Package evaluation of MIToS on Julia 1.12.0-rc2.1 (1fad90817e*) started at 2025-09-11T08:39:20.346 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.85s ################################################################################ # Installation # Installing MIToS... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [51bafb47] + MIToS v3.1.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [15f4f7f2] + AutoHashEquals v2.2.0 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.6.1 [3c28c6f8] + BioSymbols v5.2.0 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.3 [34da2185] + Compat v4.18.0 [9a962f9c] + DataAPI v1.16.0 ⌅ [864edb3b] + DataStructures v0.18.22 [8bb1440f] + DelimitedFiles v1.9.1 [ffbed154] + DocStringExtensions v0.9.5 [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 v1.7.1 [0f8b85d8] + JSON3 v1.14.3 [9c8b4983] + LightXML v0.9.2 [2ab3a3ac] + LogExpFunctions v0.3.29 [51bafb47] + MIToS v3.1.0 [e1d29d7a] + Missings v1.2.0 [86f7a689] + NamedArrays v0.10.4 [bac558e1] + OrderedCollections v1.8.1 [f9da4da7] + PairwiseListMatrices v0.11.1 [69de0a69] + Parsers v2.8.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [43287f4e] + PtrArrays v1.3.0 [3cdcf5f2] + RecipesBase v1.3.4 [ae029012] + Requires v1.3.1 [a2af1166] + SortingAlgorithms v1.2.2 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.6 [856f2bd8] + StructTypes v1.11.0 [3bb67fe8] + TranscodingStreams v0.11.3 [94ce4f54] + Libiconv_jll v1.18.0+0 [02c8fc9c] + XML2_jll v2.14.4+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [b27032c2] + LibCURL v0.6.4 [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 [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 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.11.1+1 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+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+1 [8e850ede] + nghttp2_jll v1.64.0+1 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 4.68s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 165.01s ################################################################################ # Testing # Testing MIToS Status `/tmp/jl_cAg0TL/Project.toml` [4c88cf16] Aqua v0.8.14 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.6.1 [aaaa29a8] Clustering v0.15.8 [944b1d66] CodecZlib v0.7.8 [8bb1440f] DelimitedFiles v1.9.1 [e30172f5] Documenter v1.14.1 [a0c94c4b] FastaIO v1.1.0 [1fa38f19] Format v1.3.7 [0f8b85d8] JSON3 v1.14.3 [9c8b4983] LightXML v0.9.2 [51bafb47] MIToS v3.1.0 [86f7a689] NamedArrays v0.10.4 [bac558e1] OrderedCollections v1.8.1 [f9da4da7] PairwiseListMatrices v0.11.1 [f535d66d] ROCAnalysis v0.3.6 [3cdcf5f2] RecipesBase v1.3.4 [90137ffa] StaticArrays v1.9.15 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.6 [3bb67fe8] TranscodingStreams v0.11.3 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.6.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [9a3f8284] Random v1.11.0 [9e88b42a] Serialization v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_cAg0TL/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.14 [15f4f7f2] AutoHashEquals v2.2.0 [47718e42] BioGenerics v0.1.5 [de9282ab] BioStructures v4.6.1 [3c28c6f8] BioSymbols v5.2.0 [aaaa29a8] Clustering v0.15.8 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.3 [34da2185] Compat v4.18.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.14.1 [a0c94c4b] FastaIO v1.1.0 [1a297f60] FillArrays v1.14.0 [1fa38f19] Format v1.3.7 [92fee26a] GZip v0.6.2 [d7ba0133] Git v1.5.0 [34004b35] HypergeometricFunctions v0.3.28 [b5f81e59] IOCapture v0.2.5 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.3 [b964fa9f] LaTeXStrings v1.4.0 [0e77f7df] LazilyInitializedFields v1.3.0 [9c8b4983] LightXML v0.9.2 [2ab3a3ac] LogExpFunctions v0.3.29 [51bafb47] MIToS v3.1.0 [d0879d2d] MarkdownAST v0.1.2 [e1d29d7a] Missings v1.2.0 [86f7a689] NamedArrays v0.10.4 [b8a86587] NearestNeighbors v0.4.22 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [f9da4da7] PairwiseListMatrices v0.11.1 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 ⌅ [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 v1.2.2 [276daf66] SpecialFunctions v2.5.1 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.6 [4c63d2b9] StatsFuns v1.5.0 [892a3eda] StringManipulation v0.4.1 [856f2bd8] StructTypes v1.11.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [2e619515] Expat_jll v2.7.1+0 [020c3dae] Git_LFS_jll v3.7.0+0 [f8c6e375] Git_jll v2.51.1+0 [94ce4f54] Libiconv_jll v1.18.0+0 [9bd350c2] OpenSSH_jll v10.0.1+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [02c8fc9c] XML2_jll v2.14.4+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [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 v1.12.0 [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 v1.12.0 [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 v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.1+0 [efcefdf7] PCRE2_jll v10.44.0+1 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+1 [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... Precompiling packages... 15543.0 ms ✓ BioStructures 42151.1 ms ✓ MIToS 2 dependencies successfully precompiled in 58 seconds. 68 already precompiled. Precompiling packages... 131228.7 ms ✓ DataFrames 10632.5 ms ✓ Distributions 30060.4 ms ✓ ROCAnalysis 3 dependencies successfully precompiled in 175 seconds. 64 already precompiled. Precompiling packages... 9392.6 ms ✓ BioStructures → BioStructuresDataFramesExt 1 dependency successfully precompiled in 10 seconds. 52 already precompiled. Precompiling packages... 5199.5 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 7 seconds. 50 already precompiled. Precompiling packages... 14413.7 ms ✓ MIToS → MIToSROCAnalysisExt 1 dependency successfully precompiled in 17 seconds. 103 already precompiled. Precompiling packages... 5033.9 ms ✓ Clustering 1 dependency successfully precompiled in 6 seconds. 37 already precompiled. Precompiling packages... 5309.4 ms ✓ MIToS → MIToSClusteringExt 1 dependency successfully precompiled in 6 seconds. 74 already precompiled. Test Summary: | Pass Total Time Aqua | 10 10 1m14.6s Unbound type parameters | 1 1 0.1s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 8.0s Compat bounds | 4 4 0.7s Piracy | 1 1 0.1s Persistent tasks | 1 1 31.2s Download a gz file: Error During Test at /home/pkgeval/.julia/packages/MIToS/aToo3/test/Utils/GeneralUtils.jl:136 Got exception outside of a @test RequestError: HTTP/2 503 while requesting https://www.rcsb.org/pdb/files/3NIR.pdb.gz Stacktrace: [1] #4 @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:271 [inlined] [2] open(f::Downloads.var"#4#5"{Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Nothing, String}, args::String; kwargs::@Kwargs{write::Bool, lock::Bool}) @ Base ./io.jl:410 [3] open_nolock @ /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:35 [inlined] [4] arg_write(f::Function, arg::String) @ ArgTools /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:103 [5] #download#2 @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:258 [inlined] [6] download @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:247 [inlined] [7] #6 @ ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:29 [inlined] [8] with_logstate(f::MIToS.Utils.var"#6#7"{@Kwargs{}, String, String}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:540 [9] with_logger @ ./logging/logging.jl:651 [inlined] [10] _download_file(url::String, filename::String; kargs::@Kwargs{}) @ MIToS.Utils ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:28 [11] _download_file(url::String, filename::String) @ MIToS.Utils ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:27 [12] (::Base.var"#46#47"{Base.var"#48#49"{ExponentialBackOff, Nothing, typeof(MIToS.Utils._download_file)}})(::String, ::Vararg{String}; kwargs::@Kwargs{}) @ Base ./error.jl:321 [13] #46 @ ./error.jl:304 [inlined] [14] #download_file#8 @ ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:47 [inlined] [15] download_file @ ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:46 [inlined] [16] #download_file#9 @ ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:55 [inlined] [17] download_file(url::String) @ MIToS.Utils ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:50 [18] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/Utils/GeneralUtils.jl:141 [inlined] [19] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [20] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/Utils/GeneralUtils.jl:139 [inlined] [21] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [22] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/Utils/GeneralUtils.jl:73 [23] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [24] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/tests.jl:31 [25] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [26] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/tests.jl:31 [inlined] [27] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [28] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/runtests.jl:3 [29] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [30] top-level scope @ none:6 [31] eval(m::Module, e::Any) @ Core ./boot.jl:489 [32] exec_options(opts::Base.JLOptions) @ Base ./client.jl:287 [33] _start() @ Base ./client.jl:554 Test Summary: | Pass Error Total Time Utils | 103 1 104 1m00.0s get_n_words! | 9 9 0.3s hascoordinates | 2 2 0.0s select_element | 2 2 0.4s Matrices to and from lists | 6 6 0.7s General IO | 84 1 85 57.0s lineiterator | 7 7 0.1s File checking | 4 4 0.0s Download file | 1 1 2.2s Download file: redirect | 1 1 0.6s Test _check_gzip_file | 71 71 0.0s Download a gz file | 1 1 54.1s RNG of the outermost testset: Xoshiro(0xb15890137947bd3d, 0xc361945a71536510, 0x08b785ac275ea21e, 0xc924ce0cfcf0f321, 0xa7148bda7cb1bcea) ERROR: LoadError: Some tests did not pass: 103 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MIToS/aToo3/test/tests.jl:30 in expression starting at /home/pkgeval/.julia/packages/MIToS/aToo3/test/runtests.jl:3 Testing failed after 391.22s ERROR: LoadError: Package MIToS 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:2427 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2280 [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:483 [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 653.97s: networking-related issues were detected