Package evaluation to test NCBITaxonomy on Julia 1.14.0-DEV.14 (ec5cf08762*) started at 2025-10-30T18:41:14.775


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# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.62s


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# Installation
#

Installing NCBITaxonomy...
   Resolving package versions...
   Installed NCBITaxonomy ─ v0.4.1
    Updating `~/.julia/environments/v1.14/Project.toml`
  [f88b31d2] + NCBITaxonomy v0.4.1
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [1520ce14] + AbstractTrees v0.4.5
  [69666777] + Arrow v2.8.0
  [31f734f8] + ArrowTypes v2.3.0
  [c3b6d118] + BitIntegers v0.3.5
  [5ba52731] + CodecLz4 v0.4.6
  [6b39b394] + CodecZstd v0.8.6
  [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 v0.19.1
  [e2d170a0] + DataValueInterfaces v1.0.0
  [b4f34e82] + Distances v0.10.12
  [4e289a0a] + EnumX v1.0.5
  [e2ba6199] + ExprTools v0.1.10
⌅ [92fee26a] + GZip v0.5.2
  [842dd82b] + InlineStrings v1.4.5
  [41ab1584] + InvertedIndices v1.3.1
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.1
  [b964fa9f] + LaTeXStrings v1.4.0
⌃ [6ac74813] + MD5 v0.2.1
  [e1d29d7a] + Missings v1.2.0
  [78c3b35d] + Mocking v0.8.1
  [f88b31d2] + NCBITaxonomy v0.4.1
  [bac558e1] + OrderedCollections v1.8.1
  [2dfb63ee] + PooledArrays v1.4.3
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [08abe8d2] + PrettyTables v3.1.0
  [189a3867] + Reexport v1.2.2
  [6c6a2e73] + Scratch v1.3.0
  [91c51154] + SentinelArrays v1.4.8
  [a2af1166] + SortingAlgorithms v1.2.2
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.1
  [88034a9c] + StringDistances v0.11.3
  [892a3eda] + StringManipulation v0.4.1
  [354b36f9] + StringViews v1.3.5
  [dc5dba14] + TZJData v1.5.0+2025b
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [f269a46b] + TimeZones v1.22.1
  [3bb67fe8] + TranscodingStreams v0.11.3
  [5ced341a] + Lz4_jll v1.10.1+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 v1.0.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.13.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [ca575930] + NetworkOptions v1.3.0
  [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 v1.11.0
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
  [deac9b47] + LibCURL_jll v8.16.0+0
  [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
  [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
        Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`
    Building NCBITaxonomy → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/fff23a8277e4516caa5531b1297543ff80d9521c/build.log`

Installation failed after 67.12s

ERROR: LoadError: Error building `NCBITaxonomy`: 
┌ Warning: The environmental variable NCBITAXONOMY_PATH is not set, so the tables will
│ be stored in your home directory. This is not ideal, and you really should set
│ the NCBITAXONOMY_PATH.
│ 
│ This can be done by adding `ENV["NCBITAXONOMY_PATH"]` in your Julia startup
│ file. The path will be created automatically if it does not exist.
└ @ Main ~/.julia/packages/NCBITaxonomy/obnXA/deps/build.jl:13
[ Info: Checksum of the most recent NCBI taxonomy: 01feff2c422a3853bc77e176b6245dc3
[ Info: No local taxonomy checksum found
[ Info: Downloading the taxonomy data from https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz
ERROR: LoadError: FieldError: type MD5.MD5_CTX has no field `used`, available fields: `state`, `bytecount`, `buffer`
Stacktrace:
  [1] getproperty
    @ ./Base_compiler.jl:57 [inlined]
  [2] update!(context::MD5.MD5_CTX, data::Vector{UInt8}, datalen::Int64)
    @ SHA /opt/julia/share/julia/stdlib/v1.14/SHA/src/common.jl:20
  [3] update!(context::MD5.MD5_CTX, data::Vector{UInt8})
    @ SHA /opt/julia/share/julia/stdlib/v1.14/SHA/src/common.jl:20
  [4] md5(io::IOStream, chunk_size::Int64)
    @ MD5 ~/.julia/packages/MD5/H5Cdd/src/MD5.jl:35
  [5] md5
    @ ~/.julia/packages/MD5/H5Cdd/src/MD5.jl:31 [inlined]
  [6] open(f::typeof(MD5.md5), args::String; kwargs::@Kwargs{})
    @ Base ./io.jl:427
  [7] open(f::Function, args::String)
    @ Base ./io.jl:424
  [8] download_dump(url::String, chk::SubString{String}, dest::String)
    @ Main ~/.julia/packages/NCBITaxonomy/obnXA/deps/build.jl:39
  [9] top-level scope
    @ ~/.julia/packages/NCBITaxonomy/obnXA/deps/build.jl:50
 [10] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
 [11] top-level scope
    @ none:5
 [12] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [13] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:310
 [14] _start()
    @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/NCBITaxonomy/obnXA/deps/build.jl:48
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68
  [2] (::Pkg.Operations.var"#146#147"{Bool, Pkg.Types.Context, String, PackageSpec, String})()
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:1797
  [3] withenv(::Pkg.Operations.var"#146#147"{Bool, Pkg.Types.Context, String, PackageSpec, String}, ::Pair{String, String}, ::Vararg{Pair{String}})
    @ Base ./env.jl:265
  [4] (::Pkg.Operations.var"#215#216"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#146#147"{Bool, Pkg.Types.Context, String, PackageSpec, String}, Pkg.Types.Context, PackageSpec})()
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2709
  [5] with_temp_env(fn::Pkg.Operations.var"#215#216"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#146#147"{Bool, Pkg.Types.Context, String, PackageSpec, String}, Pkg.Types.Context, PackageSpec}, temp_env::String)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2554
  [6] (::Pkg.Operations.var"#211#212"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#146#147"{Bool, Pkg.Types.Context, String, PackageSpec, String}, Pkg.Types.Context, PackageSpec, String, String})(tmp::String)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2668
  [7] mktempdir(fn::Pkg.Operations.var"#211#212"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#146#147"{Bool, Pkg.Types.Context, String, PackageSpec, String}, Pkg.Types.Context, PackageSpec, String, String}, parent::String; prefix::String)
    @ Base.Filesystem ./file.jl:936
  [8] mktempdir(fn::Function, parent::String)
    @ Base.Filesystem ./file.jl:932
  [9] #sandbox#207
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2615 [inlined]
 [10] kwcall(::@NamedTuple{preferences::Dict{String, Any}, allow_reresolve::Bool}, ::typeof(Pkg.Operations.sandbox), fn::Function, ctx::Pkg.Types.Context, target::PackageSpec, sandbox_path::String, sandbox_project_override::Pkg.Types.Project)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2605
 [11] build_versions(ctx::Pkg.Types.Context, uuids::Set{UUID}; verbose::Bool, allow_reresolve::Bool)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:1774
 [12] build_versions
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:1685 [inlined]
 [13] add(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}, new_git::Set{UUID}; allow_autoprecomp::Bool, preserve::PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2184
 [14] add
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2118 [inlined]
 [15] add(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; preserve::PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol, allow_autoprecomp::Bool, kwargs::@Kwargs{io::IOContext{IO}})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:379
 [16] add(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172
 [17] add(pkgs::Vector{PackageSpec})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161
 [18] add(pkg::PackageSpec)
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159
 [19] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:112
 [20] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [21] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:344
 [22] _start()
    @ Base ./client.jl:577
in expression starting at /PkgEval.jl/scripts/evaluate.jl:109

PkgEval skipped after 92.79s: package could not be installed