Package evaluation to test QMSimFiles on Julia 1.14.0-DEV.1299 (6d6224db99*) started at 2025-11-27T17:24:40.202 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.25s ################################################################################ # Installation # Installing QMSimFiles... Resolving package versions... Installed libaec_jll ────────────── v1.1.4+0 Installed Rmath_jll ─────────────── v0.5.1+0 Installed MPICH_jll ─────────────── v4.3.2+0 Installed HypergeometricFunctions ─ v0.3.28 Installed AliasTables ───────────── v1.1.3 Installed FillArrays ────────────── v1.15.0 Installed QMSimFiles ────────────── v0.3.4 Installed DataStructures ────────── v0.19.3 Installed MicrosoftMPI_jll ──────── v10.1.4+3 Installed DataAPI ───────────────── v1.16.0 Installed Compat ────────────────── v4.18.1 Installed OrderedCollections ────── v1.8.1 Installed StatsBase ─────────────── v0.34.8 Installed Xorg_libpciaccess_jll ─── v0.18.1+0 Installed StatsAPI ──────────────── v1.7.1 Installed Statistics ────────────── v1.11.1 Installed IrrationalConstants ───── v0.2.6 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed OpenMPI_jll ───────────── v5.0.9+0 Installed Requires ──────────────── v1.3.1 Installed HDF5_jll ──────────────── v1.14.6+0 Installed QuadGK ────────────────── v2.11.2 Installed LogExpFunctions ───────── v0.3.29 Installed Hwloc_jll ─────────────── v2.12.2+0 Installed Rmath ─────────────────── v0.9.0 Installed PtrArrays ─────────────── v1.3.0 Installed XML2_jll ──────────────── v2.13.9+0 Installed StatsFuns ─────────────── v1.5.2 Installed Reexport ──────────────── v1.2.2 Installed SpecialFunctions ──────── v2.6.1 Installed Distributions ─────────── v0.25.122 Installed Preferences ───────────── v1.5.0 Installed MPIPreferences ────────── v0.1.11 Installed Libiconv_jll ──────────── v1.18.0+0 Installed JLLWrappers ───────────── v1.7.1 Installed Missings ──────────────── v1.2.0 Installed PDMats ────────────────── v0.11.36 Installed HDF5 ──────────────────── v0.16.16 Installed MPItrampoline_jll ─────── v5.5.4+0 Installed SortingAlgorithms ─────── v1.2.2 Installed DocStringExtensions ───── v0.9.5 Installing 9 artifacts Installed artifact Rmath 121.9 KiB Installed artifact Xorg_libpciaccess 24.8 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact libaec 49.6 KiB Installed artifact Libiconv 1.9 MiB Installed artifact XML2 2.5 MiB Installed artifact Hwloc 3.5 MiB Installed artifact MPICH 3.3 MiB Installed artifact HDF5 5.7 MiB Updating `~/.julia/environments/v1.14/Project.toml` [1e04daf1] + QMSimFiles v0.3.4 Updating `~/.julia/environments/v1.14/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [34da2185] + Compat v4.18.1 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.15.0 ⌅ [f67ccb44] + HDF5 v0.16.16 [34004b35] + HypergeometricFunctions v0.3.28 [92d709cd] + IrrationalConstants v0.2.6 [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 v0.11.36 [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 v0.9.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.8 [4c63d2b9] + StatsFuns v1.5.2 ⌅ [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.2+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [7cb0a576] + MPICH_jll v4.3.2+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] + libaec_jll v1.1.4+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 v1.0.0 [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 v1.0.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [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 v8.17.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+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 v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 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 19.93s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4615.2 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ 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/i9lgt/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/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... 1116.9 ms ✓ Reexport 1156.9 ms ✓ Statistics 940.6 ms ✓ DataAPI 2487.1 ms ✓ IrrationalConstants 1005.5 ms ✓ StatsAPI 1499.3 ms ✓ Requires 1436.3 ms ✓ OrderedCollections 1042.4 ms ✓ DocStringExtensions 2036.6 ms ✓ FillArrays 823.0 ms ✓ PtrArrays 1218.0 ms ✓ SuiteSparse 1168.1 ms ✓ Compat 1161.8 ms ✓ Preferences 1360.6 ms ✓ Statistics → SparseArraysExt 1037.5 ms ✓ Missings 3517.9 ms ✓ DataStructures 1414.5 ms ✓ LogExpFunctions 1529.2 ms ✓ FillArrays → FillArraysSparseArraysExt 951.2 ms ✓ FillArrays → FillArraysStatisticsExt 994.6 ms ✓ AliasTables 1884.7 ms ✓ PDMats 874.6 ms ✓ Compat → CompatLinearAlgebraExt 1177.7 ms ✓ JLLWrappers 1350.5 ms ✓ MPIPreferences 1040.3 ms ✓ SortingAlgorithms 2152.0 ms ✓ QuadGK 2193.7 ms ✓ FillArrays → FillArraysPDMatsExt 1659.5 ms ✓ libaec_jll 1482.5 ms ✓ Xorg_libpciaccess_jll 1320.0 ms ✓ Libiconv_jll 1288.9 ms ✓ Rmath_jll 1127.6 ms ✓ MicrosoftMPI_jll 1318.6 ms ✓ OpenSpecFun_jll 4512.2 ms ✓ MPItrampoline_jll 4338.1 ms ✓ StatsBase 1593.5 ms ✓ XML2_jll 1517.1 ms ✓ Rmath 5001.9 ms ✓ SpecialFunctions 1429.3 ms ✓ PDMats → StatsBaseExt 1483.1 ms ✓ Hwloc_jll 2426.7 ms ✓ HypergeometricFunctions 4809.1 ms ✓ MPICH_jll 4504.3 ms ✓ OpenMPI_jll 2737.8 ms ✓ StatsFuns 5339.5 ms ✓ HDF5_jll 8898.6 ms ✓ Distributions 13500.3 ms ✓ HDF5 7346.2 ms ✓ QMSimFiles 48 dependencies successfully precompiled in 117 seconds. 33 already precompiled. Precompilation completed after 134.43s ################################################################################ # Testing # Testing QMSimFiles Status `/tmp/jl_C5OFrs/Project.toml` [31c24e10] Distributions v0.25.122 ⌅ [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_C5OFrs/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [34da2185] Compat v4.18.1 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.3 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [1a297f60] FillArrays v1.15.0 ⌅ [f67ccb44] HDF5 v0.16.16 [34004b35] HypergeometricFunctions v0.3.28 [92d709cd] IrrationalConstants v0.2.6 [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 v0.11.36 [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 v0.9.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.8 [4c63d2b9] StatsFuns v1.5.2 ⌅ [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.12.2+0 [94ce4f54] Libiconv_jll v1.18.0+0 [7cb0a576] MPICH_jll v4.3.2+0 [f1f71cc9] MPItrampoline_jll v5.5.4+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [fe0851c0] OpenMPI_jll v5.0.9+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 ⌅ [02c8fc9c] XML2_jll v2.13.9+0 [a65dc6b1] Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] libaec_jll v1.1.4+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 v1.0.0 [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 v1.0.0 [9e88b42a] Serialization v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [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 v8.17.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+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 v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 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 0.5s 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 2.7s Test Summary: | Pass Total Time load_QTL_effect! and read_maps: MT | 39 39 0.7s Test Summary: | Pass Total Time allele frequency | 26 26 4.4s Test Summary: | Pass Total Time generate_chromosome_set | 1 1 0.1s Test Summary: | Pass Total Time parse SNP/QTL data | 43 43 10.5s Test Summary: | Pass Total Time parse SNP/QTL data v2 | 43 43 6.4s 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 | 20 20 6.0s Test Summary: | Pass Total Time generate_gamete_with_crossover | 2 2 0.7s Test Summary: | Pass Total Time general mating | 1 1 1.0s Test Summary: | Pass Total Time general mating: MT | 1 1 1.0s Test Summary: | Pass Total Time equal sign | 3 3 5.0s Test Summary: | Pass Total Time pack/unpack genotypes | 12 12 0.6s [ Info: temporary HDF5 file: /tmp/jl_c3aVaVwlgZ [ Info: temporary HDF5 file: /tmp/jl_6TG5IrOPC1 Test Summary: | Pass Total Time save/read genotypes | 11 11 19.1s [ Info: temporary HDF5 file: /tmp/jl_ChQdQnezaN [ Info: temporary HDF5 file: /tmp/jl_yt05KFwLa9 Test Summary: | Pass Total Time save/read maps: MT | 2 2 1.4s [ Info: temporary text file: /tmp/jl_eFutoHKfCz Test Summary: | Pass Total Time export to blupf90 | 5 5 1.9s 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/v1.14/Test/src/Test.jl:1961 [inlined] [5] macro expansion @ ~/.julia/packages/QMSimFiles/vdfXH/test/runtests.jl:604 [inlined] [6] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [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:310 [10] _start() @ Base ./client.jl:577 Test Summary: | Pass Error Total Time random QTL effects | 2 1 3 6.2s RNG of the outermost testset: Xoshiro(0xc5d78d922000189b, 0xb0ef3d2c4a1fdadc, 0xabcf71f475632e50, 0xc7b03533182ff39f, 0xa983f342f29f3a18) 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 112.97s ERROR: LoadError: Package QMSimFiles 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:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [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/v1.14/Pkg/src/API.jl:572 [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/v1.14/Pkg/src/API.jl:548 [6] 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 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 303.04s: package tests unexpectedly errored