Package evaluation to test BioFetch on Julia 1.14.0-DEV.1584 (ac5fadde9b*) started at 2026-01-18T19:48:19.015


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

Installing PkgEval dependencies (TestEnv)...
  Activating project at `~/.julia/environments/v1.14`

Set-up completed after 10.25s


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

Installing BioFetch...
   Resolving package versions...
    Updating `~/.julia/environments/v1.14/Project.toml`
  [f8217676] + BioFetch v0.2.1
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [1520ce14] + AbstractTrees v0.4.5
  [67c07d97] + Automa v1.1.0
  [f8217676] + BioFetch v0.2.1
  [47718e42] + BioGenerics v0.1.5
  [7e6ae17a] + BioSequences v3.5.1
  [a0d4ced5] + BioServices v0.4.1
  [3c28c6f8] + BioSymbols v5.2.0
  [d1d4a3ce] + BitFlags v0.1.9
  [944b1d66] + CodecZlib v0.7.8
  [34da2185] + Compat v4.18.1
  [f0e56b4a] + ConcurrentUtilities v2.5.0
  [a8cc5b0e] + Crayons v4.1.1
  [9a962f9c] + DataAPI v1.16.0
  [a93c6f00] + DataFrames v1.8.1
  [864edb3b] + DataStructures v0.19.3
  [e2d170a0] + DataValueInterfaces v1.0.0
  [460bff9d] + ExceptionUnwrapping v0.1.11
  [8f5d6c58] + EzXML v1.2.3
  [c2308a5c] + FASTX v2.1.7
⌅ [4f8a0a0a] + GenomicAnnotations v0.3.8
  [708ec375] + Gumbo v0.8.3
  [cd3eb016] + HTTP v1.10.19
  [842dd82b] + InlineStrings v1.4.5
  [41ab1584] + InvertedIndices v1.3.1
  [c8e1da08] + IterTools v1.10.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.1
⌅ [682c06a0] + JSON v0.21.4
  [b964fa9f] + LaTeXStrings v1.4.0
  [e6f89c97] + LoggingExtras v1.2.0
  [739be429] + MbedTLS v1.1.9
  [e1d29d7a] + Missings v1.2.0
  [4d8831e6] + OpenSSL v1.6.1
  [bac558e1] + OrderedCollections v1.8.1
  [69de0a69] + Parsers v2.8.3
  [2dfb63ee] + PooledArrays v1.4.3
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.1
  [08abe8d2] + PrettyTables v3.1.2
  [189a3867] + Reexport v1.2.2
  [fdea26ae] + SIMD v3.7.2
  [91c51154] + SentinelArrays v1.4.9
  [777ac1f9] + SimpleBufferStream v1.2.0
  [a2af1166] + SortingAlgorithms v1.2.2
  [10745b16] + Statistics v1.11.1
  [892a3eda] + StringManipulation v0.4.2
  [354b36f9] + StringViews v1.3.6
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
⌅ [3bb67fe8] + TranscodingStreams v0.10.10
  [7200193e] + Twiddle v1.1.2
  [5c2747f8] + URIs v1.6.1
  [228000da] + XMLDict v0.4.1
  [528830af] + Gumbo_jll v0.10.2+0
  [94ce4f54] + Libiconv_jll v1.18.0+0
  [c8ffd9c3] + MbedTLS_jll v2.28.1010+0
  [02c8fc9c] + XML2_jll v2.15.1+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 v1.13.0
  [b27032c2] + LibCURL v1.0.0
  [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 v1.14.0
  [de0858da] + Printf v1.11.0
  [3fa0cd96] + REPL v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v1.0.0
  [9e88b42a] + Serialization v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [f489334b] + StyledStrings v1.13.0
  [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 v8.18.0+0
  [e37daf67] + LibGit2_jll v1.9.2+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.12.2
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [458c3c95] + OpenSSL_jll v3.5.4+0
  [efcefdf7] + PCRE2_jll v10.47.0+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 v1.68.0+1
  [3f19e933] + p7zip_jll v17.7.0+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 5.02s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...
Precompiling packages...
   1790.2 ms  ✓ BioGenerics
  17847.6 ms  ✓ Automa
  28557.3 ms  ✓ HTTP
  10171.8 ms  ✓ GenomicAnnotations
  19500.8 ms  ✓ FASTX
   4968.7 ms  ✓ BioServices
   2459.1 ms  ✓ FASTX → BioSequencesExt
  13371.4 ms  ✓ BioFetch
  8 dependencies successfully precompiled in 101 seconds. 87 already precompiled.

Precompilation completed after 116.89s


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

     Testing BioFetch
      Status `/tmp/jl_0Z9agl/Project.toml`
  [f8217676] BioFetch v0.2.1
  [a0d4ced5] BioServices v0.4.1
  [c2308a5c] FASTX v2.1.7
⌅ [4f8a0a0a] GenomicAnnotations v0.3.8
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_0Z9agl/Manifest.toml`
  [1520ce14] AbstractTrees v0.4.5
  [67c07d97] Automa v1.1.0
  [f8217676] BioFetch v0.2.1
  [47718e42] BioGenerics v0.1.5
  [7e6ae17a] BioSequences v3.5.1
  [a0d4ced5] BioServices v0.4.1
  [3c28c6f8] BioSymbols v5.2.0
  [d1d4a3ce] BitFlags v0.1.9
  [944b1d66] CodecZlib v0.7.8
  [34da2185] Compat v4.18.1
  [f0e56b4a] ConcurrentUtilities v2.5.0
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.8.1
  [864edb3b] DataStructures v0.19.3
  [e2d170a0] DataValueInterfaces v1.0.0
  [460bff9d] ExceptionUnwrapping v0.1.11
  [8f5d6c58] EzXML v1.2.3
  [c2308a5c] FASTX v2.1.7
⌅ [4f8a0a0a] GenomicAnnotations v0.3.8
  [708ec375] Gumbo v0.8.3
  [cd3eb016] HTTP v1.10.19
  [842dd82b] InlineStrings v1.4.5
  [41ab1584] InvertedIndices v1.3.1
  [c8e1da08] IterTools v1.10.0
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.7.1
⌅ [682c06a0] JSON v0.21.4
  [b964fa9f] LaTeXStrings v1.4.0
  [e6f89c97] LoggingExtras v1.2.0
  [739be429] MbedTLS v1.1.9
  [e1d29d7a] Missings v1.2.0
  [4d8831e6] OpenSSL v1.6.1
  [bac558e1] OrderedCollections v1.8.1
  [69de0a69] Parsers v2.8.3
  [2dfb63ee] PooledArrays v1.4.3
  [aea7be01] PrecompileTools v1.3.3
  [21216c6a] Preferences v1.5.1
  [08abe8d2] PrettyTables v3.1.2
  [189a3867] Reexport v1.2.2
  [fdea26ae] SIMD v3.7.2
  [91c51154] SentinelArrays v1.4.9
  [777ac1f9] SimpleBufferStream v1.2.0
  [a2af1166] SortingAlgorithms v1.2.2
  [10745b16] Statistics v1.11.1
  [892a3eda] StringManipulation v0.4.2
  [354b36f9] StringViews v1.3.6
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.1
⌅ [3bb67fe8] TranscodingStreams v0.10.10
  [7200193e] Twiddle v1.1.2
  [5c2747f8] URIs v1.6.1
  [228000da] XMLDict v0.4.1
  [528830af] Gumbo_jll v0.10.2+0
  [94ce4f54] Libiconv_jll v1.18.0+0
  [c8ffd9c3] MbedTLS_jll v2.28.1010+0
  [02c8fc9c] XML2_jll v2.15.1+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 v1.13.0
  [b27032c2] LibCURL v1.0.0
  [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 v1.14.0
  [de0858da] Printf v1.11.0
  [3fa0cd96] REPL v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v1.0.0
  [9e88b42a] Serialization v1.11.0
  [6462fe0b] Sockets v1.11.0
  [f489334b] StyledStrings v1.13.0
  [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 v8.18.0+0
  [e37daf67] LibGit2_jll v1.9.2+0
  [29816b5a] LibSSH2_jll v1.11.3+1
  [14a3606d] MozillaCACerts_jll v2025.12.2
  [4536629a] OpenBLAS_jll v0.3.29+0
  [458c3c95] OpenSSL_jll v3.5.4+0
  [efcefdf7] PCRE2_jll v10.47.0+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 v1.68.0+1
  [3f19e933] p7zip_jll v17.7.0+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for BioFetch [f8217676-c24a-4825-a874-ba6ce2a4fe08]
│   exception = Required dependency Base.PkgId(Base.UUID("d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"), "BitFlags") failed to load from a cache file.
└ @ Base loading.jl:2949
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for BioServices [a0d4ced5-b29c-5395-b614-ca030a679c4b]
│   exception = Required dependency Base.PkgId(Base.UUID("d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"), "BitFlags") failed to load from a cache file.
└ @ Base loading.jl:2949
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for HTTP [cd3eb016-35fb-5094-929b-558a96fad6f3]
│   exception = Required dependency Base.PkgId(Base.UUID("d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"), "BitFlags") failed to load from a cache file.
└ @ Base loading.jl:2949
WARNING: Detected access to binding `BioServices.EUtils` in a world prior to its definition world.
  Julia 1.12 has introduced more strict world age semantics for global bindings.
  !!! This code may malfunction under Revise.
  !!! This code will error in future versions of Julia.
Hint: Add an appropriate `invokelatest` around the access to this binding.
To make this warning an error, and hence obtain a stack trace, use `julia --depwarn=error`.
ERROR: LoadError: FieldError: type GeneDataView has no field `mem`, available fields: `parent`, `indices`, `property`
Stacktrace:
   [1] getproperty
     @ ~/.julia/packages/GenomicAnnotations/iSJX6/src/genedataview.jl:18 [inlined]
   [2] _growend!(a::Vector{Gene}, delta::Int64)
     @ Base ./array.jl:1198
   [3] _push!(a::Vector{Gene}, item::Gene)
     @ Base ./array.jl:1348
   [4] push!
     @ ./array.jl:1345 [inlined]
   [5] addgene!(chr::GenomicAnnotations.Record{Gene}, feature::Symbol, locus::Locus; kw::@Kwargs{})
     @ GenomicAnnotations ~/.julia/packages/GenomicAnnotations/iSJX6/src/record.jl:106
   [6] addgene!(chr::GenomicAnnotations.Record{Gene}, feature::Symbol, locus::Locus)
     @ GenomicAnnotations ~/.julia/packages/GenomicAnnotations/iSJX6/src/record.jl:98
   [7] parsechromosome!(stream::TranscodingStreams.NoopStream{IOBuffer}, record::GenomicAnnotations.Record{Gene})
     @ GenomicAnnotations.GenBank ~/.julia/packages/GenomicAnnotations/iSJX6/src/GenBank/reader.jl:177
   [8] tryread!
     @ ~/.julia/packages/GenomicAnnotations/iSJX6/src/GenBank/reader.jl:49 [inlined]
 ┌ [9] iterate
 │   @ ~/.julia/packages/GenomicAnnotations/iSJX6/src/GenBank/reader.jl:42 [inlined]
 ╰──── repeated 2 times
  [11] iterate
     @ ./generator.jl:45 [inlined]
  [12] grow_to!(dest::Vector{GenomicAnnotations.Record{Gene}}, itr::Base.Generator{GenomicAnnotations.GenBank.Reader{TranscodingStreams.NoopStream{IOBuffer}}, typeof(identity)})
     @ Base ./array.jl:901
  [13] collect(itr::Base.Generator{GenomicAnnotations.GenBank.Reader{TranscodingStreams.NoopStream{IOBuffer}}, typeof(identity)})
     @ Base ./array.jl:825
  [14] fetchseq_ncbi(ids::String, db::String; format::SeqFormat, range::Nothing, revstrand::Bool)
     @ BioFetch ~/.julia/packages/BioFetch/KUzgG/src/BioFetch.jl:87
  [15] fetchseq_ncbi
     @ ~/.julia/packages/BioFetch/KUzgG/src/BioFetch.jl:76 [inlined]
  [16] fetchseq(id::String, range::Nothing, revstrand::Bool; format::SeqFormat)
     @ BioFetch ~/.julia/packages/BioFetch/KUzgG/src/BioFetch.jl:67
  [17] fetchseq
     @ ~/.julia/packages/BioFetch/KUzgG/src/BioFetch.jl:61 [inlined]
  [18] kwcall(::@NamedTuple{format::SeqFormat}, ::typeof(fetchseq), id::String)
     @ BioFetch ~/.julia/packages/BioFetch/KUzgG/src/BioFetch.jl:61
  [19] top-level scope
     @ ~/.julia/packages/BioFetch/KUzgG/test/runtests.jl:7
  [20] include(mapexpr::Function, mod::Module, _path::String)
     @ Base ./Base.jl:310
  [21] top-level scope
     @ none:6
  [22] eval(m::Module, e::Any)
     @ Core ./boot.jl:489
  [23] exec_options(opts::Base.JLOptions)
     @ Base ./client.jl:310
  [24] _start()
     @ Base ./client.jl:585
in expression starting at /home/pkgeval/.julia/packages/BioFetch/KUzgG/test/runtests.jl:7

Testing failed after 227.22s

ERROR: LoadError: Package BioFetch errored during testing
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/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/v1.14/Pkg/src/Operations.jl:3122
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2987 [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/v1.14/Pkg/src/API.jl:572
  [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/v1.14/Pkg/src/API.jl:548
  [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/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/v1.14/Pkg/src/API.jl:161
  [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160
  [9] test
    @ /opt/julia/share/julia/stdlib/v1.14/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/v1.14/Pkg/src/API.jl:159
 [11] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:237
 [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:585
in expression starting at /PkgEval.jl/scripts/evaluate.jl:228

PkgEval failed after 387.68s: package tests unexpectedly errored