Package evaluation of PopGenCore on Julia 1.13.0-DEV.582 (c0a1728d50*) started at 2025-05-14T13:46:49.940 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.62s ################################################################################ # Installation # Installing PopGenCore... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [45b36091] + PopGenCore v0.7.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 ⌅ [67c07d97] + Automa v0.8.4 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [e1450e63] + BufferedStreams v1.2.2 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.16.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [ffbed154] + DocStringExtensions v0.9.4 [48062228] + FilePathsBase v0.9.24 [842dd82b] + InlineStrings v1.4.3 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.0 [69de0a69] + Parsers v2.8.3 [2dfb63ee] + PooledArrays v1.4.3 [45b36091] + PopGenCore v0.7.2 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [43287f4e] + PtrArrays v1.3.0 [189a3867] + Reexport v1.2.2 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.1 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.5 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [28eba6e3] + VariantCallFormat v0.5.6 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [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 [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 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 3.76s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 77.96s ################################################################################ # Testing # Testing PopGenCore Status `/tmp/jl_XFclT2/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.7.0 [2dfb63ee] PooledArrays v1.4.3 [45b36091] PopGenCore v0.7.2 [90137ffa] StaticArrays v1.9.13 [2913bbd2] StatsBase v0.34.5 [28eba6e3] VariantCallFormat v0.5.6 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_XFclT2/Manifest.toml` [66dad0bd] AliasTables v1.1.3 ⌅ [67c07d97] Automa v0.8.4 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.16.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [ffbed154] DocStringExtensions v0.9.4 [48062228] FilePathsBase v0.9.24 [842dd82b] InlineStrings v1.4.3 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.0 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [45b36091] PopGenCore v0.7.2 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [43287f4e] PtrArrays v1.3.0 [189a3867] Reexport v1.2.2 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.5 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [28eba6e3] VariantCallFormat v0.5.6 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [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 [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 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [4536629a] OpenBLAS_jll v0.3.29+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Running tests: PASSED: popdata.jl PASSED: types.jl PASSED: allelegenofreq.jl PASSED: allelematrices.jl [ Info: Removing 258 multialleic loci [ Info: Writing Baypass data matrix to CI_test.baypass PASSED: io.jl Renaming unique populations Assigning new population names to all samples populations: Error During Test at /home/pkgeval/.julia/packages/PopGenCore/u7lTq/test/manipulate.jl:40 Got exception outside of a @test ArgumentError: 2 samples not found: N215, N297 Stacktrace: [1] populations!(data::PopData, samples::Vector{String}, populations::Vector{String}) @ PopGenCore ~/.julia/packages/PopGenCore/u7lTq/src/Manipulate.jl:261 [2] top-level scope @ ~/.julia/packages/PopGenCore/u7lTq/test/manipulate.jl:12 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [4] macro expansion @ ~/.julia/packages/PopGenCore/u7lTq/test/manipulate.jl:41 [inlined] [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [6] macro expansion @ ~/.julia/packages/PopGenCore/u7lTq/test/manipulate.jl:62 [inlined] [7] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [8] top-level scope @ ~/.julia/packages/PopGenCore/u7lTq/test/runtests.jl:23 [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [10] macro expansion @ ~/.julia/packages/PopGenCore/u7lTq/test/runtests.jl:25 [inlined] [11] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [12] top-level scope @ none:6 [13] eval(m::Module, e::Any) @ Core ./boot.jl:489 [14] exec_options(opts::Base.JLOptions) @ Base ./client.jl:297 [15] _start() @ Base ./client.jl:564 PASSED: manipulate.jl [ Info: Removing 9 multialleic loci PASSED: utils.jl PASSED: conditionals.jl PASSED: iterators.jl Test Summary: | Pass Error Total Time All Tests | 264 1 265 4m37.9s PopData | 25 25 9.3s Data Types and Datasets | 35 35 0.5s Allele Frequncies | 25 25 37.6s Genotype Frequncies | 25 25 7.4s Genotype Counts | 11 11 2.3s AlleleMatrices.jl | 13 13 21.8s File IO | 6 6 37.1s Manipulate.jl | 35 1 36 23.3s locations | 4 4 2.1s decimal-minutes locations | 2 2 1.4s loci and genotypes | 8 8 4.1s populations | 10 1 11 8.1s exclusion | 11 11 7.6s Utilities | 47 47 14.9s Conditionals.jl | 29 29 1.8s Iterators.jl | 13 13 2.7s RNG of the outermost testset: Random.Xoshiro(0xc027c2d0c38bd93e, 0x17d95cd160b0ca22, 0xd344e27eaeb4656f, 0x84ccc6871c938a25, 0xc9a5b370172cf9d2) ERROR: LoadError: Some tests did not pass: 264 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PopGenCore/u7lTq/test/runtests.jl:22 Testing failed after 306.26s ERROR: LoadError: Package PopGenCore 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:2418 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2273 [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:498 [5] 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:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/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:309 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:331 [12] _start() @ Base ./client.jl:564 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 414.0s: package tests unexpectedly errored