Package evaluation of MIToS on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T14:23:21.193 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 7.9s ################################################################################ # Installation # Installing MIToS... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [51bafb47] + MIToS v3.0.6 Updating `~/.julia/environments/v1.11/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [15f4f7f2] + AutoHashEquals v2.2.0 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.4.2 [3c28c6f8] + BioSymbols v5.1.3 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.2 [34da2185] + Compat v4.16.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [8bb1440f] + DelimitedFiles v1.9.1 [ffbed154] + DocStringExtensions v0.9.4 [a0c94c4b] + FastaIO v1.1.0 [1fa38f19] + Format v1.3.7 [92fee26a] + GZip v0.6.2 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [0f8b85d8] + JSON3 v1.14.2 [9c8b4983] + LightXML v0.9.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [51bafb47] + MIToS v3.0.6 [e1d29d7a] + Missings v1.2.0 [86f7a689] + NamedArrays v0.10.3 [bac558e1] + OrderedCollections v1.8.0 [f9da4da7] + PairwiseListMatrices v0.11.1 [69de0a69] + Parsers v2.8.1 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [43287f4e] + PtrArrays v1.3.0 [3cdcf5f2] + RecipesBase v1.3.4 [ae029012] + Requires v1.3.1 [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 v0.34.4 [856f2bd8] + StructTypes v1.11.0 [3bb67fe8] + TranscodingStreams v0.11.3 [94ce4f54] + Libiconv_jll v1.18.0+0 [02c8fc9c] + XML2_jll v2.13.6+1 [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 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg 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 v1.11.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 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 4.0s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 210.94s ################################################################################ # Testing # Testing MIToS Status `/tmp/jl_XvknjP/Project.toml` [4c88cf16] Aqua v0.8.11 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.4.2 [aaaa29a8] Clustering v0.15.8 [944b1d66] CodecZlib v0.7.8 [8bb1440f] DelimitedFiles v1.9.1 [e30172f5] Documenter v1.10.1 [a0c94c4b] FastaIO v1.1.0 [1fa38f19] Format v1.3.7 [0f8b85d8] JSON3 v1.14.2 [9c8b4983] LightXML v0.9.1 [51bafb47] MIToS v3.0.6 [86f7a689] NamedArrays v0.10.3 [bac558e1] OrderedCollections v1.8.0 [f9da4da7] PairwiseListMatrices v0.11.1 [f535d66d] ROCAnalysis v0.3.6 [3cdcf5f2] RecipesBase v1.3.4 [90137ffa] StaticArrays v1.9.13 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.4 [3bb67fe8] TranscodingStreams v0.11.3 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.6.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [44cfe95a] Pkg v1.11.0 [9a3f8284] Random v1.11.0 [9e88b42a] Serialization v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_XvknjP/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.11 [15f4f7f2] AutoHashEquals v2.2.0 [47718e42] BioGenerics v0.1.5 [de9282ab] BioStructures v4.4.2 [3c28c6f8] BioSymbols v5.1.3 [aaaa29a8] Clustering v0.15.8 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.2 [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 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.118 [ffbed154] DocStringExtensions v0.9.4 [e30172f5] Documenter v1.10.1 [a0c94c4b] FastaIO v1.1.0 [1a297f60] FillArrays v1.13.0 [1fa38f19] Format v1.3.7 [92fee26a] GZip v0.6.2 [d7ba0133] Git v1.3.1 [34004b35] HypergeometricFunctions v0.3.28 [b5f81e59] IOCapture v0.2.5 [842dd82b] InlineStrings v1.4.3 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.2 [b964fa9f] LaTeXStrings v1.4.0 [0e77f7df] LazilyInitializedFields v1.3.0 [9c8b4983] LightXML v0.9.1 [2ab3a3ac] LogExpFunctions v0.3.29 [51bafb47] MIToS v3.0.6 [d0879d2d] MarkdownAST v0.1.2 [e1d29d7a] Missings v1.2.0 [86f7a689] NamedArrays v0.10.3 [b8a86587] NearestNeighbors v0.4.21 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.33 [f9da4da7] PairwiseListMatrices v0.11.1 [69de0a69] Parsers v2.8.1 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [f535d66d] ROCAnalysis v0.3.6 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [2792f1a3] RegistryInstances v0.1.0 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.8.0 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [4c63d2b9] StatsFuns v1.4.0 [892a3eda] StringManipulation v0.4.1 [856f2bd8] StructTypes v1.11.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [3bb67fe8] TranscodingStreams v0.11.3 [2e619515] Expat_jll v2.6.5+0 [f8c6e375] Git_jll v2.49.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [458c3c95] OpenSSL_jll v3.0.16+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [02c8fc9c] XML2_jll v2.13.6+1 [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 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.11.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.11.0 [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 v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [efcefdf7] PCRE2_jll v10.42.0+1 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling MIToS... 13660.8 ms ✓ BioStructures 2462.0 ms ✓ PairwiseListMatrices 13185.5 ms ✓ MIToS 3 dependencies successfully precompiled in 30 seconds. 70 already precompiled. Precompiling ROCAnalysis... 9470.3 ms ✓ Distributions 18057.5 ms ✓ ROCAnalysis 2 dependencies successfully precompiled in 30 seconds. 63 already precompiled. Precompiling BioStructuresDataFramesExt... 4556.9 ms ✓ BioStructures → BioStructuresDataFramesExt 1 dependency successfully precompiled in 5 seconds. 50 already precompiled. Precompiling DistributionsTestExt... 3617.8 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 5 seconds. 48 already precompiled. Precompiling MIToSROCAnalysisExt... 11009.8 ms ✓ MIToS → MIToSROCAnalysisExt 1 dependency successfully precompiled in 15 seconds. 106 already precompiled. Precompiling Clustering... 4587.6 ms ✓ NearestNeighbors 3660.3 ms ✓ Clustering 2 dependencies successfully precompiled in 9 seconds. 34 already precompiled. Precompiling MIToSClusteringExt... 4157.4 ms ✓ MIToS → MIToSClusteringExt 1 dependency successfully precompiled in 5 seconds. 77 already precompiled. Stale dependencies: Test Failed at /home/pkgeval/.julia/packages/Aqua/epbUr/src/stale_deps.jl:31 Expression: isempty(stale_deps) Evaluated: isempty(Base.PkgId[Base.PkgId(Base.UUID("44cfe95a-1eb2-52ea-b672-e2afdf69b78f"), "Pkg")]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:679 [inlined] [2] test_stale_deps(pkg::Base.PkgId; kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/epbUr/src/stale_deps.jl:31 [3] test_stale_deps @ ~/.julia/packages/Aqua/epbUr/src/stale_deps.jl:29 [inlined] [4] #test_stale_deps#34 @ ~/.julia/packages/Aqua/epbUr/src/stale_deps.jl:35 [inlined] [5] test_stale_deps @ ~/.julia/packages/Aqua/epbUr/src/stale_deps.jl:34 [inlined] [6] macro expansion @ ~/.julia/packages/Aqua/epbUr/src/Aqua.jl:90 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [8] test_all(testtarget::Module; ambiguities::Bool, unbound_args::Bool, undefined_exports::Bool, project_extras::Bool, stale_deps::Bool, deps_compat::Bool, piracies::Bool, persistent_tasks::Bool) @ Aqua ~/.julia/packages/Aqua/epbUr/src/Aqua.jl:90 Test Summary: | Pass Fail Total Time Aqua | 9 1 10 59.8s Unbound type parameters | 1 1 0.3s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 18.5s Compat bounds | 4 4 0.6s Piracy | 1 1 0.2s Persistent tasks | 1 1 23.7s ERROR: LoadError: Some tests did not pass: 9 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MIToS/HhZIN/test/tests.jl:24 in expression starting at /home/pkgeval/.julia/packages/MIToS/HhZIN/test/runtests.jl:3 Testing failed after 176.96s ERROR: LoadError: Package MIToS errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 426.52s: package has test failures