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Current time is 2020-10-26T09:26:18.835
Julia Version 1.6.0-DEV.1331
Commit bac321d949 (2020-10-25 22:53 UTC)
Platform Info:
OS: Linux (x86_64-pc-linux-gnu)
CPU: AMD EPYC 7502 32-Core Processor
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-11.0.0 (ORCJIT, znver2)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
JULIA_MAX_NUM_PRECOMPILE_FILES = 9223372036854775807
JULIA_PKG_SERVER =
Starting installation at 2020-10-26T09:26:20.557
Resolving package versions...
Installed IntelOpenMP_jll ────────────── v2018.0.3+0
Installed AbstractFFTs ───────────────── v0.5.0
Installed MKL_jll ────────────────────── v2020.2.254+0
Installed Mocking ────────────────────── v0.7.1
Installed FillArrays ─────────────────── v0.9.7
Installed FFTW ───────────────────────── v1.2.4
Installed TimeZones ──────────────────── v1.4.0
Installed Reexport ───────────────────── v0.2.0
Installed Libiconv_jll ───────────────── v1.16.0+7
Installed OpenSpecFun_jll ────────────── v0.5.3+4
Installed GLM ────────────────────────── v1.3.11
Installed HurdleDMR ──────────────────── v1.3.0
Installed Missings ───────────────────── v0.4.4
Installed OffsetArrays ───────────────── v1.3.1
Installed Intervals ──────────────────── v1.5.0
Installed Polynomials ────────────────── v1.1.10
Installed SpecialFunctions ───────────── v0.10.3
Installed MLBase ─────────────────────── v0.8.0
Installed Zlib_jll ───────────────────── v1.2.11+18
Installed PDMats ─────────────────────── v0.10.1
Installed Tables ─────────────────────── v0.2.11
Installed IterTools ──────────────────── v1.3.0
Installed ShiftedArrays ──────────────── v1.0.0
Installed JLLWrappers ────────────────── v1.1.3
Installed LambertW ───────────────────── v0.4.5
Installed TableTraits ────────────────── v1.0.0
Installed EzXML ──────────────────────── v1.1.0
Installed XML2_jll ───────────────────── v2.9.10+3
Installed SortingAlgorithms ──────────── v0.3.1
Installed StatsModels ────────────────── v0.6.15
Installed DataStructures ─────────────── v0.17.20
Installed Lasso ──────────────────────── v0.5.2
Installed StatsBase ──────────────────── v0.32.2
Installed FFTW_jll ───────────────────── v3.3.9+6
Installed QuadGK ─────────────────────── v2.4.1
Installed OrderedCollections ─────────── v1.3.1
Installed CompilerSupportLibraries_jll ─ v0.3.4+0
Installed RecipesBase ────────────────── v1.1.0
Installed LoggingExtras ──────────────── v0.3.0
Installed DataValueInterfaces ────────── v1.0.0
Installed ExprTools ──────────────────── v0.1.3
Installed Rmath_jll ──────────────────── v0.2.2+1
Installed StatsFuns ──────────────────── v0.9.5
Cloning [9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a] DataAPI from https://github.com/JuliaData/DataAPI.jl.git
[?25l Fetching: [> ] 0.0 %[2K[?25h Installed DataAPI ────────────────────── v1.3.0
Cloning [31c24e10-a181-5473-b8eb-7969acd0382f] Distributions from https://github.com/JuliaStats/Distributions.jl.git
[?25l Fetching: [> ] 0.0 %[2K[?25h Installed Distributions ──────────────── v0.23.12
Cloning [717857b8-e6f2-59f4-9121-6e50c889abd2] DSP from https://github.com/JuliaDSP/DSP.jl.git
[?25l Fetching: [> ] 0.0 %[2K[?25h Installed DSP ────────────────────────── v0.6.8
Cloning [82899510-4779-5014-852e-03e436cf321d] IteratorInterfaceExtensions from https://github.com/queryverse/IteratorInterfaceExtensions.jl.git
[?25l Fetching: [> ] 0.0 %[2K[?25h Installed IteratorInterfaceExtensions ── v1.0.0
Cloning [79098fc4-a85e-5d69-aa6a-4863f24498fa] Rmath from https://github.com/JuliaStats/Rmath.jl.git
[?25l Fetching: [> ] 0.0 %[2K[?25h Installed Rmath ──────────────────────── v0.6.1
Cloning [90137ffa-7385-5640-81b9-e52037218182] StaticArrays from https://github.com/JuliaArrays/StaticArrays.jl.git
[?25l Fetching: [> ] 0.0 %[2K[?25h Installed StaticArrays ───────────────── v0.12.4
Updating `~/.julia/environments/v1.6/Project.toml`
[f9e53bcf] + HurdleDMR v1.3.0
Updating `~/.julia/environments/v1.6/Manifest.toml`
[621f4979] + AbstractFFTs v0.5.0
[717857b8] + DSP v0.6.8
[9a962f9c] + DataAPI v1.3.0
[864edb3b] + DataStructures v0.17.20
[e2d170a0] + DataValueInterfaces v1.0.0
[31c24e10] + Distributions v0.23.12
[e2ba6199] + ExprTools v0.1.3
[8f5d6c58] + EzXML v1.1.0
[7a1cc6ca] + FFTW v1.2.4
[1a297f60] + FillArrays v0.9.7
[38e38edf] + GLM v1.3.11
[f9e53bcf] + HurdleDMR v1.3.0
[d8418881] + Intervals v1.5.0
[c8e1da08] + IterTools v1.3.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[692b3bcd] + JLLWrappers v1.1.3
[984bce1d] + LambertW v0.4.5
[b4fcebef] + Lasso v0.5.2
[e6f89c97] + LoggingExtras v0.3.0
[f0e99cf1] + MLBase v0.8.0
[e1d29d7a] + Missings v0.4.4
[78c3b35d] + Mocking v0.7.1
[6fe1bfb0] + OffsetArrays v1.3.1
[bac558e1] + OrderedCollections v1.3.1
[90014a1f] + PDMats v0.10.1
[f27b6e38] + Polynomials v1.1.10
[1fd47b50] + QuadGK v2.4.1
[3cdcf5f2] + RecipesBase v1.1.0
[189a3867] + Reexport v0.2.0
[79098fc4] + Rmath v0.6.1
[1277b4bf] + ShiftedArrays v1.0.0
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.10.3
[90137ffa] + StaticArrays v0.12.4
[2913bbd2] + StatsBase v0.32.2
[4c63d2b9] + StatsFuns v0.9.5
[3eaba693] + StatsModels v0.6.15
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v0.2.11
[f269a46b] + TimeZones v1.4.0
[e66e0078] + CompilerSupportLibraries_jll v0.3.4+0
[f5851436] + FFTW_jll v3.3.9+6
[1d5cc7b8] + IntelOpenMP_jll v2018.0.3+0
[94ce4f54] + Libiconv_jll v1.16.0+7
[856f044c] + MKL_jll v2020.2.254+0
[efe28fd5] + OpenSpecFun_jll v0.5.3+4
[f50d1b31] + Rmath_jll v0.2.2+1
[02c8fc9c] + XML2_jll v2.9.10+3
[83775a58] + Zlib_jll v1.2.11+18
[0dad84c5] + ArgTools
[56f22d72] + Artifacts
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8ba89e20] + Distributed
[f43a241f] + Downloads
[b77e0a4c] + InteractiveUtils
[b27032c2] + LibCURL
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[4607b0f0] + SuiteSparse
[fa267f1f] + TOML
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[deac9b47] + LibCURL_jll
[14a3606d] + MozillaCACerts_jll
Building TimeZones → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/2c48caca8f3912857973590a9757e1f86cbbff81/build.log`
Building FFTW ─────→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/8b7c16b56936047ca41bf25effa137ae0b381ae8/build.log`
Precompiling project... (tip: to disable auto-precompilation set ENV["JULIA_PKG_PRECOMPILE_AUTO"]=0)
[32m ✓ [39m[90mIteratorInterfaceExtensions[39m
[32m ✓ [39m[90mDataValueInterfaces[39m
[32m ✓ [39m[90mDataAPI[39m
[32m ✓ [39m[90mReexport[39m
[32m ✓ [39m[90mLoggingExtras[39m
[32m ✓ [39m[90mJLLWrappers[39m
[32m ✓ [39m[90mShiftedArrays[39m
[32m ✓ [39m[90mAbstractFFTs[39m
[32m ✓ [39m[90mTableTraits[39m
[32m ✓ [39m[90mOrderedCollections[39m
[32m ✓ [39m[90mPDMats[39m
[32m ✓ [39m[90mIterTools[39m
[32m ✓ [39m[90mOffsetArrays[39m
[32m ✓ [39m[90mLambertW[39m
[32m ✓ [39m[90mFillArrays[39m
[32m ✓ [39m[90mRmath_jll[39m
[32m ✓ [39m[90mIntelOpenMP_jll[39m
[32m ✓ [39m[90mMissings[39m
[32m ✓ [39m[90mRmath[39m
[32m ✓ [39m[90mZlib_jll[39m
[32m ✓ [39m[90mLibiconv_jll[39m
[32m ✓ [39m[90mTables[39m
[32m ✓ [39m[90mFFTW_jll[39m
[32m ✓ [39m[90mMKL_jll[39m
[32m ✓ [39m[90mCompilerSupportLibraries_jll[39m
[32m ✓ [39m[90mDataStructures[39m
[32m ✓ [39m[90mStaticArrays[39m
[32m ✓ [39m[90mOpenSpecFun_jll[39m
[32m ✓ [39m[90mXML2_jll[39m
[32m ✓ [39m[90mSortingAlgorithms[39m
[91m ✗ [39m[90mFFTW[39m
[32m ✓ [39m[90mQuadGK[39m
[32m ✓ [39m[90mEzXML[39m
[32m ✓ [39m[90mTimeZones[39m
[32m ✓ [39m[90mSpecialFunctions[39m
[32m ✓ [39m[90mIntervals[39m
[32m ✓ [39m[90mStatsBase[39m
[32m ✓ [39m[90mPolynomials[39m
[91m ✗ [39m[90mDSP[39m
[32m ✓ [39m[90mStatsFuns[39m
[32m ✓ [39m[90mMLBase[39m
[32m ✓ [39m[90mStatsModels[39m
[32m ✓ [39m[90mDistributions[39m
[32m ✓ [39m[90mGLM[39m
[91m ✗ [39m[90mLasso[39m
[91m ✗ [39mHurdleDMR
42 dependencies successfully precompiled, 4 errored (3 already precompiled)
Starting tests at 2020-10-26T09:44:38.202
Testing HurdleDMR
Status `/tmp/jl_3Dls3Z/Project.toml`
[336ed68f] CSV v0.5.23
[a93c6f00] DataFrames v0.20.0
[864edb3b] DataStructures v0.17.20
[31c24e10] Distributions v0.23.12
[38e38edf] GLM v1.3.11
[f9e53bcf] HurdleDMR v1.3.0
[984bce1d] LambertW v0.4.5
[b4fcebef] Lasso v0.5.2
[e6f89c97] LoggingExtras v0.3.0
[f0e99cf1] MLBase v0.8.0
[e1d29d7a] Missings v0.4.4
[2913bbd2] StatsBase v0.32.2
[3eaba693] StatsModels v0.6.15
[bd369af6] Tables v0.2.11
[8ba89e20] Distributed
[b77e0a4c] InteractiveUtils
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[9a3f8284] Random
[1a1011a3] SharedArrays
[2f01184e] SparseArrays
[8dfed614] Test
Status `/tmp/jl_3Dls3Z/Manifest.toml`
[621f4979] AbstractFFTs v0.5.0
[336ed68f] CSV v0.5.23
[324d7699] CategoricalArrays v0.7.7
[34da2185] Compat v3.22.0
[717857b8] DSP v0.6.8
[9a962f9c] DataAPI v1.3.0
[a93c6f00] DataFrames v0.20.0
[864edb3b] DataStructures v0.17.20
[e2d170a0] DataValueInterfaces v1.0.0
[31c24e10] Distributions v0.23.12
[e2ba6199] ExprTools v0.1.3
[8f5d6c58] EzXML v1.1.0
[7a1cc6ca] FFTW v1.2.4
[48062228] FilePathsBase v0.7.0
[1a297f60] FillArrays v0.9.7
[38e38edf] GLM v1.3.11
[f9e53bcf] HurdleDMR v1.3.0
[d8418881] Intervals v1.5.0
[41ab1584] InvertedIndices v1.0.0
[c8e1da08] IterTools v1.3.0
[82899510] IteratorInterfaceExtensions v1.0.0
[692b3bcd] JLLWrappers v1.1.3
[682c06a0] JSON v0.21.1
[984bce1d] LambertW v0.4.5
[b4fcebef] Lasso v0.5.2
[e6f89c97] LoggingExtras v0.3.0
[f0e99cf1] MLBase v0.8.0
[e1d29d7a] Missings v0.4.4
[78c3b35d] Mocking v0.7.1
[6fe1bfb0] OffsetArrays v1.3.1
[bac558e1] OrderedCollections v1.3.1
[90014a1f] PDMats v0.10.1
[69de0a69] Parsers v0.3.12
[f27b6e38] Polynomials v1.1.10
[2dfb63ee] PooledArrays v0.5.3
[1fd47b50] QuadGK v2.4.1
[3cdcf5f2] RecipesBase v1.1.0
[189a3867] Reexport v0.2.0
[79098fc4] Rmath v0.6.1
[1277b4bf] ShiftedArrays v1.0.0
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.10.3
[90137ffa] StaticArrays v0.12.4
[2913bbd2] StatsBase v0.32.2
[4c63d2b9] StatsFuns v0.9.5
[3eaba693] StatsModels v0.6.15
[3783bdb8] TableTraits v1.0.0
[bd369af6] Tables v0.2.11
[f269a46b] TimeZones v1.4.0
[ea10d353] WeakRefStrings v0.6.2
[e66e0078] CompilerSupportLibraries_jll v0.3.4+0
[f5851436] FFTW_jll v3.3.9+6
[1d5cc7b8] IntelOpenMP_jll v2018.0.3+0
[94ce4f54] Libiconv_jll v1.16.0+7
[856f044c] MKL_jll v2020.2.254+0
[efe28fd5] OpenSpecFun_jll v0.5.3+4
[f50d1b31] Rmath_jll v0.2.2+1
[02c8fc9c] XML2_jll v2.9.10+3
[83775a58] Zlib_jll v1.2.11+18
[0dad84c5] ArgTools
[56f22d72] Artifacts
[2a0f44e3] Base64
[ade2ca70] Dates
[8bb1440f] DelimitedFiles
[8ba89e20] Distributed
[f43a241f] Downloads
[9fa8497b] Future
[b77e0a4c] InteractiveUtils
[b27032c2] LibCURL
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[a63ad114] Mmap
[44cfe95a] Pkg
[de0858da] Printf
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA
[9e88b42a] Serialization
[1a1011a3] SharedArrays
[6462fe0b] Sockets
[2f01184e] SparseArrays
[10745b16] Statistics
[4607b0f0] SuiteSparse
[fa267f1f] TOML
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
[deac9b47] LibCURL_jll
[14a3606d] MozillaCACerts_jll
Testing Running tests...
[ Info: Starting 4 parallel workers for tests...
[ Info: 4 parallel workers started
PositivePoisson: Error During Test at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/positive_poisson.jl:1
Got exception outside of a @test
OverflowError: 22 is too large to look up in the table; consider using `factorial(big(22))` instead
Stacktrace:
[1] factorial_lookup
@ ./combinatorics.jl:19 [inlined]
[2] factorial
@ ./combinatorics.jl:27 [inlined]
[3] pdf(d::PositivePoisson, x::Int64)
@ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/positive_poisson.jl:71
[4] pdf
@ ~/.julia/packages/Distributions/HjzA0/src/univariates.jl:333 [inlined]
[5] logpdf
@ ~/.julia/packages/Distributions/HjzA0/src/univariates.jl:342 [inlined]
[6] loglik_obs(#unused#::PositivePoisson, y::Float64, μ::Float64, wt::Float64, ϕ::Int64)
@ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/positive_poisson.jl:143
[7] loglik
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/positive_poisson.jl:37 [inlined]
[8] _broadcast_getindex_evalf
@ ./broadcast.jl:648 [inlined]
[9] _broadcast_getindex
@ ./broadcast.jl:621 [inlined]
[10] getindex
@ ./broadcast.jl:575 [inlined]
[11] macro expansion
@ ./broadcast.jl:932 [inlined]
[12] macro expansion
@ ./simdloop.jl:77 [inlined]
[13] copyto!
@ ./broadcast.jl:931 [inlined]
[14] copyto!
@ ./broadcast.jl:886 [inlined]
[15] copy
@ ./broadcast.jl:862 [inlined]
[16] materialize(bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Nothing, var"#loglik#27"{Float64}, Tuple{Vector{Float64}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}}}})
@ Base.Broadcast ./broadcast.jl:837
[17] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/positive_poisson.jl:47 [inlined]
[18] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[19] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/positive_poisson.jl:2
[20] include(fname::String)
@ Base.MainInclude ./client.jl:444
[21] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/runtests.jl:12 [inlined]
[22] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[23] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/runtests.jl:12
[24] include(fname::String)
@ Base.MainInclude ./client.jl:444
[25] top-level scope
@ none:6
[26] eval(m::Module, e::Any)
@ Core ./boot.jl:360
[27] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:261
[28] _start()
@ Base ./client.jl:485
hurdle with Xpos == Xzero: Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:48
Expression: occursin("Hurdle regression", showstr)
Evaluated: occursin("Hurdle regression", "typename(Hurdle) regression\n\nPositive part coefficients (PositivePoisson with LogProductLogLink() link):\nGeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, PositivePoisson, LogProductLogLink}, GLM.DensePredChol{Float64, Cholesky{Float64, Matrix{Float64}}}}:\n\nCoefficients:\n───────────────────────────────────────────────────────────────────\n Coef. Std. Error z Pr(>|z|) Lower 95% Upper 95%\n───────────────────────────────────────────────────────────────────\nx1 0.671139 0.122451 5.48 <1e-07 0.431139 0.911139\nx2 -0.228583 0.0652139 -3.51 0.0005 -0.3564 -0.100766\nx3 0.096485 0.0728231 1.32 0.1852 -0.0462457 0.239216\nx4 -0.142187 0.0484524 -2.93 0.0033 -0.237152 -0.0472223\nx5 -0.0127266 0.0313033 -0.41 0.6843 -0.0740799 0.0486267\nx6 0.0187455 0.00228044 8.22 <1e-15 0.0142759 0.0232151\n───────────────────────────────────────────────────────────────────\n\nZero part coefficients (Binomial{Float64} with LogitLink() link):\nGeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Binomial{Float64}, LogitLink}, GLM.DensePredChol{Float64, Cholesky{Float64, Matrix{Float64}}}}:\n\nCoefficients:\n───────────────────────────────────────────────────────────────────\n Coef. Std. Error z Pr(>|z|) Lower 95% Upper 95%\n───────────────────────────────────────────────────────────────────\nx1 0.236796 0.295499 0.80 0.4229 -0.342371 0.815963\nx2 -0.251151 0.159094 -1.58 0.1144 -0.562969 0.0606672\nx3 0.326234 0.180805 1.80 0.0712 -0.0281381 0.680605\nx4 -0.285249 0.111123 -2.57 0.0103 -0.503046 -0.0674515\nx5 0.0222194 0.0795513 0.28 0.7800 -0.133698 0.178137\nx6 0.0801213 0.0130117 6.16 <1e-09 0.0546189 0.105624\n───────────────────────────────────────────────────────────────────\n\n")
Stacktrace:
[1] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:48 [inlined]
[2] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[3] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:39
hurdle with Xpos == Xzero: Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:88
Expression: occursin("Hurdle regression", showstr)
Evaluated: occursin("Hurdle regression", "typename(Hurdle) regression\n\nPositive part regularization path (PositivePoisson(λ=1.0) with LogProductLogLink() link):\nPositivePoisson GammaLassoPath (51) solutions for 6 predictors in 280 iterations):\n────────────────────────────────────\n λ pct_dev ncoefs\n────────────────────────────────────\n [1] 0.450305 1.24258e-9 1\n [2] 0.410301 0.0108304 1\n [3] 0.373851 0.0192856 1\n [4] 0.340639 0.0259393 1\n [5] 0.310378 0.0312114 1\n [6] 0.282805 0.0354134 1\n [7] 0.257681 0.0387795 1\n [8] 0.234789 0.0414876 1\n [9] 0.213931 0.0436745 1\n[10] 0.194926 0.0454462 1\n[11] 0.17761 0.0468855 1\n[12] 0.161831 0.0494852 2\n[13] 0.147455 0.0516661 2\n[14] 0.134355 0.0534681 2\n[15] 0.122419 0.0549582 2\n[16] 0.111544 0.0561912 2\n[17] 0.101635 0.057212 2\n[18] 0.0926057 0.0588253 3\n[19] 0.0843789 0.0604245 3\n[20] 0.0768829 0.0617551 3\n[21] 0.0700528 0.062862 3\n[22] 0.0638295 0.0637825 3\n[23] 0.0581591 0.0645481 3\n[24] 0.0529924 0.0651847 3\n[25] 0.0482847 0.0657141 3\n[26] 0.0439952 0.0663949 4\n[27] 0.0400868 0.0670034 4\n[28] 0.0365256 0.0675086 4\n[29] 0.0332808 0.0679284 4\n[30] 0.0303242 0.0682771 4\n[31] 0.0276303 0.0685666 4\n[32] 0.0251757 0.0688072 4\n[33] 0.0229391 0.0690068 4\n[34] 0.0209013 0.0691728 4\n[35] 0.0190445 0.0693105 4\n[36] 0.0173526 0.0694408 5\n[37] 0.0158111 0.069558 5\n[38] 0.0144065 0.0696551 5\n[39] 0.0131266 0.0697357 5\n[40] 0.0119605 0.0698028 5\n[41] 0.010898 0.0698583 5\n[42] 0.00992981 0.0699044 5\n[43] 0.00904767 0.0699427 5\n[44] 0.0082439 0.0699745 5\n[45] 0.00751154 0.0700009 5\n[46] 0.00684423 0.0700228 5\n[47] 0.00623621 0.070041 5\n[48] 0.0056822 0.0700561 5\n[49] 0.00517741 0.0700687 5\n[50] 0.00471746 0.0700791 5\n[51] 0.00429838 0.0700877 5\n────────────────────────────────────\nZero part regularization path (Binomial{Float64}(n=1, p=0.5) with LogitLink() link):\nBinomial GammaLassoPath (49) solutions for 6 predictors in 266 iterations):\n─────────────────────────────────────\n λ pct_dev ncoefs\n─────────────────────────────────────\n [1] 0.101577 4.32987e-15 0\n [2] 0.0925534 0.00696806 1\n [3] 0.0843312 0.0130414 1\n [4] 0.0768395 0.018352 1\n [5] 0.0700133 0.0230024 1\n [6] 0.0637935 0.0270748 1\n [7] 0.0581262 0.0306379 1\n [8] 0.0529625 0.0337503 1\n [9] 0.0482574 0.0364633 1\n[10] 0.0439704 0.0388223 1\n[11] 0.0400642 0.0408684 1\n[12] 0.036505 0.0426383 1\n[13] 0.033262 0.0441653 1\n[14] 0.0303071 0.0454791 1\n[15] 0.0276147 0.0466068 1\n[16] 0.0251615 0.0475723 1\n[17] 0.0229262 0.048397 1\n[18] 0.0208895 0.0494934 3\n[19] 0.0190337 0.0508753 3\n[20] 0.0173428 0.0520358 3\n[21] 0.0158021 0.0534522 4\n[22] 0.0143983 0.054667 4\n[23] 0.0131192 0.0556861 4\n[24] 0.0119537 0.056539 4\n[25] 0.0108918 0.0572532 4\n[26] 0.0099242 0.0578505 4\n[27] 0.00904256 0.0583501 4\n[28] 0.00823925 0.0587672 4\n[29] 0.00750729 0.0591167 4\n[30] 0.00684037 0.0594082 4\n[31] 0.00623269 0.0596514 4\n[32] 0.00567899 0.0598604 5\n[33] 0.00517449 0.0600404 5\n[34] 0.0047148 0.0601903 5\n[35] 0.00429595 0.0603158 5\n[36] 0.00391431 0.0604199 5\n[37] 0.00356657 0.0605067 5\n[38] 0.00324973 0.0605792 5\n[39] 0.00296103 0.0606393 5\n[40] 0.00269798 0.0606893 5\n[41] 0.0024583 0.060731 5\n[42] 0.00223991 0.0607657 5\n[43] 0.00204092 0.0607945 5\n[44] 0.00185961 0.0608185 5\n[45] 0.00169441 0.0608385 5\n[46] 0.00154388 0.0608551 5\n[47] 0.00140673 0.0608689 5\n[48] 0.00128176 0.0608803 5\n[49] 0.00116789 0.0608899 5\n─────────────────────────────────────\n")
Stacktrace:
[1] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:88 [inlined]
[2] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[3] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:39
hurdle degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/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:
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f05720f2723, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "failed to fit truncated counts model to positive subsample, possibly not enough variation in ypos. countmap(ypos)=OrderedCollections.OrderedDict(1.0 => 265, 2.0 => 2)", HurdleDMR, :hurdle, :HurdleDMR_3f0b480a, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/hurdle.jl", 180, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Stacktrace:
[1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure)
@ Test /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:89
[2] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:332 [inlined]
[3] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[4] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:331
hurdle degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:343
Expression: fit(Hurdle, GeneralizedLinearModel, [ones(size(X, 1)) X], ydeg; showwarnings = true)
Log Pattern: (:warn, r"failed to fit truncated counts model to positive")
Captured Logs:
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f057261a3c3, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "failed to fit truncated counts model to positive subsample, possibly not enough variation in ypos. countmap(ypos)=OrderedCollections.OrderedDict(2.0 => 1, 3.0 => 1)", HurdleDMR, :hurdle, :HurdleDMR_3f0b480a, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/hurdle.jl", 180, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Stacktrace:
[1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure)
@ Test /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:89
[2] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:343 [inlined]
[3] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[4] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:331
[ Info: Testing hurdle degenerate cases. The following warnings about step-halving are expected ...
1: λ=0.000386732571607375, pct_dev=6.491976604627858e-6
2: λ=0.00035237631582540674, pct_dev=0.004137275679515495
step-halving because obj=0.004873710484493199 > 0.0048737104844521545 + 5.348152476436496e-15 = length(scratchmu)*eps(objold)
3: λ=0.0003210721751172995, pct_dev=0.007781659027663257
4: λ=0.00029254900799187346, pct_dev=0.011000893812644796
5: λ=0.00026655976042072805, pct_dev=0.01384672457319358
6: λ=0.00024287932597443493, pct_dev=0.01636328834963452
step-halving because obj=0.004853629958394753 > 0.00485362995832963 + 5.348152476436496e-15 = length(scratchmu)*eps(objold)
7: λ=0.00022130259605833834, pct_dev=0.018588564316925682
step-halving because obj=0.004847225402105616 > 0.004847225402075316 + 5.348152476436496e-15 = length(scratchmu)*eps(objold)
8: λ=0.00020164268336002862, pct_dev=0.020555493976648687
step-halving because obj=0.004840589108480022 > 0.004840589108449965 + 5.348152476436496e-15 = length(scratchmu)*eps(objold)
9: λ=0.00018372930312084647, pct_dev=0.022292855685093316
10: λ=0.00016740729821076853, pct_dev=0.023825953055227722
11: λ=0.00015253529523157167, pct_dev=0.02517716069551157
12: λ=0.0001389844800080886, pct_dev=0.026366360317267468
13: λ=0.00012663748186144804, pct_dev=0.027411290020289636
14: λ=0.00011538735700040242, pct_dev=0.02832782749366669
15: λ=0.00010513666222536851, pct_dev=0.029130219588688777
step-halving because obj=0.0047950177502431605 > 0.004795017750074621 + 5.348152476436496e-15 = length(scratchmu)*eps(objold)
16: λ=9.579661092204997e-5, pct_dev=0.029831270237958174
step-halving because obj=0.004789253164598393 > 0.004789253164442045 + 5.348152476436496e-15 = length(scratchmu)*eps(objold)
17: λ=8.728630403425833e-5, pct_dev=0.030442496928184237
step-halving because obj=0.004783753703245748 > 0.004783753703178281 + 5.348152476436496e-15 = length(scratchmu)*eps(objold)
18: λ=7.953202935498933e-5, pct_dev=0.030974261196463515
19: λ=7.246662306655003e-5, pct_dev=0.031435879206021755
20: λ=6.60288879997001e-5, pct_dev=0.03183571788072681
21: λ=6.016306357304766e-5, pct_dev=0.03218127930818637
step-halving because obj=0.004764518539996998 > 0.004764518539672642 + 5.348152476436496e-15 = length(scratchmu)*eps(objold)
22: λ=5.481834282156947e-5, pct_dev=0.03247927557229435
23: λ=4.994843233098504e-5, pct_dev=0.03273569741126037
24: λ=4.5511151266348316e-5, pct_dev=0.03295587690875246
step-halving because obj=0.004752931599085589 > 0.00475293159876313 + 5.348152476436496e-15 = length(scratchmu)*eps(objold)
25: λ=4.1468066021834846e-5, pct_dev=0.033144545621176746
step-halving because obj=0.004749571406770409 > 0.004749571406369983 + 5.348152476436496e-15 = length(scratchmu)*eps(objold)
26: λ=3.778415732723409e-5, pct_dev=0.03330588958302205
27: λ=3.442751692778391e-5, pct_dev=0.033443599554707104
28: λ=3.136907121013224e-5, pct_dev=0.03356091938831385
29: λ=2.8582329380607118e-5, pct_dev=0.03366069162108365
30: λ=2.6043154014634736e-5, pct_dev=0.03374539711868052
31: λ=2.372955198991474e-5, pct_dev=0.033817196120928816
32: λ=2.1621483992516497e-5, pct_dev=0.033877963105122144
33: λ=1.9700690945928288e-5, pct_dev=0.03392931958095369
34: λ=1.795053585967147e-5, pct_dev=0.033972664521059515
35: λ=1.6355859727648175e-5, pct_dev=0.0340092017437984
36: λ=1.4902850228082263e-5, pct_dev=0.03403996415048871
37: λ=1.3578922087795775e-5, pct_dev=0.03406583601656832
38: λ=1.2372608074593485e-5, pct_dev=0.034087572372232255
step-halving because obj=0.0047230553668729195 > 0.004723055366334534 + 5.348152476436496e-15 = length(scratchmu)*eps(objold)
39: λ=1.1273459673583369e-5, pct_dev=0.034105816996643945
step-halving because obj=0.004721965550004314 > 0.004721965549936855 + 5.348152476436496e-15 = length(scratchmu)*eps(objold)
40: λ=1.0271956587139042e-5, pct_dev=0.0341211173866095
41: λ=9.359424274636258e-6, pct_dev=0.0341339379041421
42: λ=8.527958817731798e-6, pct_dev=0.03414467235331431
step-halving because obj=0.004719213180408082 > 0.0047192131803512295 + 5.348152476436496e-15 = length(scratchmu)*eps(objold)
Iteration: 1, deviance: 204.0380396102747, diff.dev.:284.05429274213293
Iteration: 2, deviance: 103.01893015593346, diff.dev.:101.01910945434123
Iteration: 3, deviance: 69.83490468993551, diff.dev.:33.18402546599795
Iteration: 4, deviance: 60.60747250525391, diff.dev.:9.227432184681604
Iteration: 5, deviance: 58.582063189105526, diff.dev.:2.0254093161483837
Iteration: 6, deviance: 58.153700985512415, diff.dev.:0.4283622035931103
Iteration: 7, deviance: 58.09051069391205, diff.dev.:0.06319029160036393
Iteration: 8, deviance: 58.0883485242151, diff.dev.:0.002162169696951821
Iteration: 9, deviance: 58.08834522211963, diff.dev.:3.302095471724442e-6
hurdle degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:378
Expression: fit(Hurdle, GammaLassoPath, X, y; showwarnings = true)
Log Pattern: (:warn, r"not enough variation in ypos")
Captured Logs:
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f05720f2723, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "failed to fit truncated counts model to positive subsample, possibly not enough variation in ypos. countmap(ypos)=OrderedCollections.OrderedDict(1.0 => 64, 2.0 => 1)", HurdleDMR, :hurdle, :HurdleDMR_3f0b480a, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/hurdle.jl", 180, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Stacktrace:
[1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure)
@ Test /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:89
[2] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:378 [inlined]
[3] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[4] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hurdle.jl:331
inrep with Xpos == Xzero: Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/inrep.jl:21
Expression: occursin("InclusionRepetition regression", showstr)
Evaluated: occursin("InclusionRepetition regression", "typename(InclusionRepetition) regression\n\nPositive part coefficients (Poisson{Float64} with LogLink() link):\nGeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Poisson{Float64}, LogLink}, GLM.DensePredChol{Float64, Cholesky{Float64, Matrix{Float64}}}}:\n\nCoefficients:\n───────────────────────────────────────────────────────────────────\n Coef. Std. Error z Pr(>|z|) Lower 95% Upper 95%\n───────────────────────────────────────────────────────────────────\nx1 0.245643 0.13474 1.82 0.0683 -0.018442 0.509729\nx2 -0.277031 0.0717387 -3.86 0.0001 -0.417636 -0.136426\nx3 0.116913 0.0801864 1.46 0.1448 -0.040249 0.274076\nx4 -0.172176 0.0532328 -3.23 0.0012 -0.27651 -0.0678417\nx5 -0.0153108 0.0344028 -0.45 0.6563 -0.0827391 0.0521175\nx6 0.0228528 0.00249747 9.15 <1e-19 0.0179578 0.0277478\n───────────────────────────────────────────────────────────────────\n\nZero part coefficients (Binomial{Float64} with LogitLink() link):\nGeneralizedLinearModel{GLM.GlmResp{Vector{Float64}, Binomial{Float64}, LogitLink}, GLM.DensePredChol{Float64, Cholesky{Float64, Matrix{Float64}}}}:\n\nCoefficients:\n───────────────────────────────────────────────────────────────────\n Coef. Std. Error z Pr(>|z|) Lower 95% Upper 95%\n───────────────────────────────────────────────────────────────────\nx1 0.236796 0.295499 0.80 0.4229 -0.342371 0.815963\nx2 -0.251151 0.159094 -1.58 0.1144 -0.562969 0.0606672\nx3 0.326234 0.180805 1.80 0.0712 -0.0281381 0.680605\nx4 -0.285249 0.111123 -2.57 0.0103 -0.503046 -0.0674515\nx5 0.0222194 0.0795513 0.28 0.7800 -0.133698 0.178137\nx6 0.0801213 0.0130117 6.16 <1e-09 0.0546189 0.105624\n───────────────────────────────────────────────────────────────────\n\n")
Stacktrace:
[1] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/inrep.jl:21 [inlined]
[2] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[3] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/inrep.jl:12
inrep with Xpos == Xzero: Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/inrep.jl:61
Expression: occursin("InclusionRepetition regression", showstr)
Evaluated: occursin("InclusionRepetition regression", "typename(InclusionRepetition) regression\n\nPositive part regularization path (Poisson{Float64}(λ=1.0) with LogLink() link):\nPoisson GammaLassoPath (51) solutions for 6 predictors in 281 iterations):\n────────────────────────────────────\n λ pct_dev ncoefs\n────────────────────────────────────\n [1] 0.450305 1.45336e-9 1\n [2] 0.410301 0.0112439 1\n [3] 0.373851 0.0200471 1\n [4] 0.340639 0.0269889 1\n [5] 0.310378 0.0324965 1\n [6] 0.282805 0.0368892 1\n [7] 0.257681 0.0404087 1\n [8] 0.234789 0.0432398 1\n [9] 0.213931 0.0455249 1\n[10] 0.194926 0.047375 1\n[11] 0.17761 0.0488769 1\n[12] 0.161831 0.0515822 2\n[13] 0.147455 0.053845 2\n[14] 0.134355 0.0557132 2\n[15] 0.122419 0.0572569 2\n[16] 0.111544 0.0585332 2\n[17] 0.101635 0.059589 2\n[18] 0.0926057 0.0612528 3\n[19] 0.0843789 0.0629076 3\n[20] 0.0768829 0.064284 3\n[21] 0.0700528 0.0654283 3\n[22] 0.0638295 0.0663796 3\n[23] 0.0581591 0.0671705 3\n[24] 0.0529924 0.0678279 3\n[25] 0.0482847 0.0683744 3\n[26] 0.0439952 0.0690765 4\n[27] 0.0400868 0.0697044 4\n[28] 0.0365256 0.0702257 4\n[29] 0.0332808 0.0706588 4\n[30] 0.0303242 0.0710183 4\n[31] 0.0276303 0.0713169 4\n[32] 0.0251757 0.0715649 4\n[33] 0.0229391 0.0717708 4\n[34] 0.0209013 0.0719418 4\n[35] 0.0190445 0.0720837 4\n[36] 0.0173526 0.0722178 5\n[37] 0.0158111 0.0723384 5\n[38] 0.0144065 0.0724384 5\n[39] 0.0131266 0.0725213 5\n[40] 0.0119605 0.0725903 5\n[41] 0.010898 0.0726474 5\n[42] 0.00992981 0.0726948 5\n[43] 0.00904767 0.0727342 5\n[44] 0.0082439 0.0727669 5\n[45] 0.00751154 0.0727941 5\n[46] 0.00684423 0.0728166 5\n[47] 0.00623621 0.0728353 5\n[48] 0.0056822 0.0728508 5\n[49] 0.00517741 0.0728637 5\n[50] 0.00471746 0.0728744 5\n[51] 0.00429838 0.0728833 5\n────────────────────────────────────\nZero part regularization path (Binomial{Float64}(n=1, p=0.5) with LogitLink() link):\nBinomial GammaLassoPath (49) solutions for 6 predictors in 266 iterations):\n─────────────────────────────────────\n λ pct_dev ncoefs\n─────────────────────────────────────\n [1] 0.101577 4.32987e-15 0\n [2] 0.0925534 0.00696806 1\n [3] 0.0843312 0.0130414 1\n [4] 0.0768395 0.018352 1\n [5] 0.0700133 0.0230024 1\n [6] 0.0637935 0.0270748 1\n [7] 0.0581262 0.0306379 1\n [8] 0.0529625 0.0337503 1\n [9] 0.0482574 0.0364633 1\n[10] 0.0439704 0.0388223 1\n[11] 0.0400642 0.0408684 1\n[12] 0.036505 0.0426383 1\n[13] 0.033262 0.0441653 1\n[14] 0.0303071 0.0454791 1\n[15] 0.0276147 0.0466068 1\n[16] 0.0251615 0.0475723 1\n[17] 0.0229262 0.048397 1\n[18] 0.0208895 0.0494934 3\n[19] 0.0190337 0.0508753 3\n[20] 0.0173428 0.0520358 3\n[21] 0.0158021 0.0534522 4\n[22] 0.0143983 0.054667 4\n[23] 0.0131192 0.0556861 4\n[24] 0.0119537 0.056539 4\n[25] 0.0108918 0.0572532 4\n[26] 0.0099242 0.0578505 4\n[27] 0.00904256 0.0583501 4\n[28] 0.00823925 0.0587672 4\n[29] 0.00750729 0.0591167 4\n[30] 0.00684037 0.0594082 4\n[31] 0.00623269 0.0596514 4\n[32] 0.00567899 0.0598604 5\n[33] 0.00517449 0.0600404 5\n[34] 0.0047148 0.0601903 5\n[35] 0.00429595 0.0603158 5\n[36] 0.00391431 0.0604199 5\n[37] 0.00356657 0.0605067 5\n[38] 0.00324973 0.0605792 5\n[39] 0.00296103 0.0606393 5\n[40] 0.00269798 0.0606893 5\n[41] 0.0024583 0.060731 5\n[42] 0.00223991 0.0607657 5\n[43] 0.00204092 0.0607945 5\n[44] 0.00185961 0.0608185 5\n[45] 0.00169441 0.0608385 5\n[46] 0.00154388 0.0608551 5\n[47] 0.00140673 0.0608689 5\n[48] 0.00128176 0.0608803 5\n[49] 0.00116789 0.0608899 5\n─────────────────────────────────────\n")
Stacktrace:
[1] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/inrep.jl:61 [inlined]
[2] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[3] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/inrep.jl:12
inrep degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/inrep.jl:305
Expression: fit(InclusionRepetition, GeneralizedLinearModel, [ones(size(X, 1)) X], ydeg; showwarnings = true)
Log Pattern: (:warn, r"failed to fit truncated counts model to positive")
Captured Logs:
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f0572132703, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "failed to fit truncated counts model to positive subsample, possibly not enough variation in ypos. countmap(ypos)=OrderedCollections.OrderedDict(1.0 => 1, 2.0 => 1)", HurdleDMR, :hurdle, :HurdleDMR_3f0b480a, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/hurdle.jl", 180, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Stacktrace:
[1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure)
@ Test /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:89
[2] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/inrep.jl:305 [inlined]
[3] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[4] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/inrep.jl:294
1: λ=0.00038674044876033174, pct_dev=5.408929673822449e-6
2: λ=0.00035238349319380514, pct_dev=0.004046376329978285
3: λ=0.0003210787148680711, pct_dev=0.007611478289555773
4: λ=0.0002925549667692108, pct_dev=0.010760649203050532
5: λ=0.0002665651898367098, pct_dev=0.013544519504385955
6: λ=0.00024288427305606497, pct_dev=0.016006274304332435
7: λ=0.0002213071036548711, pct_dev=0.01818307250563489
8: λ=0.00020164679051410886, pct_dev=0.02010714327092178
9: λ=0.000183733045406678, pct_dev=0.02180664182504133
10: λ=0.000167410708042241, pct_dev=0.023306323185635414
11: λ=0.00015253840214301398, pct_dev=0.024628076465672666
12: λ=0.0001389873109100814, pct_dev=0.02579135132999444
13: λ=0.0001266400612739101, pct_dev=0.026813500399619716
14: λ=0.0001153897072649705, pct_dev=0.027710055819832546
15: λ=0.00010513880369890995, pct_dev=0.028494954136865425
16: λ=9.579856215298414e-5, pct_dev=0.029180720603098842
17: λ=8.728808192321398e-5, pct_dev=0.0297786217165672
18: λ=7.953364930119035e-5, pct_dev=0.030298793003017743
19: λ=7.246809910119532e-5, pct_dev=0.030750347604051487
20: λ=6.60302329074955e-5, pct_dev=0.031141470061326393
21: λ=6.016428900294135e-5, pct_dev=0.0314794987187319
22: λ=5.481945938764883e-5, pct_dev=0.031770999359783225
23: λ=4.994944970441121e-5, pct_dev=0.03202183203722353
24: λ=4.5512078259123385e-5, pct_dev=0.032237212510321744
25: λ=4.146891066312668e-5, pct_dev=0.03242176927755969
26: λ=3.778492693292148e-5, pct_dev=0.03257959685858758
27: λ=3.442821816382316e-5, pct_dev=0.03271430573274792
28: λ=3.136971015029444e-5, pct_dev=0.032829068905250725
29: λ=2.8582911559086306e-5, pct_dev=0.03292666687394974
30: λ=2.604368447398234e-5, pct_dev=0.033009526681117785
31: λ=2.3730035324715953e-5, pct_dev=0.03307976125064971
32: λ=2.1621924389186096e-5, pct_dev=0.03313920409341786
33: λ=1.9701092218971507e-5, pct_dev=0.033189441530157016
34: λ=1.7950901484723522e-5, pct_dev=0.03323184210402219
35: λ=1.63561928715783e-5, pct_dev=0.033267583266010314
36: λ=1.4903153776423796e-5, pct_dev=0.03329767543883244
37: λ=1.3579198669739283e-5, pct_dev=0.03332298359031394
38: λ=1.2372860085759425e-5, pct_dev=0.03334424646583123
39: λ=1.127368929677188e-5, pct_dev=0.0333620936411545
40: λ=1.027216581123637e-5, pct_dev=0.033377060566930905
41: λ=9.359614911841426e-6, pct_dev=0.033389601777973676
42: λ=8.528132519253062e-6, pct_dev=0.03340010243927127
Iteration: 1, deviance: 202.88392988622178, diff.dev.:283.33062895363446
Iteration: 2, deviance: 103.34453979599364, diff.dev.:99.53939009022814
Iteration: 3, deviance: 70.86056777142211, diff.dev.:32.48397202457153
Iteration: 4, deviance: 61.88239574380505, diff.dev.:8.978172027617063
Iteration: 5, deviance: 59.91832501231312, diff.dev.:1.9640707314919297
Iteration: 6, deviance: 59.501911842558485, diff.dev.:0.4164131697546338
Iteration: 7, deviance: 59.44141711830484, diff.dev.:0.060494724253643994
Iteration: 8, deviance: 59.43942365499235, diff.dev.:0.00199346331248762
Iteration: 9, deviance: 59.439420838643315, diff.dev.:2.8163490384258694e-6
[ Info: Testing dmr degenerate cases. The 2 following warnings by workers are expected ...
┌ Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.
│ caller = macro expansion at logging.jl:340 [inlined]
└ @ Core ./logging.jl:340
┌ Warning: fitgl! failed on count dimension 2 with frequencies OrderedCollections.OrderedDict(0.0 => 200) and will return zero coefs (ErrorException("IRLS failed to converge in 30 iterations at λ = 4.3709033880452197e-7"))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/dmr.jl:412
┌ Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.
│ caller = macro expansion at logging.jl:340 [inlined]
└ @ Core ./logging.jl:340
┌ Warning: fitgl failed for countsj with frequencies OrderedCollections.OrderedDict(0.0 => 200) and will return missing path (ErrorException("IRLS failed to converge in 30 iterations at λ = 4.3709033880452197e-7"))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/dmr.jl:375
dmr degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/dmr.jl:258
Expression: dmr(covars, zcounts; parallel = false, testargs...)
Log Pattern: (:warn, r"failed on count dimension 2")
Captured Logs:
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f05721cbfa9, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "fitgl! failed on count dimension 2 with frequencies OrderedCollections.OrderedDict(0.0 => 200) and will return zero coefs (ErrorException(\"IRLS failed to converge in 30 iterations at λ = 4.3709033880452197e-7\"))", HurdleDMR, :dmr, :HurdleDMR_092e71d7, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/dmr.jl", 412, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Stacktrace:
[1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure)
@ Test /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:89
[2] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/dmr.jl:258 [inlined]
[3] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[4] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/dmr.jl:234
dmr degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/dmr.jl:262
Expression: dmrpaths(covars, zcounts; parallel = false, testargs...)
Log Pattern: (:warn, r"failed for countsj")
Captured Logs:
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f05724f37bc, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "fitgl failed for countsj with frequencies OrderedCollections.OrderedDict(0.0 => 200) and will return missing path (ErrorException(\"IRLS failed to converge in 30 iterations at λ = 4.3709033880452197e-7\"))", HurdleDMR, :dmr, :HurdleDMR_95ce04e7, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/dmr.jl", 375, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Stacktrace:
[1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure)
@ Test /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:89
[2] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/dmr.jl:262 [inlined]
[3] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[4] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/dmr.jl:234
[ Info: Testing hdmr degenerate cases. The 2 following warnings by workers are expected ...
┌ Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.
│ caller = macro expansion at logging.jl:340 [inlined]
└ @ Core ./logging.jl:340
┌ Warning: hurdle_regression! failed on count dimension 2 with frequencies OrderedCollections.OrderedDict(0.0 => 200) and will return zero coefs (ErrorException("y is all zeros! There is nothing to explain."))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:456
┌ Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.
│ caller = macro expansion at logging.jl:340 [inlined]
└ @ Core ./logging.jl:340
┌ Warning: fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(0.0 => 200) and will return missing path (ErrorException("y is all zeros! There is nothing to explain."))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:332
HDMR{InclusionRepetition} degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:291
Expression: fit(HDMRPaths{M}, covars, zcounts; parallel = false, testargs...)
Log Pattern: (:warn, rx)
Captured Logs:
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f057258ad0b, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(0.0 => 200) and will return missing path (ErrorException(\"y is all zeros! There is nothing to explain.\"))", HurdleDMR, :hdmr, :HurdleDMR_0606a6e7, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl", 332, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Stacktrace:
[1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure)
@ Test /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:89
[2] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:291 [inlined]
[3] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[4] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:247 [inlined]
[5] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1219 [inlined]
[6] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:13 [inlined]
[7] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[8] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:6
HDMR{InclusionRepetition} degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:303
Expression: fit(HDMR{M}, covars, zcounts; parallel = false, testargs...)
Log Pattern: (:warn, r"failed on count dimension 2")
Captured Logs:
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f05725856a8, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "hurdle_regression! failed on count dimension 2 with frequencies OrderedCollections.OrderedDict(0.0 => 200) and will return zero coefs (ErrorException(\"y is all zeros! There is nothing to explain.\"))", HurdleDMR, :hdmr, :HurdleDMR_ba51879f, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl", 456, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Stacktrace:
[1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure)
@ Test /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:89
[2] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:303 [inlined]
[3] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[4] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:247 [inlined]
[5] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1219 [inlined]
[6] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:13 [inlined]
[7] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[8] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:6
[ Info: Testing hdmr degenerate cases. The 12 following warnings by workers are expected ...
┌ Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.
│ caller = macro expansion at logging.jl:340 [inlined]
└ @ Core ./logging.jl:340
┌ Warning: hurdle_regression! failed on count dimension 1 with frequencies OrderedCollections.OrderedDict(1.0 => 35, 2.0 => 26, 3.0 => 20, 4.0 => 20, 5.0 => 16, 6.0 => 24, 7.0 => 18, 8.0 => 17, 9.0 => 13, 10.0 => 11) and will return zero coefs (LinearAlgebra.PosDefException(1))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:456
┌ Warning: hurdle_regression! failed on count dimension 2 with frequencies OrderedCollections.OrderedDict(1.0 => 42, 2.0 => 28, 3.0 => 19, 4.0 => 12, 5.0 => 21, 6.0 => 16, 7.0 => 20, 8.0 => 9, 9.0 => 18, 10.0 => 15) and will return zero coefs (LinearAlgebra.PosDefException(1))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:456
┌ Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.
│ caller = macro expansion at logging.jl:340 [inlined]
└ @ Core ./logging.jl:340
┌ Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.
│ caller = macro expansion at logging.jl:340 [inlined]
└ @ Core ./logging.jl:340
┌ Warning: hurdle_regression! failed on count dimension 3 with frequencies OrderedCollections.OrderedDict(1.0 => 71, 2.0 => 52, 3.0 => 19, 4.0 => 15, 5.0 => 9, 6.0 => 7, 7.0 => 4, 8.0 => 8, 9.0 => 7, 10.0 => 8) and will return zero coefs (LinearAlgebra.PosDefException(1))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:456
┌ Warning: hurdle_regression! failed on count dimension 4 with frequencies OrderedCollections.OrderedDict(1.0 => 11, 2.0 => 16, 3.0 => 34, 4.0 => 39, 5.0 => 36, 6.0 => 29, 7.0 => 16, 8.0 => 13, 9.0 => 6) and will return zero coefs (LinearAlgebra.PosDefException(1))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:456
┌ Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.
│ caller = macro expansion at logging.jl:340 [inlined]
└ @ Core ./logging.jl:340
┌ Warning: fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(1.0 => 11, 2.0 => 16, 3.0 => 34, 4.0 => 39, 5.0 => 36, 6.0 => 29, 7.0 => 16, 8.0 => 13, 9.0 => 6) and will return missing path (LinearAlgebra.PosDefException(1))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:332
┌ Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.
│ caller = macro expansion at logging.jl:340 [inlined]
└ @ Core ./logging.jl:340
┌ Warning: fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(1.0 => 71, 2.0 => 52, 3.0 => 19, 4.0 => 15, 5.0 => 9, 6.0 => 7, 7.0 => 4, 8.0 => 8, 9.0 => 7, 10.0 => 8) and will return missing path (LinearAlgebra.PosDefException(1))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:332
┌ Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.
│ caller = macro expansion at logging.jl:340 [inlined]
└ @ Core ./logging.jl:340
┌ Warning: fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(1.0 => 35, 2.0 => 26, 3.0 => 20, 4.0 => 20, 5.0 => 16, 6.0 => 24, 7.0 => 18, 8.0 => 17, 9.0 => 13, 10.0 => 11) and will return missing path (LinearAlgebra.PosDefException(1))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:332
┌ Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.
│ caller = macro expansion at logging.jl:340 [inlined]
└ @ Core ./logging.jl:340
┌ Warning: fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(1.0 => 42, 2.0 => 28, 3.0 => 19, 4.0 => 12, 5.0 => 21, 6.0 => 16, 7.0 => 20, 8.0 => 9, 9.0 => 18, 10.0 => 15) and will return missing path (LinearAlgebra.PosDefException(1))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:332
┌ Warning: fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(1.0 => 35, 2.0 => 26, 3.0 => 20, 4.0 => 20, 5.0 => 16, 6.0 => 24, 7.0 => 18, 8.0 => 17, 9.0 => 13, 10.0 => 11) and will return missing path (LinearAlgebra.PosDefException(1))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:332
┌ Warning: fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(1.0 => 42, 2.0 => 28, 3.0 => 19, 4.0 => 12, 5.0 => 21, 6.0 => 16, 7.0 => 20, 8.0 => 9, 9.0 => 18, 10.0 => 15) and will return missing path (LinearAlgebra.PosDefException(1))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:332
┌ Warning: fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(1.0 => 71, 2.0 => 52, 3.0 => 19, 4.0 => 15, 5.0 => 9, 6.0 => 7, 7.0 => 4, 8.0 => 8, 9.0 => 7, 10.0 => 8) and will return missing path (LinearAlgebra.PosDefException(1))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:332
┌ Warning: fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(1.0 => 11, 2.0 => 16, 3.0 => 34, 4.0 => 39, 5.0 => 36, 6.0 => 29, 7.0 => 16, 8.0 => 13, 9.0 => 6) and will return missing path (LinearAlgebra.PosDefException(1))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:332
HDMR{InclusionRepetition} degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:368
Expression: fit(HDMRPaths{M}, covars, zcounts; parallel = false, testargs...)
Log Pattern: warnings...
Captured Logs:
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f057259e35d, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(1.0 => 35, 2.0 => 26, 3.0 => 20, 4.0 => 20, 5.0 => 16, 6.0 => 24, 7.0 => 18, 8.0 => 17, 9.0 => 13, 10.0 => 11) and will return missing path (PosDefException(1))", HurdleDMR, :hdmr, :HurdleDMR_0606a6e7, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl", 332, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f057259e35d, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(1.0 => 42, 2.0 => 28, 3.0 => 19, 4.0 => 12, 5.0 => 21, 6.0 => 16, 7.0 => 20, 8.0 => 9, 9.0 => 18, 10.0 => 15) and will return missing path (PosDefException(1))", HurdleDMR, :hdmr, :HurdleDMR_0606a6e7, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl", 332, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f057259e35d, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(1.0 => 71, 2.0 => 52, 3.0 => 19, 4.0 => 15, 5.0 => 9, 6.0 => 7, 7.0 => 4, 8.0 => 8, 9.0 => 7, 10.0 => 8) and will return missing path (PosDefException(1))", HurdleDMR, :hdmr, :HurdleDMR_0606a6e7, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl", 332, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f057259e35d, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "fit(InclusionRepetition...) failed for countsj with frequencies OrderedCollections.OrderedDict(1.0 => 11, 2.0 => 16, 3.0 => 34, 4.0 => 39, 5.0 => 36, 6.0 => 29, 7.0 => 16, 8.0 => 13, 9.0 => 6) and will return missing path (PosDefException(1))", HurdleDMR, :hdmr, :HurdleDMR_0606a6e7, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl", 332, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Stacktrace:
[1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure)
@ Test /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:89
[2] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:368 [inlined]
[3] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[4] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:247 [inlined]
[5] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1219 [inlined]
[6] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:13 [inlined]
[7] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[8] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:6
[ Info: Testing hdmr degenerate cases. The 2 following warnings by workers are expected ...
┌ Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.
│ caller = macro expansion at logging.jl:340 [inlined]
└ @ Core ./logging.jl:340
┌ Warning: hurdle_regression! failed on count dimension 2 with frequencies OrderedCollections.OrderedDict(0.0 => 200) and will return zero coefs (ErrorException("y is all zeros! There is nothing to explain."))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:456
┌ Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.
│ caller = macro expansion at logging.jl:340 [inlined]
└ @ Core ./logging.jl:340
┌ Warning: fit(Hurdle...) failed for countsj with frequencies OrderedCollections.OrderedDict(0.0 => 200) and will return missing path (ErrorException("y is all zeros! There is nothing to explain."))
└ @ HurdleDMR ~/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl:332
HDMR{Hurdle} degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:291
Expression: fit(HDMRPaths{M}, covars, zcounts; parallel = false, testargs...)
Log Pattern: (:warn, rx)
Captured Logs:
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f05725d567b, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "fit(Hurdle...) failed for countsj with frequencies OrderedCollections.OrderedDict(0.0 => 200) and will return missing path (ErrorException(\"y is all zeros! There is nothing to explain.\"))", HurdleDMR, :hdmr, :HurdleDMR_0606a6e7, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl", 332, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Stacktrace:
[1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure)
@ Test /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:89
[2] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:291 [inlined]
[3] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[4] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:247 [inlined]
[5] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1219 [inlined]
[6] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:13 [inlined]
[7] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[8] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:6
HDMR{Hurdle} degenerate cases: Log Test Failed at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:303
Expression: fit(HDMR{M}, covars, zcounts; parallel = false, testargs...)
Log Pattern: (:warn, r"failed on count dimension 2")
Captured Logs:
Test.LogRecord(Warn, "`sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead.", Core, :depwarn, (Ptr{Nothing} @0x00007f05725d09d8, :sort), "./logging.jl", 340, Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:caller, :maxlog), Tuple{Base.StackTraces.StackFrame, Int64}}}(:caller => macro expansion at logging.jl:340 [inlined], :maxlog => 1))
Test.LogRecord(Warn, "hurdle_regression! failed on count dimension 2 with frequencies OrderedCollections.OrderedDict(0.0 => 200) and will return zero coefs (ErrorException(\"y is all zeros! There is nothing to explain.\"))", HurdleDMR, :hdmr, :HurdleDMR_ba51879f, "/home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/src/hdmr.jl", 456, Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{, Tuple{}}}())
Stacktrace:
[1] record(ts::Test.DefaultTestSet, t::Test.LogTestFailure)
@ Test /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/logging.jl:89
[2] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:303 [inlined]
[3] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[4] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:247 [inlined]
[5] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1219 [inlined]
[6] macro expansion
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:13 [inlined]
[7] macro expansion
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Test/src/Test.jl:1144 [inlined]
[8] top-level scope
@ ~/.julia/packages/HurdleDMR/9x3Z9/test/hdmr.jl:6
Test Summary: | Pass Fail Error Total
HurdleDMR | 1263 15 1 1279
PositivePoisson | 12 1 13
hurdle with Xpos == Xzero | 27 2 29
hurdle with Xpos ≠ Xzero | 21 21
hurdle with Xpos ≠ Xzero AND offset specified | 21 21
hurdle degenerate cases | 29 3 32
inrep with Xpos == Xzero | 27 2 29
inrep with Xpos ≠ Xzero | 21 21
inrep with Xpos ≠ Xzero AND offset specified | 21 21
inrep degenerate cases | 27 1 28
helpers | 87 87
logging | 2 2
dmr | 93 93
dmr degenerate cases | 15 2 17
hdmr | 854 5 859
InclusionRepetition | 428 3 431
2-part model: [h ~ x + z + cat + y, c ~ x + z + cat + y] | 97 97
2-part model: [h ~ x + z + cat + y, c ~ z + cat + y] | 97 97
2-part model: [h ~ x + z + cat, c ~ x + z + cat + y] | 94 94
2-part model: [h ~ x + z + cat, c ~ z + cat + y] | 94 94
HDMR{InclusionRepetition} degenerate cases | 46 3 49
Hurdle | 426 2 428
2-part model: [h ~ x + z + cat + y, c ~ x + z + cat + y] | 97 97
2-part model: [h ~ x + z + cat + y, c ~ z + cat + y] | 97 97
2-part model: [h ~ x + z + cat, c ~ x + z + cat + y] | 94 94
2-part model: [h ~ x + z + cat, c ~ z + cat + y] | 94 94
HDMR{Hurdle} degenerate cases | 44 2 46
mcdmr | 6 6
ERROR: LoadError: Some tests did not pass: 1263 passed, 15 failed, 1 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/HurdleDMR/9x3Z9/test/runtests.jl:10
ERROR: Package HurdleDMR errored during testing
Stacktrace:
[1] pkgerror(msg::String)
@ Pkg.Types /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:52
[2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing)
@ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1651
[3] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:334
[4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:321
[5] #test#62
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:71 [inlined]
[6] test
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:70 [inlined]
[7] #test#61
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:68 [inlined]
[8] test
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:68 [inlined]
[9] test(pkg::String; kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:67
[10] test(pkg::String)
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:67
[11] top-level scope
@ none:35