Package evaluation to test MIToS on Julia 1.13.0-DEV.1319 (9cddfda8ef*) started at 2025-10-16T18:02:02.968


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 9.0s


################################################################################
# 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 v4.7.0
  [3c28c6f8] + BioSymbols v5.2.0
  [944b1d66] + CodecZlib v0.7.8
  [861a8166] + Combinatorics v1.0.3
  [9a962f9c] + DataAPI v1.16.0
  [864edb3b] + DataStructures v0.19.1
  [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 v0.2.6
  [692b3bcd] + JLLWrappers v1.7.1
  [0f8b85d8] + JSON3 v1.14.3
  [9c8b4983] + LightXML v0.9.3
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [51bafb47] + MIToS v3.1.0
  [e1d29d7a] + Missings v1.2.0
  [86f7a689] + NamedArrays v0.10.5
  [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 v2.15.0+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
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [b27032c2] + LibCURL v0.6.4
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.13.0
  [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 v1.13.0
  [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 v8.16.0+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.9.9
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [458c3c95] + OpenSSL_jll v3.5.4+0
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [3161d3a3] + Zstd_jll v1.5.7+1
  [8e850b90] + libblastrampoline_jll v5.15.0+0
  [8e850ede] + nghttp2_jll v1.67.1+0

Installation completed after 5.78s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 57.53s


################################################################################
# Testing
#

     Testing MIToS
      Status `/tmp/jl_7jz23A/Project.toml`
  [4c88cf16] Aqua v0.8.14
  [15f4f7f2] AutoHashEquals v2.2.0
  [de9282ab] BioStructures v4.7.0
  [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 v0.9.3
  [51bafb47] MIToS v3.1.0
  [86f7a689] NamedArrays v0.10.5
  [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 v1.7.0
  [37e2e46d] LinearAlgebra v1.13.0
  [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_7jz23A/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 v4.7.0
  [3c28c6f8] BioSymbols v5.2.0
  [aaaa29a8] Clustering v0.15.8
  [944b1d66] CodecZlib v0.7.8
  [861a8166] Combinatorics v1.0.3
  [34da2185] Compat v4.18.1
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.8.0
  [864edb3b] DataStructures v0.19.1
  [e2d170a0] DataValueInterfaces v1.0.0
  [8bb1440f] DelimitedFiles v1.9.1
  [b4f34e82] Distances v0.10.12
  [31c24e10] Distributions v0.25.122
  [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 v0.2.6
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.7.1
  [682c06a0] JSON v1.1.0
  [0f8b85d8] JSON3 v1.14.3
  [b964fa9f] LaTeXStrings v1.4.0
  [0e77f7df] LazilyInitializedFields v1.3.0
  [9c8b4983] LightXML v0.9.3
  [2ab3a3ac] LogExpFunctions v0.3.29
  [51bafb47] MIToS v3.1.0
  [d0879d2d] MarkdownAST v0.1.2
  [e1d29d7a] Missings v1.2.0
  [86f7a689] NamedArrays v0.10.5
  [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 v3.1.0
  [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 v2.6.1
  [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
  [ec057cc2] StructUtils v2.5.1
  [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 v10.2.1+0
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [f50d1b31] Rmath_jll v0.5.1+0
  [02c8fc9c] XML2_jll v2.15.0+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 v1.13.0
  [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 v1.13.0
  [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 v8.16.0+0
  [e37daf67] LibGit2_jll v1.9.1+0
  [29816b5a] LibSSH2_jll v1.11.3+1
  [14a3606d] MozillaCACerts_jll v2025.9.9
  [4536629a] OpenBLAS_jll v0.3.29+0
  [05823500] OpenLibm_jll v0.8.7+0
  [458c3c95] OpenSSL_jll v3.5.4+0
  [efcefdf7] PCRE2_jll v10.46.0+0
  [bea87d4a] SuiteSparse_jll v7.10.1+0
  [83775a58] Zlib_jll v1.3.1+2
  [3161d3a3] Zstd_jll v1.5.7+1
  [8e850b90] libblastrampoline_jll v5.15.0+0
  [8e850ede] nghttp2_jll v1.67.1+0
  [3f19e933] p7zip_jll v17.6.0+0
     Testing Running tests...
ERROR: LoadError: Inconsistent dictionary sizes
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] NamedArray
    @ ~/.julia/packages/NamedArrays/f1tMK/src/namedarraytypes.jl:71 [inlined]
  [3] NamedArray
    @ ~/.julia/packages/NamedArrays/f1tMK/src/constructors.jl:43 [inlined]
  [4] macro expansion
    @ ~/.julia/packages/MIToS/aToo3/src/Information/ContingencyTables.jl:249 [inlined]
  [5] MIToS.Information.ContingencyTable{Float64, 2, MIToS.MSA.UngappedAlphabet}(alphabet::MIToS.MSA.UngappedAlphabet)
    @ MIToS.Information ~/.julia/packages/MIToS/aToo3/src/Information/ContingencyTables.jl:235
  [6] ContingencyTable
    @ ~/.julia/packages/MIToS/aToo3/src/Information/ContingencyTables.jl:260 [inlined]
  [7] MIToS.Information.ContingencyTable(matrix::Matrix{Float64}, alphabet::MIToS.MSA.UngappedAlphabet)
    @ MIToS.Information ~/.julia/packages/MIToS/aToo3/src/Information/ContingencyTables.jl:266
  [8] top-level scope
    @ ~/.julia/packages/MIToS/aToo3/src/Information/BLOSUM62.jl:35
  [9] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
 [10] top-level scope
    @ ~/.julia/packages/MIToS/aToo3/src/Information/Information.jl:113
 [11] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
 [12] top-level scope
    @ ~/.julia/packages/MIToS/aToo3/src/MIToS.jl:7
 [13] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [14] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2777
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2536
 [16] macro expansion
    @ ./loading.jl:2464 [inlined]
 [17] macro expansion
    @ ./lock.jl:376 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2428
 [19] require
    @ ./loading.jl:2404 [inlined]
 [20] eval_import_path
    @ ./module.jl:36 [inlined]
 [21] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base ./module.jl:60
 [22] _eval_using(to::Module, path::Expr)
    @ Base ./module.jl:137
 [23] top-level scope
    @ ~/.julia/packages/MIToS/aToo3/test/tests.jl:3
 [24] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
 [25] top-level scope
    @ ~/.julia/packages/MIToS/aToo3/test/runtests.jl:3
 [26] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
 [27] top-level scope
    @ none:6
 [28] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [29] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:310
 [30] _start()
    @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/MIToS/aToo3/src/Information/BLOSUM62.jl:35
in expression starting at /home/pkgeval/.julia/packages/MIToS/aToo3/src/Information/Information.jl:1
in expression starting at /home/pkgeval/.julia/packages/MIToS/aToo3/src/MIToS.jl:1
in expression starting at /home/pkgeval/.julia/packages/MIToS/aToo3/test/tests.jl:3
in expression starting at /home/pkgeval/.julia/packages/MIToS/aToo3/test/runtests.jl:3

Testing failed after 57.4s

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:2674
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2523 [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:548
  [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:525
  [6] 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:172
  [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:161
  [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:160
  [9] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:160 [inlined]
 [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String)
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:159
 [11] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [12] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [13] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:344
 [14] _start()
    @ Base ./client.jl:577
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 147.41s: package tests unexpectedly errored