Package evaluation of BioMart on Julia 1.13.0-DEV.108 (095fc99b69*) started at 2025-02-28T01:40:41.528


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 9.15s


################################################################################
# Installation
#

Installing BioMart...
   Resolving package versions...
   Installed Crayons ───────────────────── v4.1.1
   Installed XML2_jll ──────────────────── v2.13.6+1
   Installed BioGenerics ───────────────── v0.1.5
   Installed BioMart ───────────────────── v0.1.1
   Installed GenomicFeatures ───────────── v2.1.0
   Installed Preferences ───────────────── v1.4.3
   Installed BitFlags ──────────────────── v0.1.9
   Installed LoggingExtras ─────────────── v1.1.0
   Installed TableTraits ───────────────── v1.0.1
   Installed SimpleBufferStream ────────── v1.2.0
   Installed SentinelArrays ────────────── v1.4.8
   Installed Parsers ───────────────────── v2.8.1
   Installed PooledArrays ──────────────── v1.4.3
   Installed DataAPI ───────────────────── v1.16.0
   Installed Tables ────────────────────── v1.12.0
   Installed PrettyTables ──────────────── v2.4.0
   Installed ConcurrentUtilities ───────── v2.5.0
   Installed InlineStrings ─────────────── v1.4.3
   Installed Libiconv_jll ──────────────── v1.18.0+0
   Installed IteratorInterfaceExtensions ─ v1.0.0
   Installed JLLWrappers ───────────────── v1.7.0
   Installed PrecompileTools ───────────── v1.2.1
   Installed DataValueInterfaces ───────── v1.0.0
   Installed URIs ──────────────────────── v1.5.1
   Installed WorkerUtilities ───────────── v1.6.1
   Installed LaTeXStrings ──────────────── v1.4.0
   Installed OrderedCollections ────────── v1.8.0
   Installed OpenSSL ───────────────────── v1.4.3
   Installed TranscodingStreams ────────── v0.11.3
   Installed InvertedIndices ───────────── v1.3.1
   Installed Reexport ──────────────────── v1.2.2
   Installed FilePathsBase ─────────────── v0.9.23
   Installed HTTP ──────────────────────── v1.10.15
   Installed MbedTLS ───────────────────── v1.1.9
   Installed Statistics ────────────────── v1.11.1
   Installed WeakRefStrings ────────────── v1.4.2
   Installed Memoization ───────────────── v0.1.14
   Installed DataStructures ────────────── v0.18.20
   Installed IntervalTrees ─────────────── v1.1.0
   Installed MbedTLS_jll ───────────────── v2.28.6+1
   Installed Compat ────────────────────── v4.16.0
   Installed DataFrames ────────────────── v1.7.0
   Installed MacroTools ────────────────── v0.5.15
   Installed LightXML ──────────────────── v0.9.1
   Installed CodecZlib ─────────────────── v0.7.8
   Installed ExceptionUnwrapping ───────── v0.1.11
   Installed Missings ──────────────────── v1.2.0
   Installed StringManipulation ────────── v0.4.1
   Installed SortingAlgorithms ─────────── v1.2.1
   Installed CSV ───────────────────────── v0.10.15
  Installing 3 artifacts
   Installed artifact XML2     2.5 MiB
   Installed artifact MbedTLS  2.1 MiB
   Installed artifact Libiconv 1.9 MiB
    Updating `~/.julia/environments/v1.13/Project.toml`
  [d3a97c8b] + BioMart v0.1.1
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [47718e42] + BioGenerics v0.1.5
  [d3a97c8b] + BioMart v0.1.1
  [d1d4a3ce] + BitFlags v0.1.9
  [336ed68f] + CSV v0.10.15
  [944b1d66] + CodecZlib v0.7.8
  [34da2185] + Compat v4.16.0
  [f0e56b4a] + ConcurrentUtilities v2.5.0
  [a8cc5b0e] + Crayons v4.1.1
  [9a962f9c] + DataAPI v1.16.0
  [a93c6f00] + DataFrames v1.7.0
  [864edb3b] + DataStructures v0.18.20
  [e2d170a0] + DataValueInterfaces v1.0.0
  [460bff9d] + ExceptionUnwrapping v0.1.11
  [48062228] + FilePathsBase v0.9.23
⌅ [899a7d2d] + GenomicFeatures v2.1.0
  [cd3eb016] + HTTP v1.10.15
  [842dd82b] + InlineStrings v1.4.3
  [524e6230] + IntervalTrees v1.1.0
  [41ab1584] + InvertedIndices v1.3.1
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.0
  [b964fa9f] + LaTeXStrings v1.4.0
  [9c8b4983] + LightXML v0.9.1
  [e6f89c97] + LoggingExtras v1.1.0
  [1914dd2f] + MacroTools v0.5.15
  [739be429] + MbedTLS v1.1.9
⌅ [6fafb56a] + Memoization v0.1.14
  [e1d29d7a] + Missings v1.2.0
  [4d8831e6] + OpenSSL v1.4.3
  [bac558e1] + OrderedCollections v1.8.0
  [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
  [189a3867] + Reexport v1.2.2
  [91c51154] + SentinelArrays v1.4.8
  [777ac1f9] + SimpleBufferStream v1.2.0
  [a2af1166] + SortingAlgorithms v1.2.1
  [10745b16] + Statistics v1.11.1
  [892a3eda] + StringManipulation v0.4.1
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.0
  [3bb67fe8] + TranscodingStreams v0.11.3
  [5c2747f8] + URIs v1.5.1
  [ea10d353] + WeakRefStrings v1.4.2
  [76eceee3] + WorkerUtilities v1.6.1
  [94ce4f54] + Libiconv_jll v1.18.0+0
  [c8ffd9c3] + MbedTLS_jll v2.28.6+1
  [02c8fc9c] + XML2_jll v2.13.6+1
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [9fa8497b] + Future v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [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
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [f489334b] + StyledStrings v1.11.0
  [fa267f1f] + TOML v1.0.3
  [8dfed614] + Test v1.11.0
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
  [14a3606d] + MozillaCACerts_jll v2024.12.31
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [458c3c95] + OpenSSL_jll v3.0.16+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850b90] + libblastrampoline_jll v5.12.0+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 8.07s


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

Precompiling PkgEval dependencies...
Precompiling packages...
   6661.2 ms  ✓ TestEnv
  1 dependency successfully precompiled in 9 seconds. 25 already precompiled.

Precompiling package dependencies...

Precompilation completed after 325.63s


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

     Testing BioMart
      Status `/tmp/jl_4YJgnR/Project.toml`
  [d3a97c8b] BioMart v0.1.1
  [336ed68f] CSV v0.10.15
  [a93c6f00] DataFrames v1.7.0
⌅ [899a7d2d] GenomicFeatures v2.1.0
  [cd3eb016] HTTP v1.10.15
  [9c8b4983] LightXML v0.9.1
⌅ [6fafb56a] Memoization v0.1.14
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_4YJgnR/Manifest.toml`
  [47718e42] BioGenerics v0.1.5
  [d3a97c8b] BioMart v0.1.1
  [d1d4a3ce] BitFlags v0.1.9
  [336ed68f] CSV v0.10.15
  [944b1d66] CodecZlib v0.7.8
  [34da2185] Compat v4.16.0
  [f0e56b4a] ConcurrentUtilities v2.5.0
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.7.0
  [864edb3b] DataStructures v0.18.20
  [e2d170a0] DataValueInterfaces v1.0.0
  [460bff9d] ExceptionUnwrapping v0.1.11
  [48062228] FilePathsBase v0.9.23
⌅ [899a7d2d] GenomicFeatures v2.1.0
  [cd3eb016] HTTP v1.10.15
  [842dd82b] InlineStrings v1.4.3
  [524e6230] IntervalTrees v1.1.0
  [41ab1584] InvertedIndices v1.3.1
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.7.0
  [b964fa9f] LaTeXStrings v1.4.0
  [9c8b4983] LightXML v0.9.1
  [e6f89c97] LoggingExtras v1.1.0
  [1914dd2f] MacroTools v0.5.15
  [739be429] MbedTLS v1.1.9
⌅ [6fafb56a] Memoization v0.1.14
  [e1d29d7a] Missings v1.2.0
  [4d8831e6] OpenSSL v1.4.3
  [bac558e1] OrderedCollections v1.8.0
  [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
  [189a3867] Reexport v1.2.2
  [91c51154] SentinelArrays v1.4.8
  [777ac1f9] SimpleBufferStream v1.2.0
  [a2af1166] SortingAlgorithms v1.2.1
  [10745b16] Statistics v1.11.1
  [892a3eda] StringManipulation v0.4.1
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [3bb67fe8] TranscodingStreams v0.11.3
  [5c2747f8] URIs v1.5.1
  [ea10d353] WeakRefStrings v1.4.2
  [76eceee3] WorkerUtilities v1.6.1
  [94ce4f54] Libiconv_jll v1.18.0+0
  [c8ffd9c3] MbedTLS_jll v2.28.6+1
  [02c8fc9c] XML2_jll v2.13.6+1
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [9fa8497b] Future v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0
  [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
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [6462fe0b] Sockets v1.11.0
  [f489334b] StyledStrings v1.11.0
  [fa267f1f] TOML v1.0.3
  [8dfed614] Test v1.11.0
  [cf7118a7] UUIDs v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.3.0+1
  [14a3606d] MozillaCACerts_jll v2024.12.31
  [4536629a] OpenBLAS_jll v0.3.29+0
  [458c3c95] OpenSSL_jll v3.0.16+0
  [83775a58] Zlib_jll v1.3.1+2
  [8e850b90] libblastrampoline_jll v5.12.0+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
Entity: line 62: parser error : Opening and ending tag mismatch: base line 6 and head
</head>
       ^
Entity: line 92: parser error : Entity 'copy' not defined
    <p>&copy; 2024 EMBL-EBI</p>
             ^
Entity: line 96: parser error : Opening and ending tag mismatch: meta line 5 and html
</html>
       ^
Database & Dataset: Error During Test at /home/pkgeval/.julia/packages/BioMart/T5yzm/test/runtests.jl:4
  Got exception outside of a @test
  LightXML.XMLParseError{String}("Failure in parsing an XML file.")
  Stacktrace:
    [1] _check_result
      @ ~/.julia/packages/LightXML/DSNlY/src/document.jl:88 [inlined]
    [2] parse_string(s::String)
      @ LightXML ~/.julia/packages/LightXML/DSNlY/src/document.jl:99
    [3] macro expansion
      @ ~/.julia/packages/BioMart/T5yzm/src/Database.jl:35 [inlined]
    [4] (::BioMart.var"##getter#275#databases##0")()
      @ BioMart ~/.julia/packages/Memoization/ut5GT/src/Memoization.jl:163
    [5] get!(default::BioMart.var"##getter#275#databases##0", d::IdDict{Any, Any}, key::Any)
      @ Base ./iddict.jl:171
    [6] _get!(::Function, ::Vararg{Any})
      @ Memoization ~/.julia/packages/Memoization/ut5GT/src/Memoization.jl:170
    [7] databases()
      @ BioMart ~/.julia/packages/Memoization/ut5GT/src/Memoization.jl:165
    [8] top-level scope
      @ ~/.julia/packages/BioMart/T5yzm/test/runtests.jl:6
    [9] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1771 [inlined]
   [10] macro expansion
      @ ~/.julia/packages/BioMart/T5yzm/test/runtests.jl:14 [inlined]
   [11] include(mapexpr::Function, mod::Module, _path::String)
      @ Base ./Base.jl:308
   [12] top-level scope
      @ none:6
   [13] eval(m::Module, e::Any)
      @ Core ./boot.jl:488
   [14] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:294
   [15] _start()
      @ Base ./client.jl:560
Test Summary:      | Pass  Error  Total   Time
Database & Dataset |    1      1      2  34.6s
RNG of the outermost testset: Random.Xoshiro(0xef0b5a27d7c6de44, 0xb9b6a008af8f03b9, 0x52c0aed52dbc4d77, 0xa3153d911ba6d07e, 0x2f8753638cb12034)
ERROR: LoadError: Some tests did not pass: 1 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/BioMart/T5yzm/test/runtests.jl:4

Testing failed after 61.99s

ERROR: LoadError: Package BioMart 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{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/v1.13/Pkg/src/Operations.jl:2386
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2241 [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/v1.13/Pkg/src/API.jl:486
  [5] test(pkgs::Vector{Pkg.Types.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:307
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:328
 [12] _start()
    @ Base ./client.jl:560
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 438.06s: package tests unexpectedly errored