Package evaluation of GenomicOffsets on Julia 1.13.0-DEV.449 (8d6b63c3a6*) started at 2025-04-29T04:35:51.070 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.09s ################################################################################ # Installation # Installing GenomicOffsets... Resolving package versions... Installed Adapt ─────────────────── v4.3.0 Installed ScikitLearnBase ───────── v0.5.0 Installed oneTBB_jll ────────────── v2022.0.0+0 Installed IrrationalConstants ───── v0.2.4 Installed Rmath ─────────────────── v0.8.0 Installed HypergeometricFunctions ─ v0.3.28 Installed Preferences ───────────── v1.4.3 Installed OffsetArrays ──────────── v1.17.0 Installed PtrArrays ─────────────── v1.3.0 Installed Arpack_jll ────────────── v3.5.1+1 Installed StatsFuns ─────────────── v1.5.0 Installed PDMats ────────────────── v0.11.34 Installed FFTW ──────────────────── v1.8.1 Installed DataAPI ───────────────── v1.16.0 Installed FastGaussQuadrature ───── v1.0.2 Installed SpecialFunctions ──────── v2.5.1 Installed MKL_jll ───────────────── v2025.0.1+1 Installed JLLWrappers ───────────── v1.7.0 Installed AbstractFFTs ──────────── v1.5.0 Installed StaticArraysCore ──────── v1.4.3 Installed GSL_jll ───────────────── v2.8.1+0 Installed StaticArrays ──────────── v1.9.13 Installed DecisionTree ──────────── v0.12.4 Installed AbstractTrees ─────────── v0.4.5 Installed OrderedCollections ────── v1.8.0 Installed PrecompileTools ───────── v1.3.2 Installed Arpack ────────────────── v0.5.4 Installed Combinatorics ─────────── v1.0.2 Installed ChainRulesCore ────────── v1.25.1 Installed KernelDensity ─────────── v0.6.9 Installed DelimitedFiles ────────── v1.9.1 Installed GSL ───────────────────── v1.0.1 Installed MultipleTesting ───────── v0.6.0 Installed QuadGK ────────────────── v2.11.2 Installed Reexport ──────────────── v1.2.2 Installed FillArrays ────────────── v1.13.0 Installed Rmath_jll ─────────────── v0.5.1+0 Installed Statistics ────────────── v1.11.1 Installed Ratios ────────────────── v0.4.5 Installed AxisAlgorithms ────────── v1.1.0 Installed LogExpFunctions ───────── v0.3.29 Installed Requires ──────────────── v1.3.1 Installed IntelOpenMP_jll ───────── v2025.0.4+0 Installed Interpolations ────────── v0.15.1 Installed AliasTables ───────────── v1.1.3 Installed FFTW_jll ──────────────── v3.3.11+0 Installed GenomicOffsets ────────── v0.2.1 Installed DataStructures ────────── v0.18.22 Installed StatsAPI ──────────────── v1.7.0 Installed Compat ────────────────── v4.16.0 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed WoodburyMatrices ──────── v1.0.0 Installed Missings ──────────────── v1.2.0 Installed SortingAlgorithms ─────── v1.2.1 Installed MultivariateStats ─────── v0.10.3 Installed StatsBase ─────────────── v0.34.4 Installed Distributions ─────────── v0.25.119 Installed DocStringExtensions ───── v0.9.4 Installed RandomMatrices ────────── v0.5.5 Installing 6 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Installed artifact Arpack 147.2 KiB Installed artifact FFTW 2.2 MiB Installed artifact oneTBB 435.6 KiB Installed artifact GSL 4.6 MiB Updating `~/.julia/environments/v1.13/Project.toml` [496adb70] + GenomicOffsets v0.2.1 Updating `~/.julia/environments/v1.13/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [7d9fca2a] + Arpack v0.5.4 [13072b0f] + AxisAlgorithms v1.1.0 [d360d2e6] + ChainRulesCore v1.25.1 [861a8166] + Combinatorics v1.0.2 [34da2185] + Compat v4.16.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [7806a523] + DecisionTree v0.12.4 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.119 [ffbed154] + DocStringExtensions v0.9.4 [7a1cc6ca] + FFTW v1.8.1 [442a2c76] + FastGaussQuadrature v1.0.2 [1a297f60] + FillArrays v1.13.0 [92c85e6c] + GSL v1.0.1 [496adb70] + GenomicOffsets v0.2.1 [34004b35] + HypergeometricFunctions v0.3.28 [a98d9a8b] + Interpolations v0.15.1 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [5ab0869b] + KernelDensity v0.6.9 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [f8716d33] + MultipleTesting v0.6.0 [6f286f6a] + MultivariateStats v0.10.3 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.34 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [2576dda1] + RandomMatrices v0.5.5 [c84ed2f1] + Ratios v0.4.5 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [6e75b9c4] + ScikitLearnBase v0.5.0 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [4c63d2b9] + StatsFuns v1.5.0 [efce3f68] + WoodburyMatrices v1.0.0 ⌅ [68821587] + Arpack_jll v3.5.1+1 [f5851436] + FFTW_jll v3.3.11+0 [1b77fbbe] + GSL_jll v2.8.1+0 [1d5cc7b8] + IntelOpenMP_jll v2025.0.4+0 [856f044c] + MKL_jll v2025.0.1+1 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [1317d2d5] + oneTBB_jll v2022.0.0+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.12.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2024.12.31 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 12.56s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 5063.1 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 25 already precompiled. Precompiling package dependencies... Precompilation completed after 232.53s ################################################################################ # Testing # Testing GenomicOffsets Status `/tmp/jl_kQm5bD/Project.toml` [7806a523] DecisionTree v0.12.4 [31c24e10] Distributions v0.25.119 [496adb70] GenomicOffsets v0.2.1 [a98d9a8b] Interpolations v0.15.1 [5ab0869b] KernelDensity v0.6.9 [f8716d33] MultipleTesting v0.6.0 [6f286f6a] MultivariateStats v0.10.3 [2576dda1] RandomMatrices v0.5.5 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.4 [37e2e46d] LinearAlgebra v1.12.0 [9a3f8284] Random v1.11.0 [9e88b42a] Serialization v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_kQm5bD/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [7d9fca2a] Arpack v0.5.4 [13072b0f] AxisAlgorithms v1.1.0 [d360d2e6] ChainRulesCore v1.25.1 [861a8166] Combinatorics v1.0.2 [34da2185] Compat v4.16.0 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.22 [7806a523] DecisionTree v0.12.4 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.119 [ffbed154] DocStringExtensions v0.9.4 [7a1cc6ca] FFTW v1.8.1 [442a2c76] FastGaussQuadrature v1.0.2 [1a297f60] FillArrays v1.13.0 [92c85e6c] GSL v1.0.1 [496adb70] GenomicOffsets v0.2.1 [34004b35] HypergeometricFunctions v0.3.28 [a98d9a8b] Interpolations v0.15.1 [92d709cd] IrrationalConstants v0.2.4 [692b3bcd] JLLWrappers v1.7.0 [5ab0869b] KernelDensity v0.6.9 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [f8716d33] MultipleTesting v0.6.0 [6f286f6a] MultivariateStats v0.10.3 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.34 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [2576dda1] RandomMatrices v0.5.5 [c84ed2f1] Ratios v0.4.5 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.8.0 [6e75b9c4] ScikitLearnBase v0.5.0 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.1 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [4c63d2b9] StatsFuns v1.5.0 [efce3f68] WoodburyMatrices v1.0.0 ⌅ [68821587] Arpack_jll v3.5.1+1 [f5851436] FFTW_jll v3.3.11+0 [1b77fbbe] GSL_jll v2.8.1+0 [1d5cc7b8] IntelOpenMP_jll v2025.0.4+0 [856f044c] MKL_jll v2025.0.1+1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [1317d2d5] oneTBB_jll v2022.0.0+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.12.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2024.12.31 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.0.16+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... GenomicOffsets.jl: Error During Test at /home/pkgeval/.julia/packages/GenomicOffsets/1zG0f/test/runtests.jl:137 Got exception outside of a @test MethodError: no method matching mapreduce_impl(::Statistics.var"#centralizedabs2fun##0#centralizedabs2fun##1"{Float64}, ::typeof(+), ::Matrix{Float64}, ::Int64, ::Int64) The function `mapreduce_impl` exists, but no method is defined for this combination of argument types. Closest candidates are: mapreduce_impl(::Any, ::Any, ::Union{Base.AbstractBroadcasted, AbstractArray}, ::Any, ::Integer, !Matched::Integer, !Matched::Int64) @ Base reduce.jl:263 mapreduce_impl(::Any, ::Any, ::Union{Base.AbstractBroadcasted, AbstractArray}, ::Any, ::Integer, !Matched::Integer) @ Base reduce.jl:286 mapreduce_impl(::Any, !Matched::Union{typeof(max), typeof(min)}, ::Union{Base.AbstractBroadcasted, AbstractArray}, ::Any, ::Integer, !Matched::Integer) @ Base reduce.jl:649 ... Stacktrace: [1] centralize_sumabs2(A::Matrix{Float64}, m::Float64, ifirst::Int64, ilast::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:257 [2] centralize_sumabs2!(R::Matrix{Float64}, A::Matrix{Float64}, means::Matrix{Float64}) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:275 [3] varm!(R::Matrix{Float64}, A::Matrix{Float64}, m::Matrix{Float64}; corrected::Bool) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:309 [4] varm! @ ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:304 [inlined] [5] _varm @ ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:341 [inlined] [6] varm @ ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:339 [inlined] [7] _var @ ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:386 [inlined] [8] var @ ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:380 [inlined] [9] _std(A::Matrix{Float64}, corrected::Bool, mean::Nothing, dims::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:469 [10] std @ ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:461 [inlined] [11] fit(::Type{GeometricGO}, Y::Matrix{Int64}, X::Matrix{Float64}, K::Int64; center::Bool, scale::Bool, tw_threshold::Float64, λ::Float64) @ GenomicOffsets ~/.julia/packages/GenomicOffsets/1zG0f/src/Geometric_GO.jl:40 [12] fit @ ~/.julia/packages/GenomicOffsets/1zG0f/src/Geometric_GO.jl:29 [inlined] [13] #test_geometric##0 @ ./none:-1 [inlined] [14] iterate @ ./generator.jl:48 [inlined] [15] collect(itr::Base.Generator{Vector{Int64}, var"#test_geometric##0#test_geometric##1"{@NamedTuple{Y::Matrix{Int64}, X::Matrix{Float64}, Xpred::Matrix{Float64}}}}) @ Base ./array.jl:790 [16] test_geometric() @ Main ~/.julia/packages/GenomicOffsets/1zG0f/test/runtests.jl:62 [17] top-level scope @ ~/.julia/packages/GenomicOffsets/1zG0f/test/runtests.jl:138 [18] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1835 [inlined] [19] macro expansion @ ~/.julia/packages/GenomicOffsets/1zG0f/test/runtests.jl:142 [inlined] [20] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:304 [21] top-level scope @ none:6 [22] eval(m::Module, e::Any) @ Core ./boot.jl:489 [23] exec_options(opts::Base.JLOptions) @ Base ./client.jl:297 [24] _start() @ Base ./client.jl:563 Test Summary: | Pass Error Total Time GenomicOffsets.jl | 15 1 16 1m12.2s RNG of the outermost testset: Xoshiro(0x185f4b5b9bf9e373, 0xa6e4ddfa0d7c3b2a, 0xb7aff53702d387d6, 0x38bb6b2d1df34526, 0x309d9d98a4372029) ERROR: LoadError: Some tests did not pass: 15 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/GenomicOffsets/1zG0f/test/runtests.jl:137 Testing failed after 91.55s ERROR: LoadError: Package GenomicOffsets errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/Operations.jl:2414 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2269 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:486 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:303 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:331 [12] _start() @ Base ./client.jl:563 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 391.8s: package tests unexpectedly errored