Package evaluation to test HurdleDMR on Julia 1.10.10 (c8be17dcfd*) started at 2026-02-02T20:50:51.776 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.10` Set-up completed after 5.03s ################################################################################ # Installation # Installing HurdleDMR... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [f9e53bcf] + HurdleDMR v1.4.0 Updating `~/.julia/environments/v1.10/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [66dad0bd] + AliasTables v1.1.3 [0e736298] + Bessels v0.2.8 [187b0558] + ConstructionBase v1.6.0 [717857b8] + DSP v0.8.4 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [7a1cc6ca] + FFTW v1.10.0 [1a297f60] + FillArrays v1.16.0 [38e38edf] + GLM v1.9.2 [f9e53bcf] + HurdleDMR v1.4.0 [34004b35] + HypergeometricFunctions v0.3.28 [92d709cd] + IrrationalConstants v0.2.6 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 ⌅ [984bce1d] + LambertW v0.4.6 [b4fcebef] + Lasso v0.7.3 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.2.0 [f0e99cf1] + MLBase v0.9.2 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [f27b6e38] + Polynomials v4.1.0 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.5.1 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [efcf1570] + Setfield v1.1.2 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [1e83bf80] + StaticArraysCore v1.4.4 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.8 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [f5851436] + FFTW_jll v3.3.11+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 [1317d2d5] + oneTBB_jll v2022.0.0+1 [0dad84c5] + ArgTools v1.1.1 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [8ba89e20] + Distributed [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching [9fa8497b] + Future [b77e0a4c] + InteractiveUtils [4af54fe1] + LazyArtifacts [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.10.0 [de0858da] + Printf [3fa0cd96] + REPL [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [1a1011a3] + SharedArrays [6462fe0b] + Sockets [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.4.0+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.1010+0 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.23+5 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.52.0+1 [3f19e933] + p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 9.58s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 6048.9 ms ✓ HurdleDMR 1 dependency successfully precompiled in 9 seconds. 97 already precompiled. Precompilation completed after 21.39s ################################################################################ # Testing # Testing HurdleDMR Status `/tmp/jl_JqdTNv/Project.toml` [336ed68f] CSV v0.10.15 [324d7699] CategoricalArrays v1.0.2 [a93c6f00] DataFrames v1.8.1 [31c24e10] Distributions v0.25.123 [38e38edf] GLM v1.9.2 [f9e53bcf] HurdleDMR v1.4.0 ⌅ [984bce1d] LambertW v0.4.6 [b4fcebef] Lasso v0.7.3 [e6f89c97] LoggingExtras v1.2.0 [f0e99cf1] MLBase v0.9.2 [e1d29d7a] Missings v1.2.0 [2913bbd2] StatsBase v0.34.10 [3eaba693] StatsModels v0.7.8 [bd369af6] Tables v1.12.1 [8ba89e20] Distributed [b77e0a4c] InteractiveUtils [37e2e46d] LinearAlgebra [56ddb016] Logging [9a3f8284] Random [1a1011a3] SharedArrays [2f01184e] SparseArrays v1.10.0 [8dfed614] Test Status `/tmp/jl_JqdTNv/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [66dad0bd] AliasTables v1.1.3 [0e736298] Bessels v0.2.8 [336ed68f] CSV v0.10.15 [324d7699] CategoricalArrays v1.0.2 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [717857b8] DSP v0.8.4 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [7a1cc6ca] FFTW v1.10.0 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [38e38edf] GLM v1.9.2 [f9e53bcf] HurdleDMR v1.4.0 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [b964fa9f] LaTeXStrings v1.4.0 ⌅ [984bce1d] LambertW v0.4.6 [b4fcebef] Lasso v0.7.3 [2ab3a3ac] LogExpFunctions v0.3.29 [e6f89c97] LoggingExtras v1.2.0 [f0e99cf1] MLBase v0.9.2 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [69de0a69] Parsers v2.8.3 [f27b6e38] Polynomials v4.1.0 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.5.1 [08abe8d2] PrettyTables v3.1.2 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [91c51154] SentinelArrays v1.4.9 [efcf1570] Setfield v1.1.2 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [1e83bf80] StaticArraysCore v1.4.4 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.8 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [f5851436] FFTW_jll v3.3.11+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 [1317d2d5] oneTBB_jll v2022.0.0+1 [0dad84c5] ArgTools v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [8ba89e20] Distributed [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [4af54fe1] LazyArtifacts [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [a63ad114] Mmap [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.10.0 [de0858da] Printf [3fa0cd96] REPL [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [1a1011a3] SharedArrays [6462fe0b] Sockets [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.1010+0 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.23+5 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... [ Info: Starting 4 parallel workers for tests... [ Info: 4 parallel workers started WARNING: using deprecated binding Distributions.MatrixReshaped in Lasso. , use Distributions.ReshapedDistribution{2, S, D} where D<:Distributions.Distribution{Distributions.ArrayLikeVariate{1}, S} where S<:Distributions.ValueSupport instead. ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = build_model(X::Matrix{Float64}, y::Vector{Float64}, d::PositivePoisson, l::LogProductLogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Vector{Float64}, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = build_model(X::Matrix{Float64}, y::Vector{Float64}, d::PositivePoisson, l::LogProductLogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Vector{Float64}, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 hurdle degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:332 Expression: fit(Hurdle, GammaLassoPath, X, y; showwarnings = true) Log Pattern: (:warn, r"failed to fit truncated counts model to positive") Captured Logs: LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf67b06ffd, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf683037dd, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::PositivePoisson, l::LogProductLogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) LogRecord(Warn, "failed to fit truncated counts model to positive subsample, possibly not enough variation in ypos. countmap(ypos)=[1=>265, 2=>2]", HurdleDMR, :hurdle, :HurdleDMR_5f1c5b78, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 187, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf682e0713, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::PositivePoisson, l::LogProductLogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Vector{Float64}, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:332 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 hurdle degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:343 Expression: fit(Hurdle, GammaLassoPath, X, y0or1; showwarnings = true) Log Pattern: (:warn, r"ypos has no elements larger than 1") Captured Logs: LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf67b06ffd, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) LogRecord(Warn, "ypos has no elements larger than 1.0! Data may be fully described by a probability model.", HurdleDMR, :hurdle, :HurdleDMR_b1cd0eeb, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 200, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf682e0713, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::PositivePoisson, l::LogProductLogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Vector{Float64}, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:343 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 [ Info: Testing hurdle degenerate cases. The following warnings about step-halving are expected ... 1: λ=0.00038673257138011573, pct_dev=6.492056477624963e-6 step-halving because obj=0.00487623853780627 > 0.0048762385378007195 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 2: λ=0.0003523763156183366, pct_dev=0.0041372757224670265 3: λ=0.0003210721749286252, pct_dev=0.007781659157259924 4: λ=0.0002925490078199604, pct_dev=0.011000893841847548 5: λ=0.0002665597602640868, pct_dev=0.013846724619142603 6: λ=0.00024287932583170972, pct_dev=0.016363288419311672 7: λ=0.00022130259592829243, pct_dev=0.01858856439367973 step-halving because obj=0.00484722562854673 > 0.004847225628354178 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 8: λ=0.00020164268324153527, pct_dev=0.020555494005479957 9: λ=0.00018372930301288008, pct_dev=0.022292855759185604 10: λ=0.00016740729811239358, pct_dev=0.023825953112429632 11: λ=0.0001525352951419358, pct_dev=0.025177160770078588 step-halving because obj=0.00482033466522265 > 0.004820334665151485 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 12: λ=0.00013898447992641573, pct_dev=0.02636636032069528 step-halving because obj=0.004813724921507198 > 0.004813724921487546 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 13: λ=0.000126637481787031, pct_dev=0.027411290071895023 step-halving because obj=0.0048072784344947135 > 0.0048072784343059114 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 14: λ=0.00011538735693259619, pct_dev=0.028327827584448184 15: λ=0.00010513666216358598, pct_dev=0.029130219623048403 step-halving because obj=0.004795017783927299 > 0.00479501778382937 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 16: λ=9.57966108657562e-5, pct_dev=0.02983127026106236 step-halving because obj=0.004789253195216611 > 0.004789253195202084 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 17: λ=8.728630398296539e-5, pct_dev=0.030442496992046042 step-halving because obj=0.004783753731248896 > 0.004783753731089673 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 18: λ=7.953202930825311e-5, pct_dev=0.030974261250669932 step-halving because obj=0.004778528181069734 > 0.004778528180885919 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 19: λ=7.246662302396587e-5, pct_dev=0.0314358792268693 20: λ=6.602888796089887e-5, pct_dev=0.03183571795868023 21: λ=6.0163063537693424e-5, pct_dev=0.03218127937607729 22: λ=5.481834278935611e-5, pct_dev=0.032479275571307364 23: λ=4.994843230163334e-5, pct_dev=0.03273569744997884 step-halving because obj=0.004756536452854914 > 0.004756536452781726 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 24: λ=4.551115123960414e-5, pct_dev=0.03295587694970259 25: λ=4.146806599746662e-5, pct_dev=0.03314454575007297 26: λ=3.778415730503067e-5, pct_dev=0.033305889631369934 step-halving because obj=0.004746445153180686 > 0.0047464451530192 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 27: λ=3.442751690755292e-5, pct_dev=0.03344359957965104 28: λ=3.136907119169851e-5, pct_dev=0.033560919420243085 29: λ=2.858232936381104e-5, pct_dev=0.033660691594144754 30: λ=2.6043153999330735e-5, pct_dev=0.03374539727627213 31: λ=2.3729551975970305e-5, pct_dev=0.03381719626803226 32: λ=2.162148397981088e-5, pct_dev=0.03387796328352066 33: λ=1.970069093435137e-5, pct_dev=0.0339293195989383 34: λ=1.7950535849123017e-5, pct_dev=0.033972664551973564 35: λ=1.635585971803684e-5, pct_dev=0.03400920184871181 36: λ=1.4902850219324749e-5, pct_dev=0.034039964286657676 37: λ=1.3578922079816255e-5, pct_dev=0.03406583603031832 38: λ=1.2372608067322866e-5, pct_dev=0.03408757253294892 39: λ=1.1273459666958633e-5, pct_dev=0.03410581711025251 step-halving because obj=0.00472196575523354 > 0.0047219657549925475 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 40: λ=1.0271956581102827e-5, pct_dev=0.03412111728161327 step-halving because obj=0.0047209667146365245 > 0.004720966714514291 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 41: λ=9.359424269136302e-6, pct_dev=0.034133937925694524 step-halving because obj=0.004720051380043994 > 0.004720051379835151 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 42: λ=8.527958812720426e-6, pct_dev=0.03414467232168883 hurdle degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:357 Expression: fit(Hurdle, GammaLassoPath, X, y0or1; verbose = true, showwarnings = true) Log Pattern: (:warn, r"I\(y\) is all ones") Captured Logs: LogRecord(Warn, "I(y) is all ones. Data may be fully described by a poisson model.", HurdleDMR, :hurdle, :HurdleDMR_c879ab77, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 149, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf68353863, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Vector{Float64}, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf683037dd, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::PositivePoisson, l::LogProductLogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:357 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 Iteration: 1, deviance: 204.03803961035834, diff.dev.:284.05429274207955 Iteration: 2, deviance: 103.01893015603085, diff.dev.:101.01910945432749 Iteration: 3, deviance: 69.83490468997287, diff.dev.:33.184025466057975 Iteration: 4, deviance: 60.60747250524524, diff.dev.:9.227432184727633 Iteration: 5, deviance: 58.582063189783575, diff.dev.:2.0254093154616655 Iteration: 6, deviance: 58.15370098772976, diff.dev.:0.4283622020538118 Iteration: 7, deviance: 58.09051068832265, diff.dev.:0.06319029940711118 Iteration: 8, deviance: 58.08834853496279, diff.dev.:0.002162153359861918 Iteration: 9, deviance: 58.08834523345644, diff.dev.:3.301506353636796e-6 hurdle degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:363 Expression: fit(Hurdle, GeneralizedLinearModel, [ones(size(X, 1)) X], y0or1; verbose = true, showwarnings = true) Log Pattern: (:warn, r"I\(y\) is all ones") Captured Logs: LogRecord(Warn, "I(y) is all ones. Data may be fully described by a poisson model.", HurdleDMR, :hurdle, :HurdleDMR_c879ab77, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 149, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", HurdleDMR, :depwarn, (Ptr{Nothing} @0x00007dcf67bde167, :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 109, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => fitblank(::Type{GeneralizedLinearModel}, ::Matrix{Float64}, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol, Symbol}, @NamedTuple{wts::Vector{Float64}, offset::Vector{Float64}, verbose::Bool}}) at hurdle.jl:109, :maxlog => 1)) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", HurdleDMR, :depwarn, (Ptr{Nothing} @0x00007dcf6833d6fb, :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 184, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => (::HurdleDMR.var"#9#11"{GeneralizedLinearModel, Hurdle, Matrix{Float64}, Vector{Float64}, PositivePoisson, LogProductLogLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{}})() at hurdle.jl:184, :maxlog => 1)) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:363 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 hurdle degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:368 Expression: #= /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:368 =# @test_throws ErrorException fit(Hurdle, GammaLassoPath, X, y0or1; verbose = true, showwarnings = true) Log Pattern: (:warn, r"I\(y\) is all zeros") Captured Logs: LogRecord(Warn, "I(y) is all zeros. There is nothing to explain.", HurdleDMR, :hurdle, :HurdleDMR_1c5241d3, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 147, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf68353863, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Vector{Float64}, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:368 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 hurdle degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:372 Expression: fit(Hurdle, GammaLassoPath, X, y; showwarnings = true) Log Pattern: (:warn, r"not enough variation in ypos") Captured Logs: LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf67b06ffd, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf683037dd, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::PositivePoisson, l::LogProductLogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) LogRecord(Warn, "failed to fit truncated counts model to positive subsample, possibly not enough variation in ypos. countmap(ypos)=[1=>64, 2=>1]", HurdleDMR, :hurdle, :HurdleDMR_5f1c5b78, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 187, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf682e0713, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::PositivePoisson, l::LogProductLogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Vector{Float64}, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:372 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 hurdle degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:382 Expression: fit(Hurdle, GammaLassoPath, X, y; showwarnings = true) Log Pattern: (:warn, r"ypos has no elements larger than 1") Captured Logs: LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf67b06ffd, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) LogRecord(Warn, "ypos has no elements larger than 1.0! Data may be fully described by a probability model.", HurdleDMR, :hurdle, :HurdleDMR_b1cd0eeb, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 200, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf682e0713, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::PositivePoisson, l::LogProductLogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Vector{Float64}, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:382 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Poisson{Float64}, l::LogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Vector{Float64}, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Poisson{Float64}, l::LogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 inrep degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:306 Expression: fit(InclusionRepetition, GeneralizedLinearModel, [ones(size(X, 1)) X], ydeg; showwarnings = true, dropcollinear = false) Log Pattern: (:warn, r"failed to fit truncated counts model to positive") Captured Logs: LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", HurdleDMR, :depwarn, (Ptr{Nothing} @0x00007dcf6731b58b, :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 132, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => (::HurdleDMR.var"#7#8"{GeneralizedLinearModel, Float64, Matrix{Float64}, Vector{Float64}, Binomial{Float64}, LogitLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{Pair{Symbol, Bool}}})() at hurdle.jl:132, :maxlog => 1)) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", HurdleDMR, :depwarn, (Ptr{Nothing} @0x00007dcf6731d62d, :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 184, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => (::HurdleDMR.var"#9#11"{GeneralizedLinearModel, InclusionRepetition, Matrix{Float64}, Vector{Float64}, Poisson{Float64}, LogLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{Pair{Symbol, Bool}}})() at hurdle.jl:184, :maxlog => 1)) LogRecord(Warn, "failed to fit truncated counts model to positive subsample, possibly not enough variation in ypos. countmap(ypos)=[1=>1, 2=>1]", HurdleDMR, :hurdle, :HurdleDMR_5f1c5b78, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 187, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", HurdleDMR, :depwarn, (Ptr{Nothing} @0x00007dcf6731fa78, :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 109, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => fitblank(::Type{GeneralizedLinearModel}, ::Matrix{Float64}, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Any, NTuple{4, Symbol}, @NamedTuple{wts::Vector{Float64}, offset::Vector{Float64}, verbose::Bool, dropcollinear::Bool}}) at hurdle.jl:109, :maxlog => 1)) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:306 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:294 ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = (::HurdleDMR.var"#7#8"{GeneralizedLinearModel, Float64, Matrix{Float64}, Vector{Float64}, Binomial{Float64}, LogitLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{}})() at hurdle.jl:132 └ @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl:132 ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = (::HurdleDMR.var"#9#11"{GeneralizedLinearModel, InclusionRepetition, Matrix{Float64}, Vector{Float64}, Poisson{Float64}, LogLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{}})() at hurdle.jl:184 └ @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl:184 inrep degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:315 Expression: fit(InclusionRepetition, GammaLassoPath, X, y0or1; showwarnings = true) Log Pattern: (:warn, r"ypos has no elements larger than 0") Captured Logs: LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf67b06ffd, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) LogRecord(Warn, "ypos has no elements larger than 0.0! Data may be fully described by a probability model.", HurdleDMR, :hurdle, :HurdleDMR_b1cd0eeb, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 200, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf67bf92f3, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Poisson{Float64}, l::LogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Vector{Float64}, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:315 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:294 1: λ=0.00038674044876033174, pct_dev=5.408929685146724e-6 2: λ=0.00035238349319380514, pct_dev=0.004046376329942203 3: λ=0.0003210787148680711, pct_dev=0.007611478289584306 4: λ=0.0002925549667692108, pct_dev=0.010760649203109818 5: λ=0.0002665651898367098, pct_dev=0.013544519504428698 6: λ=0.00024288427305606497, pct_dev=0.01600627430443491 7: λ=0.0002213071036548711, pct_dev=0.018183072505788656 8: λ=0.00020164679051410886, pct_dev=0.020107143271123173 9: λ=0.000183733045406678, pct_dev=0.021806641825224404 10: λ=0.00016741070804224097, pct_dev=0.023306323185880773 11: λ=0.00015253840214301398, pct_dev=0.024628076465963655 12: λ=0.0001389873109100814, pct_dev=0.02579135133028554 13: λ=0.0001266400612739101, pct_dev=0.026813500399851753 14: λ=0.0001153897072649705, pct_dev=0.02771005582009123 15: λ=0.00010513880369890995, pct_dev=0.02849495413716252 16: λ=9.579856215298414e-5, pct_dev=0.02918072060338006 17: λ=8.728808192321398e-5, pct_dev=0.029778621716843645 18: λ=7.953364930119035e-5, pct_dev=0.030298793003289193 19: λ=7.246809910119532e-5, pct_dev=0.03075034760430384 20: λ=6.60302329074955e-5, pct_dev=0.03114147006159851 21: λ=6.016428900294135e-5, pct_dev=0.031479498719036436 22: λ=5.481945938764883e-5, pct_dev=0.03177099936007799 23: λ=4.994944970441121e-5, pct_dev=0.03202183203751052 24: λ=4.5512078259123385e-5, pct_dev=0.032237212510584534 25: λ=4.146891066312668e-5, pct_dev=0.03242176927783791 26: λ=3.778492693292148e-5, pct_dev=0.032579596858857696 27: λ=3.442821816382316e-5, pct_dev=0.03271430573302747 28: λ=3.136971015029444e-5, pct_dev=0.032829068905527614 29: λ=2.8582911559086306e-5, pct_dev=0.03292666687424228 30: λ=2.604368447398234e-5, pct_dev=0.033009526681392565 31: λ=2.3730035324715953e-5, pct_dev=0.03307976125094547 32: λ=2.1621924389186096e-5, pct_dev=0.03313920409372395 33: λ=1.9701092218971507e-5, pct_dev=0.03318944153045578 34: λ=1.795090148472352e-5, pct_dev=0.03323184210431507 35: λ=1.63561928715783e-5, pct_dev=0.03326758326631096 36: λ=1.4903153776423796e-5, pct_dev=0.03329767543911766 37: λ=1.3579198669739283e-5, pct_dev=0.03332298359060426 38: λ=1.2372860085759425e-5, pct_dev=0.03334424646609713 39: λ=1.127368929677188e-5, pct_dev=0.03336209364141851 40: λ=1.027216581123637e-5, pct_dev=0.033377060567176486 41: λ=9.359614911841426e-6, pct_dev=0.03338960177818728 42: λ=8.528132519253062e-6, pct_dev=0.03340010243949665 inrep degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:327 Expression: fit(InclusionRepetition, GammaLassoPath, X, y0or1; verbose = true, showwarnings = true) Log Pattern: (:warn, r"I\(y\) is all ones") Captured Logs: LogRecord(Warn, "I(y) is all ones. Data may be fully described by a poisson model.", HurdleDMR, :hurdle, :HurdleDMR_c879ab77, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 149, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf68353863, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Vector{Float64}, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf673050cd, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Poisson{Float64}, l::LogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:327 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:294 Iteration: 1, deviance: 202.88392988622184, diff.dev.:283.3306289536344 Iteration: 2, deviance: 103.34453979599401, diff.dev.:99.53939009022783 Iteration: 3, deviance: 70.86056777142231, diff.dev.:32.4839720245717 Iteration: 4, deviance: 61.882395743805034, diff.dev.:8.978172027617276 Iteration: 5, deviance: 59.91832501231315, diff.dev.:1.964070731491887 Iteration: 6, deviance: 59.50191184255864, diff.dev.:0.41641316975450593 Iteration: 7, deviance: 59.441417118304805, diff.dev.:0.06049472425383584 Iteration: 8, deviance: 59.43942365499244, diff.dev.:0.0019934633123668277 Iteration: 9, deviance: 59.43942083864344, diff.dev.:2.8163489957933052e-6 inrep degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:335 Expression: fit(InclusionRepetition, GeneralizedLinearModel, [ones(size(X, 1)) X], y0or1; verbose = true, showwarnings = true) Log Pattern: (:warn, r"I\(y\) is all ones") Captured Logs: LogRecord(Warn, "I(y) is all ones. Data may be fully described by a poisson model.", HurdleDMR, :hurdle, :HurdleDMR_c879ab77, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 149, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", HurdleDMR, :depwarn, (Ptr{Nothing} @0x00007dcf67bde167, :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 109, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => fitblank(::Type{GeneralizedLinearModel}, ::Matrix{Float64}, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol, Symbol}, @NamedTuple{wts::Vector{Float64}, offset::Vector{Float64}, verbose::Bool}}) at hurdle.jl:109, :maxlog => 1)) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", HurdleDMR, :depwarn, (Ptr{Nothing} @0x00007dcf67be9fc5, :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 184, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => (::HurdleDMR.var"#9#11"{GeneralizedLinearModel, InclusionRepetition, Matrix{Float64}, Vector{Float64}, Poisson{Float64}, LogLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{}})() at hurdle.jl:184, :maxlog => 1)) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:335 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:294 inrep degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:340 Expression: #= /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:340 =# @test_throws ErrorException fit(InclusionRepetition, GammaLassoPath, X, y0or1; verbose = true, showwarnings = true) Log Pattern: (:warn, r"I\(y\) is all zeros") Captured Logs: LogRecord(Warn, "I(y) is all zeros. There is nothing to explain.", HurdleDMR, :hurdle, :HurdleDMR_1c5241d3, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 147, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf68353863, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Vector{Float64}, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:340 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:294 inrep degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:353 Expression: fit(InclusionRepetition, GammaLassoPath, X, y; showwarnings = true) Log Pattern: (:warn, r"ypos has no elements larger than 0") Captured Logs: LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf67b06ffd, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) LogRecord(Warn, "ypos has no elements larger than 0.0! Data may be fully described by a probability model.", HurdleDMR, :hurdle, :HurdleDMR_b1cd0eeb, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 200, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf67bf92f3, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Poisson{Float64}, l::LogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Vector{Float64}, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:353 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:294 From worker 5: WARNING: using deprecated binding Distributions.MatrixReshaped in Lasso. From worker 5: , use Distributions.ReshapedDistribution{2, S, D} where D<:Distributions.Distribution{Distributions.ArrayLikeVariate{1}, S} where S<:Distributions.ValueSupport instead. From worker 2: WARNING: using deprecated binding Distributions.MatrixReshaped in Lasso. From worker 2: , use Distributions.ReshapedDistribution{2, S, D} where D<:Distributions.Distribution{Distributions.ArrayLikeVariate{1}, S} where S<:Distributions.ValueSupport instead. From worker 3: WARNING: using deprecated binding Distributions.MatrixReshaped in Lasso. From worker 3: , use Distributions.ReshapedDistribution{2, S, D} where D<:Distributions.Distribution{Distributions.ArrayLikeVariate{1}, S} where S<:Distributions.ValueSupport instead. From worker 2: ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead From worker 2: │ caller = build_model(X::SharedArrays.SharedMatrix{Float64}, y::Vector{Float64}, d::Distributions.Poisson{Float64}, l::GLM.LogLink, lp::Lasso.NaiveCoordinateDescent{Float64, true, SharedArrays.SharedMatrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 From worker 2: └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 From worker 4: WARNING: using deprecated binding Distributions.MatrixReshaped in Lasso. From worker 4: , use Distributions.ReshapedDistribution{2, S, D} where D<:Distributions.Distribution{Distributions.ArrayLikeVariate{1}, S} where S<:Distributions.ValueSupport instead. From worker 5: ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead From worker 5: │ caller = build_model(X::SharedArrays.SharedMatrix{Float64}, y::Vector{Float64}, d::Distributions.Poisson{Float64}, l::GLM.LogLink, lp::Lasso.NaiveCoordinateDescent{Float64, true, SharedArrays.SharedMatrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 From worker 5: └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 From worker 3: ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead From worker 3: │ caller = build_model(X::SharedArrays.SharedMatrix{Float64}, y::Vector{Float64}, d::Distributions.Poisson{Float64}, l::GLM.LogLink, lp::Lasso.NaiveCoordinateDescent{Float64, true, SharedArrays.SharedMatrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 From worker 3: └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 From worker 4: ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead From worker 4: │ caller = build_model(X::SharedArrays.SharedMatrix{Float64}, y::Vector{Float64}, d::Distributions.Poisson{Float64}, l::GLM.LogLink, lp::Lasso.NaiveCoordinateDescent{Float64, true, SharedArrays.SharedMatrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 From worker 4: └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 From worker 3: ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead From worker 3: │ caller = build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Distributions.Poisson{Float64}, l::GLM.LogLink, lp::Lasso.NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 From worker 3: └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 From worker 2: ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead From worker 2: │ caller = build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Distributions.Poisson{Float64}, l::GLM.LogLink, lp::Lasso.NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 From worker 2: └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 From worker 4: ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead From worker 4: │ caller = build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Distributions.Poisson{Float64}, l::GLM.LogLink, lp::Lasso.NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 From worker 4: └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 From worker 5: ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead From worker 5: │ caller = build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Distributions.Poisson{Float64}, l::GLM.LogLink, lp::Lasso.NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339 From worker 5: └ @ Lasso ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 [ Info: Testing dmr degenerate cases. The 2 following warnings by workers are expected ... From worker 3: ┌ Warning: fitgl! failed on count dimension 2 with frequencies [0=>200] and will return zero coefs (ErrorException("IRLS failed to converge in 30 iterations at λ = 4.3709033880452197e-7")) From worker 3: └ @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/dmr.jl:412 From worker 4: ┌ Warning: fitgl failed for countsj with frequencies [0=>200] and will return missing path (ErrorException("IRLS failed to converge in 30 iterations at λ = 4.3709033880452197e-7")) From worker 4: └ @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/dmr.jl:375 dmr degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/dmr.jl:263 Expression: dmr(covars, zcounts; parallel = false, testargs...) Log Pattern: (:warn, r"failed on count dimension 2") Captured Logs: LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf673050cd, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Poisson{Float64}, l::LogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) LogRecord(Warn, "fitgl! failed on count dimension 2 with frequencies [0=>200] and will return zero coefs (ErrorException(\"IRLS failed to converge in 30 iterations at λ = 4.3709033880452197e-7\"))", HurdleDMR, :dmr, :HurdleDMR_1091ca80, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/dmr.jl", 412, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/dmr.jl:263 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/dmr.jl:239 dmr degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/dmr.jl:267 Expression: dmrpaths(covars, zcounts; parallel = false, testargs...) Log Pattern: (:warn, r"failed for countsj") Captured Logs: LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Lasso, :depwarn, (Ptr{Nothing} @0x00007dcf673050cd, :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => build_model(X::Matrix{Float64}, y::Vector{Float64}, d::Poisson{Float64}, l::LogLink, lp::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, λminratio::Float64, λ::Nothing, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, ω::Nothing, intercept::Bool, irls_tol::Float64, dofit::Bool) at Lasso.jl:339, :maxlog => 1)) LogRecord(Warn, "fitgl failed for countsj with frequencies [0=>200] and will return missing path (ErrorException(\"IRLS failed to converge in 30 iterations at λ = 4.3709033880452197e-7\"))", HurdleDMR, :dmr, :HurdleDMR_74d626fa, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/dmr.jl", 375, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}()) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.10/Test/src/logging.jl:166 [2] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/dmr.jl:267 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [4] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/dmr.jl:239 [ Info: Testing hdmr degenerate cases. The 2 following warnings by workers are expected ... From worker 3: ┌ Warning: hurdle_regression! failed on count dimension 2 with frequencies [0=>200] and will return zero coefs (ErrorException("y is all zeros! There is nothing to explain.")) From worker 3: └ @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hdmr.jl:456 From worker 3: ┌ Warning: fit(InclusionRepetition...) failed for countsj with frequencies [0=>200] and will return missing path (ErrorException("y is all zeros! There is nothing to explain.")) From worker 3: └ @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hdmr.jl:332 [ Info: Testing hdmr degenerate cases. The 2 following warnings by workers are expected ... From worker 3: ┌ Warning: hurdle_regression! failed on count dimension 2 with frequencies [0=>200] and will return zero coefs (ErrorException("y is all zeros! There is nothing to explain.")) From worker 3: └ @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hdmr.jl:456 From worker 2: ┌ Warning: fit(Hurdle...) failed for countsj with frequencies [0=>200] and will return missing path (ErrorException("y is all zeros! There is nothing to explain.")) From worker 2: └ @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hdmr.jl:332 Test Summary: | Pass Fail Total Time HurdleDMR | 1750 15 1765 10m25.5s PositivePoisson | 37 37 1m07.2s hurdle with Xpos == Xzero | 29 29 58.8s hurdle with Xpos ≠ Xzero | 21 21 6.9s hurdle with Xpos ≠ Xzero AND offset specified | 21 21 4.8s hurdle degenerate cases | 24 7 31 24.7s inrep with Xpos == Xzero | 29 29 8.7s inrep with Xpos ≠ Xzero | 21 21 1.9s inrep with Xpos ≠ Xzero AND offset specified | 21 21 1.3s inrep degenerate cases | 24 6 30 5.2s helpers | 87 87 19.3s logging | 2 2 0.9s dmr | 97 97 3m26.8s dmr degenerate cases | 17 2 19 4.7s hdmr | 1314 1314 3m15.1s mcdmr | 6 6 0.0s ERROR: LoadError: Some tests did not pass: 1750 passed, 15 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/runtests.jl:10 Testing failed after 422.64s ERROR: LoadError: Package HurdleDMR errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:2034 [3] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 880.52s: package has test failures