Package evaluation to test FlxQTL on Julia 1.14.0-DEV.2291 (26145852c4*) started at 2026-06-04T18:18:07.299


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...
  Activating project at `~/.julia/environments/v1.14`

Set-up completed after 16.04s


################################################################################
# Installation
#

Installing FlxQTL...
   Resolving package versions...
    Updating `~/.julia/environments/v1.14/Project.toml`
  [ede81e08] + FlxQTL v4.0.2
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [66dad0bd] + AliasTables v1.1.3
  [9a962f9c] + DataAPI v1.16.0
  [864edb3b] + DataStructures v0.19.5
  [8bb1440f] + DelimitedFiles v1.9.1
  [31c24e10] + Distributions v0.25.126
  [ffbed154] + DocStringExtensions v0.9.5
  [1a297f60] + FillArrays v1.16.0
  [ede81e08] + FlxQTL v4.0.2
  [34004b35] + HypergeometricFunctions v0.3.28
  [92d709cd] + IrrationalConstants v0.2.6
  [692b3bcd] + JLLWrappers v1.8.0
⌅ [2ab3a3ac] + LogExpFunctions v0.3.29
  [30fc2ffe] + LossFunctions v1.2.0
  [e1d29d7a] + Missings v1.2.0
⌅ [bac558e1] + OrderedCollections v1.8.2
  [90014a1f] + PDMats v0.11.37
  [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
  [a2af1166] + SortingAlgorithms v1.2.2
  [276daf66] + SpecialFunctions v2.8.0
  [90137ffa] + StaticArrays v1.9.18
  [1e83bf80] + StaticArraysCore v1.4.4
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.8.0
  [2913bbd2] + StatsBase v0.34.11
  [4c63d2b9] + StatsFuns v2.0.1
  [efe28fd5] + OpenSpecFun_jll v0.5.6+0
  [f50d1b31] + Rmath_jll v0.5.1+0
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [8ba89e20] + Distributed v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.14.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v1.13.0
  [9e88b42a] + Serialization 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
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.5.2+0
  [4536629a] + OpenBLAS_jll v0.3.33+0
  [05823500] + OpenLibm_jll v0.8.7+0
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [8e850b90] + libblastrampoline_jll v5.15.0+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

Installation completed after 5.45s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...
Precompiling project...
   1.6 s  ✓ LossFunctions
  12.0 s  ✓ FlxQTL
  2 dependencies successfully precompiled in 15 seconds. 56 already precompiled.

Precompilation completed after 42.92s


################################################################################
# Testing
#

     Testing FlxQTL
      Status `/tmp/jl_QmNDkM/Project.toml`
  [8bb1440f] DelimitedFiles v1.9.1
  [31c24e10] Distributions v0.25.126
  [ede81e08] FlxQTL v4.0.2
  [30fc2ffe] LossFunctions v1.2.0
  [90137ffa] StaticArrays v1.9.18
  [10745b16] Statistics v1.11.1
  [2913bbd2] StatsBase v0.34.11
  [8ba89e20] Distributed v1.11.0
  [37e2e46d] LinearAlgebra v1.14.0
  [9a3f8284] Random v1.11.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_QmNDkM/Manifest.toml`
  [66dad0bd] AliasTables v1.1.3
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.19.5
  [8bb1440f] DelimitedFiles v1.9.1
  [31c24e10] Distributions v0.25.126
  [ffbed154] DocStringExtensions v0.9.5
  [1a297f60] FillArrays v1.16.0
  [ede81e08] FlxQTL v4.0.2
  [34004b35] HypergeometricFunctions v0.3.28
  [92d709cd] IrrationalConstants v0.2.6
  [692b3bcd] JLLWrappers v1.8.0
⌅ [2ab3a3ac] LogExpFunctions v0.3.29
  [30fc2ffe] LossFunctions v1.2.0
  [e1d29d7a] Missings v1.2.0
⌅ [bac558e1] OrderedCollections v1.8.2
  [90014a1f] PDMats v0.11.37
  [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
  [a2af1166] SortingAlgorithms v1.2.2
  [276daf66] SpecialFunctions v2.8.0
  [90137ffa] StaticArrays v1.9.18
  [1e83bf80] StaticArraysCore v1.4.4
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.8.0
  [2913bbd2] StatsBase v0.34.11
  [4c63d2b9] StatsFuns v2.0.1
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [f50d1b31] Rmath_jll v0.5.1+0
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [8ba89e20] Distributed v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0
  [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
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v1.13.0
  [9e88b42a] Serialization 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
  [8dfed614] Test v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.5.2+0
  [4536629a] OpenBLAS_jll v0.3.33+0
  [05823500] OpenLibm_jll v0.8.7+0
  [bea87d4a] SuiteSparse_jll v7.10.1+0
  [8e850b90] libblastrampoline_jll v5.15.0+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
rand(Random.Xoshiro(seed + myid())) = 0.02903627120676744
      From worker 2:	rand(Random.Xoshiro(seed + myid())) = 0.2293019828841396
      From worker 5:	rand(Random.Xoshiro(seed + myid())) = 0.5261301753598052
      From worker 3:	rand(Random.Xoshiro(seed + myid())) = 0.6140724580776808
      From worker 4:	rand(Random.Xoshiro(seed + myid())) = 0.8943305188090829
Positive definiteness dropping chromosome 1 is true.
Positive definiteness dropping chromosome 2 is true.
Test Passed
Test Passed
Kinship dropping chromosome 1 is corrected to be positive definite:true
Kinship dropping chromosome 2 is corrected to be positive definite:true
Test Passed
Test Passed
Kinship dropping chromosome 1 is corrected to be positive definite:true
Kinship dropping chromosome 2 is corrected to be positive definite:true
Test Passed
Test Passed
Test PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedKinship dropping chromosome 1 is corrected to be positive definite:false
Kinship dropping chromosome 2 is corrected to be positive definite:false

FlxQTL.jl: Error During Test at /home/pkgeval/.julia/packages/FlxQTL/sdovl/test/runtests.jl:5
  Got exception outside of a @test
  LoadError: ArgumentError: Cannot set a non-diagonal index in a symmetric matrix
  Stacktrace:
    [1] setindex!(A::Symmetric{Float64, Matrix{Float64}}, v::Float64, i::Int64, j::Int64)
      @ LinearAlgebra /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/symmetric.jl:313 [inlined]
    [2] _setindex!(::IndexCartesian, ::Symmetric{Float64, Matrix{Float64}}, ::Float64, ::Int64, ::Int64)
      @ Base abstractarray.jl:1488 [inlined]
    [3] setindex!(A::Symmetric{Float64, Matrix{Float64}}, v::Float64, I::CartesianIndex{2})
      @ Base abstractarray.jl:1458 [inlined]
    [4] lmul!(D::Diagonal{Float64, Vector{Float64}}, B::Symmetric{Float64, Matrix{Float64}})
      @ LinearAlgebra /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/diagonal.jl:417
    [5] cmStep!(Bnew::Matrix{Float64}, dev::Matrix{Float64}, Vg::Vector{Float64}, Ve::Array{Float64, 3}, Y::Matrix{Float64}, X::Matrix{Float64}, symXs::Matrix{Float64}, Ghat::Matrix{Float64}, Θ::Vector{Matrix{Float64}}, λg::Vector{Float64}, λc::Vector{Float64}, m::Int64)
      @ FlxQTL.EcmNestrv ~/.julia/packages/FlxQTL/sdovl/src/EcmNestrv.jl:250
    [6] fullECM(Vg::Vector{Float64}, Ve::Array{Float64, 3}, B_new::Matrix{Float64}, dev::Matrix{Float64}, Ghat::Matrix{Float64}, Θ::Vector{Matrix{Float64}}, Y::Matrix{Float64}, X::Matrix{Float64}, symXs::Matrix{Float64}, B_cur::Matrix{Float64}, τ2_cur::Float64, Σ_cur::Matrix{Float64}, λg::Vector{Float64}, λc::Vector{Float64}, m::Int64)
      @ FlxQTL.EcmNestrv ~/.julia/packages/FlxQTL/sdovl/src/EcmNestrv.jl:443
    [7] ecmLMM(Y::Matrix{Float64}, X::Matrix{Float64}, B0::Matrix{Float64}, τ2_0::Float64, Σ::Matrix{Float64}, λg::Vector{Float64}, λc::Vector{Float64}; tol::Float64)
      @ FlxQTL.EcmNestrv ~/.julia/packages/FlxQTL/sdovl/src/EcmNestrv.jl:431
    [8] nulScan(init::FlxQTL.flxMLMM.InitKc, kmin::Int64, λg::Vector{Float64}, λc::Vector{Float64}, Y1::Matrix{Float64}, Xnul_t::Matrix{Float64}, Σt::Matrix{Float64}, H0_up::Bool; ρ::Float64, itol::Float64, tol::Float64)
      @ FlxQTL.flxMLMM ~/.julia/packages/FlxQTL/sdovl/src/transformation.jl:267 [inlined]
    [9] geneScan1(cross::Int64, Tg::Matrix{Float64}, Λg::Vector{Float64}, Y::Matrix{Float64}, XX::Markers, LOCO::Bool; H0_up::Bool, Xnul::Matrix{Float64}, LogP::Bool, itol::Float64, tol0::Float64, tol::Float64, ρ::Float64)
      @ FlxQTL.flxMLMM ~/.julia/packages/FlxQTL/sdovl/src/geneScan1D.jl:296
   [10] gene1Scan(cross::Int64, Tg::Matrix{Float64}, Λg::Vector{Float64}, Y::Matrix{Float64}, XX::Markers, LOCO::Bool; penalize::Bool, m::Int64, Z::Matrix{Float64}, H0_up::Bool, Xnul::Matrix{Float64}, df_prior::Int64, Prior::Matrix{Float64}, LogP::Bool, itol::Float64, tol0::Float64, tol::Float64, ρ::Float64)
      @ FlxQTL.flxMLMM ~/.julia/packages/FlxQTL/sdovl/src/geneScan1.jl:319
   [11] top-level scope
      @ ~/.julia/packages/FlxQTL/sdovl/test/scan4cross.jl:92
   [12] include(mapexpr::Function, mod::Module, _path::String)
      @ Base Base.jl:327
   [13] top-level scope
      @ ~/.julia/packages/FlxQTL/sdovl/test/testall.jl:7
   [14] include(mapexpr::Function, mod::Module, _path::String)
      @ Base Base.jl:327
   [15] top-level scope
      @ ~/.julia/packages/FlxQTL/sdovl/test/runtests.jl:7
   [16] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined]
   [17] macro expansion
      @ ~/.julia/packages/FlxQTL/sdovl/test/runtests.jl:7 [inlined]
   [18] include(mapexpr::Function, mod::Module, _path::String)
      @ Base Base.jl:327
   [19] top-level scope
      @ none:6
   [20] eval(m::Module, e::Any)
      @ Core boot.jl:521
   [21] exec_options(opts::Base.JLOptions)
      @ Base client.jl:321
   [22] _start()
      @ Base client.jl:596
  in expression starting at /home/pkgeval/.julia/packages/FlxQTL/sdovl/test/scan4cross.jl:92
  in expression starting at /home/pkgeval/.julia/packages/FlxQTL/sdovl/test/testall.jl:7
Test Summary: | Pass  Error  Total     Time
FlxQTL.jl     |  133      1    134  4m53.9s
RNG of the outermost testset: Random.Xoshiro(0x5e5a7fd611d9cd74, 0x6252beea4b24f2f6, 0x408d6188d8861592, 0x6f4f5ec458194bb0, 0xd3413b9f96982400)
ERROR: LoadError: Some tests did not pass: 133 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/FlxQTL/sdovl/test/runtests.jl:5

Testing failed after 242.82s

ERROR: LoadError: Package FlxQTL 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:3247
  [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
  [8] include(mod::Module, _path::String)
    @ Base Base.jl:326
  [9] exec_options(opts::Base.JLOptions)
    @ Base client.jl:355
 [10] _start()
    @ Base client.jl:596
in expression starting at /PkgEval.jl/scripts/evaluate.jl:214

PkgEval failed after 404.21s: package tests unexpectedly errored