Package evaluation to test Knockoffs on Julia 1.12.7-DEV.43 (fe4faaea78*) started at 2026-06-22T01:58:12.939 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 8.33s ################################################################################ # Installation # Installing Knockoffs... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [878bf26d] + Knockoffs v3.1.4 Updating `~/.julia/environments/v1.12/Manifest.toml` [47edcb42] + ADTypes v1.22.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.6.1 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.25.0 [67c07d97] + Automa v1.2.0 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 ⌅ [0a1fb500] + BlockDiagonals v0.1.42 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [d360d2e6] + ChainRulesCore v1.26.1 [fb6a15b2] + CloseOpenIntervals v0.1.13 [aaaa29a8] + Clustering v0.15.8 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.7 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [587fd27a] + CovarianceEstimation v0.2.13 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.16.0 [a0c0ee7d] + DifferentiationInterface v0.7.18 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.127 [ffbed154] + DocStringExtensions v0.9.5 [fdbdab4c] + ElasticArrays v1.2.12 [4e289a0a] + EnumX v1.0.7 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [6a86dc24] + FiniteDiff v2.31.0 [26cc04aa] + FiniteDifferences v0.12.34 [f6369f11] + ForwardDiff v1.4.1 [38e38edf] + GLM v1.9.5 ⌃ [8d5ece8b] + GLMNet v0.7.0 ⌅ [14197337] + GenericLinearAlgebra v0.3.19 [c27321d9] + Glob v1.5.0 [3e5b6fbb] + HostCPUFeatures v0.1.18 ⌅ [b99e6be6] + Hypatia v0.7.4 [34004b35] + HypergeometricFunctions v0.3.28 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.5 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [42fd0dbc] + IterativeSolvers v0.9.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [682c06a0] + JSON v1.6.1 [4076af6c] + JuMP v1.30.1 [878bf26d] + Knockoffs v3.1.4 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 ⌃ [d3d80556] + LineSearches v7.5.1 [7a12625a] + LinearMaps v3.11.4 [2ab3a3ac] + LogExpFunctions v1.0.1 [bdcacae8] + LoopVectorization v0.12.174 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [b8f27783] + MathOptInterface v1.51.1 [e1d29d7a] + Missings v1.2.0 [d8a4904e] + MutableArithmetics v1.8.0 ⌅ [d41bc354] + NLSolversBase v7.10.0 [77ba4419] + NaNMath v1.1.4 [b8a86587] + NearestNeighbors v0.4.27 [6fe1bfb0] + OffsetArrays v1.17.0 ⌅ [429524aa] + Optim v1.13.3 ⌅ [bac558e1] + OrderedCollections v1.8.2 ⌃ [90014a1f] + PDMats v0.11.35 [69de0a69] + Parsers v2.8.6 [1d0040c9] + PolyesterWeave v0.2.2 [3a141323] + PolynomialRoots v1.0.0 [2dfb63ee] + PooledArrays v1.4.3 [85a6dd25] + PositiveFactorizations v0.2.4 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.3.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.3 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [708f8203] + Richardson v1.4.3 [79098fc4] + Rmath v0.9.0 ⌅ [f2b01f46] + Roots v2.3.0 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.46 [431bcebd] + SciMLPublic v1.0.1 [91c51154] + SentinelArrays v1.4.10 [efcf1570] + Setfield v1.1.2 [1277b4bf] + ShiftedArrays v2.0.0 [4e780e97] + SnpArrays v0.3.23 [a2af1166] + SortingAlgorithms v1.2.3 [276daf66] + SpecialFunctions v2.8.0 [aedffcd0] + Static v1.4.0 [0d7ed370] + StaticArrayInterface v1.10.0 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 ⌅ [2913bbd2] + StatsBase v0.33.10 [4c63d2b9] + StatsFuns v2.2.0 [3eaba693] + StatsModels v0.7.10 [892a3eda] + StringManipulation v0.4.4 [ec057cc2] + StructUtils v2.8.2 [9449cd9e] + TSVD v0.4.4 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [8290d209] + ThreadingUtilities v0.5.6 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [3a884ed6] + UnPack v1.0.2 [28eba6e3] + VariantCallFormat v0.5.9 [3d5dd08c] + VectorizationBase v0.21.74 [ea10d353] + WeakRefStrings v1.4.3 [efce3f68] + WoodburyMatrices v1.1.0 [76eceee3] + WorkerUtilities v1.6.1 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [ffd25f8a] + XZ_jll v5.8.3+0 [3161d3a3] + Zstd_jll v1.5.7+1 [78c6b45d] + glmnet_jll v5.0.0+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [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 v1.12.1 [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 v8.15.0+0 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 7.82s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 3099.8 ms ✓ BufferedStreams 1119.4 ms ✓ PolynomialRoots 2058.6 ms ✓ PDMats 1106.1 ms ✓ TSVD 1018.5 ms ✓ ElasticArrays 2729.6 ms ✓ TranscodingStreams 1169.9 ms ✓ LinearMaps → LinearMapsChainRulesCoreExt 8122.2 ms ✓ glmnet_jll 4623.9 ms ✓ Polynomials → PolynomialsRecipesBaseExt 6226.6 ms ✓ QuadGK 13327.9 ms ✓ StatsBase 2961.6 ms ✓ DifferentiationInterface → DifferentiationInterfaceFiniteDifferencesExt 18725.7 ms ✓ BlockDiagonals 8777.7 ms ✓ NLSolversBase 24963.5 ms ✓ Roots → RootsForwardDiffExt 118794.3 ms ✓ LoopVectorization → SpecialFunctionsExt 103070.6 ms ✓ LoopVectorization → ForwardDiffExt 7478.3 ms ✓ ToeplitzMatrices 3725.1 ms ✓ DSP → OffsetArraysExt 1441.6 ms ✓ FillArrays → FillArraysPDMatsExt 2124.9 ms ✓ CodecXz 5426.2 ms ✓ BioGenerics 1834.7 ms ✓ CodecZlib 3350.8 ms ✓ CodecZstd 22838.2 ms ✓ Automa 1809.0 ms ✓ CodecBzip2 6637.5 ms ✓ CovarianceEstimation 11085.2 ms ✓ StatsModels 36217.0 ms ✓ Clustering 13146.9 ms ✓ LineSearches 23898.3 ms ✓ ToeplitzMatrices → ToeplitzMatricesStatsBaseExt 23873.8 ms ✓ Distributions 33789.1 ms ✓ CSV 2212.9 ms ✓ BGZFStreams 96972.6 ms ✓ MathOptInterface 12827.9 ms ✓ Optim 6216.0 ms ✓ Distributions → DistributionsTestExt 9360.0 ms ✓ Distributions → DistributionsChainRulesCoreExt 29531.2 ms ✓ GLM 167305.4 ms ✓ GLMNet 16553.7 ms ✓ VariantCallFormat 171661.8 ms ✓ JuMP 18838.0 ms ✓ Hypatia 101756.9 ms ✓ Optim → OptimMOIExt 374421.0 ms ✓ SnpArrays 597071.2 ms ✓ Knockoffs 46 dependencies successfully precompiled in 2126 seconds. 209 already precompiled. 24 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 138 dependents of these packages may trigger further precompilation to work with the unexpected versions. 3 dependencies had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ ┌ SnpArrays │ [ Info: Compiling VCF parser... └ ┌ Knockoffs │ [ Info: Compiling VCF parser... └ Precompilation completed after 2144.3s ################################################################################ # Testing # Testing Knockoffs Status `/tmp/jl_LHpOoi/Project.toml` ⌅ [0a1fb500] BlockDiagonals v0.1.42 [336ed68f] CSV v0.10.16 [aaaa29a8] Clustering v0.15.8 [587fd27a] CovarianceEstimation v0.2.13 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.127 [fdbdab4c] ElasticArrays v1.2.12 [38e38edf] GLM v1.9.5 ⌃ [8d5ece8b] GLMNet v0.7.0 ⌅ [b99e6be6] Hypatia v0.7.4 [4076af6c] JuMP v1.30.1 [878bf26d] Knockoffs v3.1.4 [bdcacae8] LoopVectorization v0.12.174 ⌅ [429524aa] Optim v1.13.3 [85a6dd25] PositiveFactorizations v0.2.4 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 ⌅ [f2b01f46] Roots v2.3.0 [4e780e97] SnpArrays v0.3.23 [10745b16] Statistics v1.11.1 ⌅ [2913bbd2] StatsBase v0.33.10 [c751599d] ToeplitzMatrices v0.8.5 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.12.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_LHpOoi/Manifest.toml` [47edcb42] ADTypes v1.22.0 [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.44 [79e6a3ab] Adapt v4.6.1 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.25.0 [67c07d97] Automa v1.2.0 [28d598bf] BGZFStreams v0.3.2 [0e736298] Bessels v0.2.8 [47718e42] BioGenerics v0.1.5 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 ⌅ [0a1fb500] BlockDiagonals v0.1.42 [e1450e63] BufferedStreams v1.2.2 [2a0fbf3d] CPUSummary v0.2.7 [336ed68f] CSV v0.10.16 [d360d2e6] ChainRulesCore v1.26.1 [fb6a15b2] CloseOpenIntervals v0.1.13 [aaaa29a8] Clustering v0.15.8 [523fee87] CodecBzip2 v0.8.5 [ba30903b] CodecXz v0.7.4 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.7 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.7 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [587fd27a] CovarianceEstimation v0.2.13 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [717857b8] DSP v0.8.5 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.16.0 [a0c0ee7d] DifferentiationInterface v0.7.18 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.127 [ffbed154] DocStringExtensions v0.9.5 [fdbdab4c] ElasticArrays v1.2.12 [4e289a0a] EnumX v1.0.7 [7a1cc6ca] FFTW v1.10.0 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [6a86dc24] FiniteDiff v2.31.0 [26cc04aa] FiniteDifferences v0.12.34 [f6369f11] ForwardDiff v1.4.1 [38e38edf] GLM v1.9.5 ⌃ [8d5ece8b] GLMNet v0.7.0 ⌅ [14197337] GenericLinearAlgebra v0.3.19 [c27321d9] Glob v1.5.0 [3e5b6fbb] HostCPUFeatures v0.1.18 ⌅ [b99e6be6] Hypatia v0.7.4 [34004b35] HypergeometricFunctions v0.3.28 [615f187c] IfElse v0.1.1 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [c8e1da08] IterTools v1.10.0 [42fd0dbc] IterativeSolvers v0.9.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [682c06a0] JSON v1.6.1 [4076af6c] JuMP v1.30.1 [878bf26d] Knockoffs v3.1.4 [b964fa9f] LaTeXStrings v1.4.0 [10f19ff3] LayoutPointers v0.1.17 ⌃ [d3d80556] LineSearches v7.5.1 [7a12625a] LinearMaps v3.11.4 [2ab3a3ac] LogExpFunctions v1.0.1 [bdcacae8] LoopVectorization v0.12.174 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [b8f27783] MathOptInterface v1.51.1 [e1d29d7a] Missings v1.2.0 [d8a4904e] MutableArithmetics v1.8.0 ⌅ [d41bc354] NLSolversBase v7.10.0 [77ba4419] NaNMath v1.1.4 [b8a86587] NearestNeighbors v0.4.27 [6fe1bfb0] OffsetArrays v1.17.0 ⌅ [429524aa] Optim v1.13.3 ⌅ [bac558e1] OrderedCollections v1.8.2 ⌃ [90014a1f] PDMats v0.11.35 [69de0a69] Parsers v2.8.6 [1d0040c9] PolyesterWeave v0.2.2 [3a141323] PolynomialRoots v1.0.0 [f27b6e38] Polynomials v4.1.1 [2dfb63ee] PooledArrays v1.4.3 [85a6dd25] PositiveFactorizations v0.2.4 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.3.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.3 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [708f8203] Richardson v1.4.3 [79098fc4] Rmath v0.9.0 ⌅ [f2b01f46] Roots v2.3.0 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.46 [431bcebd] SciMLPublic v1.0.1 [91c51154] SentinelArrays v1.4.10 [efcf1570] Setfield v1.1.2 [1277b4bf] ShiftedArrays v2.0.0 [4e780e97] SnpArrays v0.3.23 [a2af1166] SortingAlgorithms v1.2.3 [276daf66] SpecialFunctions v2.8.0 [aedffcd0] Static v1.4.0 [0d7ed370] StaticArrayInterface v1.10.0 [90137ffa] StaticArrays v1.9.18 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 ⌅ [2913bbd2] StatsBase v0.33.10 [4c63d2b9] StatsFuns v2.2.0 [3eaba693] StatsModels v0.7.10 [892a3eda] StringManipulation v0.4.4 [ec057cc2] StructUtils v2.8.2 [9449cd9e] TSVD v0.4.4 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [8290d209] ThreadingUtilities v0.5.6 [c751599d] ToeplitzMatrices v0.8.5 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [3a884ed6] UnPack v1.0.2 [28eba6e3] VariantCallFormat v0.5.9 [3d5dd08c] VectorizationBase v0.21.74 [ea10d353] WeakRefStrings v1.4.3 [efce3f68] WoodburyMatrices v1.1.0 [76eceee3] WorkerUtilities v1.6.1 [6e34b625] Bzip2_jll v1.0.9+0 [f5851436] FFTW_jll v3.3.12+0 [1d5cc7b8] IntelOpenMP_jll v2025.2.0+0 [856f044c] MKL_jll v2025.2.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [ffd25f8a] XZ_jll v5.8.3+0 [3161d3a3] Zstd_jll v1.5.7+1 [78c6b45d] glmnet_jll v5.0.0+0 [1317d2d5] oneTBB_jll v2022.3.0+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL 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 v1.12.1 [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 v8.15.0+0 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.6+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Precompiling packages... 26398.2 ms ✓ Polynomials 4460.0 ms ✓ FFTW 1817.0 ms ✓ Polynomials → PolynomialsFFTWExt 3902.2 ms ✓ DSP 4036.3 ms ✓ ToeplitzMatrices 5 dependencies successfully precompiled in 41 seconds. 58 already precompiled. 49 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, CompilerSupportLibraries_jll, ConstructionBase, ConstructionBase → ConstructionBaseLinearAlgebraExt, Dates, DocStringExtensions, Downloads, FillArrays, FillArrays → FillArraysSparseArraysExt, FillArrays → FillArraysStatisticsExt, Future, IrrationalConstants, JLLWrappers, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, LogExpFunctions, Logging, MacroTools, Markdown, MozillaCACerts_jll, NetworkOptions, OpenLibm_jll, OpenSSL_jll, OpenSpecFun_jll, OrderedCollections, Pkg, Preferences, Printf, Reexport, Serialization, SparseArrays, SpecialFunctions, StaticArraysCore, Statistics, Statistics → SparseArraysExt, StyledStrings, SuiteSparse_jll, TOML, Tar, UUIDs, Unicode, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 11 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 629.9 ms ✓ AbstractFFTs → AbstractFFTsChainRulesCoreExt 1 dependency successfully precompiled in 1 seconds. 9 already precompiled. 9 dependencies precompiled but different versions are currently loaded (AbstractFFTs, ChainRulesCore, Compat, Compat → CompatLinearAlgebraExt, Dates, Printf, TOML, UUIDs and Unicode). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 1706.2 ms ✓ Polynomials → PolynomialsChainRulesCoreExt 1 dependency successfully precompiled in 2 seconds. 20 already precompiled. 20 dependencies precompiled but different versions are currently loaded (ChainRulesCore, ChainRulesCore → ChainRulesCoreSparseArraysExt, Compat, Compat → CompatLinearAlgebraExt, ConstructionBase, ConstructionBase → ConstructionBaseLinearAlgebraExt, Dates, Future, MacroTools, OrderedCollections, Polynomials, Printf, Serialization, Setfield, SparseArrays, StaticArraysCore, SuiteSparse_jll, TOML, UUIDs and Unicode). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 2008.9 ms ✓ Polynomials → PolynomialsRecipesBaseExt 1 dependency successfully precompiled in 2 seconds. 18 already precompiled. 18 dependencies precompiled but different versions are currently loaded (ConstructionBase, ConstructionBase → ConstructionBaseLinearAlgebraExt, Dates, Future, MacroTools, OrderedCollections, Polynomials, PrecompileTools, Preferences, Printf, RecipesBase, Serialization, Setfield, SparseArrays, StaticArraysCore, SuiteSparse_jll, TOML and Unicode). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 2488.2 ms ✓ Polynomials → PolynomialsMutableArithmeticsExt 1 dependency successfully precompiled in 3 seconds. 19 already precompiled. 19 dependencies precompiled but different versions are currently loaded (Base64, ConstructionBase, ConstructionBase → ConstructionBaseLinearAlgebraExt, Future, InteractiveUtils, JuliaSyntaxHighlighting, Logging, MacroTools, Markdown, MutableArithmetics, OrderedCollections, Polynomials, Serialization, Setfield, SparseArrays, StaticArraysCore, StyledStrings, SuiteSparse_jll and Test). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 2019.4 ms ✓ DSP → OffsetArraysExt 1 dependency successfully precompiled in 2 seconds. 60 already precompiled. 56 dependencies precompiled but different versions are currently loaded (AbstractFFTs, ArgTools, Base64, Bessels, CompilerSupportLibraries_jll, ConstructionBase, ConstructionBase → ConstructionBaseLinearAlgebraExt, DSP, Dates, DocStringExtensions, Downloads, FFTW, FFTW_jll, Future, IrrationalConstants, IterTools, JLLWrappers, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, LogExpFunctions, Logging, MacroTools, Markdown, MozillaCACerts_jll, NetworkOptions, OffsetArrays, OpenLibm_jll, OpenSSL_jll, OpenSpecFun_jll, OrderedCollections, Pkg, Polynomials, Polynomials → PolynomialsFFTWExt, Preferences, Printf, Reexport, Serialization, Setfield, SparseArrays, SpecialFunctions, StaticArraysCore, Statistics, Statistics → SparseArraysExt, StyledStrings, SuiteSparse_jll, TOML, Tar, UUIDs, Unicode, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 5 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 2615.2 ms ✓ ToeplitzMatrices → ToeplitzMatricesStatsBaseExt 1 dependency successfully precompiled in 3 seconds. 72 already precompiled. 68 dependencies precompiled but different versions are currently loaded (AbstractFFTs, ArgTools, Base64, Bessels, Compat, Compat → CompatLinearAlgebraExt, CompilerSupportLibraries_jll, ConstructionBase, ConstructionBase → ConstructionBaseLinearAlgebraExt, DSP, DataAPI, DataStructures, Dates, DocStringExtensions, Downloads, FFTW, FFTW_jll, FillArrays, FillArrays → FillArraysSparseArraysExt, FillArrays → FillArraysStatisticsExt, Future, InteractiveUtils, IrrationalConstants, IterTools, JLLWrappers, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, LogExpFunctions, Logging, MacroTools, Markdown, Missings, MozillaCACerts_jll, NetworkOptions, OpenLibm_jll, OpenSSL_jll, OpenSpecFun_jll, OrderedCollections, Pkg, Polynomials, Polynomials → PolynomialsFFTWExt, Preferences, Printf, Reexport, Serialization, Setfield, SortingAlgorithms, SparseArrays, SpecialFunctions, StaticArraysCore, Statistics, Statistics → SparseArraysExt, StatsAPI, StatsBase, StyledStrings, SuiteSparse_jll, TOML, Tar, ToeplitzMatrices, UUIDs, Unicode, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 5 dependents of these packages may trigger further precompilation to work with the unexpected versions. 139.139972 seconds (108.48 M allocations: 5.728 GiB, 1.97% gc time, 99.36% compilation time) Test Summary: | Pass Total Time fixed knockoffs | 10213 10213 2m25.1s 14.734071 seconds (6.38 M allocations: 503.806 MiB, 0.97% gc time, 41.97% compilation time) Test Summary: | Pass Total Time model X Guassian Knockoffs | 4 4 16.0s 10.588573 seconds (3.62 M allocations: 366.194 MiB, 7.33% gc time, 40.68% compilation time) Test Summary: | Pass Total Time model X 2nd order Knockoffs | 3 3 10.6s Test Summary: | Pass Total Time utility functions | 247484 247484 10.5s Test Summary: | Pass Total Time Symbol and string inputs agree | 15 15 1m16.2s Test Summary: | Pass Total Time MK_statistics | 16 16 2.1s Test Summary: | Pass Total Time multiple knockoff q-values | 7 7 2.5s Test Summary: | Pass Total Time q-value selection matches standard selection on simulated data | 11 11 3.5s Test Summary: | Pass Total Time select_groups returns group labels and member indices | 13 13 10.7s Test Summary: | Pass Total Time Markov chain knockoffs have the right correlation structure | 55 55 14.1s Test Summary: | Pass Total Time MVR identity covariance | 9 9 0.3s 33.724237 seconds (650.01 k allocations: 589.434 MiB, 4.63% gc time) 0.066633 seconds (108 allocations: 15.383 MiB) 0.078634 seconds (114 allocations: 15.388 MiB) 2.369409 seconds (634.82 k allocations: 82.929 MiB, 0.55% gc time, 25.96% compilation time) 2.365583 seconds (1.18 k allocations: 49.562 MiB) 2.332219 seconds (1.18 k allocations: 49.561 MiB, 0.44% gc time) Test Summary: | Pass Total Time SDP vs MVR vs ME knockoffs | 2 2 42.7s 40.339786 seconds (661.22 k allocations: 586.995 MiB, 1.80% gc time) 0.575787 seconds (80 allocations: 10.467 MiB) Test Summary: | Pass Total Time SDP vs SDP fast | 1 1 41.3s 0.676038 seconds (276.07 k allocations: 25.432 MiB, 45.42% compilation time) 0.939072 seconds (85 allocations: 10.468 MiB) Test Summary: | Pass Total Time keyword arguments | 1 1 1.6s 0.356685 seconds (108 allocations: 42.419 MiB) 3.651495 seconds (1.18 k allocations: 125.228 MiB) 4.307830 seconds (636.89 k allocations: 159.731 MiB, 14.86% compilation time) Test Summary: | Pass Total Time debiasing preserves sparsity pattern | 5 5 15.4s ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 Approximating covariance by blocks... 50%|███████ | ETA: 0:00:01 Approximating covariance by blocks... 83%|███████████▋ | ETA: 0:00:01 Approximating covariance by blocks... 100%|██████████████| Time: 0:00:03 16.772317 seconds (13.35 M allocations: 1.177 GiB, 6.23% gc time, 77.10% compilation time: 18% of which was recompilation) 0.191342 seconds (2.10 k allocations: 43.050 MiB, 4.73% gc time, 5.47% compilation time) 0.226639 seconds (3.19 k allocations: 54.172 MiB, 4.22% gc time, 5.17% compilation time) Test Summary: | Pass Total Time approximate constructions | 4 4 17.4s norm(β̂ - b) = 1.7919251278577844 norm(β̂ - b) = 1.7919251278577844 norm(β̂ - b) = 1.7919251278577844 norm(β̂ - b) = 0.7044388571689835 norm(β̂ - b) = 0.879750303505637 norm(β̂ - b) = 1.7919251278577844 norm(β̂ - b) = 1.7919251278577844 norm(β̂ - b) = 1.7919251278577844 norm(β̂ - b) = 0.7044387294061174 norm(β̂ - b) = 0.9607680773846126 norm(β̂ - b) = 1.7919251278577844 norm(β̂ - b) = 1.7919251278577844 norm(β̂ - b) = 1.7919251278577844 norm(β̂ - b) = 1.0183935821402585 norm(β̂ - b) = 1.019309911295841 Test Summary: | Total Time fit lasso Gaussian | 0 1.2s norm(β̂ - b) = 1.898369367937291 norm(β̂ - b) = 1.898369367937291 norm(β̂ - b) = 1.898369367937291 norm(β̂ - b) = 0.4880027600182147 norm(β̂ - b) = 0.6228446256183272 norm(β̂ - b) = 1.898369367937291 norm(β̂ - b) = 1.898369367937291 norm(β̂ - b) = 1.898369367937291 norm(β̂ - b) = 1.6046122369956328 norm(β̂ - b) = 1.5990540493936085 ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 839 running 1 of 1 signal (10): User defined signal 1 lognet2n_ at /home/pkgeval/.julia/artifacts/e80442d59af73a1877a108eb3fab2cd12d25dc56/lib/libglmnet.so (unknown line) lognet_ at /home/pkgeval/.julia/artifacts/e80442d59af73a1877a108eb3fab2cd12d25dc56/lib/libglmnet.so (unknown line) #glmnet!#13 at /home/pkgeval/.julia/packages/GLMNet/C8WKF/src/GLMNet.jl:368 glmnet! at /home/pkgeval/.julia/packages/GLMNet/C8WKF/src/GLMNet.jl:337 unknown function (ip: 0x78d7fa5f7532) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 #69 at /home/pkgeval/.julia/packages/GLMNet/C8WKF/src/GLMNet.jl:567 iterate at ./generator.jl:48 [inlined] collect_to! at ./array.jl:848 [inlined] collect_to_with_first! at ./array.jl:826 [inlined] _collect at ./array.jl:820 collect_similar at ./array.jl:732 [inlined] map at ./abstractarray.jl:3375 [inlined] #glmnetcv#63 at /home/pkgeval/.julia/packages/GLMNet/C8WKF/src/GLMNet.jl:559 glmnetcv at /home/pkgeval/.julia/packages/GLMNet/C8WKF/src/GLMNet.jl:527 #fit_lasso#51 at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/src/fit_lasso.jl:91 fit_lasso at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/src/fit_lasso.jl:70 [inlined] #fit_lasso#49 at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/src/fit_lasso.jl:45 fit_lasso at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/src/fit_lasso.jl:30 unknown function (ip: 0x78d7f91127fe) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_body at /source/src/interpreter.c:581 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:2873 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 _include at ./loading.jl:2933 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_65897.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [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:689 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:283 _start at ./client.jl:550 jfptr__start_61850.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [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: 0x78d844654249) 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 ============================================================== norm(β̂ - b) = 1.898369367937291 ====================================================================================== 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 ┌ 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:1361 norm(β̂ - b) = Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000078d829dfc010 Total snapshots: 871. Utilization: 100% ╎871 @Base/client.jl:550 _start() ╎ 871 @Base/client.jl:283 exec_options(opts::Base.JLOptions) ╎ 871 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 871 @Base/Base.jl:308 (::Base.IncludeInto)(fname::String) ╎ 871 @Base/Base.jl:307 include(mapexpr::Function, mod::Module, _path::S… ╎ 871 @Base/loading.jl:2933 _include(mapexpr::Function, mod::Module, _p… ╎ ╎ 871 @Base/loading.jl:2873 include_string(mapexpr::typeof(identity), … ╎ ╎ 871 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 871 @Knockoffs/…lasso.jl:30 kwcall(::@NamedTuple{d::Binomial{Float… ╎ ╎ 871 @Knockoffs/…lasso.jl:45 fit_lasso(y::Vector{Float64}, X::Matr… ╎ ╎ 871 @Knockoffs/…lasso.jl:70 fit_lasso ╎ ╎ ╎ 871 @Knockoffs/…asso.jl:91 fit_lasso(y::Vector{Float64}, ko::Kn… ╎ ╎ ╎ 871 @GLMNet/…GLMNet.jl:527 glmnetcv(X::Matrix{Float64}, y::Mat… ╎ ╎ ╎ 871 @GLMNet/…GLMNet.jl:559 glmnetcv(X::Matrix{Float64}, y::Ma… ╎ ╎ ╎ 871 @Base/…ctarray.jl:3375 map ╎ ╎ ╎ 871 @Base/array.jl:732 collect_similar ╎ ╎ ╎ ╎ 871 @Base/array.jl:820 _collect(c::UnitRange{Int64}, itr::… ╎ ╎ ╎ ╎ 871 @Base/array.jl:826 collect_to_with_first! ╎ ╎ ╎ ╎ 871 @Base/array.jl:848 collect_to! ╎ ╎ ╎ ╎ 871 @Base/…erator.jl:48 iterate ╎ ╎ ╎ ╎ 850 @GLMNet/…Net.jl:567 (::GLMNet.var"#69#70"{Vector{F… ╎ ╎ ╎ ╎ ╎ 3 @Base/…rray.jl:1342 getindex ╎ ╎ ╎ ╎ ╎ 3 @Base/…onal.jl:956 _getindex ╎ ╎ ╎ ╎ ╎ 3 @Base/…onal.jl:970 _unsafe_getindex(::IndexLine… ╎ ╎ ╎ ╎ ╎ 3 @Base/…onal.jl:979 _unsafe_getindex! ╎ ╎ ╎ ╎ ╎ 2 @Base/…sian.jl:64 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…nal.jl:981 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:929 getindex 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:920 getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:986 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:991 _setindex! ╎ ╎ ╎ ╎ ╎ 1 @Base/…sian.jl:66 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:901 iterate 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:86 - ╎ ╎ ╎ ╎ ╎ 847 @GLMNet/…et.jl:337 kwcall(::@NamedTuple{weights::… 846╎ ╎ ╎ ╎ ╎ 847 @GLMNet/…et.jl:368 glmnet!(X::Matrix{Float64}, y… ╎ ╎ ╎ ╎ 21 @GLMNet/…Net.jl:581 (::GLMNet.var"#69#70"{Vector{F… ╎ ╎ ╎ ╎ ╎ 1 @Base/…rray.jl:1342 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…onal.jl:956 _getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…onal.jl:970 _unsafe_getindex(::IndexLine… ╎ ╎ ╎ ╎ ╎ 1 @Base/…onal.jl:979 _unsafe_getindex! ╎ ╎ ╎ ╎ ╎ 1 @Base/…sian.jl:66 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:901 iterate 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:86 - ╎ ╎ ╎ ╎ ╎ 20 @GLMNet/…et.jl:184 kwcall(::@NamedTuple{offsets::… ╎ ╎ ╎ ╎ ╎ 20 @GLMNet/…et.jl:184 loss ╎ ╎ ╎ ╎ ╎ 20 @GLMNet/…et.jl:191 loss(path::GLMNet.GLMNetPath… ╎ ╎ ╎ ╎ ╎ 20 @GLMNet/…et.jl:105 predict 1╎ ╎ ╎ ╎ ╎ 1 @GLMNet/…t.jl:0 predict(path::GLMNet.GLMNetPa… 1╎ ╎ ╎ ╎ ╎ 16 @GLMNet/…t.jl:119 predict(path::GLMNet.GLMNet… ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ay.jl:1345 getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:928 getindex 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:699 checkbounds ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ay.jl:929 getindex 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:919 getindex 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ls.jl:920 getindex ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ay.jl:929 getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1377 _to_linear_index ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:3052 _sub2ind ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:3068 _sub2ind ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:3084 _sub2ind_recurse ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:3084 _sub2ind_recurse 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:88 * 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ls.jl:920 getindex 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…at.jl:497 * ╎ ╎ ╎ ╎ ╎ 3 @GLMNet/…t.jl:120 predict(path::GLMNet.GLMNet… 2╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…nge.jl:921 iterate 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…on.jl:637 == 1.898369367937291 norm(β̂ - b) = 1.662231193450143 norm(β̂ - b) = 1.6604119549015366 norm(β̂ - b) = 1.6604633394479436 Test Summary: | Total Time fit lasso logistic | 0 40.2s poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#406 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] wait at ./process.jl:693 wait at ./process.jl:686 jfptr_wait_30048.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 subprocess_handler at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2556 unknown function (ip: 0x797971781483) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 #205 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2496 withenv at ./env.jl:265 #190 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2311 with_temp_env at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2164 #186 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2278 #mktempdir#21 at ./file.jl:936 unknown function (ip: 0x79797177649c) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 mktempdir at ./file.jl:932 mktempdir at ./file.jl:932 #sandbox#182 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2225 [inlined] sandbox at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2215 unknown function (ip: 0x79797176cae9) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 #test#193 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2481 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2387 [inlined] #test#174 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:552 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:529 unknown function (ip: 0x79797176c051) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 #test#84 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:169 unknown function (ip: 0x797971768250) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:158 #test#82 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [inlined] #test#81 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 [inlined] test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 unknown function (ip: 0x79797176106f) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [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:689 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:2873 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 _include at ./loading.jl:2933 include at ./Base.jl:306 exec_options at ./client.jl:317 _start at ./client.jl:550 jfptr__start_61850.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [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: 0x79798c027249) 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:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007979717fc010 Total snapshots: 646. Utilization: 0% ╎646 @Base/client.jl:550 _start() ╎ 646 @Base/client.jl:317 exec_options(opts::Base.JLOptions) ╎ 646 @Base/Base.jl:306 include(mod::Module, _path::String) ╎ 646 @Base/loading.jl:2933 _include(mapexpr::Function, mod::Module, _pat… ╎ 646 @Base/loading.jl:2873 include_string(mapexpr::typeof(identity), mo… ╎ 646 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 646 @Pkg/src/API.jl:156 kwcall(::@NamedTuple{julia_args::Cmd}, ::typ… ╎ ╎ 646 @Pkg/src/API.jl:156 #test#81 ╎ ╎ 646 @Pkg/src/API.jl:157 test ╎ ╎ 646 @Pkg/src/API.jl:157 test(pkgs::Vector{String}; kwargs::Base.P… ╎ ╎ 646 @Pkg/src/API.jl:158 kwcall(::@NamedTuple{julia_args::Cmd}, :… ╎ ╎ ╎ 646 @Pkg/src/API.jl:169 test(pkgs::Vector{PackageSpec}; io::IOC… ╎ ╎ ╎ 646 @Pkg/src/API.jl:529 kwcall(::@NamedTuple{julia_args::Cmd, … ╎ ╎ ╎ 646 @Pkg/src/API.jl:552 test(ctx::Pkg.Types.Context, pkgs::Ve… ╎ ╎ ╎ 646 @Pkg/…erations.jl:2387 test ╎ ╎ ╎ 646 @Pkg/…erations.jl:2481 test(ctx::Pkg.Types.Context, pkg… ╎ ╎ ╎ ╎ 646 @Pkg/…rations.jl:2215 kwcall(::@NamedTuple{preferences… ╎ ╎ ╎ ╎ 646 @Pkg/…rations.jl:2225 #sandbox#182 ╎ ╎ ╎ ╎ 646 @Base/file.jl:932 mktempdir(fn::Function) ╎ ╎ ╎ ╎ 646 @Base/file.jl:932 mktempdir(fn::Function, parent::S… ╎ ╎ ╎ ╎ 646 @Base/file.jl:936 mktempdir(fn::Pkg.Operations.var… ╎ ╎ ╎ ╎ ╎ 646 @Pkg/…tions.jl:2278 (::Pkg.Operations.var"#186#18… ╎ ╎ ╎ ╎ ╎ 646 @Pkg/…tions.jl:2164 with_temp_env(fn::Pkg.Operat… ╎ ╎ ╎ ╎ ╎ 646 @Pkg/…tions.jl:2311 (::Pkg.Operations.var"#190#… ╎ ╎ ╎ ╎ ╎ 646 @Base/env.jl:265 withenv(::Pkg.Operations.var"… ╎ ╎ ╎ ╎ ╎ 646 @Pkg/…ions.jl:2496 (::Pkg.Operations.var"#205… ╎ ╎ ╎ ╎ ╎ ╎ 646 @Pkg/…ons.jl:2556 subprocess_handler(cmd::Cm… ╎ ╎ ╎ ╎ ╎ ╎ 646 @Base/…ss.jl:686 wait(x::Base.Process) ╎ ╎ ╎ ╎ ╎ ╎ 646 @Base/…ss.jl:693 wait(x::Base.Process, syn… ╎ ╎ ╎ ╎ ╎ ╎ 646 @Base/…on.jl:136 wait ╎ ╎ ╎ ╎ ╎ ╎ 646 @Base/…on.jl:141 wait(c::Base.GenericCon… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 646 @Base/…sk.jl:1228 wait() 645╎ ╎ ╎ ╎ ╎ ╎ ╎ 646 @Base/…sk.jl:1216 poptask(W::Base.Intr… Test Summary: | Pass Total Time predict via knockoff-filter | 15 15 2.9s 0.020983 seconds (861 allocations: 9.952 MiB, 63.64% compilation time) [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 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:1216 wait at ./task.jl:1228 #wait#406 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] _trywait at ./asyncevent.jl:185 profile_printing_listener at ./Base.jl:332 #start_profile_listener##0 at ./Base.jl:352 jfptr_YY.start_profile_listenerYY.YY.0_14326.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) Allocations: 26089884 (Pool: 26089190; Big: 694); GC: 28 [839] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/test/runtests.jl:743 _ZN4llvm21BranchProbabilityInfo9calculateERKNS_8FunctionERKNS_8LoopInfoEPKNS_17TargetLibraryInfoEPNS_13DominatorTreeEPNS_17PostDominatorTreeE at /opt/julia/bin/../lib/julia/libLLVM.so.18.1jl (unknown line) _ZN4llvm32BranchProbabilityInfoWrapperPass13runOnFunctionERNS_8FunctionE 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:3528 _jl_invoke at /source/src/gf.c:4006 [inlined] ijl_apply_generic at /source/src/gf.c:4214 get_PCA_vectors at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/src/group.jl:2230 #solve_group_sdp_hybrid#217 at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/src/group.jl:971 solve_group_sdp_hybrid at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/src/group.jl:953 [inlined] #solve_s_group#105 at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/src/group.jl:405 solve_s_group at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/src/group.jl:349 [inlined] #modelX_gaussian_group_knockoffs#96 at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/src/group.jl:123 modelX_gaussian_group_knockoffs at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/src/group.jl:109 unknown function (ip: 0x78d7f917f9da) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 macro expansion at ./timing.jl:697 [inlined] macro expansion at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/test/runtests.jl:772 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.12/Test/src/Test.jl:1777 [inlined] top-level scope at /home/pkgeval/.julia/packages/Knockoffs/ROZEa/test/runtests.jl:745 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_invoke at /source/src/gf.c:4021 jl_toplevel_eval_flex at /source/src/toplevel.c:1024 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:2873 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 _include at ./loading.jl:2933 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_65897.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [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:689 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:283 _start at ./client.jl:550 jfptr__start_61850.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2397 [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: 0x78d844654249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) Allocations: 280381629 (Pool: 280337783; Big: 43846); GC: 110 PkgEval terminated after 2721.93s: test duration exceeded the time limit