Package evaluation of Infernal on Julia 1.13.0-DEV.974 (7bbb213719*) started at 2025-08-12T16:09:50.891 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 11.07s ################################################################################ # Installation # Installing Infernal... Resolving package versions... Installed InlineStrings ─────────────── v1.4.4 Installed OrderedCollections ────────── v1.8.1 Installed Infernal_jll ──────────────── v1.1.5+0 Installed CodecZlib ─────────────────── v0.7.8 Installed Compat ────────────────────── v4.18.0 Installed FilePathsBase ─────────────── v0.9.24 Installed DataStructures ────────────── v0.18.22 Installed TranscodingStreams ────────── v0.11.3 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed DataAPI ───────────────────── v1.16.0 Installed InvertedIndices ───────────── v1.3.1 Installed Statistics ────────────────── v1.11.1 Installed DataValueInterfaces ───────── v1.0.0 Installed SentinelArrays ────────────── v1.4.8 Installed PrecompileTools ───────────── v1.3.2 Installed Parsers ───────────────────── v2.8.3 Installed Tables ────────────────────── v1.12.1 Installed StringManipulation ────────── v0.4.1 Installed GSL_jll ───────────────────── v2.7.2+0 Installed Infernal ──────────────────── v1.4.1 Installed PrettyTables ──────────────── v2.4.0 Installed Reexport ──────────────────── v1.2.2 Installed Missings ──────────────────── v1.2.0 Installed WeakRefStrings ────────────── v1.4.2 Installed DataFrames ────────────────── v1.7.0 Installed PooledArrays ──────────────── v1.4.3 Installed Preferences ───────────────── v1.5.0 Installed JLLWrappers ───────────────── v1.7.1 Installed TableTraits ───────────────── v1.0.1 Installed LaTeXStrings ──────────────── v1.4.0 Installed Crayons ───────────────────── v4.1.1 Installed WorkerUtilities ───────────── v1.6.1 Installed SortingAlgorithms ─────────── v1.2.2 Installed CSV ───────────────────────── v0.10.15 Installing 2 artifacts Installed artifact GSL 4.4 MiB Installed artifact Infernal 15.0 MiB Updating `~/.julia/environments/v1.13/Project.toml` [4aa08641] + Infernal v1.4.1 Updating `~/.julia/environments/v1.13/Manifest.toml` [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.0 [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 [48062228] + FilePathsBase v0.9.24 [4aa08641] + Infernal v1.4.1 [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 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [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 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.2 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 ⌅ [1b77fbbe] + GSL_jll v2.7.2+0 [5109d7c4] + Infernal_jll v1.1.5+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 [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 v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [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 [e37daf67] + LibGit2_jll v1.9.1+0 [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 [efcefdf7] + PCRE2_jll v10.45.0+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` Installation completed after 9.73s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4580.3 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompilation completed after 356.24s ################################################################################ # Testing # Testing Infernal Status `/tmp/jl_sNL8hp/Project.toml` ⌃ [4c88cf16] Aqua v0.8.13 ⌃ [7e6ae17a] BioSequences v3.4.1 [c2308a5c] FASTX v2.1.7 [4aa08641] Infernal v1.4.1 [38c5b72b] Rfam v3.2.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_sNL8hp/Manifest.toml` ⌃ [4c88cf16] Aqua v0.8.13 [67c07d97] Automa v1.1.0 [47718e42] BioGenerics v0.1.5 ⌃ [7e6ae17a] BioSequences v3.4.1 [3c28c6f8] BioSymbols v5.2.0 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 ⌃ [34da2185] Compat v4.16.0 [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 [c2308a5c] FASTX v2.1.7 [48062228] FilePathsBase v0.9.24 [4aa08641] Infernal v1.4.1 [842dd82b] InlineStrings v1.4.4 [41ab1584] InvertedIndices v1.3.1 [82899510] IteratorInterfaceExtensions v1.0.0 ⌃ [692b3bcd] JLLWrappers v1.7.0 [b964fa9f] LaTeXStrings v1.4.0 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 ⌃ [aea7be01] PrecompileTools v1.2.1 ⌃ [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [189a3867] Reexport v1.2.2 [38c5b72b] Rfam v3.2.0 [fdea26ae] SIMD v3.7.1 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [10745b16] Statistics v1.11.1 [892a3eda] StringManipulation v0.4.1 ⌃ [354b36f9] StringViews v1.3.4 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [7200193e] Twiddle v1.1.2 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 ⌅ [1b77fbbe] GSL_jll v2.7.2+0 [be1be57a] Gzip_jll v1.14.0+0 [5109d7c4] Infernal_jll v1.1.5+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 [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 v1.13.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [f489334b] StyledStrings v1.11.0 [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 v8.15.0+1 [e37daf67] LibGit2_jll v1.9.1+0 [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 [efcefdf7] PCRE2_jll v10.45.0+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 ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Precompiling packages... 1332.7 ms ✓ Preferences 1326.7 ms ✓ JLLWrappers 1475.4 ms ✓ Gzip_jll 1823.2 ms ✓ Rfam 4 dependencies successfully precompiled in 6 seconds. 16 already precompiled. [ Info: RFAM Directory /tmp set. [ Info: Rfam version 14.8 set. Precompiling packages... 1330.2 ms ✓ Compat 958.1 ms ✓ Compat → CompatLinearAlgebraExt 6953.5 ms ✓ Aqua 3 dependencies successfully precompiled in 9 seconds. 30 already precompiled. Precompiling packages... 1021.6 ms ✓ PrecompileTools 4167.2 ms ✓ DataStructures 1481.4 ms ✓ GSL_jll 3550.2 ms ✓ StringManipulation 17885.0 ms ✓ Parsers 1839.2 ms ✓ SortingAlgorithms 2038.4 ms ✓ Infernal_jll 26399.9 ms ✓ PrettyTables 1055.4 ms ✓ InlineStrings → ParsersExt 82277.3 ms ✓ DataFrames 2709.5 ms ✓ WeakRefStrings 28999.4 ms ✓ CSV 6492.7 ms ✓ Infernal 13 dependencies successfully precompiled in 180 seconds. 54 already precompiled. Piracy: Error During Test at /home/pkgeval/.julia/packages/Aqua/1UuaV/src/Aqua.jl:103 Got exception outside of a @test FieldError: type Core.TypeName has no field `mt`, available fields: `name`, `module`, `singletonname`, `names`, `atomicfields`, `constfields`, `wrapper`, `Typeofwrapper`, `cache`, `linearcache`, `partial`, `hash`, `max_args`, `n_uninitialized`, `flags`, `cache_entry_count`, `max_methods`, `constprop_heuristic` Stacktrace: [1] getproperty(x::Core.TypeName, f::Symbol) @ Base ./Base_compiler.jl:57 [2] all_methods(mods::Module; skip_deprecated::Bool) @ Aqua.Piracy ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:55 [3] all_methods @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:21 [inlined] [4] #hunt#30 @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:194 [inlined] [5] hunt @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:193 [inlined] [6] test_piracies(m::Module; broken::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:219 [7] test_piracies @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:218 [inlined] [8] macro expansion @ ~/.julia/packages/Aqua/1UuaV/src/Aqua.jl:104 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1929 [inlined] [10] test_all(testtarget::Module; ambiguities::Bool, unbound_args::Bool, undefined_exports::Bool, project_extras::Bool, stale_deps::Bool, deps_compat::Bool, piracies::Bool, persistent_tasks::Bool, undocumented_names::Bool) @ Aqua ~/.julia/packages/Aqua/1UuaV/src/Aqua.jl:104 [11] kwcall(::@NamedTuple{ambiguities::Bool}, ::typeof(Aqua.test_all), testtarget::Module) @ Aqua ~/.julia/packages/Aqua/1UuaV/src/Aqua.jl:59 [12] top-level scope @ ~/.julia/packages/Infernal/ft6w4/test/aqua.jl:6 [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1929 [inlined] [14] macro expansion @ ~/.julia/packages/Infernal/ft6w4/test/aqua.jl:6 [inlined] [15] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:312 [16] top-level scope @ ~/.julia/packages/Infernal/ft6w4/test/runtests.jl:6 [17] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:312 [18] top-level scope @ none:6 [19] eval(m::Module, e::Any) @ Core ./boot.jl:489 [20] exec_options(opts::Base.JLOptions) @ Base ./client.jl:286 [21] _start() @ Base ./client.jl:553 Test Summary: | Pass Error Total Time aqua | 9 1 10 2m01.2s Unbound type parameters | 1 1 0.1s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.4s Stale dependencies | 1 1 9.9s Compat bounds | 4 4 0.7s Piracy | 1 1 6.5s Persistent tasks | 1 1 1m26.1s RNG of the outermost testset: Random.Xoshiro(0xef933f5bcc9f4e9d, 0x980f52ff2b806dcd, 0x45301bfeebc9a8ae, 0x65e76256b438fa7d, 0xdb0574b2d79fbcd5) ERROR: LoadError: Some tests did not pass: 9 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/Infernal/ft6w4/test/aqua.jl:5 in expression starting at /home/pkgeval/.julia/packages/Infernal/ft6w4/test/runtests.jl:6 Testing failed after 345.21s ERROR: LoadError: Package Infernal errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/Operations.jl:2672 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2521 [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/v1.13/Pkg/src/API.jl:538 [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/v1.13/Pkg/src/API.jl:515 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:168 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:157 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [9] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:311 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:320 [14] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 763.83s: package tests unexpectedly errored