Package evaluation of MIToS on Julia 1.13.0-DEV.733 (c0ecfe9bcc*) started at 2025-06-12T18:15:53.921 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 7.4s ################################################################################ # 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 v4.5.0 [3c28c6f8] + BioSymbols v5.2.0 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.3 [34da2185] + Compat v4.16.0 [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 v0.9.1 [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 v2.13.6+1 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.7.0 [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 v8.12.1+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 v5.12.0+0 [8e850ede] + nghttp2_jll v1.65.0+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 4.01s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 268.18s ################################################################################ # Testing # Testing MIToS Status `/tmp/jl_lQ73Py/Project.toml` [4c88cf16] Aqua v0.8.13 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.5.0 [aaaa29a8] Clustering v0.15.8 [944b1d66] CodecZlib v0.7.8 [8bb1440f] DelimitedFiles v1.9.1 [e30172f5] Documenter v1.12.0 [a0c94c4b] FastaIO v1.1.0 [1fa38f19] Format v1.3.7 [0f8b85d8] JSON3 v1.14.3 [9c8b4983] LightXML v0.9.1 [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_lQ73Py/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 v4.5.0 [3c28c6f8] BioSymbols v5.2.0 [aaaa29a8] Clustering v0.15.8 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.3 [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 v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.12.0 [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 v1.4.3 [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 v1.14.3 [b964fa9f] LaTeXStrings v1.4.0 [0e77f7df] LazilyInitializedFields v1.3.0 [9c8b4983] LightXML v0.9.1 [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 v2.49.0+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 v2.13.6+1 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [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 v8.12.1+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 v3.5.0+0 [efcefdf7] PCRE2_jll v10.44.0+1 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.65.0+0 [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... 12830.5 ms ✓ BioStructures 29555.2 ms ✓ MIToS 2 dependencies successfully precompiled in 44 seconds. 68 already precompiled. Precompiling packages... 116026.9 ms ✓ DataFrames 10544.1 ms ✓ Distributions 27551.0 ms ✓ ROCAnalysis 3 dependencies successfully precompiled in 156 seconds. 63 already precompiled. Precompiling packages... 10353.0 ms ✓ BioStructures → BioStructuresDataFramesExt 1 dependency successfully precompiled in 11 seconds. 52 already precompiled. Precompiling packages... 4777.3 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 6 seconds. 49 already precompiled. Precompiling packages... 16559.1 ms ✓ MIToS → MIToSROCAnalysisExt 1 dependency successfully precompiled in 18 seconds. 102 already precompiled. Precompiling packages... 5174.9 ms ✓ Clustering 1 dependency successfully precompiled in 6 seconds. 37 already precompiled. Precompiling packages... 5930.9 ms ✓ MIToS → MIToSClusteringExt 1 dependency successfully precompiled in 7 seconds. 74 already precompiled. Test Summary: | Pass Total Time Aqua | 10 10 1m05.2s 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 6.1s Compat bounds | 4 4 0.5s Piracy | 1 1 0.0s Persistent tasks | 1 1 43.3s Test Summary: | Pass Total Time Utils | 105 105 7.2s get_n_words! | 9 9 0.4s 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 8m06.5s Residue | 20634 20634 2.6s Alphabet | 69 69 1.3s Three letters name | 11 11 0.2s Annotations | 76 76 5.3s MultipleSequenceAlignment | 331 331 17.3s GeneralParserMethods | 49 49 18.5s IO | 210 210 41.5s Test using MSA files | 220 220 10.0s MSAEditing.jl | 79 79 22.9s MSA Stats | 44 44 1.2s AnnotatedSequence | 124 124 3.9s Shuffle | 117 117 30.7s Identity | 4226 4226 6.7s Clusters | 100 100 0.0s Hobohm I | 9 9 2.6s MSA Annotations | 15 15 0.5s getindex | 199 199 7.4s hcat | 109 109 6.3s vcat | 48 48 2.3s _find_gaps | 1 1 1.5s join MSAs | 443 443 17.2s ┌ 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 1m06.9s ContingencyTables | 442 442 18.4s Counters | 201 201 15.3s Information Measures | 49 49 3.2s Iterations | 26 26 11.4s CorrectedMutualInformation | 55 55 14.9s Pairwise Gap Percentage | 10 10 1.2s ┌ 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 ┌ 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 Download mmCIF format: Error During Test at /home/pkgeval/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:28 Got exception outside of a @test RequestError: Operation too slow. Less than 1 bytes/sec transferred the last 20 seconds while requesting https://alphafold.ebi.ac.uk/api/prediction/A0A0C5B5G6 Stacktrace: [1] (::Downloads.var"#26#27"{IOBuffer, Base.DevNull, String, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool})(easy::Downloads.Curl.Easy) @ Downloads /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:479 [2] with_handle(f::Downloads.var"#26#27"{IOBuffer, Base.DevNull, String, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, handle::Downloads.Curl.Easy) @ Downloads.Curl /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Curl/Curl.jl:105 [3] #24 @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:390 [inlined] [4] arg_write(f::Downloads.var"#24#25"{Base.DevNull, String, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, arg::IOBuffer) @ ArgTools /opt/julia/share/julia/stdlib/v1.13/ArgTools/src/ArgTools.jl:134 [5] #22 @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:389 [inlined] [6] arg_read @ /opt/julia/share/julia/stdlib/v1.13/ArgTools/src/ArgTools.jl:76 [inlined] [7] #request#9 @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:388 [inlined] [8] request @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:355 [inlined] [9] query_alphafolddb(uniprot_accession::String) @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AlphaFoldDB.jl:13 [10] download_alphafold_structure(uniprot_accession::String; format::Type{MMCIFFile}) @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AlphaFoldDB.jl:48 [11] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:2 [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1837 [inlined] [13] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:16 [inlined] [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1837 [inlined] [15] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:29 [inlined] [16] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1837 [inlined] [17] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:29 [inlined] [18] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [19] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/tests.jl:68 [20] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1837 [inlined] [21] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/tests.jl:73 [inlined] [22] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [23] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/runtests.jl:3 [24] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [25] top-level scope @ none:6 [26] eval(m::Module, e::Any) @ Core ./boot.jl:489 [27] exec_options(opts::Base.JLOptions) @ Base ./client.jl:290 [28] _start() @ Base ./client.jl:557 Unsupported format: Test Failed at /home/pkgeval/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:42 Expression: download_alphafold_structure("A0A0C5B5G6", format = UnsupportedFormat) Expected: ArgumentError Thrown: Downloads.RequestError RequestError: Operation too slow. Less than 1 bytes/sec transferred the last 20 seconds while requesting https://alphafold.ebi.ac.uk/api/prediction/A0A0C5B5G6 Stacktrace: [1] (::Downloads.var"#26#27"{IOBuffer, Base.DevNull, String, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool})(easy::Downloads.Curl.Easy) @ Downloads /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:479 [2] with_handle(f::Downloads.var"#26#27"{IOBuffer, Base.DevNull, String, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, handle::Downloads.Curl.Easy) @ Downloads.Curl /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Curl/Curl.jl:105 [3] #24 @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:390 [inlined] [4] arg_write(f::Downloads.var"#24#25"{Base.DevNull, String, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, arg::IOBuffer) @ ArgTools /opt/julia/share/julia/stdlib/v1.13/ArgTools/src/ArgTools.jl:134 [5] #22 @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:389 [inlined] [6] arg_read @ /opt/julia/share/julia/stdlib/v1.13/ArgTools/src/ArgTools.jl:76 [inlined] [7] #request#9 @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:388 [inlined] [8] request @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:355 [inlined] [9] query_alphafolddb(uniprot_accession::String) @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AlphaFoldDB.jl:13 [10] download_alphafold_structure(uniprot_accession::String; format::Type{UnsupportedFormat}) @ MIToS.PDB ~/.julia/packages/MIToS/aToo3/src/PDB/AlphaFoldDB.jl:48 [11] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:2 [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1837 [inlined] [13] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:16 [inlined] [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1837 [inlined] [15] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:41 [inlined] [16] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1837 [inlined] [17] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:42 [inlined] [18] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:824 [inlined] [19] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:42 [inlined] Stacktrace: [1] top-level scope @ ~/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:2 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1837 [inlined] [3] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:16 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1837 [inlined] [5] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:41 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1837 [inlined] [7] macro expansion @ ~/.julia/packages/MIToS/aToo3/test/PDB/AlphaFoldDB.jl:42 [inlined] Test Summary: | Pass Fail Error Total Time PDB | 13776 1 1 13778 2m42.9s Parse PDB and PDBML | 139 139 23.2s RESTful PDB Interface | 10 10 1.4s Write PDB files | 16 16 3.6s Contacts | 13304 13304 12.8s Kabsch algorithm | 63 63 50.5s AtomsData internals | 187 187 1.3s Check amino acid residues | 8 8 0.0s Extract protein sequences from PDB | 44 44 1.7s AlphaFoldDB Tests | 5 1 1 7 1m05.2s query_alphafolddb tests | 3 3 8.2s download_alphafold_structure tests | 1 1 1 3 56.9s Download PDB format | 1 1 6.8s Download mmCIF format | 1 1 23.3s Unsupported format | 1 1 26.8s _extract_filename_from_url tests | 1 1 0.0s RNG of the outermost testset: Xoshiro(0x54700c3ddf223444, 0x09d51148976efc25, 0x7b5ed2bce65a6db7, 0x4fe3a8fcee05d3f0, 0x0a02fcb2a75c18d6) ERROR: LoadError: Some tests did not pass: 13776 passed, 1 failed, 1 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 1012.64s 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:2421 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2276 [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:324 [12] _start() @ Base ./client.jl:557 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1381.06s: package is using an unknown package