Package evaluation of HMMER on Julia 1.13.0-DEV.820 (69a2a571e8*) started at 2025-07-07T09:21:57.756 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.56s ################################################################################ # Installation # Installing HMMER... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [59c5aa83] + HMMER v1.5.1 Updating `~/.julia/environments/v1.13/Manifest.toml` [59c5aa83] + HMMER v1.5.1 [692b3bcd] + JLLWrappers v1.7.0 [21216c6a] + Preferences v1.4.3 ⌅ [1b77fbbe] + GSL_jll v2.7.2+0 [9a00dd6d] + HMMER_jll v3.4.0+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 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown 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 v8.14.1+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [458c3c95] + OpenSSL_jll v3.5.1+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [83775a58] + Zlib_jll v1.3.1+2 [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 To see why use `status --outdated -m` Installation completed after 1.37s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 53.9s ################################################################################ # Testing # Testing HMMER Status `/tmp/jl_d14O9U/Project.toml` ⌅ [4c88cf16] Aqua v0.7.4 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [c2308a5c] FASTX v2.1.7 [59c5aa83] HMMER v1.5.1 [275cd14a] Pfam v2.2.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_d14O9U/Manifest.toml` ⌅ [4c88cf16] Aqua v0.7.4 [67c07d97] Automa v1.1.0 [47718e42] BioGenerics v0.1.5 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.17.0 [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 [59c5aa83] HMMER v1.5.1 [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 [275cd14a] Pfam v2.2.0 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.4 [189a3867] Reexport v1.2.2 [fdea26ae] SIMD v3.7.1 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [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 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 ⌅ [1b77fbbe] GSL_jll v2.7.2+0 [be1be57a] Gzip_jll v1.14.0+0 [9a00dd6d] HMMER_jll v3.4.0+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed 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 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [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 [6462fe0b] Sockets 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 v8.14.1+1 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.1+0 [efcefdf7] PCRE2_jll v10.45.0+0 [83775a58] Zlib_jll v1.3.1+2 [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. Testing Running tests... [ Info: PFAM directory /tmp/jl_a9tXCp set. [ Info: Pfam version 35.0 set. [ Info: Downloading pdbmap to /tmp/jl_a9tXCp/35.0/Pfam-A.hmm ... 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(bytes): 271631746 Time: 0:01:31 Downloaded (bytes): 273303746 Time: 0:01:31 Downloaded (bytes): 275015746 Time: 0:01:31 Downloaded (bytes): 276775746 Time: 0:01:32 Downloaded (bytes): 278575746 Time: 0:01:32 Downloaded (bytes): 280423746 Time: 0:01:32 Downloaded (bytes): 282311746 Time: 0:01:32 Downloaded (bytes): 284223746 Time: 0:01:32 Downloaded (bytes): 286183746 Time: 0:01:32 Downloaded (bytes): 288199746 Time: 0:01:32 Downloaded (bytes): 290263746 Time: 0:01:32 Downloaded (bytes): 292359746 Time: 0:01:33Precompiling packages... 1600.1 ms ✓ GSL_jll 1916.1 ms ✓ HMMER_jll 4744.0 ms ✓ HMMER 3 dependencies successfully precompiled in 8 seconds. 29 already precompiled. ┌ Warning: `isbindingresolved(m::Module, var::Symbol)` is deprecated, use `true` instead. │ caller = walkmodules(f::Aqua.var"#undefined_exports##0#undefined_exports##1"{Vector{Symbol}}, x::Module) at exports.jl:5 └ @ Core ~/.julia/packages/Aqua/rmHe1/src/exports.jl:5 Piracy: Error During Test at /home/pkgeval/.julia/packages/Aqua/rmHe1/src/Aqua.jl:99 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/rmHe1/src/piracy.jl:55 [3] hunt(mod::Module; skip_deprecated::Bool, kwargs::@Kwargs{}) @ Aqua.Piracy ~/.julia/packages/Aqua/rmHe1/src/piracy.jl:194 [4] hunt(mod::Module) @ Aqua.Piracy ~/.julia/packages/Aqua/rmHe1/src/piracy.jl:193 [5] test_piracy(m::Module; broken::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/rmHe1/src/piracy.jl:218 [6] test_piracy(m::Module) @ Aqua ~/.julia/packages/Aqua/rmHe1/src/piracy.jl:217 [7] macro expansion @ ~/.julia/packages/Aqua/rmHe1/src/Aqua.jl:101 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [9] test_all(testtarget::Module; ambiguities::Bool, unbound_args::Bool, undefined_exports::Bool, project_extras::Bool, stale_deps::Bool, deps_compat::Bool, project_toml_formatting::Bool, piracy::Bool) @ Aqua ~/.julia/packages/Aqua/rmHe1/src/Aqua.jl:100 [10] test_all(testtarget::Module) @ Aqua ~/.julia/packages/Aqua/rmHe1/src/Aqua.jl:53 [11] top-level scope @ ~/.julia/packages/HMMER/3OXmS/test/aqua.jl:6 [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [13] macro expansion @ ~/.julia/packages/HMMER/3OXmS/test/aqua.jl:6 [inlined] [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [15] top-level scope @ ~/.julia/packages/HMMER/3OXmS/test/runtests.jl:10 [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [17] top-level scope @ none:6 [18] eval(m::Module, e::Any) @ Core ./boot.jl:489 [19] exec_options(opts::Base.JLOptions) @ Base ./client.jl:290 [20] _start() @ Base ./client.jl:557 Test Summary: | Pass Error Total Time aqua | 8 1 9 36.6s Method ambiguity | 1 1 7.4s Unbound type parameters | 1 1 0.1s Undefined exports | 1 1 2.8s Compare Project.toml and test/Project.toml | 1 1 0.4s Stale dependencies | 1 1 8.2s Compat bounds | 1 1 2.8s Project.toml formatting | 2 2 0.6s Piracy | 1 1 2.6s RNG of the outermost testset: Random.Xoshiro(0x126de62eb3ea1697, 0x7f0ce7c996b8b9cc, 0xd2f2a32c32071912, 0xca0a7cbc6b7cf5cb, 0x349b368f62a279e2) ERROR: LoadError: Some tests did not pass: 8 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/HMMER/3OXmS/test/aqua.jl:5 in expression starting at /home/pkgeval/.julia/packages/HMMER/3OXmS/test/runtests.jl:10 Testing failed after 84.0s ERROR: LoadError: Package HMMER 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:2446 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2301 [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:500 [5] 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:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:309 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:324 [12] _start() @ Base ./client.jl:557 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 249.69s: package tests unexpectedly errored