Package evaluation of OnlinePCA on Julia 1.12.0-rc2.1 (1fad90817e*) started at 2025-09-11T14:23:34.428 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.77s ################################################################################ # Installation # Installing OnlinePCA... Resolving package versions... Installed PlotlyJS ─ v0.18.17 Installed WebIO ──── v0.8.21 Updating `~/.julia/environments/v1.12/Project.toml` [975b03d1] + OnlinePCA v0.3.10 Updating `~/.julia/environments/v1.12/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 v3.30.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.1 [34da2185] + Compat v4.18.0 [f0e56b4a] + ConcurrentUtilities v2.5.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [460bff9d] + ExceptionUnwrapping v0.1.11 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.14.0 [53c48c17] + FixedPointNumbers v0.8.5 [de31a74c] + FunctionalCollections v0.5.0 [38e38edf] + GLM v1.9.0 [f67ccb44] + HDF5 v0.17.2 [cd3eb016] + HTTP v1.10.17 [9fb69e20] + Hiccup v0.2.2 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [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 v1.1.0 [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 v1.5.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [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 v2.4.0 [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 v0.8.0 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [777ac1f9] + SimpleBufferStream v1.2.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.6 [4c63d2b9] + StatsFuns v1.5.0 [3eaba693] + StatsModels v0.7.6 [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 v4.3.1+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [c8ffd9c3] + MbedTLS_jll v2.28.6+2 [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 v2.13.8+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0 [3161d3a3] + Zstd_jll v1.5.7+1 [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 v1.6.0 [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 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [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 v8.11.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+1 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.5.0+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 27.36s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 530.67s ################################################################################ # Testing # Testing OnlinePCA Test Could not use exact versions of packages in manifest. Re-resolving dependencies Updating `/tmp/jl_QoEDwC/Project.toml` [31c24e10] ↑ Distributions v0.25.111 ⇒ v0.25.120 [1a297f60] ↑ FillArrays v1.12.0 ⇒ v1.14.0 [975b03d1] + OnlinePCA v0.3.10 [10745b16] ↑ Statistics v1.10.0 ⇒ v1.11.1 [37e2e46d] ~ LinearAlgebra ⇒ v1.12.0 [2f01184e] ↑ SparseArrays v1.10.0 ⇒ v1.12.0 [8dfed614] ~ Test ⇒ v1.11.0 Updating `/tmp/jl_QoEDwC/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 v3.30.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.1 [34da2185] ↑ Compat v4.16.0 ⇒ v4.18.0 [f0e56b4a] + ConcurrentUtilities v2.5.0 [a8cc5b0e] + Crayons v4.1.1 [a93c6f00] + DataFrames v1.7.1 ⌅ [864edb3b] ↑ DataStructures v0.18.20 ⇒ v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [31c24e10] ↑ Distributions v0.25.111 ⇒ v0.25.120 [ffbed154] ↑ DocStringExtensions v0.9.3 ⇒ v0.9.5 [460bff9d] + ExceptionUnwrapping v0.1.11 [48062228] + FilePathsBase v0.9.24 [1a297f60] ↑ FillArrays v1.12.0 ⇒ v1.14.0 [53c48c17] + FixedPointNumbers v0.8.5 [de31a74c] + FunctionalCollections v0.5.0 [38e38edf] + GLM v1.9.0 [f67ccb44] + HDF5 v0.17.2 [cd3eb016] + HTTP v1.10.17 [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 ⇒ v0.2.4 [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 v1.1.0 [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 v1.5.0 [bac558e1] ↑ OrderedCollections v1.6.3 ⇒ v1.8.1 [90014a1f] ↑ PDMats v0.11.31 ⇒ v0.11.35 [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 v2.4.0 [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 ⇒ v0.8.0 [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 ⇒ v2.5.1 [10745b16] ↑ Statistics v1.10.0 ⇒ v1.11.1 [82ae8749] ↑ StatsAPI v1.7.0 ⇒ v1.7.1 [2913bbd2] ↑ StatsBase v0.34.3 ⇒ v0.34.6 [4c63d2b9] ↑ StatsFuns v1.3.1 ⇒ v1.5.0 [3eaba693] + StatsModels v0.7.6 [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 v4.3.1+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [c8ffd9c3] ↑ MbedTLS_jll v2.28.2+1 ⇒ v2.28.6+2 [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 v2.13.8+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0 [3161d3a3] + Zstd_jll v1.5.7+1 [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 [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 [76f85450] ~ LibGit2 ⇒ v1.11.0 [8f399da3] ~ Libdl ⇒ v1.11.0 [37e2e46d] ~ LinearAlgebra ⇒ v1.12.0 [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 ⇒ v1.12.0 [de0858da] ~ Printf ⇒ v1.11.0 [3fa0cd96] ~ REPL ⇒ v1.11.0 [9a3f8284] ~ Random ⇒ v1.11.0 [9e88b42a] ~ Serialization ⇒ v1.11.0 [6462fe0b] ~ Sockets ⇒ v1.11.0 [2f01184e] ↑ SparseArrays v1.10.0 ⇒ v1.12.0 [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 ⇒ v8.11.1+1 [e37daf67] ↑ LibGit2_jll v1.6.4+0 ⇒ v1.9.0+0 [29816b5a] ↑ LibSSH2_jll v1.11.0+1 ⇒ v1.11.3+1 [14a3606d] ↑ MozillaCACerts_jll v2023.1.10 ⇒ v2025.5.20 [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 v3.5.1+0 [bea87d4a] ↑ SuiteSparse_jll v7.2.1+1 ⇒ v7.8.3+2 [83775a58] ↑ Zlib_jll v1.2.13+1 ⇒ v1.3.1+2 [8e850b90] ↑ libblastrampoline_jll v5.8.0+1 ⇒ v5.13.1+1 [8e850ede] ↑ nghttp2_jll v1.52.0+1 ⇒ v1.64.0+1 [3f19e933] ↑ p7zip_jll v17.4.0+2 ⇒ v17.5.0+2 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_QoEDwC/Project.toml` [c7e460c6] ArgParse v1.2.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [1a297f60] FillArrays v1.14.0 [4d4711f2] MatrixMarket v0.5.2 [975b03d1] OnlinePCA v0.3.10 [10745b16] Statistics v1.11.1 [37e2e46d] LinearAlgebra v1.12.0 [2f01184e] SparseArrays v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_QoEDwC/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 v3.30.0 [3da002f7] ColorTypes v0.12.1 [c3611d14] ColorVectorSpace v0.11.0 [5ae59095] Colors v0.13.1 [34da2185] Compat v4.18.0 [f0e56b4a] ConcurrentUtilities v2.5.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [460bff9d] ExceptionUnwrapping v0.1.11 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.14.0 [53c48c17] FixedPointNumbers v0.8.5 [de31a74c] FunctionalCollections v0.5.0 [38e38edf] GLM v1.9.0 [f67ccb44] HDF5 v0.17.2 [cd3eb016] HTTP v1.10.17 [9fb69e20] Hiccup v0.2.2 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [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 v1.1.0 [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 v1.5.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [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 v2.4.0 [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 v0.8.0 [91c51154] SentinelArrays v1.4.8 [1277b4bf] ShiftedArrays v2.0.0 [777ac1f9] SimpleBufferStream v1.2.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.5.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.6 [4c63d2b9] StatsFuns v1.5.0 [3eaba693] StatsModels v0.7.6 [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 v4.3.1+0 [f1f71cc9] MPItrampoline_jll v5.5.4+0 [c8ffd9c3] MbedTLS_jll v2.28.6+2 [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 v2.13.8+0 [a65dc6b1] Xorg_libpciaccess_jll v0.18.1+0 [3161d3a3] Zstd_jll v1.5.7+1 [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 v1.6.0 [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 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [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 v8.11.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.1+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+1 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... 10514.0 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 13 seconds. 50 already precompiled. /tmp/jl_rTNBYE 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) ####### Precompiling packages... 2009.8 ms ✓ TextWrap 1300.8 ms ✓ WorkerUtilities 1171.9 ms ✓ ShiftedArrays 7387.2 ms ✓ Lazy 1560.9 ms ✓ Mustache 1584.2 ms ✓ MatrixMarket 2173.9 ms ✓ Widgets 1789.7 ms ✓ Kaleido_jll 1233.4 ms ✓ Pidfile 1586.1 ms ✓ FunctionalCollections 1784.4 ms ✓ Hiccup 3688.3 ms ✓ QuadGK 209984.1 ms ✓ DataFrames 1103.0 ms ✓ InlineStrings → ParsersExt 2146.6 ms ✓ CodecZstd 22206.2 ms ✓ PlotlyBase 4421.1 ms ✓ WebSockets 2371.9 ms ✓ ArgParse 18380.8 ms ✓ StatsModels 3437.3 ms ✓ PlotlyKaleido 1126.2 ms ✓ AssetRegistry 14139.0 ms ✓ Distributions 2378.3 ms ✓ WeakRefStrings 316215.0 ms ✓ PlotlyBase → DataFramesExt 12735.0 ms ✓ Mux 9496.6 ms ✓ WebIO 6046.6 ms ✓ Distributions → DistributionsTestExt 8144.0 ms ✓ GLM 26866.4 ms ✓ PlotlyBase → DistributionsExt 71616.3 ms ✓ CSV 7267.3 ms ✓ JSExpr 12096.0 ms ✓ Blink 25831.1 ms ✓ PlotlyJS 11452.6 ms ✓ PlotlyJS → CSVExt 229343.5 ms ✓ PlotlyJS → DataFramesExt 285270.5 ms ✓ OnlinePCA 36 dependencies successfully precompiled in 1336 seconds. 127 already precompiled. 2 dependencies had output during precompilation: ┌ 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`. └ ┌ 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. └ Parsed args: binfile => /tmp/jl_rTNBYE/Data.zst csvfile => /tmp/jl_rTNBYE/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_rTNBYE/Data.mtx binfile => /tmp/jl_rTNBYE/Data.mtx.zst ####### Binarization of Binary COO (Julia API) ####### ####### Binarization of Binary COO (Command line) ####### Parsed args: binfile => /tmp/jl_rTNBYE/Data.bincoo.zst bincoofile => /tmp/jl_rTNBYE/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_rTNBYE/Data.zst mode => dense outdir => /tmp/jl_ajxmD4 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_rTNBYE/Data.mtx.zst mode => sparse_mm outdir => /tmp/jl_4MQNPX 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_ajxmD4/Feature_Means.csv binfile => /tmp/jl_rTNBYE/Data.zst rowcv2list => /tmp/jl_ajxmD4/Feature_CV2s.csv rowvarlist => /tmp/jl_ajxmD4/Feature_Vars.csv outdir => /tmp/jl_ajxmD4 Highly Variable Genes are calculated... ####### Filtering (Julia API) ####### ####### Filtering (Command line) ####### Parsed args: samplelist => /tmp/jl_ajxmD4/Sample_NoCounts.csv thr1 => 10 direct2 => + direct1 => + thr2 => 10 outdir => /tmp/jl_ajxmD4 input => /tmp/jl_rTNBYE/Data.zst featurelist => /tmp/jl_ajxmD4/Feature_Means.csv Parsed args: samplelist => thr1 => 10 direct2 => + direct1 => + thr2 => 10 outdir => /tmp/jl_ajxmD4 input => /tmp/jl_rTNBYE/Data.zst featurelist => /tmp/jl_ajxmD4/Feature_Means.csv Parsed args: samplelist => /tmp/jl_ajxmD4/Sample_NoCounts.csv thr1 => 10 direct2 => + direct1 => + thr2 => 10 outdir => /tmp/jl_ajxmD4 input => /tmp/jl_rTNBYE/Data.zst featurelist => ####### GD (Julia API) ####### ####### GD (Command line) ####### Parsed args: logdir => "/tmp/jl_ajxmD4" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_ajxmD4" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_rTNBYE/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_ajxmD4/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Parsed args: logdir => "/tmp/jl_ajxmD4" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_ajxmD4" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => "/tmp/jl_ajxmD4/Eigen_vectors.csv" colsumlist => "" input => "/tmp/jl_rTNBYE/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_ajxmD4/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Parsed args: logdir => "/tmp/jl_ajxmD4" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_ajxmD4" rowvarlist => "" lower => 0 initV => "/tmp/jl_ajxmD4/Loadings.csv" cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_rTNBYE/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_ajxmD4/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Parsed args: logdir => "/tmp/jl_ajxmD4" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_ajxmD4" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_rTNBYE/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_ajxmD4/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false ####### Oja (Julia API) ####### Progress: 1%|▎ | ETA: 0:02:59 Progress: 1%|▍ | ETA: 0:03:26 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Progress: 1%|▎ | ETA: 0:02:40 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:02:52 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:01:12 Progress: 100%|█████████████████████████████████████████| Time: 0:00:00 ####### Oja (Command line) ####### Parsed args: logdir => "/tmp/jl_ajxmD4" scale => "ftt" upper => 1.0f38 scheduling => "robbins-monro" offsetStoch => 1.0f-6 outdir => "/tmp/jl_ajxmD4" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_rTNBYE/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_ajxmD4/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:05:43 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Parsed args: logdir => "/tmp/jl_ajxmD4" scale => "ftt" upper => 1.0f38 scheduling => "momentum" offsetStoch => 1.0f-6 outdir => "/tmp/jl_ajxmD4" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_rTNBYE/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_ajxmD4/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:06:38 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Parsed args: logdir => "/tmp/jl_ajxmD4" scale => "ftt" upper => 1.0f38 scheduling => "nag" offsetStoch => 1.0f-6 outdir => "/tmp/jl_ajxmD4" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_rTNBYE/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_ajxmD4/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:08:19 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 Parsed args: logdir => "/tmp/jl_ajxmD4" scale => "ftt" upper => 1.0f38 scheduling => "adagrad" offsetStoch => 1.0f-6 outdir => "/tmp/jl_ajxmD4" rowvarlist => "" lower => 0 initV => nothing cper => 1.0f0 pseudocount => 1.0f0 g => 0.9f0 offsetFull => 1.0f-20 initW => nothing colsumlist => "" input => "/tmp/jl_rTNBYE/Data.zst" numepoch => "1" evalfreq => 5000 stepsize => "1.0e-15" rowmeanlist => "/tmp/jl_ajxmD4/Feature_FTTMeans.csv" expvar => 0.1f0 epsilon => 1.0f-8 dim => "3" perm => false Progress: 1%|▎ | ETA: 0:07:51 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 ####### SGD (Julia API) ####### Progress: 1%|▎ | ETA: 0:02:53 Progress: 1%|▍ | ETA: 0:03:42 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 Progress: 1%|▎ | ETA: 0:03:40 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:04:04 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 Progress: 1%|▎ | ETA: 0:02:35 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ####### SGD (Command line) ####### ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 683 running 1 of 1 signal (10): User defined signal 1 jl_is_va_tuple at /source/src/julia_internal.h:1168 [inlined] jl_is_va_tuple at /source/src/julia_internal.h:1164 [inlined] obviously_unequal at /source/src/subtype.c:466 ijl_types_equal at /source/src/subtype.c:2325 jl_specializations_get_linfo_ at /source/src/gf.c:237 jl_restore_system_image_from_stream_ at /source/src/staticdata.c:4162 jl_restore_package_image_from_stream at /source/src/staticdata.c:4414 jl_restore_incremental_from_buf at /source/src/staticdata.c:4483 ijl_restore_package_image_from_file at /source/src/staticdata.c:4550 #_include_from_serialized#862 at ./loading.jl:1270 _include_from_serialized at ./loading.jl:1246 [inlined] #_require_search_from_serialized#878 at ./loading.jl:2074 _require_search_from_serialized at ./loading.jl:1981 [inlined] __require_prelocked at ./loading.jl:2599 _require_prelocked at ./loading.jl:2465 macro expansion at ./loading.jl:2393 [inlined] macro expansion at ./lock.jl:376 [inlined] __require at ./loading.jl:2358 jfptr___require_63569.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [inlined] jl_f_invoke_in_world at /source/src/builtins.c:894 require at ./loading.jl:2334 jfptr_require_102915.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [inlined] call_require at /source/src/toplevel.c:494 [inlined] eval_import_path at /source/src/toplevel.c:532 jl_toplevel_eval_flex at /source/src/toplevel.c:830 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2843 _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 _include at ./loading.jl:2903 include at ./Base.jl:305 exec_options at ./client.jl:321 _start at ./client.jl:554 jfptr__start_103313.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7c29680fd249) 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) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 201 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 poptask at ./task.jl:1187 wait at ./task.jl:1199 #wait#398 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] wait at ./process.jl:694 wait at ./process.jl:687 [inlined] success at ./process.jl:556 #run#703 at ./process.jl:513 run at ./process.jl:510 unknown function (ip: 0x77b4d23881ab) at (unknown file) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [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:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2843 _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 _include at ./loading.jl:2903 include at ./Base.jl:306 IncludeInto at ./Base.jl:307 jfptr_IncludeInto_81501.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [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:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2843 _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 _include at ./loading.jl:2903 include at ./Base.jl:306 IncludeInto at ./Base.jl:307 jfptr_IncludeInto_81501.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [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:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 exec_options at ./client.jl:287 _start at ./client.jl:554 jfptr__start_103313.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x77b4d3890249) 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) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== 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 poptask at ./task.jl:1187 wait at ./task.jl:1199 #wait#398 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] wait at ./process.jl:694 wait at ./process.jl:687 jfptr_wait_88991.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 subprocess_handler at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2445 unknown function (ip: 0x71c313591ca3) at (unknown file) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 #204 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2385 withenv at ./env.jl:265 #189 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2204 with_temp_env at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2062 #185 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2171 #mktempdir#21 at ./file.jl:899 unknown function (ip: 0x71c31358663c) at (unknown file) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 mktempdir at ./file.jl:895 mktempdir at ./file.jl:895 #sandbox#181 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2118 [inlined] sandbox at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2110 unknown function (ip: 0x71c313582d21) at (unknown file) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 #test#192 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2370 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2280 [inlined] #test#170 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:483 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:462 unknown function (ip: 0x71c313582951) at (unknown file) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 #test#84 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:164 unknown function (ip: 0x71c31357fc20) at (unknown file) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:153 #test#82 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [inlined] #test#81 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 [inlined] test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 unknown function (ip: 0x71c31357813f) at (unknown file) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [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:693 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2843 _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 _include at ./loading.jl:2903 include at ./Base.jl:305 exec_options at ./client.jl:321 _start at ./client.jl:554 jfptr__start_103313.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x71c32f7d8249) 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) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ 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/v1.12/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000071c3155fc010 Total snapshots: 126. Utilization: 0% ╎126 @Base/client.jl:554 _start() ╎ 126 @Base/client.jl:321 exec_options(opts::Base.JLOptions) ╎ 126 @Base/Base.jl:305 include(mod::Module, _path::String) ╎ 126 @Base/loading.jl:2903 _include(mapexpr::Function, mod::Module, _pat… ╎ 126 @Base/loading.jl:2843 include_string(mapexpr::typeof(identity), mo… ╎ 126 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 126 @Pkg/src/API.jl:151 kwcall(::@NamedTuple{julia_args::Cmd}, ::typ… ╎ ╎ 126 @Pkg/src/API.jl:151 #test#81 ╎ ╎ 126 @Pkg/src/API.jl:152 test ╎ ╎ 126 @Pkg/src/API.jl:152 test(pkgs::Vector{String}; kwargs::Base.P… ╎ ╎ 126 @Pkg/src/API.jl:153 kwcall(::@NamedTuple{julia_args::Cmd}, :… ╎ ╎ ╎ 126 @Pkg/src/API.jl:164 test(pkgs::Vector{PackageSpec}; io::IOC… ╎ ╎ ╎ 126 @Pkg/src/API.jl:462 kwcall(::@NamedTuple{julia_args::Cmd, … ╎ ╎ ╎ 126 @Pkg/src/API.jl:483 test(ctx::Pkg.Types.Context, pkgs::Ve… ╎ ╎ ╎ 126 @Pkg/…erations.jl:2280 test ╎ ╎ ╎ 126 @Pkg/…erations.jl:2370 test(ctx::Pkg.Types.Context, pkg… ╎ ╎ ╎ ╎ 126 @Pkg/…rations.jl:2110 kwcall(::@NamedTuple{preferences… ╎ ╎ ╎ ╎ 126 @Pkg/…rations.jl:2118 #sandbox#181 ╎ ╎ ╎ ╎ 126 @Base/file.jl:895 mktempdir(fn::Function) ╎ ╎ ╎ ╎ 126 @Base/file.jl:895 mktempdir(fn::Function, parent::S… ╎ ╎ ╎ ╎ 126 @Base/file.jl:899 mktempdir(fn::Pkg.Operations.var… ╎ ╎ ╎ ╎ ╎ 126 @Pkg/…tions.jl:2171 (::Pkg.Operations.var"#185#18… ╎ ╎ ╎ ╎ ╎ 126 @Pkg/…tions.jl:2062 with_temp_env(fn::Pkg.Operat… ╎ ╎ ╎ ╎ ╎ 126 @Pkg/…tions.jl:2204 (::Pkg.Operations.var"#189#… ╎ ╎ ╎ ╎ ╎ 126 @Base/env.jl:265 withenv(::Pkg.Operations.var"… ╎ ╎ ╎ ╎ ╎ 126 @Pkg/…ions.jl:2385 (::Pkg.Operations.var"#204… ╎ ╎ ╎ ╎ ╎ ╎ 126 @Pkg/…ons.jl:2445 subprocess_handler(cmd::Cm… ╎ ╎ ╎ ╎ ╎ ╎ 126 @Base/…ss.jl:687 wait(x::Base.Process) ╎ ╎ ╎ ╎ ╎ ╎ 126 @Base/…ss.jl:694 wait(x::Base.Process, syn… ╎ ╎ ╎ ╎ ╎ ╎ 126 @Base/…on.jl:136 wait ╎ ╎ ╎ ╎ ╎ ╎ 126 @Base/…on.jl:141 wait(c::Base.GenericCon… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 126 @Base/…sk.jl:1199 wait() 125╎ ╎ ╎ ╎ ╎ ╎ ╎ 126 @Base/…sk.jl:1187 poptask(W::Base.Intr… [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 poptask at ./task.jl:1187 wait at ./task.jl:1199 #wait#398 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] _trywait at ./asyncevent.jl:185 profile_printing_listener at ./Base.jl:331 #start_profile_listener##0 at ./Base.jl:351 jfptr_YY.start_profile_listenerYY.YY.0_45490.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 30402375 (Pool: 30401759; Big: 616); GC: 28 [201] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/OnlinePCA/AhPWT/test/test_sgd.jl:58 _ZN4llvm16DwarfCompileUnit24constructInlinedScopeDIEEPNS_12LexicalScopeERNS_3DIEE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm16DwarfCompileUnit17constructScopeDIEEPNS_12LexicalScopeERNS_3DIEE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm16DwarfCompileUnit25createAndAddScopeChildrenEPNS_12LexicalScopeERNS_3DIEE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm16DwarfCompileUnit25createAndAddScopeChildrenEPNS_12LexicalScopeERNS_3DIEE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm16DwarfCompileUnit27constructSubprogramScopeDIEEPKNS_12DISubprogramEPNS_12LexicalScopeE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm10DwarfDebug15endFunctionImplEPKNS_15MachineFunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) [683] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/OnlinePCA/AhPWT/bin/sgd:138 _ZN4llvm16DebugHandlerBase11endFunctionEPKNS_15MachineFunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm10AsmPrinter16emitFunctionBodyEv at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN12_GLOBAL__N_111DAGCombiner3RunEN4llvm12CombineLevelE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm12SelectionDAG7CombineENS_12CombineLevelEPNS_9AAResultsENS_15CodeGenOptLevelE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm16SelectionDAGISel17CodeGenAndEmitDAGEv at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm16SelectionDAGISel20SelectAllBasicBlocksERKNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm16SelectionDAGISel20runOnMachineFunctionERNS_15MachineFunctionE.part.0 at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN12_GLOBAL__N_115X86DAGToDAGISel20runOnMachineFunctionERN4llvm15MachineFunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm19MachineFunctionPass13runOnFunctionERNS_8FunctionE.part.0 at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm13FPPassManager13runOnFunctionERNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm13FPPassManager11runOnModuleERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm6legacy15PassManagerImpl3runERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm3orc14SimpleCompilerclERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm13X86AsmPrinter20runOnMachineFunctionERNS_15MachineFunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm19MachineFunctionPass13runOnFunctionERNS_8FunctionE.part.0 at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm13FPPassManager13runOnFunctionERNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm13FPPassManager11runOnModuleERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm6legacy15PassManagerImpl3runERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm3orc14SimpleCompilerclERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) operator() at /source/src/jitlayers.cpp:1561 addModule at /source/src/jitlayers.cpp:2044 jl_compile_codeinst_now at /source/src/jitlayers.cpp:626 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:824 jl_compile_method_internal at /source/src/gf.c:3520 _jl_invoke at /source/src/gf.c:3997 [inlined] ijl_apply_generic at /source/src/gf.c:4205 #handle_message#6 at ./logging/ConsoleLogger.jl:162 handle_message at ./logging/ConsoleLogger.jl:110 unknown function (ip: 0x7c2966b4444d) at (unknown file) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [inlined] jl_f_invoke_in_world at /source/src/builtins.c:894 #invokelatest_gr#232 at ./reflection.jl:1280 [inlined] invokelatest_gr at ./reflection.jl:1274 [inlined] #handle_message_nothrow#2 at ./logging/logging.jl:432 handle_message_nothrow at ./logging/logging.jl:429 _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_invoke at /source/src/gf.c:4012 tojlinvoke2016.1 at /opt/julia/share/julia/compiled/v1.12/Profile/nGhxz_X6ROR.so (unknown line) macro expansion at ./logging/logging.jl:417 [inlined] #warning_empty#40 at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1362 operator() at /source/src/jitlayers.cpp:1561 addModule at /source/src/jitlayers.cpp:2044 jl_compile_codeinst_now at /source/src/jitlayers.cpp:626 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:824 jl_compile_method_internal at /source/src/gf.c:3520 _jl_invoke at /source/src/gf.c:3997 [inlined] ijl_apply_generic at /source/src/gf.c:4205 warning_empty at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1360 [inlined] #print#5 at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:358 print at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:271 [inlined] print at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:271 [inlined] print at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:271 _peek_report at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:94 unknown function (ip: 0x7c2966b2d8ef) at (unknown file) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [inlined] jl_f_invokelatest at /source/src/builtins.c:875 profile_printing_listener at ./Base.jl:333 #start_profile_listener##0 at ./Base.jl:351 jfptr_YY.start_profile_listenerYY.YY.0_45490.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 18923313 (Pool: 18923093; Big: 220); GC: 17 jl_apply at /source/src/julia.h:2381 [inlined] jl_f_invokelatest at /source/src/builtins.c:875 profile_printing_listener at ./Base.jl:333 #start_profile_listener##0 at ./Base.jl:351 jfptr_YY.start_profile_listenerYY.YY.0_45490.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4005 [inlined] ijl_apply_generic at /source/src/gf.c:4205 jl_apply at /source/src/julia.h:2381 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 70982234 (Pool: 70981378; Big: 856); GC: 70 PkgEval terminated after 2737.94s: test duration exceeded the time limit