Package evaluation to test BiobakeryUtils on Julia 1.14.0-DEV.65 (b05afe0f25*) started at 2025-11-11T22:00:57.409 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.38s ################################################################################ # Installation # Installing BiobakeryUtils... Resolving package versions... Installed Rmath_jll ─────────────────── v0.5.1+0 Installed VersionParsing ────────────── v1.3.0 Installed Indexing ──────────────────── v1.1.1 Installed FilePathsBase ─────────────── v0.9.24 Installed FillArrays ────────────────── v1.15.0 Installed MultivariateStats ─────────── v0.10.3 Installed DataStructures ────────────── v0.19.3 Installed InlineStrings ─────────────── v1.4.5 Installed HypergeometricFunctions ───── v0.3.28 Installed AliasTables ───────────────── v1.1.3 Installed CodecZlib ─────────────────── v0.7.8 Installed StatsBase ─────────────────── v0.34.8 Installed Compat ────────────────────── v4.18.1 Installed OrderedCollections ────────── v1.8.1 Installed TranscodingStreams ────────── v0.11.3 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed RecipesBase ───────────────── v1.3.4 Installed DataAPI ───────────────────── v1.16.0 Installed StatsAPI ──────────────────── v1.7.1 Installed EcoBase ───────────────────── v0.1.7 Installed Statistics ────────────────── v1.11.1 Installed DataValueInterfaces ───────── v1.0.0 Installed PrecompileTools ───────────── v1.3.3 Installed SentinelArrays ────────────── v1.4.8 Installed Conda ─────────────────────── v1.10.3 Installed StructUtils ───────────────── v2.6.0 Installed IrrationalConstants ───────── v0.2.6 Installed Distances ─────────────────── v0.10.12 Installed InlineTest ────────────────── v0.2.0 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed QuadGK ────────────────────── v2.11.2 Installed LogExpFunctions ───────────── v0.3.29 Installed Parsers ───────────────────── v2.8.3 Installed Rmath ─────────────────────── v0.9.0 Installed Arpack_jll ────────────────── v3.5.1+1 Installed JSON ──────────────────────── v1.2.1 Installed StatsFuns ─────────────────── v1.5.2 Installed Distributions ─────────────── v0.25.122 Installed Tables ────────────────────── v1.12.1 Installed Arpack ────────────────────── v0.5.4 Installed PtrArrays ─────────────────── v1.3.0 Installed Reexport ──────────────────── v1.2.2 Installed Missings ──────────────────── v1.2.0 Installed SpecialFunctions ──────────── v2.6.1 Installed Preferences ───────────────── v1.5.0 Installed WeakRefStrings ────────────── v1.4.2 Installed PooledArrays ──────────────── v1.4.3 Installed JLLWrappers ───────────────── v1.7.1 Installed TableTraits ───────────────── v1.0.1 Installed PDMats ────────────────────── v0.11.36 Installed ReTest ────────────────────── v0.3.4 Installed WorkerUtilities ───────────── v1.6.1 Installed SortingAlgorithms ─────────── v1.2.2 Installed CSV ───────────────────────── v0.10.15 Installed Dictionaries ──────────────── v0.3.29 Installed DocStringExtensions ───────── v0.9.5 Installed Microbiome ────────────────── v0.10.1 Installed BiobakeryUtils ────────────── v0.7.0 Installing 3 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Arpack 147.2 KiB Updating `~/.julia/environments/v1.14/Project.toml` [fa5322f5] + BiobakeryUtils v0.7.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [7d9fca2a] + Arpack v0.5.4 [fa5322f5] + BiobakeryUtils v0.7.0 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.1 [8f4d0f93] + Conda v1.10.3 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 ⌅ [85a47980] + Dictionaries v0.3.29 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [a58aae7d] + EcoBase v0.1.7 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.15.0 [34004b35] + HypergeometricFunctions v0.3.28 [313cdc1a] + Indexing v1.1.1 [842dd82b] + InlineStrings v1.4.5 [bd334432] + InlineTest v0.2.0 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.2.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [3bd8f0ae] + Microbiome v0.10.1 [e1d29d7a] + Missings v1.2.0 [6f286f6a] + MultivariateStats v0.10.3 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.36 [69de0a69] + Parsers v2.8.3 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [e0db7c4e] + ReTest v0.3.4 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.8 [4c63d2b9] + StatsFuns v1.5.2 [ec057cc2] + StructUtils v2.6.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [81def892] + VersionParsing v1.3.0 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 ⌅ [68821587] + Arpack_jll v3.5.1+1 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+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 [b27032c2] + LibCURL v1.0.0 [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 v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [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 v8.16.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Building Conda → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/8f06b0cfa4c514c7b9546756dbae91fcfbc92dc9/build.log` Installation completed after 15.23s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4852.2 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 1696.6 ms ✓ InlineStrings 780.6 ms ✓ Reexport 1117.4 ms ✓ Statistics 853.4 ms ✓ DataAPI 2136.6 ms ✓ IrrationalConstants 751.7 ms ✓ DataValueInterfaces 831.4 ms ✓ StatsAPI 1230.8 ms ✓ OrderedCollections 1071.6 ms ✓ DocStringExtensions 880.7 ms ✓ VersionParsing 790.8 ms ✓ Indexing 966.2 ms ✓ WorkerUtilities 2427.2 ms ✓ FillArrays 796.0 ms ✓ PtrArrays 1253.5 ms ✓ TranscodingStreams 740.8 ms ✓ IteratorInterfaceExtensions 1228.1 ms ✓ SuiteSparse 3287.8 ms ✓ SentinelArrays 1428.6 ms ✓ StructUtils 1139.6 ms ✓ Compat 1132.4 ms ✓ Preferences 1509.2 ms ✓ InlineTest 1300.8 ms ✓ Statistics → SparseArraysExt 938.7 ms ✓ Missings 996.3 ms ✓ PooledArrays 1437.7 ms ✓ Distances 3771.4 ms ✓ DataStructures 1612.2 ms ✓ LogExpFunctions 2039.3 ms ✓ Dictionaries 1516.6 ms ✓ FillArrays → FillArraysSparseArraysExt 907.5 ms ✓ FillArrays → FillArraysStatisticsExt 929.3 ms ✓ AliasTables 908.3 ms ✓ CodecZlib 731.4 ms ✓ TableTraits 1809.8 ms ✓ PDMats 809.1 ms ✓ Compat → CompatLinearAlgebraExt 1170.5 ms ✓ JLLWrappers 875.0 ms ✓ PrecompileTools 1264.2 ms ✓ Distances → DistancesSparseArraysExt 1055.3 ms ✓ SortingAlgorithms 2319.0 ms ✓ QuadGK 1751.0 ms ✓ Tables 1434.2 ms ✓ FillArrays → FillArraysPDMatsExt 2165.3 ms ✓ FilePathsBase 1442.7 ms ✓ Rmath_jll 1444.0 ms ✓ OpenSpecFun_jll 1401.1 ms ✓ Arpack_jll 3063.7 ms ✓ RecipesBase 18053.2 ms ✓ Parsers WARNING: Imported binding Test.pop_testset was undeclared at import time during import to Testset. WARNING: Imported binding Test.push_testset was undeclared at import time during import to Testset. ┌ Error: Precompilation failed, this is the captured stdout (114 chars): └ @ ReTest ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:36  Pass | Time / Compile / GC | Alloc ΔRSS | ReTest._ReTestPrecompileTests:  ┌ Error: And this is the captured stderr (0 chars): └ @ ReTest ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:39  ERROR: LoadError: TaskFailedException Stacktrace:  [1] #wait#580  @ ./task.jl:363 [inlined]  [2] wait  @ ./task.jl:360 [inlined]  [3] retest(::Union{Regex, AbstractString, Integer, Module, Symbol, Tuple, ReTest.Pattern, AbstractArray, Pair{Module, <:Union{Regex, AbstractString, Integer, Symbol, Tuple, ReTest.Pattern, AbstractArray}}}, ::Vararg{Union{Regex, AbstractString, Integer, Module, Symbol, Tuple, ReTest.Pattern, AbstractArray, Pair{Module, <:Union{Regex, AbstractString, Integer, Symbol, Tuple, ReTest.Pattern, AbstractArray}}}}; dry::Bool, stats::Bool, shuffle::Bool, group::Bool, verbose::Bool, recursive::Bool, id::Nothing, strict::Bool, dup::Bool, static::Nothing, load::Bool, seed::Bool, marks::Bool, tag::Vector{Symbol}, spin::Bool, clear::Bool)  @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1186  [4] kwcall(::@NamedTuple{recursive::Bool, stats::Bool, spin::Bool}, ::typeof(InlineTest.retest), ::Union{Regex, AbstractString, Integer, Module, Symbol, Tuple, ReTest.Pattern, AbstractArray, Pair{Module, <:Union{Regex, AbstractString, Integer, Symbol, Tuple, ReTest.Pattern, AbstractArray}}}, ::Vararg{Union{Regex, AbstractString, Integer, Module, Symbol, Tuple, ReTest.Pattern, AbstractArray, Pair{Module, <:Union{Regex, AbstractString, Integer, Symbol, Tuple, ReTest.Pattern, AbstractArray}}}})  @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:750  [5] #137  @ ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:26 [inlined]  [6] redirect_stdio(f::ReTest.var"#137#138"; stdin::Nothing, stderr::Pipe, stdout::Pipe)  @ Base ./stream.jl:1449  [7] kwcall(::@NamedTuple{stderr::Pipe, stdout::Pipe}, ::typeof(redirect_stdio), f::Function)  @ Base ./stream.jl:1412  [8] macro expansion  @ ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:25 [inlined]  [9] macro expansion  @ ~/.julia/packages/PrecompileTools/gn08A/src/workloads.jl:73 [inlined]  [10] macro expansion  @ ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:23 [inlined]  [11] macro expansion  @ ~/.julia/packages/PrecompileTools/gn08A/src/workloads.jl:121 [inlined]  [12] top-level scope  @ ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:118  [13] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:310  [14] top-level scope  @ ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1751  [15] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [16] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3151  [17] top-level scope  @ stdin:5  [18] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [19] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2997  [20] include_string  @ ./loading.jl:3007 [inlined]  [21] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [22] _start()  @ Base ./client.jl:577   nested task error: TaskFailedException   nested task error: UndefVarError: `push_testset` not defined in `ReTest.Testset`  Suggestion: this global was defined as `Test.push_testset` but not assigned a value.  Stacktrace:  [1] top-level scope  @ ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:517  [2] macro expansion  @ ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:12 [inlined]  [3] macro expansion  @ ~/.julia/packages/ReTest/3Ikse/src/testset.jl:517 [inlined]  [4] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [5] (::ReTest.var"#110#111"{ReTest.Testset.Format})(mod::Module, ts::ReTest.TestsetExpr, pat::ReTest.And, chan::@NamedTuple{out::Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, compute::Channel{Nothing}, preview::Nothing})  @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1154  [6] #local_remotecall_thunk##0  @ /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:425 [inlined]  [7] run_work_thunk(thunk::Distributed.var"#local_remotecall_thunk##0#local_remotecall_thunk##1"{ReTest.var"#110#111"{ReTest.Testset.Format}, Tuple{Module, ReTest.TestsetExpr, ReTest.And, @NamedTuple{out::Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, compute::Channel{Nothing}, preview::Nothing}}, @Kwargs{}}, print_error::Bool)  @ Distributed /opt/julia/share/julia/stdlib/v1.14/Distributed/src/process_messages.jl:70  [8] remotecall_fetch(::Function, ::Distributed.LocalProcess, ::Module, ::Vararg{Any}; kwargs::@Kwargs{})  @ Distributed /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:450  [9] remotecall_fetch  @ /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:449 [inlined]  [10] remotecall_fetch  @ /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:492 [inlined]  [11] (::ReTest.var"#106#107"{Int64, ReTest.Testset.Format, Nothing, ReTest.Testset.ReTestSet, Base.Threads.Atomic{Bool}, Channel{Nothing}, Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, Vector{Any}, ReTest.And, Module})()  @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1151  Stacktrace:  [1] remotecall_fetch(::Function, ::Distributed.LocalProcess, ::Module, ::Vararg{Any}; kwargs::@Kwargs{})  @ Distributed /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:451  [2] remotecall_fetch  @ /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:449 [inlined]  [3] remotecall_fetch  @ /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:492 [inlined]  [4] (::ReTest.var"#106#107"{Int64, ReTest.Testset.Format, Nothing, ReTest.Testset.ReTestSet, Base.Threads.Atomic{Bool}, Channel{Nothing}, Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, Vector{Any}, ReTest.And, Module})()  @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1151  Stacktrace:  [1] sync_end(c::Channel{Any})  @ Base ./task.jl:630  [2] macro expansion  @ ./task.jl:663 [inlined]  [3] (::ReTest.var"#96#97"{Bool, ReTest.Testset.Format, Bool, Base.RefValue{Int64}, Bool, ReTest.var"#take_latest!#91", Nothing, ReentrantLock, Bool, ReTest.Testset.ReTestSet, Base.Threads.Atomic{Bool}, Base.RefValue{Exception}, Channel{Nothing}, Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, Vector{Any}, ReTest.And, Module})()  @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1104 in expression starting at /home/pkgeval/.julia/packages/ReTest/3Ikse/src/precompile.jl:19 in expression starting at /home/pkgeval/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1 in expression starting at stdin:5 Precompilation completed after 126.69s ################################################################################ # Testing # Testing BiobakeryUtils Status `/tmp/jl_XDpSQr/Project.toml` [fa5322f5] BiobakeryUtils v0.7.0 [336ed68f] CSV v0.10.15 [8bb1440f] DelimitedFiles v1.9.1 [3bd8f0ae] Microbiome v0.10.1 [e0db7c4e] ReTest v0.3.4 [9a3f8284] Random v1.11.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_XDpSQr/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [7d9fca2a] Arpack v0.5.4 [fa5322f5] BiobakeryUtils v0.7.0 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 [8f4d0f93] Conda v1.10.3 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 ⌅ [85a47980] Dictionaries v0.3.29 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [a58aae7d] EcoBase v0.1.7 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [34004b35] HypergeometricFunctions v0.3.28 [313cdc1a] Indexing v1.1.1 [842dd82b] InlineStrings v1.4.5 [bd334432] InlineTest v0.2.0 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.2.1 [2ab3a3ac] LogExpFunctions v0.3.29 [3bd8f0ae] Microbiome v0.10.1 [e1d29d7a] Missings v1.2.0 [6f286f6a] MultivariateStats v0.10.3 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.36 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [e0db7c4e] ReTest v0.3.4 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.8 [4c63d2b9] StatsFuns v1.5.2 [ec057cc2] StructUtils v2.6.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [81def892] VersionParsing v1.3.0 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 ⌅ [68821587] Arpack_jll v3.5.1+1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+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 [b27032c2] LibCURL v1.0.0 [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 v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... WARNING: Imported binding Test.pop_testset was undeclared at import time during import to Testset. WARNING: Imported binding Test.push_testset was undeclared at import time during import to Testset. ┌ Error: Precompilation failed, this is the captured stdout (114 chars): └ @ ReTest ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:36  Pass | Time / Compile / GC | Alloc ΔRSS | ReTest._ReTestPrecompileTests:  ┌ Error: And this is the captured stderr (0 chars): └ @ ReTest ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:39  ERROR: LoadError: TaskFailedException Stacktrace:  [1] #wait#580  @ ./task.jl:363 [inlined]  [2] wait  @ ./task.jl:360 [inlined]  [3] retest(::Union{Regex, AbstractString, Integer, Module, Symbol, Tuple, ReTest.Pattern, AbstractArray, Pair{Module, <:Union{Regex, AbstractString, Integer, Symbol, Tuple, ReTest.Pattern, AbstractArray}}}, ::Vararg{Union{Regex, AbstractString, Integer, Module, Symbol, Tuple, ReTest.Pattern, AbstractArray, Pair{Module, <:Union{Regex, AbstractString, Integer, Symbol, Tuple, ReTest.Pattern, AbstractArray}}}}; dry::Bool, stats::Bool, shuffle::Bool, group::Bool, verbose::Bool, recursive::Bool, id::Nothing, strict::Bool, dup::Bool, static::Nothing, load::Bool, seed::Bool, marks::Bool, tag::Vector{Symbol}, spin::Bool, clear::Bool)  @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1186  [4] kwcall(::@NamedTuple{recursive::Bool, stats::Bool, spin::Bool}, ::typeof(InlineTest.retest), ::Union{Regex, AbstractString, Integer, Module, Symbol, Tuple, ReTest.Pattern, AbstractArray, Pair{Module, <:Union{Regex, AbstractString, Integer, Symbol, Tuple, ReTest.Pattern, AbstractArray}}}, ::Vararg{Union{Regex, AbstractString, Integer, Module, Symbol, Tuple, ReTest.Pattern, AbstractArray, Pair{Module, <:Union{Regex, AbstractString, Integer, Symbol, Tuple, ReTest.Pattern, AbstractArray}}}})  @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:750  [5] #137  @ ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:26 [inlined]  [6] redirect_stdio(f::ReTest.var"#137#138"; stdin::Nothing, stderr::Pipe, stdout::Pipe)  @ Base ./stream.jl:1449  [7] kwcall(::@NamedTuple{stderr::Pipe, stdout::Pipe}, ::typeof(redirect_stdio), f::Function)  @ Base ./stream.jl:1412  [8] macro expansion  @ ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:25 [inlined]  [9] macro expansion  @ ~/.julia/packages/PrecompileTools/gn08A/src/workloads.jl:73 [inlined]  [10] macro expansion  @ ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:23 [inlined]  [11] macro expansion  @ ~/.julia/packages/PrecompileTools/gn08A/src/workloads.jl:121 [inlined]  [12] top-level scope  @ ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:118  [13] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:310  [14] top-level scope  @ ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1751  [15] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [16] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3151  [17] top-level scope  @ stdin:5  [18] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [19] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2997  [20] include_string  @ ./loading.jl:3007 [inlined]  [21] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [22] _start()  @ Base ./client.jl:577   nested task error: TaskFailedException   nested task error: UndefVarError: `push_testset` not defined in `ReTest.Testset`  Suggestion: this global was defined as `Test.push_testset` but not assigned a value.  Stacktrace:  [1] top-level scope  @ ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:517  [2] macro expansion  @ ~/.julia/packages/ReTest/3Ikse/src/precompile.jl:12 [inlined]  [3] macro expansion  @ ~/.julia/packages/ReTest/3Ikse/src/testset.jl:517 [inlined]  [4] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [5] (::ReTest.var"#110#111"{ReTest.Testset.Format})(mod::Module, ts::ReTest.TestsetExpr, pat::ReTest.And, chan::@NamedTuple{out::Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, compute::Channel{Nothing}, preview::Nothing})  @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1154  [6] #local_remotecall_thunk##0  @ /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:425 [inlined]  [7] run_work_thunk(thunk::Distributed.var"#local_remotecall_thunk##0#local_remotecall_thunk##1"{ReTest.var"#110#111"{ReTest.Testset.Format}, Tuple{Module, ReTest.TestsetExpr, ReTest.And, @NamedTuple{out::Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, compute::Channel{Nothing}, preview::Nothing}}, @Kwargs{}}, print_error::Bool)  @ Distributed /opt/julia/share/julia/stdlib/v1.14/Distributed/src/process_messages.jl:70  [8] remotecall_fetch(::Function, ::Distributed.LocalProcess, ::Module, ::Vararg{Any}; kwargs::@Kwargs{})  @ Distributed /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:450  [9] remotecall_fetch  @ /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:449 [inlined]  [10] remotecall_fetch  @ /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:492 [inlined]  [11] (::ReTest.var"#106#107"{Int64, ReTest.Testset.Format, Nothing, ReTest.Testset.ReTestSet, Base.Threads.Atomic{Bool}, Channel{Nothing}, Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, Vector{Any}, ReTest.And, Module})()  @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1151  Stacktrace:  [1] remotecall_fetch(::Function, ::Distributed.LocalProcess, ::Module, ::Vararg{Any}; kwargs::@Kwargs{})  @ Distributed /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:451  [2] remotecall_fetch  @ /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:449 [inlined]  [3] remotecall_fetch  @ /opt/julia/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:492 [inlined]  [4] (::ReTest.var"#106#107"{Int64, ReTest.Testset.Format, Nothing, ReTest.Testset.ReTestSet, Base.Threads.Atomic{Bool}, Channel{Nothing}, Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, Vector{Any}, ReTest.And, Module})()  @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1151  Stacktrace:  [1] sync_end(c::Channel{Any})  @ Base ./task.jl:630  [2] macro expansion  @ ./task.jl:663 [inlined]  [3] (::ReTest.var"#96#97"{Bool, ReTest.Testset.Format, Bool, Base.RefValue{Int64}, Bool, ReTest.var"#take_latest!#91", Nothing, ReentrantLock, Bool, ReTest.Testset.ReTestSet, Base.Threads.Atomic{Bool}, Base.RefValue{Exception}, Channel{Nothing}, Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, Vector{Any}, ReTest.And, Module})()  @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1104 in expression starting at /home/pkgeval/.julia/packages/ReTest/3Ikse/src/precompile.jl:19 in expression starting at /home/pkgeval/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1 in expression starting at stdin:5 1 dependency had output during precompilation: ┌ ReTest │ [Output was shown above] └ ERROR: LoadError: The following 1 package failed to precompile: ReTest Failed to precompile ReTest [e0db7c4e-2690-44b9-bad6-7687da720f89] to "/home/pkgeval/.julia/compiled/v1.14/ReTest/jl_gni2XX" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/BiobakeryUtilsTests.jl:1 in expression starting at /home/pkgeval/.julia/packages/BiobakeryUtils/ypFMk/test/runtests.jl:1 Testing failed after 35.0s ERROR: LoadError: Package BiobakeryUtils 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:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [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:572 [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:548 [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:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 206.74s: package fails to precompile