Package evaluation of MIToS on Julia 1.13.0-DEV.791 (d5209bd37d*) started at 2025-07-04T14:33:31.172 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 7.83s ################################################################################ # Installation # Installing MIToS... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [51bafb47] + MIToS v3.1.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [15f4f7f2] + AutoHashEquals v2.2.0 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.6.0 [3c28c6f8] + BioSymbols v5.2.0 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.3 [34da2185] + Compat v4.17.0 [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 v1.7.0 [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 v1.3.2 [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 v1.7.1 [2913bbd2] + StatsBase v0.34.5 [856f2bd8] + StructTypes v1.11.0 [3bb67fe8] + TranscodingStreams v0.11.3 [94ce4f54] + Libiconv_jll v1.18.0+0 [02c8fc9c] + XML2_jll v2.14.1+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 v1.12.0 [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 v8.14.1+1 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 Installation completed after 2.92s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 173.71s ################################################################################ # Testing # Testing MIToS Status `/tmp/jl_ModwYK/Project.toml` [4c88cf16] Aqua v0.8.13 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.6.0 [aaaa29a8] Clustering v0.15.8 [944b1d66] CodecZlib v0.7.8 [8bb1440f] DelimitedFiles v1.9.1 [e30172f5] Documenter v1.13.0 [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 v1.9.13 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.5 [3bb67fe8] TranscodingStreams v0.11.3 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [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_ModwYK/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.13 [15f4f7f2] AutoHashEquals v2.2.0 [47718e42] BioGenerics v0.1.5 [de9282ab] BioStructures v4.6.0 [3c28c6f8] BioSymbols v5.2.0 [aaaa29a8] Clustering v0.15.8 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.3 [34da2185] Compat v4.17.0 [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 v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.13.0 [a0c94c4b] FastaIO v1.1.0 [1a297f60] FillArrays v1.13.0 [1fa38f19] Format v1.3.7 [92fee26a] GZip v0.6.2 [d7ba0133] Git v1.4.0 [34004b35] HypergeometricFunctions v0.3.28 [b5f81e59] IOCapture v0.2.5 [842dd82b] InlineStrings v1.4.4 [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 v1.14.3 [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 v0.4.21 [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 v1.3.2 [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 v2.5.1 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.5 [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 v2.6.5+0 [f8c6e375] Git_jll v2.50.0+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 v2.14.1+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 [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 v1.13.0 [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 v8.14.1+1 [e37daf67] LibGit2_jll v1.9.1+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 v3.5.0+0 [efcefdf7] PCRE2_jll v10.45.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Testing Running tests... Precompiling packages... 1341.8 ms ✓ BioGenerics 3821.0 ms ✓ PairwiseListMatrices 15375.6 ms ✓ BioStructures 15017.2 ms ✓ MIToS 4 dependencies successfully precompiled in 36 seconds. 66 already precompiled. Precompiling packages... 82628.5 ms ✓ DataFrames 26231.9 ms ✓ ROCAnalysis 2 dependencies successfully precompiled in 111 seconds. 64 already precompiled. Precompiling packages... 9939.6 ms ✓ BioStructures → BioStructuresDataFramesExt 1 dependency successfully precompiled in 10 seconds. 52 already precompiled. Precompiling packages... 4442.7 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 5 seconds. 49 already precompiled. Precompiling packages... 14649.0 ms ✓ MIToS → MIToSROCAnalysisExt 1 dependency successfully precompiled in 16 seconds. 102 already precompiled. Precompiling packages... 5139.4 ms ✓ Clustering 1 dependency successfully precompiled in 5 seconds. 37 already precompiled. Precompiling packages... 5809.2 ms ✓ MIToS → MIToSClusteringExt 1 dependency successfully precompiled in 6 seconds. 74 already precompiled. Test Summary: | Pass Total Time Aqua | 10 10 1m24.0s Unbound type parameters | 1 1 0.2s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 9.0s Compat bounds | 4 4 0.7s Piracy | 1 1 0.1s Persistent tasks | 1 1 56.4s Test Summary: | Pass Total Time Utils | 105 105 7.1s get_n_words! | 9 9 0.5s hascoordinates | 2 2 0.0s select_element | 2 2 0.4s Matrices to and from lists | 6 6 0.7s General IO | 86 86 3.1s ┌ Warning: Sequence identifier seq is taken; using seq(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier seq is taken; using seq(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier seq is taken; using seq(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier seq is taken; using seq(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier a is taken; using a(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier b is taken; using b(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier b is taken; using b(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier a is taken; using a(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier b is taken; using b(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier b is taken; using b(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier item(1) is taken; using item(1)(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier item(1) is taken; using item(1)(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier x is taken; using x(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier x is taken; using x(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier x(1) is taken; using x(1)(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier x(1) is taken; using x(1)(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier x is taken; using x(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier x is taken; using x(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier x(1) is taken; using x(1)(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier x(1) is taken; using x(1)(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: indexing is deprecated for OrderedSet, please rewrite your code to use iteration │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: Sequence identifier SEQUENCE is taken; using SEQUENCE(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier dupl is taken; using dupl(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: Sequence identifier SEQUENCE is taken; using SEQUENCE(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/GeneralParserMethods.jl:205 ┌ Warning: The second argument should be a feature name, not the sequence identifier: AZBR. │ Possible sequence features: Type and Title └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/MultipleSequenceAlignment.jl:658 ┌ Warning: The second argument should be a feature name, not the sequence identifier: AZBR. │ Possible sequence features: Type and Title └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/MultipleSequenceAlignment.jl:658 ┌ Warning: There was no possible to match the ColMap annotations. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/Concatenation.jl:71 ┌ Warning: There was no possible to match the ColMap annotations. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/Concatenation.jl:71 ┌ Warning: Sequence order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/Concatenation.jl:1005 ┌ Warning: Column order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/Concatenation.jl:1018 ┌ Warning: Sequence order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/Concatenation.jl:1005 ┌ Warning: Sequence order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/Concatenation.jl:1005 ┌ Warning: Column order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/Concatenation.jl:1018 ┌ Warning: Column order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/aToo3/src/MSA/Concatenation.jl:1018 Test Summary: | Pass Total Time MSA | 27114 27114 8m02.8s Residue | 20634 20634 2.8s Alphabet | 69 69 1.4s Three letters name | 11 11 0.2s Annotations | 76 76 5.6s MultipleSequenceAlignment | 331 331 19.4s GeneralParserMethods | 49 49 19.3s IO | 210 210 42.6s Test using MSA files | 220 220 10.0s MSAEditing.jl | 79 79 24.4s MSA Stats | 44 44 1.3s AnnotatedSequence | 124 124 4.2s Shuffle | 117 117 30.9s Identity | 4226 4226 7.1s Clusters | 100 100 0.0s Hobohm I | 9 9 2.6s MSA Annotations | 15 15 0.6s getindex | 199 199 7.5s hcat | 109 109 6.3s vcat | 48 48 2.4s _find_gaps | 1 1 1.5s join MSAs | 443 443 18.4s ┌ Warning: Assignment to `gaussdca_installed` in soft scope is ambiguous because a global variable by the same name exists: `gaussdca_installed` will be treated as a new local. Disambiguate by using `local gaussdca_installed` to suppress this warning or `global gaussdca_installed` to assign to the existing global variable. └ @ ~/.julia/packages/MIToS/aToo3/test/Information/Externals.jl:11 ┌ Warning: GaussDCA.jl not gaussdca_installed: ArgumentError("Package Pkg not found in current path.") └ @ Main ~/.julia/packages/MIToS/aToo3/test/Information/Externals.jl:13 Test Summary: | Pass Total Time Information | 783 783 1m11.5s ContingencyTables | 442 442 19.3s Counters | 201 201 17.4s Information Measures | 49 49 3.4s Iterations | 26 26 11.9s CorrectedMutualInformation | 55 55 15.6s Pairwise Gap Percentage | 10 10 1.3s 2VQC.xml.gz:1: parser error : Start tag expected, '<' not found  ^ Test downloadpdb: Error During Test at /home/pkgeval/.julia/packages/MIToS/aToo3/test/PDB/PDB.jl:18 Got exception outside of a @test LightXML.XMLParseError{String}("Failure in parsing an XML file.") Stacktrace: [1] _check_result @ ~/.julia/packages/LightXML/PG9aQ/src/document.jl:88 [inlined] [2] parse_file(filename::String) @ LightXML ~/.julia/packages/LightXML/PG9aQ/src/document.jl:92 [3] _read(::String, ::String, ::Type{PDBML}; kargs::@Kwargs{}) @ MIToS.Utils ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:92 [4] _read @ ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:83 [inlined] [5] read_file(::String, ::Type{PDBML}; kargs::@Kwargs{}) @ MIToS.Utils ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:136 [6] read_file(::String, ::Type{PDBML}) @ MIToS.Utils ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:117 [7] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/PDB/PDB.jl:3 [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [9] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/PDB.jl:20 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [11] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/PDB.jl:25 [inlined] [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [13] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/tests.jl:68 [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [15] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/tests.jl:68 [inlined] [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [17] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/runtests.jl:3 [18] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [19] top-level scope @ none:6 [20] eval(m::Module, e::Any) @ Core ./boot.jl:489 [21] exec_options(opts::Base.JLOptions) @ Base ./client.jl:290 [22] _start() @ Base ./client.jl:557 /home/pkgeval/.julia/packages/MIToS/aToo3/test/data/1H4A.xml.gz:1: parser error : Start tag expected, '<' not found  ^ 1H4A: Chain A (auth) == Chain X (label): Error During Test at /home/pkgeval/.julia/packages/MIToS/aToo3/test/PDB/PDB.jl:66 Got exception outside of a @test LightXML.XMLParseError{String}("Failure in parsing an XML file.") Stacktrace: [1] _check_result @ ~/.julia/packages/LightXML/PG9aQ/src/document.jl:88 [inlined] [2] parse_file(filename::String) @ LightXML ~/.julia/packages/LightXML/PG9aQ/src/document.jl:92 [3] _read(::String, ::String, ::Type{PDBML}; kargs::@Kwargs{label::Bool}) @ MIToS.Utils ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:92 [4] _read @ ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:83 [inlined] [5] read_file(::String, ::Type{PDBML}; kargs::@Kwargs{label::Bool}) @ MIToS.Utils ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:136 [6] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/PDB/PDB.jl:3 [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [8] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/PDB.jl:68 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [10] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/PDB.jl:69 [inlined] [11] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [12] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/tests.jl:68 [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [14] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/tests.jl:68 [inlined] [15] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [16] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/runtests.jl:3 [17] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [18] top-level scope @ none:6 [19] eval(m::Module, e::Any) @ Core ./boot.jl:489 [20] exec_options(opts::Base.JLOptions) @ Base ./client.jl:290 [21] _start() @ Base ./client.jl:557 ┌ Warning: There is no alpha carbon in residue │ PDBe_number number name group model chain │ "" "115" "ASN" "ATOM" "1" "E" └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/Kabsch.jl:85 ┌ Warning: There is no alpha carbon in residue │ PDBe_number number name group model chain │ "97" "115" "ASN" "ATOM" "1" "A" └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/Kabsch.jl:85 ┌ Warning: RESIDUE NAG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE FUL is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE NDG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE BMA is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE MAN is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE NAG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE GAL is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE MAN is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE NAG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE NAG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE FUC is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE NDG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE BMA is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE MAN is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE NAG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE GAL is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE MAN is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 ┌ Warning: RESIDUE NAG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AtomsData.jl:844 /home/pkgeval/.julia/packages/MIToS/aToo3/test/data/1AKS.xml.gz:1: parser error : Start tag expected, '<' not found  ^ 1AKS: Error During Test at /home/pkgeval/.julia/packages/MIToS/aToo3/test/PDB/Contacts.jl:111 Got exception outside of a @test LightXML.XMLParseError{String}("Failure in parsing an XML file.") Stacktrace: [1] _check_result @ ~/.julia/packages/LightXML/PG9aQ/src/document.jl:88 [inlined] [2] parse_file(filename::String) @ LightXML ~/.julia/packages/LightXML/PG9aQ/src/document.jl:92 [3] _read(::String, ::String, ::Type{PDBML}; kargs::@Kwargs{}) @ MIToS.Utils ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:92 [4] _read @ ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:83 [inlined] [5] read_file(::String, ::Type{PDBML}; kargs::@Kwargs{}) @ MIToS.Utils ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:136 [6] read_file(::String, ::Type{PDBML}) @ MIToS.Utils ~/.julia/packages/MIToS/aToo3/src/Utils/Read.jl:117 [7] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/PDB/Contacts.jl:3 [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [9] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/Contacts.jl:113 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [11] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/Contacts.jl:113 [inlined] [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [13] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/tests.jl:68 [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [15] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/tests.jl:69 [inlined] [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [17] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/runtests.jl:3 [18] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [19] top-level scope @ none:6 [20] eval(m::Module, e::Any) @ Core ./boot.jl:489 [21] exec_options(opts::Base.JLOptions) @ Base ./client.jl:290 [22] _start() @ Base ./client.jl:557 ┌ Warning: Using 2 residues for RMSD calculation because there are 1 residues without CA: [2] └ @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/Kabsch.jl:266 Test Summary: | Pass Error Total Time PDB | 13441 3 13444 2m25.0s Parse PDB and PDBML | 131 2 133 22.8s 2VQC: Missings | 2 2 2.7s Test downloadpdb | 1 1 3.9s 1H4A: Chain A (auth) == Chain X (label) | 1 1 1.2s 1SSX: Residues with insert codes, 15A 15B | 19 19 3.5s read_file with occupancyfilter=true | 5 5 0.6s CBN: Identical PDBe ResNum for Residue 22 | 4 4 0.3s 1AS5: NMR | 3 3 0.6s 1DPO: Inserted residues lack insertion letters | 8 8 1.3s 1IGY: Insertions | 4 4 1.9s 1HAG | 4 4 1.4s 1NSA | 4 4 1.5s 1IAO | 12 12 2.9s 3BTT | 2 2 0.9s Foldseek | 64 64 0.1s RESTful PDB Interface | 10 10 12.6s Write PDB files | 16 16 3.7s Contacts | 12975 1 12976 13.7s Piccolo | 12950 12950 8.8s 1AKS | 1 1 1.0s Vectorized contact/distance | 20 20 2.4s Proximity Mean | 5 5 1.5s Kabsch algorithm | 63 63 53.2s AtomsData internals | 187 187 1.2s Check amino acid residues | 8 8 0.1s Extract protein sequences from PDB | 44 44 1.5s AlphaFoldDB Tests | 7 7 33.1s RNG of the outermost testset: Xoshiro(0xd80f1b51cdde6de5, 0xd54558518435dc1a, 0xd16ce531c5d9f68f, 0x4ba277ba195409e0, 0x8070e455e90e181e) ERROR: LoadError: Some tests did not pass: 13441 passed, 0 failed, 3 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MIToS/aToo3/test/tests.jl:67 in expression starting at /home/pkgeval/.julia/packages/MIToS/aToo3/test/runtests.jl:3 Testing failed after 984.18s ERROR: LoadError: Package MIToS 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:2423 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2278 [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:500 [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:324 [12] _start() @ Base ./client.jl:557 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1228.65s: package is using an unknown package