Package evaluation of NCBITaxonomy on Julia 1.13.0-DEV.985 (9c94e7ae32*) started at 2025-08-17T18:36:53.213 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.87s ################################################################################ # Installation # Installing NCBITaxonomy... Resolving package versions... Installed NCBITaxonomy ─ v0.4.1 Updating `~/.julia/environments/v1.13/Project.toml` [f88b31d2] + NCBITaxonomy v0.4.1 Updating `~/.julia/environments/v1.13/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 v4.18.0 [f0e56b4a] + ConcurrentUtilities v2.5.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 ⌅ [864edb3b] + DataStructures v0.18.22 [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 v1.4.4 [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 v1.3.2 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v2.4.0 [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 v1.22.0 [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 v0.6.4 [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 [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 v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+1 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.7.15 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.2+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+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 290.38s ERROR: LoadError: Error building `NCBITaxonomy`: Precompiling packages... 1243.4 ms ✓ MD5 1 dependency successfully precompiled in 1 seconds Precompiling packages... 1540.1 ms ✓ GZip 1 dependency successfully precompiled in 2 seconds Precompiling packages... 1757.2 ms ✓ InlineStrings 858.5 ms ✓ PooledArrays 966.0 ms ✓ StringViews 1115.6 ms ✓ TZJData 1408.3 ms ✓ BitIntegers 998.5 ms ✓ ArrowTypes 2171.7 ms ✓ CodecZstd 5818.6 ms ✓ SentinelArrays 1269.5 ms ✓ Mocking 1608.7 ms ✓ Lz4_jll 906.4 ms ✓ InlineStrings → ArrowTypesExt 16215.8 ms ✓ TimeZones 1804.8 ms ✓ CodecLz4 Info Given Arrow was explicitly requested, output will be shown live  WARNING: Constructor for type "Type" was extended in `Flatbuf` without explicit qualification or import.  NOTE: Assumed "Type" refers to `Base.Type`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function Type end`.  Hint: To silence the warning, qualify `Type` as `Base.Type` in the method signature or explicitly `import Base: Type`. 14260.6 ms ✓ Arrow 14 dependencies successfully precompiled in 51 seconds. 35 already precompiled. 2 dependencies had output during precompilation: ┌ BitIntegers │ WARNING: Imported binding GMP.ispos was undeclared at import time during import to BitIntegers. └ ┌ Arrow │ [Output was shown above] └ Precompiling packages... 1000.2 ms ✓ InvertedIndices 4756.5 ms ✓ Crayons 5337.6 ms ✓ StringManipulation 51440.0 ms ✓ PrettyTables 154488.2 ms ✓ DataFrames 5 dependencies successfully precompiled in 218 seconds. 30 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 [ Info: Checksum of the most recent NCBI taxonomy: 5951066eecdebf4693feeec3a13e70ae [ 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: Wrong checksum for the NCBI taxonomy archive file - unable to download Stacktrace: [1] download_dump(url::String, chk::SubString{String}, dest::String) @ Main ~/.julia/packages/NCBITaxonomy/obnXA/deps/build.jl:40 [2] top-level scope @ ~/.julia/packages/NCBITaxonomy/obnXA/deps/build.jl:50 [3] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:309 [4] top-level scope @ none:5 [5] eval(m::Module, e::Any) @ Core ./boot.jl:489 [6] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [7] _start() @ Base ./client.jl:563 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/v1.13/Pkg/src/Types.jl:68 [2] (::Pkg.Operations.var"#145#146"{Bool, Pkg.Types.Context, String, PackageSpec, String})() @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:1590 [3] withenv(::Pkg.Operations.var"#145#146"{Bool, Pkg.Types.Context, String, PackageSpec, String}, ::Pair{String, String}, ::Vararg{Pair{String}}) @ Base ./env.jl:265 [4] (::Pkg.Operations.var"#208#209"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#145#146"{Bool, Pkg.Types.Context, String, PackageSpec, String}, Pkg.Types.Context, PackageSpec})() @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2445 [5] with_temp_env(fn::Pkg.Operations.var"#208#209"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#145#146"{Bool, Pkg.Types.Context, String, PackageSpec, String}, Pkg.Types.Context, PackageSpec}, temp_env::String) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2291 [6] (::Pkg.Operations.var"#204#205"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#145#146"{Bool, Pkg.Types.Context, String, PackageSpec, String}, Pkg.Types.Context, PackageSpec, String, String})(tmp::String) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2404 [7] mktempdir(fn::Pkg.Operations.var"#204#205"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#145#146"{Bool, Pkg.Types.Context, String, PackageSpec, String}, Pkg.Types.Context, PackageSpec, String, String}, parent::String; prefix::String) @ Base.Filesystem ./file.jl:899 [8] mktempdir(fn::Function, parent::String) @ Base.Filesystem ./file.jl:895 [9] #sandbox#200 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2351 [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/v1.13/Pkg/src/Operations.jl:2341 [11] build_versions(ctx::Pkg.Types.Context, uuids::Set{UUID}; verbose::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:1567 [12] build_versions @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:1479 [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/v1.13/Pkg/src/Operations.jl:1923 [14] add @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:1868 [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/v1.13/Pkg/src/API.jl:354 [16] add(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:168 [17] add(pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:157 [18] add(pkg::PackageSpec) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [19] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:112 [20] include(mod::Module, _path::String) @ Base ./Base.jl:308 [21] exec_options(opts::Base.JLOptions) @ Base ./client.jl:330 [22] _start() @ Base ./client.jl:563 in expression starting at /PkgEval.jl/scripts/evaluate.jl:109 PkgEval skipped after 314.71s: package could not be installed