Package evaluation to test FlxQTL on Julia 1.14.0-DEV.30 (073666df8b*) started at 2025-11-04T17:13:42.429


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 10.89s


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

Installing FlxQTL...
   Resolving package versions...
    Updating `~/.julia/environments/v1.14/Project.toml`
  [ede81e08] + FlxQTL v3.0.1
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [66dad0bd] + AliasTables v1.1.3
  [9a962f9c] + DataAPI v1.16.0
  [864edb3b] + DataStructures v0.19.2
  [8bb1440f] + DelimitedFiles v1.9.1
  [31c24e10] + Distributions v0.25.122
  [ffbed154] + DocStringExtensions v0.9.5
  [1a297f60] + FillArrays v1.14.0
  [ede81e08] + FlxQTL v3.0.1
  [34004b35] + HypergeometricFunctions v0.3.28
  [92d709cd] + IrrationalConstants v0.2.6
  [692b3bcd] + JLLWrappers v1.7.1
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [30fc2ffe] + LossFunctions v1.1.1
  [e1d29d7a] + Missings v1.2.0
  [bac558e1] + OrderedCollections v1.8.1
  [90014a1f] + PDMats v0.11.36
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [43287f4e] + PtrArrays v1.3.0
  [1fd47b50] + QuadGK v2.11.2
  [189a3867] + Reexport v1.2.2
  [79098fc4] + Rmath v0.9.0
  [a2af1166] + SortingAlgorithms v1.2.2
  [276daf66] + SpecialFunctions v2.6.1
  [90137ffa] + StaticArrays v1.9.15
  [1e83bf80] + StaticArraysCore v1.4.4
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.1
  [2913bbd2] + StatsBase v0.34.7
  [4c63d2b9] + StatsFuns v1.5.2
  [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 v1.12.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.13.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v1.0.0
  [9e88b42a] + Serialization v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [2f01184e] + SparseArrays v1.13.0
  [f489334b] + StyledStrings v1.11.0
  [4607b0f0] + SuiteSparse
  [fa267f1f] + TOML v1.0.3
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [05823500] + OpenLibm_jll v0.8.7+0
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [8e850b90] + libblastrampoline_jll v5.15.0+0

Installation completed after 5.7s


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

Precompiling PkgEval dependencies...

┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled
│   exception =
│    UndefVarError: `project_rel_path` not defined in `TestEnv`
│    Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value.
│    Stacktrace:
│     [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec)
│       @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:75
│     [2] test_dir_has_project_file
│       @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined]
│     [3] maybe_gen_project_override!
│       @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined]
│     [4] activate(pkg::String; allow_reresolve::Bool)
│       @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12
│     [5] activate(pkg::String)
│       @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:9
│     [6] top-level scope
│       @ /PkgEval.jl/scripts/precompile.jl:24
│     [7] include(mod::Module, _path::String)
│       @ Base ./Base.jl:309
│     [8] exec_options(opts::Base.JLOptions)
│       @ Base ./client.jl:344
│     [9] _start()
│       @ Base ./client.jl:577
└ @ Main /PkgEval.jl/scripts/precompile.jl:26
Precompiling package dependencies...
Precompiling packages...
   1979.1 ms  ✓ LossFunctions
   5340.9 ms  ✓ StatsBase
   6185.1 ms  ✓ SpecialFunctions
   2376.5 ms  ✓ PDMats → StatsBaseExt
   2996.9 ms  ✓ HypergeometricFunctions
   3462.5 ms  ✓ StatsFuns
  11809.0 ms  ✓ Distributions
   6117.2 ms  ✓ FlxQTL
  8 dependencies successfully precompiled in 42 seconds. 45 already precompiled.

Precompilation completed after 57.53s


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

     Testing FlxQTL
      Status `/tmp/jl_AtlUeC/Project.toml`
  [8bb1440f] DelimitedFiles v1.9.1
  [31c24e10] Distributions v0.25.122
  [ede81e08] FlxQTL v3.0.1
  [30fc2ffe] LossFunctions v1.1.1
  [90137ffa] StaticArrays v1.9.15
  [10745b16] Statistics v1.11.1
  [2913bbd2] StatsBase v0.34.7
  [8ba89e20] Distributed v1.11.0
  [37e2e46d] LinearAlgebra v1.13.0
  [9a3f8284] Random v1.11.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_AtlUeC/Manifest.toml`
  [66dad0bd] AliasTables v1.1.3
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.19.2
  [8bb1440f] DelimitedFiles v1.9.1
  [31c24e10] Distributions v0.25.122
  [ffbed154] DocStringExtensions v0.9.5
  [1a297f60] FillArrays v1.14.0
  [ede81e08] FlxQTL v3.0.1
  [34004b35] HypergeometricFunctions v0.3.28
  [92d709cd] IrrationalConstants v0.2.6
  [692b3bcd] JLLWrappers v1.7.1
  [2ab3a3ac] LogExpFunctions v0.3.29
  [30fc2ffe] LossFunctions v1.1.1
  [e1d29d7a] Missings v1.2.0
  [bac558e1] OrderedCollections v1.8.1
  [90014a1f] PDMats v0.11.36
  [aea7be01] PrecompileTools v1.3.3
  [21216c6a] Preferences v1.5.0
  [43287f4e] PtrArrays v1.3.0
  [1fd47b50] QuadGK v2.11.2
  [189a3867] Reexport v1.2.2
  [79098fc4] Rmath v0.9.0
  [a2af1166] SortingAlgorithms v1.2.2
  [276daf66] SpecialFunctions v2.6.1
  [90137ffa] StaticArrays v1.9.15
  [1e83bf80] StaticArraysCore v1.4.4
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.1
  [2913bbd2] StatsBase v0.34.7
  [4c63d2b9] StatsFuns v1.5.2
  [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 v1.12.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.13.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v1.0.0
  [9e88b42a] Serialization v1.11.0
  [6462fe0b] Sockets v1.11.0
  [2f01184e] SparseArrays v1.13.0
  [f489334b] StyledStrings v1.11.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [8dfed614] Test v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.3.0+1
  [4536629a] OpenBLAS_jll v0.3.29+0
  [05823500] OpenLibm_jll v0.8.7+0
  [bea87d4a] SuiteSparse_jll v7.10.1+0
  [8e850b90] libblastrampoline_jll v5.15.0+0
     Testing Running tests...
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:isposdef(K_loco[:,:,l])
Kinship dropping chromosome 2 is corrected to be positive definite:isposdef(K_loco[:,:,l])
Test Passed
Test Passed
Kinship dropping chromosome 1 is corrected to be positive definite:isposdef(K_loco[:,:,l])
Kinship dropping chromosome 2 is corrected to be positive definite:isposdef(K_loco[:,:,l])
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
Kinship dropping chromosome 2 is corrected to be positive definite
  0.096072 seconds (366.07 k allocations: 33.606 MiB)
  0.002308 seconds (7.56 k allocations: 667.641 KiB)
  0.099727 seconds (366.07 k allocations: 33.606 MiB)
  0.001845 seconds (7.30 k allocations: 642.328 KiB)
  0.429591 seconds (29.81 k allocations: 2.754 MiB, 98.24% gc time)
  0.031661 seconds (172.81 k allocations: 14.746 MiB)
  0.006196 seconds (29.81 k allocations: 2.754 MiB)
  0.045818 seconds (243.07 k allocations: 20.747 MiB)
  0.005978 seconds (29.81 k allocations: 2.754 MiB)
  0.023735 seconds (121.17 k allocations: 10.375 MiB)
  0.005864 seconds (29.81 k allocations: 2.754 MiB)
  0.038975 seconds (116.08 k allocations: 9.936 MiB, 45.23% gc time)
Test PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest Passed 16.074190 seconds (47.18 M allocations: 7.414 GiB, 7.09% gc time)
  0.027867 seconds (82.19 k allocations: 12.380 MiB, 13.88% gc time)
 15.827624 seconds (47.18 M allocations: 7.415 GiB, 6.81% gc time)
 16.157586 seconds (47.18 M allocations: 7.415 GiB, 6.60% gc time)
Test PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest PassedTest Passed
Test Passed
  9.559434 seconds (30.18 M allocations: 4.778 GiB, 9.00% gc time)
  0.775884 seconds (2.70 M allocations: 396.087 MiB, 8.55% gc time)
  8.063340 seconds (23.17 M allocations: 3.641 GiB, 8.27% gc time)
 47.299884 seconds (143.73 M allocations: 20.444 GiB, 8.50% gc time)
  8.437004 seconds (23.17 M allocations: 3.642 GiB, 8.65% gc time)
 48.360012 seconds (143.73 M allocations: 20.444 GiB, 8.30% gc time)
  8.061970 seconds (23.17 M allocations: 3.642 GiB, 8.65% gc time)
 49.122377 seconds (143.73 M allocations: 20.444 GiB, 8.32% gc time)
 11.207443 seconds (30.18 M allocations: 4.779 GiB, 8.11% gc time)
  0.894200 seconds (2.70 M allocations: 396.089 MiB, 8.87% gc time)
 11.226985 seconds (30.18 M allocations: 4.779 GiB, 8.37% gc time)
  0.936665 seconds (2.70 M allocations: 396.089 MiB, 7.23% gc time)
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
  8.452133 seconds (23.17 M allocations: 3.641 GiB, 8.45% gc time)
 41.043048 seconds (125.85 M allocations: 18.057 GiB, 8.27% gc time)
  7.801675 seconds (23.17 M allocations: 3.642 GiB, 8.34% gc time)
  8.057809 seconds (23.17 M allocations: 3.642 GiB, 8.07% gc time)
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Passed
Test Summary: | Pass  Total      Time
FlxQTL.jl     |  244    244  21m47.4s
     Testing FlxQTL tests passed 

Testing completed after 1200.16s

PkgEval succeeded after 1441.8s