Package evaluation to test BioSequenceMappings on Julia 1.14.0-DEV.1372 (893635dc59*) started at 2025-12-16T15:05:05.756


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...
  Activating project at `~/.julia/environments/v1.14`

Set-up completed after 9.82s


################################################################################
# Installation
#

Installing BioSequenceMappings...
   Resolving package versions...
    Updating `~/.julia/environments/v1.14/Project.toml`
  [a84bc454] + BioSequenceMappings v0.1.6
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [79e6a3ab] + Adapt v4.4.0
  [dce04be8] + ArgCheck v2.5.0
  [a9b6321e] + Atomix v1.1.2
  [67c07d97] + Automa v1.1.0
  [47718e42] + BioGenerics v0.1.5
  [a84bc454] + BioSequenceMappings v0.1.6
  [d360d2e6] + ChainRulesCore v1.26.0
  [34da2185] + Compat v4.18.1
  [c2308a5c] + FASTX v2.1.7
  [46192b85] + GPUArraysCore v0.2.0
  [076d061b] + HashArrayMappedTries v0.2.0
  [63c18a36] + KernelAbstractions v0.9.39
  [1914dd2f] + MacroTools v0.5.16
  [872c559c] + NNlib v0.9.32
  [0b1bfda6] + OneHotArrays v0.2.10
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [ae029012] + Requires v1.3.1
  [fdea26ae] + SIMD v3.7.2
  [7e506255] + ScopedValues v1.5.0
  [90137ffa] + StaticArrays v1.9.15
  [1e83bf80] + StaticArraysCore v1.4.4
  [10745b16] + Statistics v1.11.1
  [354b36f9] + StringViews v1.3.6
  [3bb67fe8] + TranscodingStreams v0.11.3
  [013be700] + UnsafeAtomics v0.3.0
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates 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
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v1.0.0
  [f489334b] + StyledStrings v1.13.0
  [fa267f1f] + TOML v1.0.3
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [8e850b90] + libblastrampoline_jll v5.15.0+0

Installation completed after 3.85s


################################################################################
# Precompilation
#

ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing)
The function `setindex!` exists, but no method is defined for this combination of argument types.
Stacktrace:
 [1] top-level scope
   @ /PkgEval.jl/scripts/precompile.jl:10
 [2] include(mod::Module, _path::String)
   @ Base ./Base.jl:309
 [3] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:344
 [4] _start()
   @ Base ./client.jl:577
in expression starting at /PkgEval.jl/scripts/precompile.jl:6

caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull)
The function `setindex!` exists, but no method is defined for this combination of argument types.
Stacktrace:
 [1] top-level scope
   @ /PkgEval.jl/scripts/precompile.jl:7
 [2] include(mod::Module, _path::String)
   @ Base ./Base.jl:309
 [3] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:344
 [4] _start()
   @ Base ./client.jl:577

Precompilation failed after 13.53s



################################################################################
# Testing
#

     Testing BioSequenceMappings
      Status `/tmp/jl_Ytt9Gw/Project.toml`
  [6e4b80f9] BenchmarkTools v1.6.3
  [a84bc454] BioSequenceMappings v0.1.6
  [e41cd558] DCAUtils v1.1.0
  [9a3f8284] Random v1.11.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_Ytt9Gw/Manifest.toml`
  [79e6a3ab] Adapt v4.4.0
  [dce04be8] ArgCheck v2.5.0
  [a9b6321e] Atomix v1.1.2
  [67c07d97] Automa v1.1.0
  [6e4b80f9] BenchmarkTools v1.6.3
  [47718e42] BioGenerics v0.1.5
  [a84bc454] BioSequenceMappings v0.1.6
  [d360d2e6] ChainRulesCore v1.26.0
  [34da2185] Compat v4.18.1
  [e41cd558] DCAUtils v1.1.0
  [c2308a5c] FASTX v2.1.7
  [a0c94c4b] FastaIO v1.1.0
  [46192b85] GPUArraysCore v0.2.0
  [92fee26a] GZip v0.6.2
  [076d061b] HashArrayMappedTries v0.2.0
  [682c06a0] JSON v1.3.0
  [63c18a36] KernelAbstractions v0.9.39
  [1914dd2f] MacroTools v0.5.16
  [872c559c] NNlib v0.9.32
  [0b1bfda6] OneHotArrays v0.2.10
  [69de0a69] Parsers v2.8.3
  [aea7be01] PrecompileTools v1.3.3
  [21216c6a] Preferences v1.5.0
  [ae029012] Requires v1.3.1
  [fdea26ae] SIMD v3.7.2
  [7e506255] ScopedValues v1.5.0
  [90137ffa] StaticArrays v1.9.15
  [1e83bf80] StaticArraysCore v1.4.4
  [10745b16] Statistics v1.11.1
  [354b36f9] StringViews v1.3.6
  [ec057cc2] StructUtils v2.6.0
  [3bb67fe8] TranscodingStreams v0.11.3
  [013be700] UnsafeAtomics v0.3.0
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates 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
  [de0858da] Printf v1.11.0
  [9abbd945] Profile v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v1.0.0
  [9e88b42a] Serialization 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
  [4536629a] OpenBLAS_jll v0.3.29+0
  [83775a58] Zlib_jll v1.3.1+2
  [8e850b90] libblastrampoline_jll v5.15.0+0
     Testing Running tests...
WARNING: Wrapping `Vararg` directly in UnionAll is deprecated (wrap the tuple instead).
You may need to write `f(x::Vararg{T})` rather than `f(x::Vararg{<:T})` or `f(x::Vararg{T}) where T` instead of `f(x::Vararg{T} where T)`.
To make this warning an error, and hence obtain a stack trace, use `julia --depwarn=error`.

  1 dependency had output during precompilation:
┌ BioSequenceMappings
│  [Output was shown above]
└  
# Alphabet
# Alignment
┌ Warning: I should write a test for `find_sequence` and `match_sequences`
└ @ Main ~/.julia/packages/BioSequenceMappings/Yj4fV/test/alignments/methods.jl:16
# IO
[ Info: Tests: warning will be produced below
┌ Warning: Could not find a default alphabet for characters ['-', '.', 'A', 'C', 'G']
│  Using Alphabet{Char,Int64}: ['-', '.', 'A', 'C', 'G']
└ @ BioSequenceMappings ~/.julia/packages/BioSequenceMappings/Yj4fV/src/IO.jl:62
Test Summary:          | Pass  Total   Time
BioSequenceMappings.jl |  165    165  42.5s
     Testing BioSequenceMappings tests passed 

Testing completed after 80.35s

PkgEval succeeded after 119.11s