms ✓ WeakRefStrings 33707.1 ms ✓ DataFrames 11704.3 ms ✓ HTTP 579.3 ms ✓ Hwloc_jll 1027.9 ms ✓ HypergeometricFunctions 1121.1 ms ✓ Widgets 947.0 ms ✓ ColorVectorSpace → SpecialFunctionsExt 4556.3 ms ✓ ColorSchemes 11339.4 ms ✓ CSV 1451.5 ms ✓ WebSockets 1987.3 ms ✓ Mux 451.3 ms ✓ OpenMPI_jll 594.5 ms ✓ MPICH_jll 1382.9 ms ✓ StatsFuns 3339.2 ms ✓ PlotlyBase 2200.7 ms ✓ WebIO 784.5 ms ✓ HDF5_jll 1604.3 ms ✓ StatsModels 5022.4 ms ✓ Distributions 3475.1 ms ✓ PlotlyBase → DataFramesExt 2247.9 ms ✓ JSExpr 5203.1 ms ✓ HDF5 1523.0 ms ✓ Distributions → DistributionsTestExt 1883.9 ms ✓ GLM 1754.7 ms ✓ PlotlyBase → DistributionsExt 3483.4 ms ✓ Blink 5518.7 ms ✓ PlotlyJS 3416.7 ms ✓ PlotlyJS → CSVExt 4969.0 ms ✓ PlotlyJS → DataFramesExt 4411.1 ms ✓ OnlinePCA 125 dependencies successfully precompiled in 230 seconds. 7 already precompiled. Precompilation completed after 243.58s ################################################################################ # Testing # Testing OnlinePCA Status `/tmp/jl_bpt7KI/Project.toml` [c7e460c6] ArgParse v1.2.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.123 [1a297f60] FillArrays v1.16.0 [4d4711f2] MatrixMarket v0.5.2 [975b03d1] OnlinePCA v0.3.10 [37e2e46d] LinearAlgebra [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [8dfed614] Test Status `/tmp/jl_bpt7KI/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [c7e460c6] ArgParse v1.2.0 [bf4720bc] AssetRegistry v0.1.1 [d1d4a3ce] BitFlags v0.1.9 [ad839575] Blink v0.12.9 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.7 [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 v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [460bff9d] ExceptionUnwrapping v0.1.11 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [53c48c17] FixedPointNumbers v0.8.5 [de31a74c] FunctionalCollections v0.5.0 [38e38edf] GLM v1.9.2 [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 v1.6.1 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.3 [fa939f87] Pidfile v1.3.0 [a03496cd] PlotlyBase v0.8.23 [f0f68f2c] PlotlyJS v0.18.17 [f2990250] PlotlyKaleido v2.3.1 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [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 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [91c51154] SentinelArrays v1.4.9 [1277b4bf] ShiftedArrays v2.0.0 [777ac1f9] SimpleBufferStream v1.2.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.8 [892a3eda] StringManipulation v0.4.2 [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 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [fe0851c0] OpenMPI_jll v5.0.9+0 [458c3c95] OpenSSL_jll v3.5.5+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 [3161d3a3] Zstd_jll v1.5.7+1 [477f73a3] libaec_jll v1.1.5+0 [0dad84c5] ArgTools v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [8ba89e20] Distributed [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [4af54fe1] LazyArtifacts [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [a63ad114] Mmap [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.10.0 [de0858da] Printf [3fa0cd96] REPL [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [6462fe0b] Sockets [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.1010+0 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.23+5 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... /tmp/jl_wTMUCm 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_wTMUCm/Data.zst csvfile => /tmp/jl_wTMUCm/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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 ####### Binarization of MM (Julia API) ####### ####### Binarization of MM (Command line) ####### Parsed args: mmfile => /tmp/jl_wTMUCm/Data.mtx binfile => /tmp/jl_wTMUCm/Data.mtx.zst ####### Binarization of Binary COO (Julia API) ####### ####### Binarization of Binary COO (Command line) ####### Parsed args: binfile => /tmp/jl_wTMUCm/Data.bincoo.zst bincoofile => /tmp/jl_wTMUCm/Data.bincoo ####### Summarization (Julia API) ####### 1 / 2 : Column-wise statistics are calculated... 2 / 2 : Row-wise statistics are calculated... ####### Summarization (Command line) ####### Parsed args: pseudocount => 1.0 binfile => /tmp/jl_wTMUCm/Data.zst mode => dense outdir => /tmp/jl_UG81Wy 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: pseudocount => 1.0 binfile => /tmp/jl_wTMUCm/Data.mtx.zst mode => sparse_mm outdir => /tmp/jl_77dtm0 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: rowmeanlist => /tmp/jl_UG81Wy/Feature_Means.csv binfile => /tmp/jl_wTMUCm/Data.zst rowcv2list => /tmp/jl_UG81Wy/Feature_CV2s.csv rowvarlist => /tmp/jl_UG81Wy/Feature_Vars.csv outdir => /tmp/jl_UG81Wy Highly Variable Genes are calculated... ####### Filtering (Julia API) ####### ####### Filtering (Command line) ####### Parsed args: samplelist => /tmp/jl_UG81Wy/Sample_NoCounts.csv thr1 => 10 direct2 => + direct1 => + thr2 => 10 outdir => /tmp/jl_UG81Wy input => /tmp/jl_wTMUCm/Data.zst featurelist => /tmp/jl_UG81Wy/Feature_Means.csv Parsed args: samplelist => thr1 => 10 direct2 => + direct1 => + thr2 => 10 outdir => /tmp/jl_UG81Wy input => /tmp/jl_wTMUCm/Data.zst featurelist => /tmp/jl_UG81Wy/Feature_Means.csv Parsed args: samplelist => /tmp/jl_UG81Wy/Sample_NoCounts.csv thr1 => 10 direct2 => + direct1 => + thr2 => 10 outdir => /tmp/jl_UG81Wy input => /tmp/jl_wTMUCm/Data.zst featurelist => ####### GD (Julia API) ####### ####### GD (Command line) ####### Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => "/tmp/jl_UG81Wy/Eigen_vectors.csv" colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => "/tmp/jl_UG81Wy/Loadings.csv" cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false ####### Oja (Julia API) ####### Progress: 1%|▎ | ETA: 0:01:15 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:01:12 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Progress: 1%|▎ | ETA: 0:00:54 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Progress: 1%|▎ | ETA: 0:00:53 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 ####### Oja (Command line) ####### Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:03:28 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:03:37 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:04:34 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:04:16 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 ####### SGD (Julia API) ####### Progress: 1%|▎ | ETA: 0:01:16 Progress: 1%|▍ | ETA: 0:01:37 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Progress: 1%|▎ | ETA: 0:01:29 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Progress: 1%|▎ | ETA: 0:01:11 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Progress: 1%|▎ | ETA: 0:02:08 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 ####### SGD (Command line) ####### Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:03:33 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:03:53 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:04:47 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:04:35 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 ####### CCIPCA (Julia API) ####### Progress: 1%|▎ | ETA: 0:00:47 Progress: 1%|▍ | ETA: 0:00:51 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 ####### CCIPCA (Command line) ####### Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 offsetStoch => 1.0f-15 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:05:47 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 ####### RSGD (Julia API) ####### Progress: 1%|▎ | ETA: 0:11:50 Progress: 1%|▍ | ETA: 0:08:39 Progress: 100%|█████████████████████████████████████████| Time: 0:00:05 Progress: 1%|▎ | ETA: 0:01:28 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Progress: 1%|▎ | ETA: 0:01:43 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Progress: 1%|▎ | ETA: 0:02:06 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 ####### RSGD (Command line) ####### Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:09:49 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:10:30 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:10:41 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:11:05 Progress: 100%|█████████████████████████████████████████| Time: 0:00:05 ####### SVRG (Julia API) ####### Progress: 1%|▎ | ETA: 0:02:22 Progress: 1%|▍ | ETA: 0:02:48 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:02:28 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Progress: 1%|▎ | ETA: 0:03:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:03:21 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### SVRG (Command line) ####### Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:09:09 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:09:00 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:10:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:09:12 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 ####### RSVRG (Julia API) ####### Progress: 1%|▎ | ETA: 0:02:15 Progress: 1%|▍ | ETA: 0:02:44 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:02:21 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Progress: 1%|▎ | ETA: 0:02:42 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:03:17 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### RSVRG (Command line) ####### Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:15:34 Progress: 100%|█████████████████████████████████████████| Time: 0:00:07 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:16:07 Progress: 100%|█████████████████████████████████████████| Time: 0:00:07 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:16:06 Progress: 100%|█████████████████████████████████████████| Time: 0:00:07 Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 numbatch => 100 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:15:20 Progress: 100%|█████████████████████████████████████████| Time: 0:00:06 ####### Orthogonal Iteration (Julia API) ####### Progress: 0%|▏ | ETA: 0:03:35 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 ####### Orthogonal Iteration (Command line) ####### Parsed args: logdir => "/tmp/jl_UG81Wy" upper => 1.0f38 scale => "ftt" outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "3" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 dim => "3" perm => false Progress: 0%|▏ | ETA: 0:15:32 Progress: 33%|█████████████▊ | ETA: 0:00:07 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 ####### Randomized Block Krylov Iteration (Julia API) ####### Q' A Q' A' A svd(Q' A' A) Q*U ####### Randomized Block Krylov Iteration (Command line) ####### Parsed args: logdir => "/tmp/jl_UG81Wy" upper => 1.0f38 scale => "ftt" outdir => "/tmp/jl_UG81Wy" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "3" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 dim => "3" perm => false Progress: 0%|▏ | ETA: 0:15:03 Progress: 67%|███████████████████████████▍ | ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Q' A Q' A' A svd(Q' A' A) Q*U ####### ARNOLDI (Julia API) ####### Progress: 20%|████████▎ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 ####### ARNOLDI (Command line) ####### Parsed args: scale => "ftt" outdir => "/tmp/jl_UG81Wy" rowvarlist => "" cper => 1.0f0 pseudocount => 1.0f0 colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "3" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 dim => "3" perm => false Progress: 67%|███████████████████████████▍ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 ####### LANCZOS (Julia API) ####### ####### LANCZOS (Command line) ####### Parsed args: scale => "ftt" outdir => "/tmp/jl_UG81Wy" rowvarlist => "" cper => 1.0f0 pseudocount => 1.0f0 colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" numepoch => "3" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" expvar => 0.1f0 dim => "3" perm => false Progress: 67%|███████████████████████████▍ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 ####### HALKO (Julia API) ####### Random Projection : Y = A Ω Progress: 1%|▎ | ETA: 0:00:24 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 QR factorization : Q = qr(Y) Subspace iterations (1/2) : qr(A' Q) qr(A' Q) Subspace iterations (2/2) : Y = qr(A qr(A' Q)) Q = qr(Y) Subspace iterations (1/2) : qr(A' Q) qr(A' Q) Subspace iterations (2/2) : Y = qr(A qr(A' Q)) Q = qr(Y) Subspace iterations (1/2) : qr(A' Q) qr(A' Q) Subspace iterations (2/2) : Y = qr(A qr(A' Q)) Q = qr(Y) Calculation of small matrix : B = Q' A SVD with small matrix : svd(B) ####### HALKO (Command line) ####### Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" noversamples => 5 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" initV => nothing cper => 1.0f0 niter => 3 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" dim => "3" perm => false Random Projection : Y = A Ω Progress: 1%|▎ | ETA: 0:04:25 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 QR factorization : Q = qr(Y) Subspace iterations (1/2) : qr(A' Q) Progress: 1%|▎ | ETA: 0:00:55 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 qr(A' Q) Subspace iterations (2/2) : Y = qr(A qr(A' Q)) Q = qr(Y) Subspace iterations (1/2) : qr(A' Q) qr(A' Q) Subspace iterations (2/2) : Y = qr(A qr(A' Q)) Q = qr(Y) Subspace iterations (1/2) : qr(A' Q) qr(A' Q) Subspace iterations (2/2) : Y = qr(A qr(A' Q)) Q = qr(Y) Calculation of small matrix : B = Q' A SVD with small matrix : svd(B) ####### ALGORITHM971 (Julia API) ####### Random Projection : Y = A Ω LU factorization : L = lu(Y) Normalized power iterations (1/3) : A' L L = lu(A' L) Normalized power iterations (2/3) : Y = A lu(A' L) Normalized power iterations (3/3) : L = lu(A lu(A' L)) Normalized power iterations (1/3) : A' L L = lu(A' L) Normalized power iterations (2/3) : Y = A lu(A' L) Normalized power iterations (3/3) : L = lu(A lu(A' L)) Normalized power iterations (1/3) : A' L L = lu(A' L) Normalized power iterations (2/3) : Y = A lu(A' L) QR factorization (3/3) : Q = qr(A lu(A' L)) Calculation of small matrix : B = Q' A SVD with small matrix : svd(B) ####### ALGORITHM971 (Command line) ####### Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" noversamples => 5 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" initV => nothing cper => 1.0f0 niter => 3 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" dim => "3" perm => false Random Projection : Y = A Ω Progress: 1%|▎ | ETA: 0:04:26 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 LU factorization : L = lu(Y) Normalized power iterations (1/3) : A' L Progress: 1%|▎ | ETA: 0:00:53 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 L = lu(A' L) Normalized power iterations (2/3) : Y = A lu(A' L) Normalized power iterations (3/3) : L = lu(A lu(A' L)) Normalized power iterations (1/3) : A' L L = lu(A' L) Normalized power iterations (2/3) : Y = A lu(A' L) Normalized power iterations (3/3) : L = lu(A lu(A' L)) Normalized power iterations (1/3) : A' L L = lu(A' L) Normalized power iterations (2/3) : Y = A lu(A' L) QR factorization (3/3) : Q = qr(A lu(A' L)) Calculation of small matrix : B = Q' A SVD with small matrix : svd(B) ####### SINGLEPASS (Julia API) ####### Random Projection : Y = A Ω, Ytilde = A' Ωtilde QR factorization : Q = qr(Y), Qtilde = qr(Ytilde) Solve linear equation : Ωtilde' Q B = Ytilde' Qtilde for B SVD with small matrix : svd(B) ####### SINGLEPASS (Command line) ####### Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" noversamples => 5 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" initV => nothing cper => 1.0f0 niter => 3 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" dim => "3" perm => false Random Projection : Y = A Ω, Ytilde = A' Ωtilde Progress: 1%|▎ | ETA: 0:01:24 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 QR factorization : Q = qr(Y), Qtilde = qr(Ytilde) Solve linear equation : Ωtilde' Q B = Ytilde' Qtilde for B SVD with small matrix : svd(B) ####### SINGLEPASS2 (Julia API) ####### Random Projection : G = A Ω, H = A' A Ω Subspace iterations (1/2) : Q = qr(Yi) Subspace iterations (2/2) : Q = qr(Qi - Q(Q' Qi)) Subspace iterations (1/2) : Q = qr(Yi) Subspace iterations (2/2) : Q = qr(Qi - Q(Q' Qi)) Subspace iterations (1/2) : Q = qr(Yi) Subspace iterations (2/2) : Q = qr(Qi - Q(Q' Qi)) SVD with small matrix : svd(B) ####### SINGLEPASS2 (Command line) ####### Parsed args: logdir => "/tmp/jl_UG81Wy" scale => "ftt" noversamples => 5 outdir => "/tmp/jl_UG81Wy" rowvarlist => "" initV => nothing cper => 1.0f0 niter => 3 pseudocount => 1.0f0 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.zst" rowmeanlist => "/tmp/jl_UG81Wy/Feature_FTTMeans.csv" dim => "3" perm => false Random Projection : G = A Ω, H = A' A Ω Progress: 1%|▎ | ETA: 0:01:25 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Subspace iterations (1/2) : Q = qr(Yi) Subspace iterations (2/2) : Q = qr(Qi - Q(Q' Qi)) Subspace iterations (1/2) : Q = qr(Yi) Subspace iterations (2/2) : Q = qr(Qi - Q(Q' Qi)) Subspace iterations (1/2) : Q = qr(Yi) Subspace iterations (2/2) : Q = qr(Qi - Q(Q' Qi)) SVD with small matrix : svd(B) ####### Sparse Randomized SVD (Julia API) ####### Initial Setting... Progress: 40%|████████████████▍ | ETA: 0:00:03 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Random Projection : Y = A Ω Progress: 40%|████████████████▍ | ETA: 0:00:00 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 LU factorization : L = lu(Y) ##### Iteration 1 / 3 ##### Normalized power iterations (1/3) : A' L Progress: 40%|████████████████▍ | ETA: 0:00:00 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Normalized power iterations (2/3) : A A' L LU decomposition (3/3) : L = lu(A A' L) ##### Iteration 2 / 3 ##### Normalized power iterations (1/3) : A' L Normalized power iterations (2/3) : A A' L LU decomposition (3/3) : L = lu(A A' L) ##### Iteration 3 / 3 ##### Normalized power iterations (1/3) : A' L Normalized power iterations (2/3) : A A' L QR decomposition (3/3) : Q = qr(A A' L) Small matrix computation : B = Q' A Progress: 40%|████████████████▍ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 SVD : B = U Σ V' ####### Sparse Randomized SVD (Command line) ####### Parsed args: logdir => "/tmp/jl_77dtm0" scale => "ftt" noversamples => 5 outdir => "/tmp/jl_77dtm0" rowvarlist => "" initV => nothing cper => 1.0f0 niter => 3 initW => nothing colsumlist => "" input => "/tmp/jl_wTMUCm/Data.mtx.zst" rowmeanlist => "/tmp/jl_77dtm0/Feature_FTTMeans.csv" dim => "3" perm => false chunksize => "51" Initial Setting... Progress: 40%|████████████████▍ | ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Random Projection : Y = A Ω Progress: 40%|████████████████▍ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 LU factorization : L = lu(Y) ##### Iteration 1 / 3 ##### Normalized power iterations (1/3) : A' L Progress: 40%|████████████████▍ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 Normalized power iterations (2/3) : A A' L LU decomposition (3/3) : L = lu(A A' L) ##### Iteration 2 / 3 ##### Normalized power iterations (1/3) : A' L Normalized power iterations (2/3) : A A' L LU decomposition (3/3) : L = lu(A A' L) ##### Iteration 3 / 3 ##### Normalized power iterations (1/3) : A' L Normalized power iterations (2/3) : A A' L QR decomposition (3/3) : Q = qr(A A' L) Small matrix computation : B = Q' A Progress: 40%|████████████████▍ | ETA: 0:00:00 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 SVD : B = U Σ V' ####### Exact Out-of-Core PCA (Dense, Julia API) ####### # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation Progress: 2 Time: 0:00:02 Progress: 6 Time: 0:00:02 # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation Progress: 2 Time: 0:00:01 Progress: 6 Time: 0:00:01 # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues ####### Exact Out-of-Core PCA (Dense, Command line) ####### Parsed args: pseudocount => 1.0f0 mode => "dense" dim => "3" outdir => "/tmp/jl_UG81Wy" input => "/tmp/jl_wTMUCm/Data.zst" scale => "raw" chunksize => "51" # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation Progress: 2 Time: 0:00:01 Progress: 6 Time: 0:00:01 # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation Progress: 2 Time: 0:00:00 Progress: 6 Time: 0:00:00 # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues ####### Exact Out-of-Core PCA (MM-Sparse, Julia API) ####### # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation Progress: 2 Time: 0:00:01 Progress: 6 Time: 0:00:01 # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation Progress: 2 Time: 0:00:00 Progress: 6 Time: 0:00:00 # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues ####### Exact Out-of-Core PCA (MM-Sparse, Command line) ####### Parsed args: pseudocount => 1.0f0 mode => "sparse_mm" dim => "3" outdir => "/tmp/jl_77dtm0" input => "/tmp/jl_wTMUCm/Data.mtx.zst" scale => "raw" chunksize => "51" # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation Progress: 2 Time: 0:00:00 Progress: 6 Time: 0:00:00 # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation Progress: 2 Time: 0:00:00 Progress: 6 Time: 0:00:00 # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues ####### Exact Out-of-Core PCA (BinCOO-Sparse, Julia API) ####### # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation Progress: 2 Time: 0:00:00 Progress: 6 Time: 0:00:00 # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues ####### Exact Out-of-Core PCA (BinCOO-Sparse, Command line) ####### Parsed args: pseudocount => 1.0f0 mode => "sparse_bincoo" dim => "3" outdir => "/tmp/jl_77dtm0" input => "/tmp/jl_wTMUCm/Data.bincoo.zst" scale => "raw" chunksize => "51" # 1. Column-wise Mean # 2. Out-of-Core Covariance Matrix Calculation Progress: 2 Time: 0:00:00 Progress: 6 Time: 0:00:00 # 3. PC Score (Z = XV) is being calculated. # 4. Out-of-Core PC Score Calculation Progress: 2 Time: 0:00:00 Progress: 6 Time: 0:00:00 # 5. Delayed Centering Correction # 6. Normalize W and Calculate Eigenvalues Inner product (Dense): 0.6409028976339882 Inner product (Sparse MM): 0.9999999807041767 Inner product (Sparse BinCOO): 0.9999999807041767 Test Failed at /home/pkgeval/.julia/packages/OnlinePCA/AhPWT/test/test_exact_ooc_pca.jl:84 Expression: inner_prod1 > 0.7 Evaluated: 0.6409028976339882 > 0.7 ERROR: LoadError: There was an error during testing in expression starting at /home/pkgeval/.julia/packages/OnlinePCA/AhPWT/test/test_exact_ooc_pca.jl:84 in expression starting at /home/pkgeval/.julia/packages/OnlinePCA/AhPWT/test/runtests.jl:83 Testing failed after 929.2s ERROR: LoadError: Package OnlinePCA errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:2034 [3] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1235.64s: package tests unexpectedly errored