Package evaluation to test NCBITaxonomy on Julia 1.11.8 (29b3528cce*) started at 2026-01-20T09:46:32.386


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# Set-up
#

Installing PkgEval dependencies (TestEnv)...
  Activating project at `~/.julia/environments/v1.11`

Set-up completed after 8.45s


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# Installation
#

Installing NCBITaxonomy...
   Resolving package versions...
   Installed NCBITaxonomy ─ v0.4.1
    Updating `~/.julia/environments/v1.11/Project.toml`
  [f88b31d2] + NCBITaxonomy v0.4.1
    Updating `~/.julia/environments/v1.11/Manifest.toml`
  [1520ce14] + AbstractTrees v0.4.5
  [69666777] + Arrow v2.8.1
  [31f734f8] + ArrowTypes v2.3.0
  [c3b6d118] + BitIntegers v0.3.7
  [5ba52731] + CodecLz4 v0.4.6
  [6b39b394] + CodecZstd v0.8.7
  [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
  [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 v0.2.3
  [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 v1.2.1
  [21216c6a] + Preferences v1.5.1
  [08abe8d2] + PrettyTables v3.1.2
  [189a3867] + Reexport v1.2.2
  [6c6a2e73] + Scratch v1.3.0
  [91c51154] + SentinelArrays v1.4.9
  [a2af1166] + SortingAlgorithms v1.2.2
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.8.0
  [88034a9c] + StringDistances v0.11.3
  [892a3eda] + StringManipulation v0.4.2
  [354b36f9] + StringViews v1.3.6
  [dc5dba14] + TZJData v1.5.0+2025b
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [f269a46b] + TimeZones v1.22.2
  [3bb67fe8] + TranscodingStreams v0.11.3
  [5ced341a] + Lz4_jll v1.10.1+0
  [3161d3a3] + Zstd_jll v1.5.7+1
  [0dad84c5] + ArgTools v1.1.2
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching v1.11.0
  [9fa8497b] + Future v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [b27032c2] + LibCURL v0.6.4
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [ca575930] + NetworkOptions v1.2.0
  [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
  [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 v1.1.1+0
  [deac9b47] + LibCURL_jll v8.6.0+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.6+0
  [14a3606d] + MozillaCACerts_jll v2023.12.12
  [4536629a] + OpenBLAS_jll v0.3.27+1
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.11.0+0
  [8e850ede] + nghttp2_jll v1.59.0+0
  [3f19e933] + p7zip_jll v17.4.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
    Building NCBITaxonomy → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/fff23a8277e4516caa5531b1297543ff80d9521c/build.log`

Installation failed after 233.0s

ERROR: LoadError: Error building `NCBITaxonomy`: 
Precompiling MD5...
   1448.6 ms  ✓ MD5
  1 dependency successfully precompiled in 2 seconds
Precompiling GZip...
   1152.2 ms  ✓ GZip
  1 dependency successfully precompiled in 1 seconds
Precompiling Arrow...
   1330.4 ms  ✓ StringViews
    925.3 ms  ✓ ArrowTypes
   1308.0 ms  ✓ BitIntegers
    980.4 ms  ✓ TZJData
   1025.3 ms  ✓ Mocking
   2747.8 ms  ✓ CodecZstd
   2313.1 ms  ✓ CodecLz4
    929.0 ms  ✓ InlineStrings → ArrowTypesExt
  17039.1 ms  ✓ TimeZones
  10851.5 ms  ✓ Arrow
  10 dependencies successfully precompiled in 40 seconds. 39 already precompiled.
Precompiling DataFrames...
   2937.7 ms  ✓ DataStructures
  70535.5 ms  ✓ PrettyTables
    798.4 ms  ✓ SortingAlgorithms
  98333.9 ms  ✓ DataFrames
  4 dependencies successfully precompiled in 174 seconds. 31 already precompiled.
┌ 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
ERROR: LoadError: RequestError: SSL connection timeout while requesting https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz.md5
Stacktrace:
  [1] (::Downloads.var"#9#19"{IOStream, Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool})(easy::Downloads.Curl.Easy)
    @ Downloads /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:452
  [2] with_handle(f::Downloads.var"#9#19"{IOStream, Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, handle::Downloads.Curl.Easy)
    @ Downloads.Curl /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Curl/Curl.jl:105
  [3] #8
    @ /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:363 [inlined]
  [4] arg_write(f::Downloads.var"#8#18"{Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, arg::IOStream)
    @ ArgTools /opt/julia/share/julia/stdlib/v1.11/ArgTools/src/ArgTools.jl:134
  [5] #7
    @ /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:362 [inlined]
  [6] arg_read
    @ /opt/julia/share/julia/stdlib/v1.11/ArgTools/src/ArgTools.jl:76 [inlined]
  [7] request(url::String; input::Nothing, output::IOStream, method::Nothing, headers::Vector{Pair{String, String}}, timeout::Float64, progress::Nothing, verbose::Bool, debug::Nothing, throw::Bool, downloader::Nothing, interrupt::Nothing)
    @ Downloads /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:361
  [8] request
    @ /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:328 [inlined]
  [9] #3
    @ /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:259 [inlined]
 [10] arg_write(f::Downloads.var"#3#4"{Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Nothing, String}, arg::Nothing)
    @ ArgTools /opt/julia/share/julia/stdlib/v1.11/ArgTools/src/ArgTools.jl:123
 [11] #download#2
    @ /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:258 [inlined]
 [12] download(url::String, output::Nothing)
    @ Downloads /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:247
 [13] #invokelatest#2
    @ ./essentials.jl:1055 [inlined]
 [14] invokelatest
    @ ./essentials.jl:1052 [inlined]
 [15] do_download(url::String, path::Nothing)
    @ Base ./download.jl:24
 [16] download(url::String)
    @ Base ./download.jl:20
 [17] top-level scope
    @ ~/.julia/packages/NCBITaxonomy/obnXA/deps/build.jl:25
 [18] include(fname::String)
    @ Main ./sysimg.jl:38
 [19] top-level scope
    @ none:5
in expression starting at /home/pkgeval/.julia/packages/NCBITaxonomy/obnXA/deps/build.jl:25
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68
  [2] (::Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String})()
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1195
  [3] withenv(::Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, ::Pair{String, String}, ::Vararg{Pair{String}})
    @ Base ./env.jl:265
  [4] (::Pkg.Operations.var"#118#123"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.PackageSpec})()
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1935
  [5] with_temp_env(fn::Pkg.Operations.var"#118#123"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.PackageSpec}, temp_env::String)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1793
  [6] (::Pkg.Operations.var"#116#121"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, String})(tmp::String)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1902
  [7] mktempdir(fn::Pkg.Operations.var"#116#121"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#67#74"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, String}, parent::String; prefix::String)
    @ Base.Filesystem ./file.jl:819
  [8] mktempdir(fn::Function, parent::String)
    @ Base.Filesystem ./file.jl:815
  [9] mktempdir
    @ ./file.jl:815 [inlined]
 [10] #sandbox#115
    @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1849 [inlined]
 [11] build_versions(ctx::Pkg.Types.Context, uuids::Set{UUID}; verbose::Bool)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1176
 [12] build_versions
    @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1094 [inlined]
 [13] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{UUID}; allow_autoprecomp::Bool, preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol)
    @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1472
 [14] add
    @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1418 [inlined]
 [15] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol, allow_autoprecomp::Bool, kwargs::@Kwargs{io::IOContext{IO}})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:312
 [16] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159
 [17] add(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:148
 [18] add(pkg::Pkg.Types.PackageSpec)
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146
 [19] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:116
in expression starting at /PkgEval.jl/scripts/evaluate.jl:113

PkgEval skipped after 288.48s: package could not be installed