Package evaluation to test HurdleDMR on Julia 1.14.0-DEV.1475 (42ad41c179*) started at 2026-01-04T18:29:34.600 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 8.73s ################################################################################ # Installation # Installing HurdleDMR... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [f9e53bcf] + HurdleDMR v1.4.0 Updating `~/.julia/environments/v1.14/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 v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [7a1cc6ca] + FFTW v1.10.0 [1a297f60] + FillArrays v1.15.0 [38e38edf] + GLM v1.9.1 [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 v1.3.3 [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 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.9 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.7 [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 v1.1.2 [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 v1.13.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v1.0.0 [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 v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.17.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+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 v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 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 3.96s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 Precompilation failed after 13.29s ################################################################################ # Testing # Testing HurdleDMR Status `/tmp/jl_OhASTD/Project.toml` [336ed68f] CSV v0.10.15 [324d7699] CategoricalArrays v1.0.2 [a93c6f00] DataFrames v1.8.1 [31c24e10] Distributions v0.25.122 [38e38edf] GLM v1.9.1 [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 v0.34.9 [3eaba693] StatsModels v0.7.7 [bd369af6] Tables v1.12.1 [8ba89e20] Distributed v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [9a3f8284] Random v1.11.0 [1a1011a3] SharedArrays v1.11.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_OhASTD/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 v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [7a1cc6ca] FFTW v1.10.0 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [38e38edf] GLM v1.9.1 [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 v1.3.3 [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 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.9 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.7 [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 v1.1.2 [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 v1.13.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v1.0.0 [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 v1.14.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [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 v8.17.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+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 v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 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: `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 └ @ Core ~/.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 └ @ Core ~/.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 └ @ Core ~/.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", Core, :depwarn, (Ptr{Nothing}(0x00007c77209b0d38), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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", Core, :depwarn, (Ptr{Nothing}(0x00007c77209338d8), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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_4fdd95a4, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 187, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Core, :depwarn, (Ptr{Nothing}(0x00007c7720912835), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:332 [inlined] 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", Core, :depwarn, (Ptr{Nothing}(0x00007c77209b0d38), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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_e1675784, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 200, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Core, :depwarn, (Ptr{Nothing}(0x00007c7720912835), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:343 [inlined] [ Info: Testing hurdle degenerate cases. The following warnings about step-halving are expected ... 1: λ=0.0003867325713801151, pct_dev=6.4920500555398775e-6 2: λ=0.00035237631561833594, pct_dev=0.0041372757265244475 3: λ=0.0003210721749286246, pct_dev=0.007781659140974062 step-halving because obj=0.004869923554307433 > 0.004869923554286684 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 4: λ=0.0002925490078199599, pct_dev=0.01100089384295544 5: λ=0.00026655976026408637, pct_dev=0.013846724599090088 step-halving because obj=0.004859664140970761 > 0.004859664140896032 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 6: λ=0.0002428793258317093, pct_dev=0.01636328839414891 7: λ=0.00022130259592829205, pct_dev=0.018588564388426487 step-halving because obj=0.004847225400817916 > 0.00484722540075796 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 8: λ=0.00020164268324153491, pct_dev=0.02055549401335177 9: λ=0.00018372930301287975, pct_dev=0.022292855750670304 step-halving because obj=0.0048338356088028795 > 0.004833835608731584 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 10: λ=0.00016740729811239328, pct_dev=0.02382595308919 11: λ=0.00015253529514193552, pct_dev=0.025177160747647642 12: λ=0.00013898447992641573, pct_dev=0.026366360340590256 step-halving because obj=0.004813724752516016 > 0.004813724752439465 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 13: λ=0.0001266374817870308, pct_dev=0.027411290060179838 14: λ=0.00011538735693259597, pct_dev=0.02832782760514796 15: λ=0.00010513666216358598, pct_dev=0.029130219623084264 step-halving because obj=0.004795017704131979 > 0.0047950177040689155 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 16: λ=9.579661086575603e-5, pct_dev=0.029831270255508135 17: λ=8.728630398296524e-5, pct_dev=0.03044249701160484 step-halving because obj=0.00478375368838985 > 0.004783753688225356 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 18: λ=7.953202930825296e-5, pct_dev=0.030974261264354097 19: λ=7.246662302396573e-5, pct_dev=0.03143587922357194 step-halving because obj=0.004773580706219157 > 0.004773580706204912 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 20: λ=6.602888796089875e-5, pct_dev=0.031835717928628604 step-halving because obj=0.004768911734506395 > 0.004768911734442515 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 21: λ=6.0163063537693315e-5, pct_dev=0.03218127932430337 step-halving because obj=0.004764518513801181 > 0.004764518513690922 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 22: λ=5.4818342789356005e-5, pct_dev=0.03247927563964026 step-halving because obj=0.004760395813052424 > 0.004760395813005317 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 23: λ=4.994843230163325e-5, pct_dev=0.03273569739793325 step-halving because obj=0.004756536416093103 > 0.0047565364159685075 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 24: λ=4.551115123960406e-5, pct_dev=0.032955876967414977 25: λ=4.146806599746655e-5, pct_dev=0.033144545754554056 step-halving because obj=0.004749571385363883 > 0.004749571384914886 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 26: λ=3.7784157305030604e-5, pct_dev=0.03330588962782388 step-halving because obj=0.004746445123916796 > 0.004746445123833794 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 27: λ=3.442751690755286e-5, pct_dev=0.03344359956516718 28: λ=3.136907119169851e-5, pct_dev=0.033560919438132886 29: λ=2.8582329363810993e-5, pct_dev=0.033660691596692494 30: λ=2.6043153999330687e-5, pct_dev=0.033745397194471116 31: λ=2.3729551975970305e-5, pct_dev=0.03381719627438984 32: λ=2.1621483979810843e-5, pct_dev=0.0338779632349111 33: λ=1.9700690934351336e-5, pct_dev=0.03392931965391821 34: λ=1.7950535849123017e-5, pct_dev=0.03397266462569737 35: λ=1.6355859718036814e-5, pct_dev=0.03400920184598999 36: λ=1.4902850219324724e-5, pct_dev=0.034039964256540545 37: λ=1.3578922079816255e-5, pct_dev=0.03406583614021719 38: λ=1.2372608067322844e-5, pct_dev=0.03408757254554551 39: λ=1.1273459666958612e-5, pct_dev=0.034105817134283956 step-halving because obj=0.004721965746409653 > 0.004721965746131991 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 40: λ=1.0271956581102827e-5, pct_dev=0.0341211173125513 41: λ=9.359424269136285e-6, pct_dev=0.034133937955958205 step-halving because obj=0.004720051492593788 > 0.004720051492333895 + 5.348152476436496e-15 = length(scratchmu)*eps(objold) 42: λ=8.52795881272041e-6, pct_dev=0.034144672335046033 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_d98f5ec1, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 149, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Core, :depwarn, (Ptr{Nothing}(0x00007c7720993475), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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", Core, :depwarn, (Ptr{Nothing}(0x00007c77209338d8), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:357 [inlined] Iteration: 1, deviance: 204.0380396103584, diff.dev.:284.0542927420774 Iteration: 2, deviance: 103.01893015603056, diff.dev.:101.01910945432783 Iteration: 3, deviance: 69.83490468997296, diff.dev.:33.184025466057605 Iteration: 4, deviance: 60.60747250524526, diff.dev.:9.227432184727697 Iteration: 5, deviance: 58.58206318978401, diff.dev.:2.0254093154612534 Iteration: 6, deviance: 58.15370098772986, diff.dev.:0.42836220205414577 Iteration: 7, deviance: 58.09051068832338, diff.dev.:0.0631902994064859 Iteration: 8, deviance: 58.0883485349626, diff.dev.:0.002162153360778518 Iteration: 9, deviance: 58.08834523345594, diff.dev.:3.3015066591701725e-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_d98f5ec1, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 149, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Core, :depwarn, (Ptr{Nothing}(0x00007c77206bb0f3), :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 109, Base.Pairs{Symbol, Any, Nothing, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => fitblank(::Type{GeneralizedLinearModel}, ::Matrix{Float64}, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Any, Nothing, @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", Core, :depwarn, (Ptr{Nothing}(0x00007c772095ba21), :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 184, Base.Pairs{Symbol, Any, Nothing, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => (::HurdleDMR.var"#fitpos##0#fitpos##1"{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/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:363 [inlined] 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_8f59d6f8, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 147, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Core, :depwarn, (Ptr{Nothing}(0x00007c7720993475), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:368 [inlined] 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", Core, :depwarn, (Ptr{Nothing}(0x00007c77209b0d38), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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", Core, :depwarn, (Ptr{Nothing}(0x00007c77209338d8), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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_4fdd95a4, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 187, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Core, :depwarn, (Ptr{Nothing}(0x00007c7720912835), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:372 [inlined] 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", Core, :depwarn, (Ptr{Nothing}(0x00007c77209b0d38), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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_e1675784, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 200, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Core, :depwarn, (Ptr{Nothing}(0x00007c7720912835), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:382 [inlined] ┌ 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 └ @ Core ~/.julia/packages/Lasso/IMm8z/src/Lasso.jl:339 inrep with Xpos == Xzero: Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:70 Expression: ≈(coefsJCVmin[1 + p:var"end"], coefsR1[1 + p:var"end"], rtol = 0.3) Evaluated: sparsevec([1, 2, 3, 4, 6], [0.3507196311410343, -0.17850670231930268, 0.20272441527374593, -0.1962182608092539, 0.0726719167711444], 6) ≈ [0.23679601243522808, -0.2511511286179945, 0.3262335836130562, -0.2852487157850386, 0.02221939709900889, 0.08012135468658138] (rtol=0.3) Stacktrace: [1] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:12 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [3] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:70 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:773 [inlined] ┌ 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 └ @ Core ~/.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 └ @ Core ~/.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", Core, :depwarn, (Ptr{Nothing}(0x00007c7720716ed0), :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 132, Base.Pairs{Symbol, Any, Nothing, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => (::HurdleDMR.var"#fitzero##0#fitzero##1"{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", Core, :depwarn, (Ptr{Nothing}(0x00007c772071a6a5), :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 184, Base.Pairs{Symbol, Any, Nothing, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => (::HurdleDMR.var"#fitpos##0#fitpos##1"{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_4fdd95a4, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 187, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Core, :depwarn, (Ptr{Nothing}(0x00007c772071dac8), :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 109, Base.Pairs{Symbol, Any, Nothing, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => fitblank(::Type{GeneralizedLinearModel}, ::Matrix{Float64}, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Any, Nothing, @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/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:294 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:306 [inlined] ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = (::HurdleDMR.var"#fitzero##0#fitzero##1"{GeneralizedLinearModel, Float64, Matrix{Float64}, Vector{Float64}, Binomial{Float64}, LogitLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{}})() at hurdle.jl:132 └ @ Core ~/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl:132 ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = (::HurdleDMR.var"#fitpos##0#fitpos##1"{GeneralizedLinearModel, InclusionRepetition, Matrix{Float64}, Vector{Float64}, Poisson{Float64}, LogLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{}})() at hurdle.jl:184 └ @ Core ~/.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", Core, :depwarn, (Ptr{Nothing}(0x00007c77209b0d38), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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_e1675784, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 200, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Core, :depwarn, (Ptr{Nothing}(0x00007c77206d7985), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:294 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:315 [inlined] 1: λ=0.0003867404487603311, pct_dev=5.408929609651558e-6 2: λ=0.00035238349319380454, pct_dev=0.00404637632992999 3: λ=0.0003210787148680705, pct_dev=0.007611478289548668 4: λ=0.00029255496676921025, pct_dev=0.010760649203022998 5: λ=0.0002665651898367093, pct_dev=0.013544519504349761 6: λ=0.00024288427305606454, pct_dev=0.01600627430437984 7: λ=0.0002213071036548707, pct_dev=0.018183072505749243 8: λ=0.0002016467905141085, pct_dev=0.020107143271063666 9: λ=0.00018373304540667768, pct_dev=0.021806641825166673 10: λ=0.00016741070804224067, pct_dev=0.023306323185832145 11: λ=0.0001525384021430137, pct_dev=0.024628076465984083 12: λ=0.00013898731091008113, pct_dev=0.025791351330280765 13: λ=0.00012664006127390988, pct_dev=0.026813500399933576 14: λ=0.00011538970726497029, pct_dev=0.027710055820079793 15: λ=0.00010513880369890977, pct_dev=0.028494954137210482 16: λ=9.579856215298396e-5, pct_dev=0.029180720603450894 17: λ=8.728808192321398e-5, pct_dev=0.029778621716890386 18: λ=7.953364930119022e-5, pct_dev=0.030298793003348368 19: λ=7.24680991011952e-5, pct_dev=0.03075034760436579 20: λ=6.60302329074955e-5, pct_dev=0.03114147006166046 21: λ=6.016428900294124e-5, pct_dev=0.031479498719058197 22: λ=5.4819459387648735e-5, pct_dev=0.03177099936014183 23: λ=4.994944970441121e-5, pct_dev=0.0320218320375687 24: λ=4.5512078259123303e-5, pct_dev=0.03223721251067668 25: λ=4.14689106631266e-5, pct_dev=0.0324217692778942 26: λ=3.778492693292141e-5, pct_dev=0.03257959685890033 27: λ=3.44282181638231e-5, pct_dev=0.03271430573306522 28: λ=3.136971015029439e-5, pct_dev=0.03282906890559156 29: λ=2.8582911559086256e-5, pct_dev=0.03292666687426704 30: λ=2.604368447398234e-5, pct_dev=0.03300952668148138 31: λ=2.3730035324715912e-5, pct_dev=0.03307976125098355 32: λ=2.1621924389186055e-5, pct_dev=0.03313920409378046 33: λ=1.9701092218971507e-5, pct_dev=0.03318944153047776 34: λ=1.795090148472349e-5, pct_dev=0.03323184210438024 35: λ=1.6356192871578274e-5, pct_dev=0.03326758326639567 36: λ=1.4903153776423796e-5, pct_dev=0.0332976754391876 37: λ=1.357919866973926e-5, pct_dev=0.03332298359068986 38: λ=1.2372860085759403e-5, pct_dev=0.03334424646617373 39: λ=1.127368929677188e-5, pct_dev=0.03336209364150067 40: λ=1.0272165811236351e-5, pct_dev=0.03337706056729062 41: λ=9.35961491184141e-6, pct_dev=0.03338960177831951 42: λ=8.528132519253062e-6, pct_dev=0.03340010243959779 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_d98f5ec1, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 149, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Core, :depwarn, (Ptr{Nothing}(0x00007c7720993475), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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", Core, :depwarn, (Ptr{Nothing}(0x00007c77206e9578), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:294 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:327 [inlined] Iteration: 1, deviance: 202.8839298862207, diff.dev.:283.33062895363287 Iteration: 2, deviance: 103.34453979599422, diff.dev.:99.53939009022648 Iteration: 3, deviance: 70.86056777142119, diff.dev.:32.483972024573035 Iteration: 4, deviance: 61.88239574380623, diff.dev.:8.97817202761496 Iteration: 5, deviance: 59.918325012312735, diff.dev.:1.9640707314934929 Iteration: 6, deviance: 59.50191184255809, diff.dev.:0.41641316975464804 Iteration: 7, deviance: 59.4414171183051, diff.dev.:0.060494724252990295 Iteration: 8, deviance: 59.439423654992964, diff.dev.:0.0019934633121323486 Iteration: 9, deviance: 59.43942083864354, diff.dev.:2.8163494221189467e-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_d98f5ec1, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 149, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Core, :depwarn, (Ptr{Nothing}(0x00007c77206bb0f3), :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 109, Base.Pairs{Symbol, Any, Nothing, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => fitblank(::Type{GeneralizedLinearModel}, ::Matrix{Float64}, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Any, Nothing, @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", Core, :depwarn, (Ptr{Nothing}(0x00007c77206c5253), :fit), "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 184, Base.Pairs{Symbol, Any, Nothing, @NamedTuple{caller::Base.StackTraces.StackFrame, maxlog::Int64}}(:caller => (::HurdleDMR.var"#fitpos##0#fitpos##1"{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/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:294 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:335 [inlined] 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_8f59d6f8, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 147, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Core, :depwarn, (Ptr{Nothing}(0x00007c7720993475), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:294 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:340 [inlined] 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", Core, :depwarn, (Ptr{Nothing}(0x00007c77209b0d38), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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_e1675784, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl", 200, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) LogRecord(Warn, "`wts` keyword argument is deprecated, use `weights` instead", Core, :depwarn, (Ptr{Nothing}(0x00007c77206d7985), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:294 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:353 [inlined] 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: └ @ Core ~/.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::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: └ @ Core ~/.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: └ @ Core ~/.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::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: └ @ Core ~/.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: └ @ Core ~/.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: └ @ Core ~/.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: └ @ Core ~/.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: └ @ Core ~/.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 3: ┌ 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 3: └ @ 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", Core, :depwarn, (Ptr{Nothing}(0x00007c77206e9578), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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_7d955524, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/dmr.jl", 412, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/dmr.jl:239 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/dmr.jl:263 [inlined] 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", Core, :depwarn, (Ptr{Nothing}(0x00007c77206e9578), :fit), "/home/pkgeval/.julia/packages/Lasso/IMm8z/src/Lasso.jl", 339, Base.Pairs{Symbol, Any, Nothing, @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_ccd64b70, "/home/pkgeval/.julia/packages/HurdleDMR/i6kx1/src/dmr.jl", 375, Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}()) Stacktrace: [1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure) @ Test /opt/julia/share/julia/stdlib/v1.14/Test/src/logging.jl:166 [2] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/dmr.jl:239 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1995 [inlined] [4] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/dmr.jl:267 [inlined] [ 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 3: ┌ 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 3: └ @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hdmr.jl:332 Test Summary: | Pass Fail Total Time HurdleDMR | 1749 16 1765 8m57.3s PositivePoisson | 37 37 43.0s hurdle with Xpos == Xzero | 29 29 47.9s hurdle with Xpos ≠ Xzero | 21 21 4.6s hurdle with Xpos ≠ Xzero AND offset specified | 21 21 4.0s hurdle degenerate cases | 24 7 31 21.7s inrep with Xpos == Xzero | 28 1 29 8.4s inrep with Xpos ≠ Xzero | 21 21 1.3s inrep with Xpos ≠ Xzero AND offset specified | 21 21 1.4s inrep degenerate cases | 24 6 30 3.6s helpers | 87 87 13.9s logging | 2 2 0.6s dmr | 97 97 3m20.2s dmr degenerate cases | 17 2 19 6.6s hdmr | 1314 1314 2m42.3s mcdmr | 6 6 0.0s RNG of the outermost testset: Xoshiro(0x2d451e553497fb47, 0xc5514c6c358bc46d, 0xd163dcfaa3d2f13b, 0xf58f09bfaffb4529, 0x4b1598bcd838e2d4) ERROR: LoadError: Some tests did not pass: 1749 passed, 16 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/runtests.jl:10 Testing failed after 637.04s ERROR: LoadError: Package HurdleDMR errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{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/v1.14/Pkg/src/Operations.jl:3067 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2916 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{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::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:237 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:228 PkgEval failed after 777.01s: package has test failures