Package evaluation of QMSimFiles on Julia 1.13.0-DEV.974 (7bbb213719*) started at 2025-08-12T17:33:29.102


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 9.72s


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

Installing QMSimFiles...
   Resolving package versions...
   Installed HDF5 ─ v0.16.16
    Updating `~/.julia/environments/v1.13/Project.toml`
  [1e04daf1] + QMSimFiles v0.3.4
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [66dad0bd] + AliasTables v1.1.3
  [34da2185] + Compat v4.18.0
  [9a962f9c] + DataAPI v1.16.0
  [864edb3b] + DataStructures v0.19.0
  [31c24e10] + Distributions v0.25.120
  [ffbed154] + DocStringExtensions v0.9.5
  [1a297f60] + FillArrays v1.13.0
⌅ [f67ccb44] + HDF5 v0.16.16
  [34004b35] + HypergeometricFunctions v0.3.28
  [92d709cd] + IrrationalConstants v0.2.4
  [692b3bcd] + JLLWrappers v1.7.1
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [3da0fdf6] + MPIPreferences v0.1.11
  [e1d29d7a] + Missings v1.2.0
  [bac558e1] + OrderedCollections v1.8.1
  [90014a1f] + PDMats v0.11.35
  [21216c6a] + Preferences v1.5.0
  [43287f4e] + PtrArrays v1.3.0
  [1e04daf1] + QMSimFiles v0.3.4
  [1fd47b50] + QuadGK v2.11.2
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [79098fc4] + Rmath v0.8.0
  [a2af1166] + SortingAlgorithms v1.2.2
  [276daf66] + SpecialFunctions v2.5.1
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.1
  [2913bbd2] + StatsBase v0.34.6
  [4c63d2b9] + StatsFuns v1.5.0
  [0234f1f7] + HDF5_jll v1.14.6+0
  [e33a78d0] + Hwloc_jll v2.12.1+0
  [7cb0a576] + MPICH_jll v4.3.1+0
  [f1f71cc9] + MPItrampoline_jll v5.5.4+0
  [9237b28f] + MicrosoftMPI_jll v10.1.4+3
  [fe0851c0] + OpenMPI_jll v5.0.8+0
  [efe28fd5] + OpenSpecFun_jll v0.5.6+0
  [f50d1b31] + Rmath_jll v0.5.1+0
  [477f73a3] + libaec_jll v1.1.3+0
  [0dad84c5] + ArgTools v1.1.2
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [f43a241f] + Downloads v1.7.0
  [7b1f6079] + FileWatching 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 v1.13.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [ca575930] + NetworkOptions v1.3.0
  [44cfe95a] + Pkg v1.13.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [2f01184e] + SparseArrays v1.13.0
  [f489334b] + StyledStrings v1.11.0
  [4607b0f0] + SuiteSparse
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
  [deac9b47] + LibCURL_jll v8.15.0+1
  [e37daf67] + LibGit2_jll v1.9.1+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.7.15
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [05823500] + OpenLibm_jll v0.8.5+0
  [458c3c95] + OpenSSL_jll v3.5.2+0
  [efcefdf7] + PCRE2_jll v10.45.0+0
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [3161d3a3] + Zstd_jll v1.5.7+1
  [8e850b90] + libblastrampoline_jll v5.13.1+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`
    Building HDF5 → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/114e20044677badbc631ee6fdc80a67920561a29/build.log`

Installation completed after 15.4s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 51.28s


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

     Testing QMSimFiles
      Status `/tmp/jl_iYgxSG/Project.toml`
  [31c24e10] Distributions v0.25.120
⌅ [f67ccb44] HDF5 v0.16.16
  [1e04daf1] QMSimFiles v0.3.4
  [10745b16] Statistics v1.11.1
  [37e2e46d] LinearAlgebra v1.13.0
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_iYgxSG/Manifest.toml`
  [66dad0bd] AliasTables v1.1.3
  [34da2185] Compat v4.18.0
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.19.0
  [31c24e10] Distributions v0.25.120
  [ffbed154] DocStringExtensions v0.9.5
  [1a297f60] FillArrays v1.13.0
⌅ [f67ccb44] HDF5 v0.16.16
  [34004b35] HypergeometricFunctions v0.3.28
  [92d709cd] IrrationalConstants v0.2.4
  [692b3bcd] JLLWrappers v1.7.1
  [2ab3a3ac] LogExpFunctions v0.3.29
  [3da0fdf6] MPIPreferences v0.1.11
  [e1d29d7a] Missings v1.2.0
  [bac558e1] OrderedCollections v1.8.1
  [90014a1f] PDMats v0.11.35
  [21216c6a] Preferences v1.5.0
  [43287f4e] PtrArrays v1.3.0
  [1e04daf1] QMSimFiles v0.3.4
  [1fd47b50] QuadGK v2.11.2
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.1
  [79098fc4] Rmath v0.8.0
  [a2af1166] SortingAlgorithms v1.2.2
  [276daf66] SpecialFunctions v2.5.1
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.1
  [2913bbd2] StatsBase v0.34.6
  [4c63d2b9] StatsFuns v1.5.0
  [0234f1f7] HDF5_jll v1.14.6+0
  [e33a78d0] Hwloc_jll v2.12.1+0
  [7cb0a576] MPICH_jll v4.3.1+0
  [f1f71cc9] MPItrampoline_jll v5.5.4+0
  [9237b28f] MicrosoftMPI_jll v10.1.4+3
  [fe0851c0] OpenMPI_jll v5.0.8+0
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [f50d1b31] Rmath_jll v0.5.1+0
  [477f73a3] libaec_jll v1.1.3+0
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates 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 v1.13.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.3.0
  [44cfe95a] Pkg v1.13.0
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [2f01184e] SparseArrays v1.13.0
  [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 v8.15.0+1
  [e37daf67] LibGit2_jll v1.9.1+0
  [29816b5a] LibSSH2_jll v1.11.3+1
  [14a3606d] MozillaCACerts_jll v2025.7.15
  [4536629a] OpenBLAS_jll v0.3.29+0
  [05823500] OpenLibm_jll v0.8.5+0
  [458c3c95] OpenSSL_jll v3.5.2+0
  [efcefdf7] PCRE2_jll v10.45.0+0
  [bea87d4a] SuiteSparse_jll v7.10.1+0
  [83775a58] Zlib_jll v1.3.1+2
  [3161d3a3] Zstd_jll v1.5.7+1
  [8e850b90] libblastrampoline_jll v5.13.1+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...
Test Summary:             | Pass  Total  Time
get_number_of_chromosomes |    2      2  1.6s
Test Summary:      | Pass  Total  Time
get_number_of_loci |    2      2  0.3s
Test Summary:            | Pass  Total  Time
get_number_of_QTL_allele |    3      3  1.4s
Test Summary:              | Pass  Total  Time
get_leading_width_standard |    4      4  0.0s
Test Summary:      | Pass  Total  Time
load_SNP_QTL_maps! |   12     12  2.2s
Test Summary:                  | Pass  Total  Time
load_QTL_effect! and read_maps |   39     39  3.3s
Test Summary:                      | Pass  Total  Time
load_QTL_effect! and read_maps: MT |   39     39  0.8s
Test Summary:    | Pass  Total  Time
allele frequency |   26     26  4.3s
Test Summary:           | Pass  Total  Time
generate_chromosome_set |    1      1  0.1s
Test Summary:      | Pass  Total   Time
parse SNP/QTL data |   43     43  10.8s
Test Summary:         | Pass  Total  Time
parse SNP/QTL data v2 |   43     43  6.7s
Test Summary:          | Pass  Total  Time
parse SNP/QTL data: MT |   12     12  0.0s
Test Summary:     | Pass  Total  Time
number_of_crosses |    1      1  0.3s
Test Summary:         | Pass  Total  Time
location_of_crossover |   24     24  6.1s
Test Summary:                  | Pass  Total  Time
generate_gamete_with_crossover |    2      2  0.6s
Test Summary:  | Pass  Total  Time
general mating |    1      1  1.0s
Test Summary:      | Pass  Total  Time
general mating: MT |    1      1  1.1s
Test Summary: | Pass  Total  Time
equal sign    |    3      3  5.3s
Test Summary:         | Pass  Total  Time
pack/unpack genotypes |   12     12  0.6s
[ Info: temporary HDF5 file: /tmp/jl_YJCZkpcrEj
[ Info: temporary HDF5 file: /tmp/jl_CVg1QlwrmL
Test Summary:       | Pass  Total   Time
save/read genotypes |   11     11  20.3s
[ Info: temporary HDF5 file: /tmp/jl_ObEZ8DK5Up
[ Info: temporary HDF5 file: /tmp/jl_ojiRE3WH8l
Test Summary:      | Pass  Total  Time
save/read maps: MT |    2      2  1.5s
[ Info: temporary text file: /tmp/jl_I3m9i3IxIZ
Test Summary:     | Pass  Total  Time
export to blupf90 |    5      5  2.0s

random QTL effects: Error During Test at /home/pkgeval/.julia/packages/QMSimFiles/vdfXH/test/runtests.jl:566
  Got exception outside of a @test
  BoundsError: attempt to access Float64 at index [2]
  Stacktrace:
    [1] getindex
      @ ./number.jl:98 [inlined]
    [2] rand_effQTL!(effQTL::Array{Float64, 3}, dist::Gamma{Float64})
      @ QMSimFiles ~/.julia/packages/QMSimFiles/vdfXH/src/update.jl:101
    [3] top-level scope
      @ ~/.julia/packages/QMSimFiles/vdfXH/test/runtests.jl:567
    [4] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1929 [inlined]
    [5] macro expansion
      @ ~/.julia/packages/QMSimFiles/vdfXH/test/runtests.jl:604 [inlined]
    [6] include(mapexpr::Function, mod::Module, _path::String)
      @ Base ./Base.jl:312
    [7] top-level scope
      @ none:6
    [8] eval(m::Module, e::Any)
      @ Core ./boot.jl:489
    [9] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:286
   [10] _start()
      @ Base ./client.jl:553
Test Summary:      | Pass  Error  Total  Time
random QTL effects |    2      1      3  6.6s
RNG of the outermost testset: Xoshiro(0x0145cc3c5a93619c, 0xb7c99fdc8ac8b1a2, 0xe0cbfd984c09d05f, 0x7a800301d37e19be, 0xe61eb4d83f913c8f)
ERROR: LoadError: Some tests did not pass: 2 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/QMSimFiles/vdfXH/test/runtests.jl:566

Testing failed after 106.28s

ERROR: LoadError: Package QMSimFiles 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:2672
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2521 [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:538
  [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:515
  [6] 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:168
  [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:157
  [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156
  [9] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined]
 [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String)
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155
 [11] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [12] include(mod::Module, _path::String)
    @ Base ./Base.jl:311
 [13] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:320
 [14] _start()
    @ Base ./client.jl:553
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 198.38s: package tests unexpectedly errored