Package evaluation to test HurdleDMR on Julia 1.14.0-DEV.3055 (7e75a8061a*) started at 2026-08-27T22:59:46.964 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.58s ################################################################################ # 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 [7d9f7c33] + Accessors v0.1.45 [66dad0bd] + AliasTables v1.1.3 [0e736298] + Bessels v0.2.8 [38540f10] + CommonSolve v0.2.14 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [717857b8] + DSP v0.8.6 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.6 [e2d170a0] + DataValueInterfaces v1.0.0 [31c24e10] + Distributions v0.25.131 [ffbed154] + DocStringExtensions v0.9.5 [7a1cc6ca] + FFTW v1.10.0 [1a297f60] + FillArrays v1.17.0 [38e38edf] + GLM v1.9.5 [a0844989] + Gamma v1.2.0 [f9e53bcf] + HurdleDMR v1.4.0 [34004b35] + HypergeometricFunctions v0.3.30 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 ⌅ [984bce1d] + LambertW v0.4.6 [b4fcebef] + Lasso v0.7.5 [2ab3a3ac] + LogExpFunctions v1.0.1 [e6f89c97] + LoggingExtras v1.2.0 [f0e99cf1] + MLBase v0.9.2 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 ⌅ [bac558e1] + OrderedCollections v1.8.2 [90014a1f] + PDMats v0.11.41 [f27b6e38] + Polynomials v4.1.1 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.3 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v3.0.7 [efcf1570] + Setfield v1.1.2 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.3 [276daf66] + SpecialFunctions v2.9.0 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.13 [4c63d2b9] + StatsFuns v2.2.1 [3eaba693] + StatsModels v0.7.10 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.14.0 [f5851436] + FFTW_jll v3.3.12+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [856f044c] + MKL_jll v2025.2.0+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.2+0 [1317d2d5] + oneTBB_jll v2022.3.0+0 [0dad84c5] + ArgTools v1.2.0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.12.0 [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 v1.14.0 [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 v1.13.0 [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 v1.5.7+0 [deac9b47] + LibCURL_jll v8.21.0+0 [e37daf67] + LibGit2_jll v1.9.7+0 [29816b5a] + LibSSH2_jll v1.11.104+0 [14a3606d] + MozillaCACerts_jll v2026.8.13 [4536629a] + OpenBLAS_jll v0.3.34+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.8+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.70.0+0 [3f19e933] + p7zip_jll v17.8.2+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 4.93s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 3.6 s ✓ MLBase 8.0 s ✓ GLM 8.7 s ✓ Lasso 8.5 s ✓ HurdleDMR 4 dependencies successfully precompiled in 31 seconds. 137 already precompiled. Precompilation completed after 55.09s ################################################################################ # Testing # Testing HurdleDMR Status `/tmp/jl_1ZfY1a/Project.toml` [336ed68f] CSV v0.10.17 [324d7699] CategoricalArrays v1.1.1 [a93c6f00] DataFrames v1.8.2 [31c24e10] Distributions v0.25.131 [38e38edf] GLM v1.9.5 [f9e53bcf] HurdleDMR v1.4.0 ⌅ [984bce1d] LambertW v0.4.6 [b4fcebef] Lasso v0.7.5 [e6f89c97] LoggingExtras v1.2.0 [f0e99cf1] MLBase v0.9.2 [e1d29d7a] Missings v1.2.0 [2913bbd2] StatsBase v0.34.13 [3eaba693] StatsModels v0.7.10 [bd369af6] Tables v1.14.0 [8ba89e20] Distributed v1.12.0 [b77e0a4c] InteractiveUtils v1.11.0 [37e2e46d] LinearAlgebra v1.14.0 [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_1ZfY1a/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [7d9f7c33] Accessors v0.1.45 [66dad0bd] AliasTables v1.1.3 [0e736298] Bessels v0.2.8 [336ed68f] CSV v0.10.17 [324d7699] CategoricalArrays v1.1.1 [944b1d66] CodecZlib v0.7.9 [38540f10] CommonSolve v0.2.14 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.2.0 [717857b8] DSP v0.8.6 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.6 [e2d170a0] DataValueInterfaces v1.0.0 [31c24e10] Distributions v0.25.131 [ffbed154] DocStringExtensions v0.9.5 [7a1cc6ca] FFTW v1.10.0 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.17.0 [38e38edf] GLM v1.9.5 [a0844989] Gamma v1.2.0 [f9e53bcf] HurdleDMR v1.4.0 [34004b35] HypergeometricFunctions v0.3.30 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [b964fa9f] LaTeXStrings v1.4.1 ⌅ [984bce1d] LambertW v0.4.6 [b4fcebef] Lasso v0.7.5 [2ab3a3ac] LogExpFunctions v1.0.1 [e6f89c97] LoggingExtras v1.2.0 [f0e99cf1] MLBase v0.9.2 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 ⌅ [bac558e1] OrderedCollections v1.8.2 [90014a1f] PDMats v0.11.41 ⌅ [69de0a69] Parsers v2.8.7 [f27b6e38] Polynomials v4.1.1 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.4.8 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.3 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v3.0.7 [91c51154] SentinelArrays v1.4.10 [efcf1570] Setfield v1.1.2 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.3 [276daf66] SpecialFunctions v2.9.0 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.13 [4c63d2b9] StatsFuns v2.2.1 [3eaba693] StatsModels v0.7.10 [892a3eda] StringManipulation v0.5.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.14.0 [3bb67fe8] TranscodingStreams v0.11.3 [ea10d353] WeakRefStrings v1.4.3 [76eceee3] WorkerUtilities v1.6.1 [f5851436] FFTW_jll v3.3.12+0 [1d5cc7b8] IntelOpenMP_jll v2025.2.0+0 [856f044c] MKL_jll v2025.2.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.2+0 [1317d2d5] oneTBB_jll v2022.3.0+0 [0dad84c5] ArgTools v1.2.0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.12.0 [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 v1.14.0 [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 v1.13.0 [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 v1.5.7+0 [deac9b47] LibCURL_jll v8.21.0+0 [e37daf67] LibGit2_jll v1.9.7+0 [29816b5a] LibSSH2_jll v1.11.104+0 [14a3606d] MozillaCACerts_jll v2026.8.13 [4536629a] OpenBLAS_jll v0.3.34+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.8+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.70.0+0 [3f19e933] p7zip_jll v17.8.2+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 hurdle with Xpos == Xzero: Error During Test at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:27 Got exception outside of a @test FieldError: type NaiveCoordinateDescent has no field `beta0`, available fields: `X`, `μy`, `μX`, `Xssq`, `residuals`, `residualoffset`, `weights`, `oldy`, `weightsum`, `coefitr`, `dev`, `α`, `maxiter`, `maxncoef`, `tol`, `ω` Stacktrace: [1] getproperty(x::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, f::Symbol) @ Base Base_compiler.jl:58 [inlined] [2] coef(x::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}) @ GLM ~/.julia/packages/GLM/US8qj/src/linpred.jl:287 [3] coef(obj::GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, PositivePoisson, LogProductLogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}) @ GLM ~/.julia/packages/GLM/US8qj/src/linpred.jl:288 [4] coeftable(mm::GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, PositivePoisson, LogProductLogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}; level::Float64) @ GLM ~/.julia/packages/GLM/US8qj/src/glmfit.jl:243 [5] coeftable(mm::GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, PositivePoisson, LogProductLogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}) @ GLM ~/.julia/packages/GLM/US8qj/src/glmfit.jl:242 [6] show(io::IOContext{IOBuffer}, obj::GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, PositivePoisson, LogProductLogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}) @ GLM ~/.julia/packages/GLM/US8qj/src/linpred.jl:258 [7] _show_default(io::IOBuffer, x::Any) @ Base show.jl:536 [8] show_default(io::IOBuffer, x::GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, PositivePoisson, LogProductLogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}) @ Base show.jl:519 [inlined] [9] show(io::IOBuffer, x::GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, PositivePoisson, LogProductLogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}) @ Base show.jl:514 [inlined] [10] print(io::IOBuffer, x::GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, PositivePoisson, LogProductLogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}) @ Base strings/io.jl:35 [11] print(::IOBuffer, ::GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, PositivePoisson, LogProductLogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}, ::String) @ Base strings/io.jl:46 [12] println(io::IOBuffer, xs::GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, PositivePoisson, LogProductLogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}) @ Base strings/io.jl:75 [inlined] [13] show(io::IOBuffer, tpm::Hurdle{GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Binomial{Float64}, LogitLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}, GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, PositivePoisson, LogProductLogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}}) @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl:348 [14] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:39 [15] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [16] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:86 [inlined] hurdle degenerate cases: Error During Test at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:332 Test threw exception Expression: fit(Hurdle, GammaLassoPath, X, y; showwarnings = true) MethodError: no method matching reducedim1(::Matrix{Float64}, ::Adjoint{Float64, Matrix{Float64}}) The function `reducedim1` exists, but no method is defined for this combination of argument types. Closest candidates are: reducedim1(::Any) @ Base reducedim.jl:1229 Stacktrace: [1] centralize_sumabs2!(R::Matrix{Float64}, A::Adjoint{Float64, Matrix{Float64}}, means::Matrix{Float64}) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:282 [2] varm!(R::Matrix{Float64}, A::Adjoint{Float64, Matrix{Float64}}, m::Matrix{Float64}; corrected::Bool) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:309 [3] _varm(A::Adjoint{Float64, Matrix{Float64}}, m::Matrix{Float64}, corrected::Bool, region::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:341 [4] varm(A::Adjoint{Float64, Matrix{Float64}}, m::Matrix{Float64}; corrected::Bool, dims::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:339 [inlined] [5] _var(A::Adjoint{Float64, Matrix{Float64}}, corrected::Bool, mean::Nothing, dims::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:386 [inlined] [6] var(A::Adjoint{Float64, Matrix{Float64}}; corrected::Bool, mean::Nothing, dims::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:380 [inlined] [7] _std(A::Adjoint{Float64, Matrix{Float64}}, corrected::Bool, mean::Nothing, dims::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:469 [8] std(A::Adjoint{Float64, Matrix{Float64}}; corrected::Bool, mean::Nothing, dims::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:461 [inlined] [9] standardizeX(X::Adjoint{Float64, Matrix{Float64}}, standardize::Bool) @ Lasso ~/.julia/packages/Lasso/DdoId/src/Lasso.jl:363 [10] fit(::Type{GammaLassoPath}, X::Adjoint{Float64, Matrix{Float64}}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink; γ::Float64, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, λminratio::Float64, λ::Nothing, standardize::Bool, intercept::Bool, algorithm::Core.TypeEgal{NaiveCoordinateDescent}, dofit::Bool, irls_tol::Float64, randomize::Bool, rng::Nothing, maxncoef::Int64, penalty_factor::Nothing, standardizeω::Bool, fitargs::@Kwargs{verbose::Bool}) @ Lasso ~/.julia/packages/Lasso/DdoId/src/gammalasso.jl:78 [11] (::HurdleDMR.var"#fitzero##0#fitzero##1"{GammaLassoPath, Float64, Adjoint{Float64, Matrix{Float64}}, Vector{Float64}, Binomial{Float64}, LogitLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{}})() @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl:132 [12] with_logstate(f::HurdleDMR.var"#fitzero##0#fitzero##1"{GammaLassoPath, Float64, Adjoint{Float64, Matrix{Float64}}, Vector{Float64}, Binomial{Float64}, LogitLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging logging/logging.jl:542 [13] with_logger(f::HurdleDMR.var"#fitzero##0#fitzero##1"{GammaLassoPath, Float64, Adjoint{Float64, Matrix{Float64}}, Vector{Float64}, Binomial{Float64}, LogitLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{}}, logger::AbstractLogger) @ Base.CoreLogging logging/logging.jl:653 [inlined] [14] fitzero(::Core.TypeEgal{GammaLassoPath}, ::Adjoint{Float64, Matrix{Float64}}, ::Vector{Float64}, ::Binomial{Float64}, ::LogitLink, ::Bool, ::Vector{Float64}, ::Vector{Float64}, ::Bool, ::Bool) @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl:129 [inlined] [15] fit(::Type{Hurdle}, ::Core.TypeEgal{GammaLassoPath}, X::Adjoint{Float64, Matrix{Float64}}, y::Vector{Float64}, dzero::Binomial{Float64}, dpos::PositivePoisson, lzero::LogitLink, lpos::LogProductLogLink; Xpos::Nothing, dofit::Bool, wts::Vector{Float64}, offsetzero::Vector{Float64}, offsetpos::Vector{Float64}, offset::Vector{Float64}, verbose::Bool, showwarnings::Bool, fitargs::@Kwargs{}) @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl:271 [16] (::var"#54#55")() @ Main none:-1 [17] with_logstate(f::var"#54#55", logstate::Base.CoreLogging.LogState) @ Base.CoreLogging logging/logging.jl:542 [18] with_logger(f::Function, logger::TestLogger) @ Base.CoreLogging logging/logging.jl:653 [19] collect_test_logs(f::Function; kwargs::@Kwargs{}) @ Test /opt/julia/share/julia/stdlib/v1.14/Test/src/logging.jl:126 [inlined] [20] collect_test_logs(f::Function) @ Test /opt/julia/share/julia/stdlib/v1.14/Test/src/logging.jl:124 [inlined] [21] match_logs(f::Function, patterns::Tuple{Symbol, Regex}; match_mode::Symbol, kwargs::@Kwargs{}) @ Test /opt/julia/share/julia/stdlib/v1.14/Test/src/logging.jl:307 [inlined] [22] match_logs(f::Function, patterns::Tuple{Symbol, Regex}) @ Test /opt/julia/share/julia/stdlib/v1.14/Test/src/logging.jl:306 [23] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 [24] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [25] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:332 [inlined] hurdle degenerate cases: Error During Test at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:328 Got exception outside of a @test MethodError: no method matching coef(::Nothing; select::MinAICc) The function `coef` exists, but no method is defined for this combination of argument types. Closest candidates are: coef(!Matched::DMRPaths) got unsupported keyword argument "select" @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/dmr.jl:164 coef(!Matched::DMRPaths, !Matched::SegSelect) got unsupported keyword argument "select" @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/dmr.jl:164 coef(!Matched::RegularizationPath, !Matched::MinCVKfold{S}; kwargs...) where S<:CVSegSelect @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl:402 ... Stacktrace: [1] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:331 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [3] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/hurdle.jl:333 [inlined] inrep with Xpos == Xzero: Error During Test at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:10 Got exception outside of a @test FieldError: type NaiveCoordinateDescent has no field `beta0`, available fields: `X`, `μy`, `μX`, `Xssq`, `residuals`, `residualoffset`, `weights`, `oldy`, `weightsum`, `coefitr`, `dev`, `α`, `maxiter`, `maxncoef`, `tol`, `ω` Stacktrace: [1] getproperty(x::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}, f::Symbol) @ Base Base_compiler.jl:58 [inlined] [2] coef(x::NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}) @ GLM ~/.julia/packages/GLM/US8qj/src/linpred.jl:287 [3] coef(obj::GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Poisson{Float64}, LogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}) @ GLM ~/.julia/packages/GLM/US8qj/src/linpred.jl:288 [4] coeftable(mm::GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Poisson{Float64}, LogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}; level::Float64) @ GLM ~/.julia/packages/GLM/US8qj/src/glmfit.jl:243 [5] coeftable(mm::GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Poisson{Float64}, LogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}) @ GLM ~/.julia/packages/GLM/US8qj/src/glmfit.jl:242 [6] show(io::IOContext{IOBuffer}, obj::GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Poisson{Float64}, LogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}) @ GLM ~/.julia/packages/GLM/US8qj/src/linpred.jl:258 [7] _show_default(io::IOBuffer, x::Any) @ Base show.jl:536 [8] show_default(io::IOBuffer, x::GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Poisson{Float64}, LogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}) @ Base show.jl:519 [inlined] [9] show(io::IOBuffer, x::GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Poisson{Float64}, LogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}) @ Base show.jl:514 [inlined] [10] print(io::IOBuffer, x::GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Poisson{Float64}, LogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}) @ Base strings/io.jl:35 [11] print(::IOBuffer, ::GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Poisson{Float64}, LogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}, ::String) @ Base strings/io.jl:46 [12] println(io::IOBuffer, xs::GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Poisson{Float64}, LogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}) @ Base strings/io.jl:75 [inlined] [13] show(io::IOBuffer, tpm::InclusionRepetition{GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Binomial{Float64}, LogitLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}, GammaLassoPath{GeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Poisson{Float64}, LogLink}, NaiveCoordinateDescent{Float64, true, Matrix{Float64}, Lasso.RandomCoefficientIterator, Vector{Float64}}}, Float64}}) @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl:348 [14] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:12 [15] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [16] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:59 [inlined] ┌ Warning: failed to fit zero counts model, possibly not enough variation in I(y). countmap(Iy)=[0=>5899, 1=>267] └ @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl:135 ┌ Warning: X'=[5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 5.0 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0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) └ @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl:140 inrep degenerate cases: Error During Test at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:291 Got exception outside of a @test MethodError: no method matching reducedim1(::Matrix{Float64}, ::Adjoint{Float64, Matrix{Float64}}) The function `reducedim1` exists, but no method is defined for this combination of argument types. Closest candidates are: reducedim1(::Any) @ Base reducedim.jl:1229 Stacktrace: [1] centralize_sumabs2!(R::Matrix{Float64}, A::Adjoint{Float64, Matrix{Float64}}, means::Matrix{Float64}) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:282 [2] varm!(R::Matrix{Float64}, A::Adjoint{Float64, Matrix{Float64}}, m::Matrix{Float64}; corrected::Bool) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:309 [3] _varm(A::Adjoint{Float64, Matrix{Float64}}, m::Matrix{Float64}, corrected::Bool, region::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:341 [4] varm(A::Adjoint{Float64, Matrix{Float64}}, m::Matrix{Float64}; corrected::Bool, dims::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:339 [inlined] [5] _var(A::Adjoint{Float64, Matrix{Float64}}, corrected::Bool, mean::Nothing, dims::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:386 [inlined] [6] var(A::Adjoint{Float64, Matrix{Float64}}; corrected::Bool, mean::Nothing, dims::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:380 [inlined] [7] _std(A::Adjoint{Float64, Matrix{Float64}}, corrected::Bool, mean::Nothing, dims::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:469 [8] std(A::Adjoint{Float64, Matrix{Float64}}; corrected::Bool, mean::Nothing, dims::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:461 [inlined] [9] standardizeX(X::Adjoint{Float64, Matrix{Float64}}, standardize::Bool) @ Lasso ~/.julia/packages/Lasso/DdoId/src/Lasso.jl:363 [10] fit(::Type{GammaLassoPath}, X::Adjoint{Float64, Matrix{Float64}}, y::Vector{Float64}, d::Binomial{Float64}, l::LogitLink; γ::Float64, wts::Vector{Float64}, offset::Vector{Float64}, α::Float64, nλ::Int64, λminratio::Float64, λ::Nothing, standardize::Bool, intercept::Bool, algorithm::Core.TypeEgal{NaiveCoordinateDescent}, dofit::Bool, irls_tol::Float64, randomize::Bool, rng::Nothing, maxncoef::Int64, penalty_factor::Nothing, standardizeω::Bool, fitargs::@Kwargs{verbose::Bool}) @ Lasso ~/.julia/packages/Lasso/DdoId/src/gammalasso.jl:78 [11] (::HurdleDMR.var"#fitzero##0#fitzero##1"{GammaLassoPath, Float64, Adjoint{Float64, Matrix{Float64}}, Vector{Float64}, Binomial{Float64}, LogitLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{}})() @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl:132 [12] with_logstate(f::HurdleDMR.var"#fitzero##0#fitzero##1"{GammaLassoPath, Float64, Adjoint{Float64, Matrix{Float64}}, Vector{Float64}, Binomial{Float64}, LogitLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging logging/logging.jl:542 [13] with_logger(f::HurdleDMR.var"#fitzero##0#fitzero##1"{GammaLassoPath, Float64, Adjoint{Float64, Matrix{Float64}}, Vector{Float64}, Binomial{Float64}, LogitLink, Bool, Vector{Float64}, Vector{Float64}, Bool, Tuple{}}, logger::AbstractLogger) @ Base.CoreLogging logging/logging.jl:653 [inlined] [14] fitzero(::Core.TypeEgal{GammaLassoPath}, ::Adjoint{Float64, Matrix{Float64}}, ::Vector{Float64}, ::Binomial{Float64}, ::LogitLink, ::Bool, ::Vector{Float64}, ::Vector{Float64}, ::Bool, ::Bool) @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/hurdle.jl:129 [inlined] [15] fit(::Type{InclusionRepetition}, ::Core.TypeEgal{GammaLassoPath}, X::Adjoint{Float64, Matrix{Float64}}, y::Vector{Float64}, dzero::Binomial{Float64}, dpos::Poisson{Float64}, lzero::LogitLink, lpos::LogLink; Xpos::Nothing, dofit::Bool, wts::Vector{Float64}, offsetzero::Vector{Float64}, offsetpos::Vector{Float64}, offset::Vector{Float64}, verbose::Bool, showwarnings::Bool, fitargs::@Kwargs{}) @ HurdleDMR ~/.julia/packages/HurdleDMR/i6kx1/src/inrep.jl:83 [16] top-level scope @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:294 [17] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [18] macro expansion @ ~/.julia/packages/HurdleDMR/i6kx1/test/inrep.jl:295 [inlined] [ 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 [ 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 Error Total Time HurdleDMR | 1676 5 1681 12m16.7s PositivePoisson | 37 37 1m13.9s hurdle with Xpos == Xzero | 15 1 16 35.8s hurdle with Xpos ≠ Xzero | 21 21 26.8s hurdle with Xpos ≠ Xzero AND offset specified | 21 21 5.6s hurdle degenerate cases | 2 2 27.5s inrep with Xpos == Xzero | 15 1 16 9.4s inrep with Xpos ≠ Xzero | 21 21 2.7s inrep with Xpos ≠ Xzero AND offset specified | 21 21 1.6s inrep degenerate cases | 1 1 0.7s helpers | 87 87 26.9s logging | 2 2 1.3s dmr | 97 97 4m54.6s dmr degenerate cases | 19 19 13.4s hdmr | 1314 1314 3m07.1s mcdmr | 6 6 0.0s RNG of the outermost testset: Xoshiro(0xc24b4a7d178f7dc3, 0x5f5b7feeb34dc32d, 0xb0070bf2f272f373, 0x6ff3eedae720b68f, 0x602c8e043f9c8672) ERROR: LoadError: Some tests did not pass: 1676 passed, 0 failed, 5 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/HurdleDMR/i6kx1/test/runtests.jl:10 Testing failed after 633.48s 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:3283 [3] 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:587 [4] 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 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 999.4s: package tests unexpectedly errored