Package evaluation to test BioMart on Julia 1.14.0-DEV.1893 (b4aba01002*) started at 2026-03-19T23:39:36.656 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.24s ################################################################################ # Installation # Installing BioMart... Resolving package versions... Installed URIs ──────────────────────── v1.6.1 Installed MacroTools ────────────────── v0.5.16 Installed LightXML ──────────────────── v0.9.3 Installed InlineStrings ─────────────── v1.4.5 Installed FilePathsBase ─────────────── v0.9.24 Installed GenomicFeatures ───────────── v2.1.0 Installed DataStructures ────────────── v0.18.22 Installed CSV ───────────────────────── v0.10.16 Installed CodecZlib ─────────────────── v0.7.8 Installed Memoization ───────────────── v0.1.14 Installed ExceptionUnwrapping ───────── v0.1.11 Installed ConcurrentUtilities ───────── v2.5.1 Installed Compat ────────────────────── v4.18.1 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed OrderedCollections ────────── v1.8.1 Installed TranscodingStreams ────────── v0.11.3 Installed DataAPI ───────────────────── v1.16.0 Installed InvertedIndices ───────────── v1.3.1 Installed DataValueInterfaces ───────── v1.0.0 Installed SentinelArrays ────────────── v1.4.9 Installed Statistics ────────────────── v1.11.1 Installed MbedTLS ───────────────────── v1.1.10 Installed OpenSSL ───────────────────── v1.6.1 Installed PrecompileTools ───────────── v1.3.3 Installed LoggingExtras ─────────────── v1.2.0 Installed BitFlags ──────────────────── v0.1.9 Installed Parsers ───────────────────── v2.8.3 Installed StringManipulation ────────── v0.4.4 Installed BioMart ───────────────────── v0.1.1 Installed HTTP ──────────────────────── v1.11.0 Installed Tables ────────────────────── v1.12.1 Installed BioGenerics ───────────────── v0.1.5 Installed XML2_jll ──────────────────── v2.15.1+0 Installed Reexport ──────────────────── v1.2.2 Installed Preferences ───────────────── v1.5.2 Installed WeakRefStrings ────────────── v1.4.2 Installed SimpleBufferStream ────────── v1.2.0 Installed Missings ──────────────────── v1.2.0 Installed PrettyTables ──────────────── v3.2.3 Installed PooledArrays ──────────────── v1.4.3 Installed JLLWrappers ───────────────── v1.7.1 Installed DataFrames ────────────────── v1.8.1 Installed TableTraits ───────────────── v1.0.1 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed MbedTLS_jll ───────────────── v2.28.1010+0 Installed LaTeXStrings ──────────────── v1.4.0 Installed Crayons ───────────────────── v4.1.1 Installed WorkerUtilities ───────────── v1.6.1 Installed SortingAlgorithms ─────────── v1.2.2 Installed IntervalTrees ─────────────── v1.1.0 Installing 4 artifacts Installed artifact Libiconv 1.9 MiB Installed artifact MbedTLS 2.2 MiB Installed artifact XML2 2.2 MiB Installed artifact testfiles 6.2 MiB Updating `~/.julia/environments/v1.14/Project.toml` [d3a97c8b] + BioMart v0.1.1 Updating `~/.julia/environments/v1.14/Manifest.toml` [47718e42] + BioGenerics v0.1.5 [d3a97c8b] + BioMart v0.1.1 [d1d4a3ce] + BitFlags v0.1.9 [336ed68f] + CSV v0.10.16 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.1 [f0e56b4a] + ConcurrentUtilities v2.5.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [460bff9d] + ExceptionUnwrapping v0.1.11 [48062228] + FilePathsBase v0.9.24 ⌅ [899a7d2d] + GenomicFeatures v2.1.0 [cd3eb016] + HTTP v1.11.0 [842dd82b] + InlineStrings v1.4.5 [524e6230] + IntervalTrees v1.1.0 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [b964fa9f] + LaTeXStrings v1.4.0 [9c8b4983] + LightXML v0.9.3 [e6f89c97] + LoggingExtras v1.2.0 [1914dd2f] + MacroTools v0.5.16 [739be429] + MbedTLS v1.1.10 ⌅ [6fafb56a] + Memoization v0.1.14 [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 v1.5.2 [08abe8d2] + PrettyTables v3.2.3 [189a3867] + Reexport v1.2.2 [91c51154] + SentinelArrays v1.4.9 [777ac1f9] + SimpleBufferStream v1.2.0 [a2af1166] + SortingAlgorithms v1.2.2 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.4 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [5c2747f8] + URIs v1.6.1 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [94ce4f54] + Libiconv_jll v1.18.0+0 [c8ffd9c3] + MbedTLS_jll v2.28.1010+0 [02c8fc9c] + XML2_jll v2.15.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [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 [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 [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 v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.30+0 [458c3c95] + OpenSSL_jll v3.5.5+0 [83775a58] + Zlib_jll v1.3.2+0 [8e850b90] + libblastrampoline_jll v5.15.0+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 10.98s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 8924.1 ms ✓ TestEnv 1 dependency successfully precompiled in 9 seconds. 27 already precompiled. 26 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, PCRE2_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, Zstd_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling package dependencies... Precompiling packages... 5436.1 ms ✓ MacroTools 2260.7 ms ✓ InlineStrings 1039.4 ms ✓ Reexport 1602.2 ms ✓ Statistics 1296.5 ms ✓ DataAPI 973.6 ms ✓ DataValueInterfaces 2160.1 ms ✓ URIs 1857.3 ms ✓ OrderedCollections 1043.0 ms ✓ InvertedIndices 1130.9 ms ✓ BitFlags 2280.3 ms ✓ ConcurrentUtilities 2215.3 ms ✓ WorkerUtilities 1925.0 ms ✓ IntervalTrees 1935.5 ms ✓ TranscodingStreams 1350.7 ms ✓ SimpleBufferStream 1059.7 ms ✓ IteratorInterfaceExtensions 1204.2 ms ✓ LaTeXStrings 3348.2 ms ✓ Crayons 3528.0 ms ✓ SentinelArrays 1683.9 ms ✓ LoggingExtras 1400.0 ms ✓ Compat 1802.2 ms ✓ Preferences 1948.9 ms ✓ ExceptionUnwrapping 1014.6 ms ✓ Memoization 1278.2 ms ✓ Missings 1392.9 ms ✓ PooledArrays 5974.6 ms ✓ OpenSSL 2497.8 ms ✓ BioGenerics 2183.0 ms ✓ CodecZlib 1804.5 ms ✓ TableTraits 2412.5 ms ✓ Compat → CompatLinearAlgebraExt 3652.3 ms ✓ JLLWrappers 3713.2 ms ✓ PrecompileTools 4341.4 ms ✓ Tables 7063.0 ms ✓ FilePathsBase 13496.4 ms ✓ DataStructures 7982.8 ms ✓ Libiconv_jll 6884.5 ms ✓ MbedTLS_jll 12197.1 ms ✓ StringManipulation 34758.4 ms ✓ Parsers 6636.4 ms ✓ FilePathsBase → FilePathsBaseTestExt 2988.5 ms ✓ FilePathsBase → FilePathsBaseMmapExt 2920.9 ms ✓ SortingAlgorithms 4117.6 ms ✓ GenomicFeatures 5314.4 ms ✓ XML2_jll 6268.0 ms ✓ MbedTLS 70543.7 ms ✓ PrettyTables 2913.0 ms ✓ InlineStrings → ParsersExt 3061.9 ms ✓ LightXML 58695.4 ms ✓ HTTP 152476.1 ms ✓ DataFrames 4005.8 ms ✓ WeakRefStrings 48961.1 ms ✓ CSV 29578.3 ms ✓ BioMart 54 dependencies successfully precompiled in 556 seconds. 20 already precompiled. 13 dependencies precompiled but different versions are currently loaded (Base64, Dates, JuliaSyntaxHighlighting, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Printf, StyledStrings, TOML, UUIDs and Zlib_jll). Restart julia to access the new versions. Otherwise, 33 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompilation completed after 343.03s ################################################################################ # Testing # Testing BioMart Status `/tmp/jl_NHZAnl/Project.toml` [d3a97c8b] BioMart v0.1.1 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.1 ⌅ [899a7d2d] GenomicFeatures v2.1.0 [cd3eb016] HTTP v1.11.0 [9c8b4983] LightXML v0.9.3 ⌅ [6fafb56a] Memoization v0.1.14 [8dfed614] Test v1.11.0 Status `/tmp/jl_NHZAnl/Manifest.toml` [47718e42] BioGenerics v0.1.5 [d3a97c8b] BioMart v0.1.1 [d1d4a3ce] BitFlags v0.1.9 [336ed68f] CSV v0.10.16 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 [f0e56b4a] ConcurrentUtilities v2.5.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [460bff9d] ExceptionUnwrapping v0.1.11 [48062228] FilePathsBase v0.9.24 ⌅ [899a7d2d] GenomicFeatures v2.1.0 [cd3eb016] HTTP v1.11.0 [842dd82b] InlineStrings v1.4.5 [524e6230] IntervalTrees v1.1.0 [41ab1584] InvertedIndices v1.3.1 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [b964fa9f] LaTeXStrings v1.4.0 [9c8b4983] LightXML v0.9.3 [e6f89c97] LoggingExtras v1.2.0 [1914dd2f] MacroTools v0.5.16 [739be429] MbedTLS v1.1.10 ⌅ [6fafb56a] Memoization v0.1.14 [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 v1.5.2 [08abe8d2] PrettyTables v3.2.3 [189a3867] Reexport v1.2.2 [91c51154] SentinelArrays v1.4.9 [777ac1f9] SimpleBufferStream v1.2.0 [a2af1166] SortingAlgorithms v1.2.2 [10745b16] Statistics v1.11.1 [892a3eda] StringManipulation v0.4.4 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [5c2747f8] URIs v1.6.1 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [94ce4f54] Libiconv_jll v1.18.0+0 [c8ffd9c3] MbedTLS_jll v2.28.1010+0 [02c8fc9c] XML2_jll v2.15.1+0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [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 [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 [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 v2025.12.2 [4536629a] OpenBLAS_jll v0.3.30+0 [458c3c95] OpenSSL_jll v3.5.5+0 [83775a58] Zlib_jll v1.3.2+0 [8e850b90] libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Test Summary: | Pass Total Time Database & Dataset | 2 2 38.4s Test Summary: | Pass Total Time Low level API | 1 1 1m08.6s Higher level API: Error During Test at /home/pkgeval/.julia/packages/BioMart/T5yzm/test/runtests.jl:52 Test threw exception Expression: d[1, 1] == "EGFR" BoundsError: attempt to access 0×1 DataFrame at index [1, 1] Stacktrace: [1] getindex(df::DataFrames.DataFrame, row_ind::Int64, col_ind::Int64) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/dataframe/dataframe.jl:514 [2] top-level scope @ ~/.julia/packages/BioMart/T5yzm/test/runtests.jl:38 [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [4] macro expansion @ ~/.julia/packages/BioMart/T5yzm/test/runtests.jl:52 [inlined] [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:778 [inlined] Test Summary: | Pass Error Total Time Higher level API | 4 1 5 32.5s RNG of the outermost testset: Random.Xoshiro(0x4e64cbe72184256a, 0x20a88c3647b7f927, 0x522d165b94101180, 0xea4dfb979b1187b5, 0xb361c1791a771e52) ERROR: LoadError: Some tests did not pass: 4 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BioMart/T5yzm/test/runtests.jl:36 Testing failed after 137.84s ERROR: LoadError: Package BioMart 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:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [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:586 [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:562 [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:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:323 [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:214 PkgEval failed after 953.97s: package tests unexpectedly errored