Package evaluation of GeneExpressionProgramming on Julia 1.13.0-DEV.888 (0e1aa6c7eb*) started at 2025-07-23T01:38:35.696 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.29s ################################################################################ # Installation # Installing GeneExpressionProgramming... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [2f0a5bb0] + GeneExpressionProgramming v0.5.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.15.0 [621f4979] + AbstractFFTs v1.5.0 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [dce04be8] + ArgCheck v2.5.0 [4fba245c] + ArrayInterface v7.19.0 [a9b6321e] + Atomix v1.1.1 [198e06fe] + BangBang v0.4.4 [9718e550] + Baselet v0.1.1 [6e4b80f9] + BenchmarkTools v1.6.0 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [fa961155] + CEnum v0.5.0 [2a0fbf3d] + CPUSummary v0.2.6 [336ed68f] + CSV v0.10.15 [082447d4] + ChainRules v1.72.5 [d360d2e6] + ChainRulesCore v1.25.2 [fb6a15b2] + CloseOpenIntervals v0.1.13 [944b1d66] + CodecZlib v0.7.8 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.17.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [6add18c4] + ContextVariablesX v0.1.3 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [244e2a9f] + DefineSingletons v0.1.2 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.3 [8d63f2c5] + DispatchDoctor v0.4.26 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 ⌅ [a40a106e] + DynamicExpressions v1.10.1 [4e289a0a] + EnumX v1.0.5 [f151be2c] + EnzymeCore v0.8.12 [cc61a311] + FLoops v0.2.2 [b9860ae5] + FLoopsBase v0.1.1 [5789e2e9] + FileIO v1.17.0 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [6a86dc24] + FiniteDiff v2.27.0 [587475ba] + Flux v0.16.4 ⌅ [f6369f11] + ForwardDiff v0.10.38 [d9f16b24] + Functors v0.5.2 [0c68f7d7] + GPUArrays v11.2.3 [46192b85] + GPUArraysCore v0.2.0 [92fee26a] + GZip v0.6.2 [2f0a5bb0] + GeneExpressionProgramming v0.5.0 [076d061b] + HashArrayMappedTries v0.2.0 [3e5b6fbb] + HostCPUFeatures v0.1.17 [34004b35] + HypergeometricFunctions v0.3.28 [7869d1d1] + IRTools v0.4.15 [615f187c] + IfElse v0.1.1 [22cec73e] + InitialValues v0.3.1 [842dd82b] + InlineStrings v1.4.4 [85a1e053] + Interfaces v0.3.2 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [b14d175d] + JuliaVariables v0.2.4 [63c18a36] + KernelAbstractions v0.9.37 [929cbde3] + LLVM v9.4.2 [8ac3fa9e] + LRUCache v1.6.2 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 [d3d80556] + LineSearches v7.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.172 [c2834f40] + MLCore v1.0.0 [7e8f7934] + MLDataDevices v1.11.0 [d8e11817] + MLStyle v0.4.17 [f1d291b0] + MLUtils v0.4.8 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [128add7d] + MicroCollections v0.2.0 [e1d29d7a] + Missings v1.2.0 [d41bc354] + NLSolversBase v7.10.0 [872c559c] + NNlib v0.9.30 [77ba4419] + NaNMath v1.1.3 [71a1bf82] + NameResolution v0.1.5 [b8a86587] + NearestNeighbors v0.4.22 [6fe1bfb0] + OffsetArrays v1.17.0 [0b1bfda6] + OneHotArrays v0.2.10 [429524aa] + Optim v1.13.2 [3bd65402] + Optimisers v0.4.6 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [85a6dd25] + PositiveFactorizations v0.2.4 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [8162dcfd] + PrettyPrint v0.2.0 [08abe8d2] + PrettyTables v2.4.0 [33c8b6b6] + ProgressLogging v0.1.5 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [c1ae055f] + RealDot v0.1.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [fdea26ae] + SIMD v3.7.1 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [7e506255] + ScopedValues v1.4.0 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [605ecd9f] + ShowCases v0.1.0 [699a6c99] + SimpleTraits v0.9.4 [a2af1166] + SortingAlgorithms v1.2.1 [dc90abb0] + SparseInverseSubset v0.1.2 [276daf66] + SpecialFunctions v2.5.1 [171d559e] + SplittablesBase v0.1.15 [aedffcd0] + Static v1.2.0 [0d7ed370] + StaticArrayInterface v1.8.0 [90137ffa] + StaticArrays v1.9.14 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 [892a3eda] + StringManipulation v0.4.1 [09ab397b] + StructArrays v0.7.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [48a634ad] + Tensors v1.16.2 [8290d209] + ThreadingUtilities v0.5.5 [3bb67fe8] + TranscodingStreams v0.11.3 [28d57a85] + Transducers v0.4.84 [3a884ed6] + UnPack v1.0.2 [013be700] + UnsafeAtomics v0.3.0 [3d5dd08c] + VectorizationBase v0.21.71 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 ⌅ [e88e6eb3] + Zygote v0.6.77 [700de1a5] + ZygoteRules v0.2.7 [dad2f222] + LLVMExtra_jll v0.0.37+2 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+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 v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [9abbd945] + Profile 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 v1.13.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.14.1+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.7.15 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 [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` Installation completed after 5.86s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 565.98s ################################################################################ # Testing # Testing GeneExpressionProgramming Status `/tmp/jl_Q4IQnZ/Project.toml` [6e4b80f9] BenchmarkTools v1.6.0 [336ed68f] CSV v0.10.15 [d360d2e6] ChainRulesCore v1.25.2 [a93c6f00] DataFrames v1.7.0 [31c24e10] Distributions v0.25.120 ⌅ [a40a106e] DynamicExpressions v1.10.1 [5789e2e9] FileIO v1.17.0 [587475ba] Flux v0.16.4 ⌅ [f6369f11] ForwardDiff v0.10.38 [92fee26a] GZip v0.6.2 [2f0a5bb0] GeneExpressionProgramming v0.5.0 [682c06a0] JSON v0.21.4 [8ac3fa9e] LRUCache v1.6.2 [d3d80556] LineSearches v7.4.0 [bdcacae8] LoopVectorization v0.12.172 [b8a86587] NearestNeighbors v0.4.22 [429524aa] Optim v1.13.2 [bac558e1] OrderedCollections v1.8.1 [aea7be01] PrecompileTools v1.3.2 [92933f4c] ProgressMeter v1.10.4 [90137ffa] StaticArrays v1.9.14 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.5 [48a634ad] Tensors v1.16.2 ⌅ [e88e6eb3] Zygote v0.6.77 [ade2ca70] Dates 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v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.14.1+1 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.7.15 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+0 [efcefdf7] PCRE2_jll v10.45.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 [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... Test Summary: | Pass Total Time SymbolicEntities Tests | 15 15 21.8s ("Lib Entries:", total_len_lib) = ("Lib Entries:", 7420) "Genes before test" = "Genes before test" gene = Int8[1, 4, 1, 2, 7, 8, 7, 3, 4, 7, 7, 8, 1, 4, 8, 7, 8] "Genes after test" = "Genes after test" gene = Int8[2, 8, 2, 7, 1, 7, 7, 3, 4, 7, 7, 8, 1, 4, 8, 7, 8] "Correction" = "Correction" correction = 0.0f0 dim4 = Float16[1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0] Test Summary: | Pass Total Time SBP Tests | 18 18 16.3s Test Summary: | Pass Total Time dominates_ function | 13 13 0.5s Test Summary: | Pass Total Time calculate_fronts function | 11 11 1.9s [ Info: Dict(3 => 1.0, 2 => 1.0, 1 => Inf, 4 => 1.0, 5 => Inf) Test Summary: | Pass Total Time assign_crowding_distance function | 8 8 5.3s Test Summary: | Pass Total Time nsga_selection function | 8 8 6.1s WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in mean_squared_error(AbstractArray{T, N} where N, AbstractArray{T, N} where N) where {T<:AbstractFloat} at /home/pkgeval/.julia/packages/GeneExpressionProgramming/MyvTo/src/Losses.jl Training: 2%|▌ | ETA: 0:58:05 (35.56 s/it) epoch_: 2 duplicates_per_epoch: 52 train_loss: 1.972152e-32 validation_loss: 1.972152e-32         Training: 5%|█▍ | ETA: 0:22:37 (14.29 s/it) epoch_: 5 duplicates_per_epoch: 86 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 8%|██▏ | ETA: 0:13:43 ( 8.95 s/it) epoch_: 8 duplicates_per_epoch: 65 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 10%|██▊ | ETA: 0:10:45 ( 7.17 s/it) epoch_: 10 duplicates_per_epoch: 62 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 12%|███▎ | ETA: 0:08:46 ( 5.98 s/it) epoch_: 12 duplicates_per_epoch: 64 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 14%|███▊ | ETA: 0:07:22 ( 5.14 s/it) epoch_: 14 duplicates_per_epoch: 54 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 16%|████▍ | ETA: 0:06:18 ( 4.50 s/it) epoch_: 16 duplicates_per_epoch: 71 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 18%|████▉ | ETA: 0:05:29 ( 4.01 s/it) epoch_: 18 duplicates_per_epoch: 101 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 20%|█████▍ | ETA: 0:04:49 ( 3.61 s/it) epoch_: 20 duplicates_per_epoch: 87 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 22%|██████ | ETA: 0:04:17 ( 3.29 s/it) epoch_: 22 duplicates_per_epoch: 129 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 24%|██████▌ | ETA: 0:03:50 ( 3.02 s/it) epoch_: 24 duplicates_per_epoch: 181 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 26%|███████ | ETA: 0:03:27 ( 2.79 s/it) epoch_: 26 duplicates_per_epoch: 262 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 29%|███████▉ | ETA: 0:02:58 ( 2.51 s/it) epoch_: 29 duplicates_per_epoch: 430 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 32%|████████▋ | ETA: 0:02:35 ( 2.28 s/it) epoch_: 32 duplicates_per_epoch: 515 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 35%|█████████▌ | ETA: 0:02:16 ( 2.09 s/it) epoch_: 35 duplicates_per_epoch: 505 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 38%|██████████▎ | ETA: 0:01:59 ( 1.92 s/it) epoch_: 38 duplicates_per_epoch: 508 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 41%|███████████▏ | ETA: 0:01:46 ( 1.79 s/it) epoch_: 41 duplicates_per_epoch: 526 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 44%|███████████▉ | ETA: 0:01:33 ( 1.67 s/it) epoch_: 44 duplicates_per_epoch: 435 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 47%|████████████▊ | ETA: 0:01:23 ( 1.56 s/it) epoch_: 47 duplicates_per_epoch: 441 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 50%|█████████████▌ | ETA: 0:01:14 ( 1.47 s/it) epoch_: 50 duplicates_per_epoch: 451 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 53%|██████████████▎ | ETA: 0:01:05 ( 1.39 s/it) epoch_: 53 duplicates_per_epoch: 476 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 56%|███████████████▏ | ETA: 0:00:58 ( 1.32 s/it) epoch_: 56 duplicates_per_epoch: 567 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 59%|███████████████▉ | ETA: 0:00:51 ( 1.25 s/it) epoch_: 59 duplicates_per_epoch: 512 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 63%|█████████████████ | ETA: 0:00:44 ( 1.18 s/it) epoch_: 63 duplicates_per_epoch: 482 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 67%|██████████████████▏ | ETA: 0:00:37 ( 1.11 s/it) epoch_: 67 duplicates_per_epoch: 489 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 70%|██████████████████▉ | ETA: 0:00:32 ( 1.06 s/it) epoch_: 70 duplicates_per_epoch: 589 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 73%|███████████████████▊ | ETA: 0:00:28 ( 1.02 s/it) epoch_: 73 duplicates_per_epoch: 566 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 76%|████████████████████▌ | ETA: 0:00:24 ( 0.98 s/it) epoch_: 76 duplicates_per_epoch: 658 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 79%|█████████████████████▍ | ETA: 0:00:20 ( 0.95 s/it) epoch_: 79 duplicates_per_epoch: 654 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 82%|██████████████████████▏ | ETA: 0:00:16 ( 0.91 s/it) epoch_: 82 duplicates_per_epoch: 651 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 86%|███████████████████████▎ | ETA: 0:00:12 ( 0.87 s/it) epoch_: 86 duplicates_per_epoch: 655 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 89%|████████████████████████ | ETA: 0:00:09 ( 0.84 s/it) epoch_: 89 duplicates_per_epoch: 655 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 92%|████████████████████████▉ | ETA: 0:00:07 ( 0.82 s/it) epoch_: 92 duplicates_per_epoch: 667 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 95%|█████████████████████████▋ | ETA: 0:00:04 ( 0.79 s/it) epoch_: 95 duplicates_per_epoch: 650 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 98%|██████████████████████████▌| ETA: 0:00:02 ( 0.77 s/it) epoch_: 98 duplicates_per_epoch: 668 train_loss: 0.000000e+00 validation_loss: 0.000000e+00         Training: 100%|███████████████████████████| Time: 0:01:33 ( 0.93 s/it) epoch_: 100 duplicates_per_epoch: 657 train_loss: 0.000000e+00 validation_loss: 0.000000e+00 Test Summary: | Pass Total Time GepRegressor Tests | 24 24 1m59.5s Test Summary: | Pass Total Time TensorRegUtils | 7 7 5.6s Test Summary: | Pass Total Time All Node Operations | 9 9 1.4s Testing GeneExpressionProgramming tests passed Testing completed after 255.88s PkgEval succeeded after 859.14s