Package evaluation to test QMSimFiles on Julia 1.14.0-DEV.1260 (89243d1cdf*) started at 2025-11-16T18:40:46.532 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.37s ################################################################################ # Installation # Installing QMSimFiles... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed libaec_jll ────────────── v1.1.4+0 Installed MPICH_jll ─────────────── v4.3.2+0 Installed FillArrays ────────────── v1.15.0 Installed HypergeometricFunctions ─ v0.3.28 Installed AliasTables ───────────── v1.1.3 Installed QMSimFiles ────────────── v0.3.4 Installed DataStructures ────────── v0.19.3 Installed OrderedCollections ────── v1.8.1 Installed MicrosoftMPI_jll ──────── v10.1.4+3 Installed Compat ────────────────── v4.18.1 Installed Xorg_libpciaccess_jll ─── v0.18.1+0 Installed DataAPI ───────────────── v1.16.0 Installed StatsAPI ──────────────── v1.7.1 Installed StatsBase ─────────────── v0.34.8 Installed Statistics ────────────── v1.11.1 Installed IrrationalConstants ───── v0.2.6 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed Hwloc_jll ─────────────── v2.12.2+0 Installed Requires ──────────────── v1.3.1 Installed QuadGK ────────────────── v2.11.2 Installed OpenMPI_jll ───────────── v5.0.9+0 Installed HDF5_jll ──────────────── v1.14.6+0 Installed LogExpFunctions ───────── v0.3.29 Installed XML2_jll ──────────────── v2.13.9+0 Installed Rmath ─────────────────── v0.9.0 Installed PtrArrays ─────────────── v1.3.0 Installed Reexport ──────────────── v1.2.2 Installed StatsFuns ─────────────── v1.5.2 Installed SpecialFunctions ──────── v2.6.1 Installed Preferences ───────────── v1.5.0 Installed Distributions ─────────── v0.25.122 Installed MPIPreferences ────────── v0.1.11 Installed Libiconv_jll ──────────── v1.18.0+0 Installed Missings ──────────────── v1.2.0 Installed JLLWrappers ───────────── v1.7.1 Installed PDMats ────────────────── v0.11.36 Installed MPItrampoline_jll ─────── v5.5.4+0 Installed HDF5 ──────────────────── v0.16.16 Installed SortingAlgorithms ─────── v1.2.2 Installed DocStringExtensions ───── v0.9.5 Installing 9 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact libaec 49.6 KiB Installed artifact Xorg_libpciaccess 24.8 KiB Installed artifact XML2 2.5 MiB Installed artifact MPICH 3.3 MiB Installed artifact Libiconv 1.9 MiB Installed artifact Hwloc 3.5 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 v1.11.0 [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 v8.16.0+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 19.89s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4529.4 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... 843.5 ms ✓ Reexport 1140.1 ms ✓ Statistics 881.0 ms ✓ DataAPI 2232.5 ms ✓ IrrationalConstants 840.9 ms ✓ StatsAPI 1178.8 ms ✓ Requires 1284.6 ms ✓ OrderedCollections 1108.3 ms ✓ DocStringExtensions 2149.0 ms ✓ FillArrays 843.9 ms ✓ PtrArrays 1245.9 ms ✓ SuiteSparse 1106.8 ms ✓ Compat 1144.8 ms ✓ Preferences 1321.8 ms ✓ Statistics → SparseArraysExt 1008.6 ms ✓ Missings 3521.5 ms ✓ DataStructures 1457.6 ms ✓ LogExpFunctions 1523.2 ms ✓ FillArrays → FillArraysSparseArraysExt 949.9 ms ✓ FillArrays → FillArraysStatisticsExt 969.8 ms ✓ AliasTables 1848.2 ms ✓ PDMats 814.9 ms ✓ Compat → CompatLinearAlgebraExt 1175.6 ms ✓ JLLWrappers 1455.2 ms ✓ MPIPreferences 1078.8 ms ✓ SortingAlgorithms 2396.1 ms ✓ QuadGK 1493.8 ms ✓ FillArrays → FillArraysPDMatsExt 1487.1 ms ✓ libaec_jll 1471.2 ms ✓ Xorg_libpciaccess_jll 1462.3 ms ✓ Libiconv_jll 1443.3 ms ✓ Rmath_jll 1166.8 ms ✓ MicrosoftMPI_jll 1388.3 ms ✓ OpenSpecFun_jll 4200.3 ms ✓ MPItrampoline_jll 4041.9 ms ✓ StatsBase 1416.3 ms ✓ XML2_jll 1369.4 ms ✓ Rmath 4719.6 ms ✓ SpecialFunctions 1382.2 ms ✓ PDMats → StatsBaseExt 2073.1 ms ✓ Hwloc_jll 2547.7 ms ✓ HypergeometricFunctions 4818.2 ms ✓ MPICH_jll 4471.8 ms ✓ OpenMPI_jll 2851.6 ms ✓ StatsFuns 5568.0 ms ✓ HDF5_jll 9266.6 ms ✓ Distributions 12955.6 ms ✓ HDF5 7414.2 ms ✓ QMSimFiles 48 dependencies successfully precompiled in 115 seconds. 33 already precompiled. Precompilation completed after 134.78s ################################################################################ # Testing # Testing QMSimFiles Status `/tmp/jl_tHoWgN/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_tHoWgN/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 v1.11.0 [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 v8.16.0+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 1.8s Test Summary: | Pass Total Time load_QTL_effect! and read_maps | 39 39 2.0s Test Summary: | Pass Total Time load_QTL_effect! and read_maps: MT | 39 39 0.6s Test Summary: | Pass Total Time allele frequency | 26 26 3.5s Test Summary: | Pass Total Time generate_chromosome_set | 1 1 0.1s Test Summary: | Pass Total Time parse SNP/QTL data | 43 43 10.6s Test Summary: | Pass Total Time parse SNP/QTL data v2 | 43 43 6.6s 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 | 22 22 5.0s 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 1.1s Test Summary: | Pass Total Time equal sign | 3 3 4.9s Test Summary: | Pass Total Time pack/unpack genotypes | 12 12 0.6s [ Info: temporary HDF5 file: /tmp/jl_Y7yFIfUFwn [ Info: temporary HDF5 file: /tmp/jl_izcF6Pg9ih Test Summary: | Pass Total Time save/read genotypes | 11 11 19.8s [ Info: temporary HDF5 file: /tmp/jl_SDy521Sxs9 [ Info: temporary HDF5 file: /tmp/jl_ARSlWTM7gH Test Summary: | Pass Total Time save/read maps: MT | 2 2 1.4s [ Info: temporary text file: /tmp/jl_WvMX8B8rQ9 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 6.7s RNG of the outermost testset: Xoshiro(0x5ca78351354407b9, 0x165877b7df42587d, 0x1c30e0b1322091a7, 0xe650c56689103ebf, 0x78dab3bc8d1fa0ac) 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 112.44s 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 303.81s: package tests unexpectedly errored