Package evaluation to test QMSimFiles on Julia 1.14.0-DEV.2113 (886384998d*) started at 2026-05-03T20:03:00.019 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.43s ################################################################################ # Installation # Installing QMSimFiles... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed libaec_jll ────────────── v1.1.6+0 Installed MPICH_jll ─────────────── v4.3.2+0 Installed FillArrays ────────────── v1.16.0 Installed QMSimFiles ────────────── v0.3.4 Installed DataStructures ────────── v0.19.4 Installed HypergeometricFunctions ─ v0.3.28 Installed AliasTables ───────────── v1.1.3 Installed MicrosoftMPI_jll ──────── v10.1.4+3 (no artifacts on this platform) Installed OrderedCollections ────── v1.8.1 Installed DataAPI ───────────────── v1.16.0 Installed StatsAPI ──────────────── v1.8.0 Installed StatsBase ─────────────── v0.34.10 Installed Xorg_libpciaccess_jll ─── v0.19.0+0 Installed Statistics ────────────── v1.11.1 Installed Compat ────────────────── v4.18.1 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed LogExpFunctions ───────── v0.3.29 Installed IrrationalConstants ───── v0.2.6 Installed Requires ──────────────── v1.3.1 Installed HDF5_jll ──────────────── v1.14.6+0 Installed QuadGK ────────────────── v2.11.3 Installed Hwloc_jll ─────────────── v2.13.0+1 Installed OpenMPI_jll ───────────── v5.0.11+0 Installed Rmath ─────────────────── v0.9.0 Installed Reexport ──────────────── v1.2.2 Installed StatsFuns ─────────────── v1.5.2 Installed PtrArrays ─────────────── v1.4.0 Installed XML2_jll ──────────────── v2.13.9+0 Installed Distributions ─────────── v0.25.125 Installed Missings ──────────────── v1.2.0 Installed SpecialFunctions ──────── v2.7.2 Installed Preferences ───────────── v1.5.2 Installed Libiconv_jll ──────────── v1.18.0+0 Installed JLLWrappers ───────────── v1.7.1 Installed MPIPreferences ────────── v0.1.12 Installed MPItrampoline_jll ─────── v5.5.6+0 Installed PDMats ────────────────── v0.11.37 Installed SortingAlgorithms ─────── v1.2.2 Installed DocStringExtensions ───── v0.9.5 Installed HDF5 ──────────────────── v0.16.16 Installing 9 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Installed artifact Xorg_libpciaccess 26.2 KiB Installed artifact libaec 50.0 KiB Installed artifact MPICH 3.3 MiB Installed artifact Libiconv 1.9 MiB Installed artifact XML2 2.5 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 v0.19.4 [31c24e10] + Distributions v0.25.125 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 ⌅ [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 v0.1.12 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [21216c6a] + Preferences v1.5.2 [43287f4e] + PtrArrays v1.4.0 [1e04daf1] + QMSimFiles v0.3.4 [1fd47b50] + QuadGK v2.11.3 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.7.2 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 ⌅ [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.13.0+1 [94ce4f54] + Libiconv_jll v1.18.0+0 ⌅ [7cb0a576] + MPICH_jll v4.3.2+0 [f1f71cc9] + MPItrampoline_jll v5.5.6+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.11+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 v0.19.0+0 [477f73a3] + libaec_jll v1.1.6+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 v1.13.0 [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 v1.14.0 [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 v1.5.1+0 [deac9b47] + LibCURL_jll v8.19.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2026.3.19 [4536629a] + OpenBLAS_jll v0.3.33+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+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 22.42s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 5.4 s ✓ TestEnv 1 dependency successfully precompiled in 6 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 0.9 s ✓ Reexport 1.2 s ✓ Statistics 0.9 s ✓ DataAPI 2.2 s ✓ IrrationalConstants 0.9 s ✓ StatsAPI 1.4 s ✓ OrderedCollections 1.1 s ✓ DocStringExtensions 2.3 s ✓ FillArrays 0.9 s ✓ PtrArrays 1.3 s ✓ Requires 2.1 s ✓ PDMats 1.2 s ✓ Compat 1.5 s ✓ Preferences 1.5 s ✓ Statistics → SparseArraysExt 1.0 s ✓ Missings 3.8 s ✓ DataStructures 1.4 s ✓ LogExpFunctions 1.8 s ✓ FillArrays → FillArraysSparseArraysExt 1.1 s ✓ FillArrays → FillArraysStatisticsExt 1.1 s ✓ AliasTables 1.7 s ✓ FillArrays → FillArraysPDMatsExt 0.9 s ✓ Compat → CompatLinearAlgebraExt 1.6 s ✓ JLLWrappers 2.3 s ✓ MPIPreferences 1.2 s ✓ SortingAlgorithms 2.4 s ✓ QuadGK 2.3 s ✓ libaec_jll 2.3 s ✓ Xorg_libpciaccess_jll 2.3 s ✓ Libiconv_jll 2.4 s ✓ Rmath_jll 1.6 s ✓ MicrosoftMPI_jll 2.3 s ✓ OpenSpecFun_jll 5.1 s ✓ MPItrampoline_jll 5.0 s ✓ StatsBase 2.5 s ✓ XML2_jll 2.0 s ✓ Rmath 5.7 s ✓ SpecialFunctions 1.7 s ✓ PDMats → StatsBaseExt 2.4 s ✓ Hwloc_jll 2.7 s ✓ HypergeometricFunctions 5.9 s ✓ MPICH_jll 5.1 s ✓ OpenMPI_jll 3.1 s ✓ StatsFuns 6.4 s ✓ HDF5_jll 10.2 s ✓ Distributions 14.9 s ✓ HDF5 4.3 s ✓ Distributions → DistributionsTestExt 8.1 s ✓ QMSimFiles 48 dependencies successfully precompiled in 138 seconds. 36 already precompiled. Precompilation completed after 176.23s ################################################################################ # Testing # Testing QMSimFiles Status `/tmp/jl_RT1qZ0/Project.toml` [31c24e10] Distributions v0.25.125 ⌅ [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_RT1qZ0/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [34da2185] Compat v4.18.1 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.4 [31c24e10] Distributions v0.25.125 [ffbed154] DocStringExtensions v0.9.5 [1a297f60] FillArrays v1.16.0 ⌅ [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 v0.1.12 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [21216c6a] Preferences v1.5.2 [43287f4e] PtrArrays v1.4.0 [1e04daf1] QMSimFiles v0.3.4 [1fd47b50] QuadGK v2.11.3 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.7.2 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 ⌅ [0234f1f7] HDF5_jll v1.14.6+0 [e33a78d0] Hwloc_jll v2.13.0+1 [94ce4f54] Libiconv_jll v1.18.0+0 ⌅ [7cb0a576] MPICH_jll v4.3.2+0 [f1f71cc9] MPItrampoline_jll v5.5.6+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [fe0851c0] OpenMPI_jll v5.0.11+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 v0.19.0+0 [477f73a3] libaec_jll v1.1.6+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 v1.13.0 [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 v1.14.0 [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 v1.5.1+0 [deac9b47] LibCURL_jll v8.19.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2026.3.19 [4536629a] OpenBLAS_jll v0.3.33+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.6+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+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 0.6s 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 1.5s 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 1.9s Test Summary: | Pass Total Time load_QTL_effect! and read_maps: MT | 39 39 0.9s Test Summary: | Pass Total Time allele frequency | 26 26 4.8s Test Summary: | Pass Total Time generate_chromosome_set | 1 1 0.1s Test Summary: | Pass Total Time parse SNP/QTL data | 43 43 10.4s 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 0.2s Test Summary: | Pass Total Time location_of_crossover | 24 24 5.7s 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 5.2s Test Summary: | Pass Total Time pack/unpack genotypes | 12 12 0.7s [ Info: temporary HDF5 file: /tmp/jl_F07gZmjsr8 [ Info: temporary HDF5 file: /tmp/jl_Pazm123SVm Test Summary: | Pass Total Time save/read genotypes | 11 11 18.5s [ Info: temporary HDF5 file: /tmp/jl_jIneD0N0ZK [ Info: temporary HDF5 file: /tmp/jl_lej49ero9s Test Summary: | Pass Total Time save/read maps: MT | 2 2 1.5s [ Info: temporary text file: /tmp/jl_NmTcdODqh4 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] iterate(r::UnitRange{Int64}) @ Base ./number.jl:104 [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:2246 [inlined] [5] macro expansion @ ~/.julia/packages/QMSimFiles/vdfXH/test/runtests.jl:604 [inlined] [6] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [7] top-level scope @ none:6 [8] eval(m::Module, e::Any) @ Core ./boot.jl:517 [9] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [10] _start() @ Base ./client.jl:593 Test Summary: | Pass Error Total Time random QTL effects | 2 1 3 6.3s RNG of the outermost testset: Xoshiro(0xd589d38e616ef1ba, 0x455a338cf2b57013, 0xfd4585a51b6a5e4d, 0x9eb673ac72fd8b0b, 0xeef13425e791e6c1) 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 103.64s 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:3162 [3] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [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:586 [5] 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 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [12] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 358.25s: package tests unexpectedly errored