Package evaluation of TMLECLI on Julia 1.13.0-DEV.791 (d5209bd37d*) started at 2025-07-04T23:39:05.110 ################################################################################ # Set-up # Set-up completed after 0.19s ################################################################################ # Installation # Installing TMLECLI... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [2573d147] + TMLECLI v0.10.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.15.0 [da404889] + ARFFFiles v1.5.0 [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [dce04be8] + ArgCheck v2.5.0 [c7e460c6] + ArgParse v1.2.0 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.19.0 [69666777] + Arrow v2.8.0 [31f734f8] + ArrowTypes v2.3.0 [a9b6321e] + Atomix v1.1.1 [15f4f7f2] + AutoHashEquals v2.2.0 [fbb218c0] + BSON v0.3.9 [198e06fe] + BangBang v0.4.4 [9718e550] + Baselet v0.1.1 [d1d4a3ce] + BitFlags v0.1.9 [c3b6d118] + BitIntegers v0.3.5 [fa961155] + CEnum v0.5.0 [336ed68f] + CSV v0.10.15 [324d7699] + CategoricalArrays v0.10.8 [af321ab8] + CategoricalDistributions v0.1.15 [082447d4] + ChainRules v1.72.5 [d360d2e6] + ChainRulesCore v1.25.2 [5ba52731] + CodecLz4 v0.4.6 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.6 [3da002f7] + ColorTypes v0.12.1 [861a8166] + Combinatorics v1.0.3 [38540f10] + CommonSolve v0.2.4 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.17.0 [a33af91c] + CompositionsBase v0.1.2 [ed09eef8] + ComputationalResources v0.3.2 [f0e56b4a] + ConcurrentUtilities v2.5.0 [5218b696] + Configurations v0.17.6 [187b0558] + ConstructionBase v1.6.0 [6add18c4] + ContextVariablesX v0.1.3 [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 [85a47980] + Dictionaries v0.4.5 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 ⌅ [a0c0ee7d] + DifferentiationInterface v0.6.54 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [792122b4] + EarlyStopping v0.3.0 [4e289a0a] + EnumX v1.0.5 [f6006082] + EvoTrees v0.17.3 [460bff9d] + ExceptionUnwrapping v0.1.11 [e2ba6199] + ExprTools v0.1.10 [55351af7] + ExproniconLite v0.10.14 [411431e0] + Extents v0.1.6 [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 [53c48c17] + FixedPointNumbers v0.8.5 [f6369f11] + ForwardDiff v1.0.1 [38e38edf] + GLM v1.9.0 ⌃ [8d5ece8b] + GLMNet v0.7.0 [46192b85] + GPUArraysCore v0.2.0 [68eda718] + GeoFormatTypes v0.4.4 [cf35fbd7] + GeoInterface v1.4.1 [5c1252a2] + GeometryBasics v0.5.9 [c27321d9] + Glob v1.3.1 [86223c79] + Graphs v1.13.0 [cd3eb016] + HTTP v1.10.17 [076d061b] + HashArrayMappedTries v0.2.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.5 [7869d1d1] + IRTools v0.4.15 [313cdc1a] + Indexing v1.1.1 [d25df0c9] + Inflate v0.1.5 [22cec73e] + InitialValues v0.3.1 [842dd82b] + InlineStrings v1.4.4 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [c8e1da08] + IterTools v1.10.0 [b3c1a2ee] + IterationControl v0.5.4 [42fd0dbc] + IterativeSolvers v0.9.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [033835bb] + JLD2 v0.5.15 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.3 [b14d175d] + JuliaVariables v0.2.4 [63c18a36] + KernelAbstractions v0.9.36 [b964fa9f] + LaTeXStrings v1.4.0 [a5e1c1ea] + LatinHypercubeSampling v1.9.0 ⌅ [92ad9a40] + LearnAPI v0.1.0 [d3d80556] + LineSearches v7.4.0 [7a12625a] + LinearMaps v3.11.4 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.1.0 [c2834f40] + MLCore v1.0.0 ⌅ [64a0f543] + MLFlowClient v0.4.7 ⌃ [add582a8] + MLJ v0.20.0 ⌃ [a7f614a8] + MLJBase v1.7.0 [50ed68f4] + MLJEnsembles v0.4.3 ⌅ [7b7b8358] + MLJFlow v0.2.0 [caf8df21] + MLJGLMInterface v0.3.7 [614be32b] + MLJIteration v0.6.3 [6ee0df7b] + MLJLinearModels v0.10.1 [e80e1ace] + MLJModelInterface v1.11.1 ⌅ [d491faf4] + MLJModels v0.16.17 [03970b2e] + MLJTuning v0.8.8 [54119dfa] + MLJXGBoostInterface v0.3.12 [d8e11817] + MLStyle v0.4.17 [f1d291b0] + MLUtils v0.4.8 [1914dd2f] + MacroTools v0.5.16 [739be429] + MbedTLS v1.1.9 [fa8bd995] + MetaGraphsNext v0.7.3 [128add7d] + MicroCollections v0.2.0 [e1d29d7a] + Missings v1.2.0 [78c3b35d] + Mocking v0.8.1 [d41bc354] + NLSolversBase v7.10.0 [872c559c] + NNlib v0.9.30 [77ba4419] + NaNMath v1.1.3 [71a1bf82] + NameResolution v0.1.5 [46757867] + NetworkLayout v0.4.10 [8b6db2d4] + OpenML v0.3.2 [4d8831e6] + OpenSSL v1.5.0 [429524aa] + Optim v1.13.2 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [9b87118b] + PackageCompiler v2.2.1 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [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 [54e16d92] + PrettyPrinting v0.4.2 [08abe8d2] + PrettyTables v2.4.0 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [05181044] + RelocatableFolders v1.0.1 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [f2b01f46] + Roots v2.2.8 [321657f4] + ScientificTypes v3.1.0 [30f210dd] + ScientificTypesBase v3.0.0 [7e506255] + ScopedValues v1.3.0 [6c6a2e73] + Scratch v1.3.0 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [1277b4bf] + ShiftedArrays v2.0.0 [605ecd9f] + ShowCases v0.1.0 [777ac1f9] + SimpleBufferStream v1.2.0 [699a6c99] + SimpleTraits v0.9.4 [a2af1166] + SortingAlgorithms v1.2.1 [dc90abb0] + SparseInverseSubset v0.1.2 [a0a7dd2c] + SparseMatricesCSR v0.6.9 [276daf66] + SpecialFunctions v2.5.1 [03a91e81] + SplitApplyCombine v1.2.3 [171d559e] + SplittablesBase v0.1.15 [860ef19b] + StableRNGs v1.0.3 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 ⌅ [a19d573c] + StatisticalMeasures v0.1.7 [c062fc1d] + StatisticalMeasuresBase v0.1.2 [64bff920] + StatisticalTraits v3.4.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.0 [3eaba693] + StatsModels v0.7.4 [69024149] + StringEncodings v0.3.7 [892a3eda] + StringManipulation v0.4.1 [354b36f9] + StringViews v1.3.4 [09ab397b] + StructArrays v0.7.1 [856f2bd8] + StructTypes v1.11.0 ⌅ [8afdd2fb] + TMLE v0.18.1 [2573d147] + TMLECLI v0.10.2 [dc5dba14] + TZJData v1.5.0+2025b [ab02a1b2] + TableOperations v1.2.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [b718987f] + TextWrap v1.0.2 [f269a46b] + TimeZones v1.21.3 [3bb67fe8] + TranscodingStreams v0.11.3 [28d57a85] + Transducers v0.4.84 [5c2747f8] + URIs v1.6.1 [3a884ed6] + UnPack v1.0.2 [013be700] + UnsafeAtomics v0.3.0 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [009559a3] + XGBoost v2.5.1 [ddb6d928] + YAML v0.4.14 [e88e6eb3] + Zygote v0.7.10 [700de1a5] + ZygoteRules v0.2.7 [4ee394cb] + CUDA_Driver_jll v12.9.0+0 [76a88914] + CUDA_Runtime_jll v0.18.0+0 [5ae413db] + EarCut_jll v2.2.4+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [5ced341a] + Lz4_jll v1.10.1+0 [c8ffd9c3] + MbedTLS_jll v2.28.6+2 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [a5c6f535] + XGBoost_jll v2.0.1+0 [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 [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 v1.13.0 [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 [1a1011a3] + SharedArrays 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 v8.14.1+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.0+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 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 15.87s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml` No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml` Precompiling package dependencies... Precompiling packages... 53496.3 ms ✓ StatisticalMeasuresBase 33383.0 ms ✓ EvoTrees 9821.9 ms ✓ ScientificTypes ✗ GLMNet 69112.7 ms ✓ DifferentiationInterface → DifferentiationInterfaceZygoteExt 29982.7 ms ✓ MLJGLMInterface 10239.3 ms ✓ Optim 6999.8 ms ✓ CategoricalDistributions 79944.5 ms ? MLJLinearModels 126450.7 ms ✓ MLJBase 15360.1 ms ✓ MLJEnsembles 44761.9 ms ✓ StatisticalMeasures 25606.3 ms ✓ MLJModels 15479.6 ms ✓ MLJIteration 17195.1 ms ✓ MLJFlow 25030.0 ms ✓ MLJTuning 11532.1 ms ✓ StatisticalMeasures → ScientificTypesExt 13003.4 ms ✓ MLJBase → DefaultMeasuresExt 159129.9 ms ✓ TMLE 36005.5 ms ✓ MLJ 473352.8 ms ✓ TMLE → YAMLExt 113714.3 ms ? TMLE → JSONExt 66500.4 ms ? TMLECLI 19 dependencies successfully precompiled in 1461 seconds. 324 already precompiled. 3 dependencies failed but may be precompilable after restarting julia 3 dependencies had output during precompilation: ┌ MLJLinearModels │ WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Statistics.cov), SparseArrays.SparseMatrixCSC{Tv, Ti} where Ti<:Integer where Tv) in module SparseArraysExt at /home/pkgeval/.julia/packages/Statistics/gbcbG/ext/SparseArraysExt.jl:14 overwritten in module SparseArraysExt on the same line (check for duplicate calls to `include`). │ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. └ ┌ TMLECLI │ WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Statistics.cov), SparseArrays.SparseMatrixCSC{Tv, Ti} where Ti<:Integer where Tv) in module SparseArraysExt at /home/pkgeval/.julia/packages/Statistics/gbcbG/ext/SparseArraysExt.jl:14 overwritten in module SparseArraysExt on the same line (check for duplicate calls to `include`). │ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. └ ┌ TMLE → JSONExt │ WARNING: Method definition cov(FillArrays.AbstractFill{T, 2, Axes} where Axes) where {T<:Number} in module FillArraysStatisticsExt at /home/pkgeval/.julia/packages/FillArrays/lVl4c/ext/FillArraysStatisticsExt.jl:23 overwritten in module FillArraysStatisticsExt on the same line (check for duplicate calls to `include`). │ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. └ Precompilation completed after 1459.83s ################################################################################ # Loading # Loading TMLECLI... Precompiling packages... 14486.6 ms ✓ EvoTrees 9801.0 ms ✓ CategoricalDistributions ✗ GLMNet 30966.6 ms ✓ MLJGLMInterface 89001.8 ms ✓ MLJLinearModels 118360.1 ms ? MLJBase 66846.6 ms ✓ MLJEnsembles 43825.9 ms ✓ StatisticalMeasures 25882.6 ms ✓ MLJModels 40575.9 ms ✓ MLJIteration 26838.2 ms ✓ MLJFlow 24281.6 ms ✓ MLJTuning 11961.7 ms ✓ StatisticalMeasures → ScientificTypesExt 13356.4 ms ✓ MLJBase → DefaultMeasuresExt 200478.4 ms ✓ TMLE 53484.5 ms ✓ MLJ 363822.7 ms ✓ TMLE → YAMLExt ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 403 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1213 wait_forever at ./task.jl:1150 jfptr_wait_forever_62247.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] start_task at /source/src/task.c:1249 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000797ee6f64a60 Total snapshots: 484. Utilization: 0% ╎484 @Base/task.jl:1150 wait_forever() 483╎ 484 @Base/task.jl:1213 wait() ====================================================================================== 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 wait at ./task.jl:1213 wait_forever at ./task.jl:1150 jfptr_wait_forever_62247.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] start_task at /source/src/task.c:1249 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000711a8e5ca0e0 Total snapshots: 471. Utilization: 0% ╎471 @Base/task.jl:1150 wait_forever() 470╎ 471 @Base/task.jl:1213 wait() [403] signal 15: Terminated in expression starting at none:1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1213 wait_forever at ./task.jl:1150 jfptr_wait_forever_62247.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 16885074 (Pool: 16884829; Big: 245); GC: 36 PkgEval terminated after 2763.52s: test duration exceeded the time limit