Package evaluation of QMSimFiles on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T17:06:39.704 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.47s ################################################################################ # Installation # Installing QMSimFiles... Resolving package versions... Installed HDF5 ─ v0.16.16 Updating `~/.julia/environments/v1.12/Project.toml` [1e04daf1] + QMSimFiles v0.3.4 Updating `~/.julia/environments/v1.12/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [34da2185] + Compat v4.17.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [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 v1.7.0 [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 v1.4.3 [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 v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [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 v1.6.0 [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 v1.12.0 [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 v1.12.0 [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 v8.11.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.64.0+1 [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 15.78s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 34.69s ################################################################################ # Testing # Testing QMSimFiles Status `/tmp/jl_ZQNOeq/Project.toml` [31c24e10] Distributions v0.25.120 ⌅ [f67ccb44] HDF5 v0.16.16 [1e04daf1] QMSimFiles v0.3.4 [10745b16] Statistics v1.11.1 [37e2e46d] LinearAlgebra v1.12.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_ZQNOeq/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [34da2185] Compat v4.17.0 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.22 [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 v1.7.0 [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 v1.4.3 [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 v1.2.1 [276daf66] SpecialFunctions v2.5.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.5 [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 v1.6.0 [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 v1.12.0 [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 v1.12.0 [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 v8.11.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.64.0+1 [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 0.1s Test Summary: | Pass Total Time get_number_of_QTL_allele | 3 3 1.0s Test Summary: | Pass Total Time get_leading_width_standard | 4 4 0.1s 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 1.8s 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 3.8s Test Summary: | Pass Total Time generate_chromosome_set | 1 1 0.1s Test Summary: | Pass Total Time parse SNP/QTL data | 43 43 9.8s Test Summary: | Pass Total Time parse SNP/QTL data v2 | 43 43 6.1s 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 6.2s Test Summary: | Pass Total Time generate_gamete_with_crossover | 2 2 0.8s Test Summary: | Pass Total Time general mating | 1 1 1.2s Test Summary: | Pass Total Time general mating: MT | 1 1 1.1s Test Summary: | Pass Total Time equal sign | 3 3 3.8s Test Summary: | Pass Total Time pack/unpack genotypes | 12 12 0.6s [ Info: temporary HDF5 file: /tmp/jl_yp6dyje1eD [ Info: temporary HDF5 file: /tmp/jl_idqHiNAp2l Test Summary: | Pass Total Time save/read genotypes | 11 11 22.5s [ Info: temporary HDF5 file: /tmp/jl_2VYdqvI1Ep [ Info: temporary HDF5 file: /tmp/jl_GFQLkP29ef Test Summary: | Pass Total Time save/read maps: MT | 2 2 1.6s [ Info: temporary text file: /tmp/jl_wd8PcbkTKh 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/v1.12/Test/src/Test.jl:1776 [inlined] [5] macro expansion @ ~/.julia/packages/QMSimFiles/vdfXH/test/runtests.jl:604 [inlined] [6] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [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:287 [10] _start() @ Base ./client.jl:554 Test Summary: | Pass Error Total Time random QTL effects | 2 1 3 6.4s RNG of the outermost testset: Xoshiro(0xde2a8d7b08e93156, 0x68cf104a51248401, 0x999cc113d8e583a3, 0x3436ffda4ed7004d, 0x862882b560b351a3) 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 102.68s ERROR: LoadError: Package QMSimFiles errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/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/v1.12/Pkg/src/Operations.jl:2458 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2313 [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/v1.12/Pkg/src/API.jl:511 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:305 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:321 [12] _start() @ Base ./client.jl:554 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 180.58s: package tests unexpectedly errored