Package evaluation to test BioSequenceMappings on Julia 1.14.0-DEV.14 (ec5cf08762*) started at 2025-11-02T15:46:36.368


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 9.7s


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

Installing BioSequenceMappings...
   Resolving package versions...
   Installed HashArrayMappedTries ─ v0.2.0
   Installed Compat ─────────────── v4.18.1
   Installed MacroTools ─────────── v0.5.16
   Installed Adapt ──────────────── v4.4.0
   Installed StringViews ────────── v1.3.5
   Installed TranscodingStreams ─── v0.11.3
   Installed BioSequenceMappings ── v0.1.6
   Installed NNlib ──────────────── v0.9.31
   Installed SIMD ───────────────── v3.7.2
   Installed ArgCheck ───────────── v2.5.0
   Installed Statistics ─────────── v1.11.1
   Installed Atomix ─────────────── v1.1.2
   Installed StaticArraysCore ───── v1.4.4
   Installed StaticArrays ───────── v1.9.15
   Installed PrecompileTools ────── v1.3.3
   Installed ChainRulesCore ─────── v1.26.0
   Installed GPUArraysCore ──────── v0.2.0
   Installed Requires ───────────── v1.3.1
   Installed UnsafeAtomics ──────── v0.3.0
   Installed ScopedValues ───────── v1.5.0
   Installed KernelAbstractions ─── v0.9.38
   Installed Preferences ────────── v1.5.0
   Installed BioGenerics ────────── v0.1.5
   Installed Automa ─────────────── v1.1.0
   Installed FASTX ──────────────── v2.1.7
   Installed OneHotArrays ───────── v0.2.10
    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 v0.9.38
  [1914dd2f] + MacroTools v0.5.16
  [872c559c] + NNlib v0.9.31
  [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 v1.3.5
  [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 v1.12.0
  [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 v1.11.0
  [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 5.11s


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

Precompiling PkgEval dependencies...
Precompiling packages...
   4862.2 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...
   4286.8 ms  ✓ MacroTools
    934.7 ms  ✓ StaticArraysCore
    886.5 ms  ✓ HashArrayMappedTries
    960.1 ms  ✓ ArgCheck
   3544.1 ms  ✓ UnsafeAtomics
   1109.1 ms  ✓ Statistics
   1236.8 ms  ✓ TranscodingStreams
   1071.2 ms  ✓ StringViews
   1137.9 ms  ✓ Requires
   1130.4 ms  ✓ Preferences
   1106.1 ms  ✓ Compat
    857.1 ms  ✓ ScopedValues
    936.2 ms  ✓ Atomix
    876.6 ms  ✓ BioGenerics
    886.4 ms  ✓ Adapt
    856.0 ms  ✓ PrecompileTools
   1027.1 ms  ✓ Compat → CompatLinearAlgebraExt
   1162.0 ms  ✓ GPUArraysCore
  13324.1 ms  ✓ StaticArrays


Precompilation completed after 70.36s


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

     Testing BioSequenceMappings
      Status `/tmp/jl_a03Rtu/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_a03Rtu/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 v1.2.0
  [63c18a36] KernelAbstractions v0.9.38
  [1914dd2f] MacroTools v0.5.16
  [872c559c] NNlib v0.9.31
  [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 v1.3.5
  [ec057cc2] StructUtils v2.5.1
  [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 v1.12.0
  [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 v1.11.0
  [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...
ERROR: LoadError: UndefVarError: `T` not defined in `SIMD`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
   [1] top-level scope
     @ ~/.julia/packages/SIMD/UiGbs/src/arrayops.jl:4
   [2] include(mapexpr::Function, mod::Module, _path::String)
     @ Base ./Base.jl:310
   [3] top-level scope
     @ ~/.julia/packages/SIMD/UiGbs/src/SIMD.jl:25
   [4] include(mod::Module, _path::String)
     @ Base ./Base.jl:309
   [5] __require_prelocked(pkg::Base.PkgId, env::String)
     @ Base ./loading.jl:2817
   [6] _require_prelocked(uuidkey::Base.PkgId, env::String)
     @ Base ./loading.jl:2576
   [7] macro expansion
     @ ./loading.jl:2504 [inlined]
   [8] macro expansion
     @ ./lock.jl:376 [inlined]
   [9] __require(into::Module, mod::Symbol)
     @ Base ./loading.jl:2468
  [10] require
     @ ./loading.jl:2444 [inlined]
  [11] eval_import_path
     @ ./module.jl:36 [inlined]
  [12] eval_import_path_all(at::Module, path::Expr, keyword::String)
     @ Base ./module.jl:60
  [13] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})
     @ Base ./module.jl:101
  [14] top-level scope
     @ ~/.julia/packages/Automa/EyNRt/src/Automa.jl:4
  [15] include(mod::Module, _path::String)
     @ Base ./Base.jl:309
  [16] __require_prelocked(pkg::Base.PkgId, env::String)
     @ Base ./loading.jl:2817
  [17] _require_prelocked(uuidkey::Base.PkgId, env::String)
     @ Base ./loading.jl:2576
  [18] macro expansion
     @ ./loading.jl:2504 [inlined]
  [19] macro expansion
     @ ./lock.jl:376 [inlined]
  [20] __require(into::Module, mod::Symbol)
     @ Base ./loading.jl:2468
  [21] require
     @ ./loading.jl:2444 [inlined]
  [22] eval_import_path
     @ ./module.jl:36 [inlined]
  [23] eval_import_path_all(at::Module, path::Expr, keyword::String)
     @ Base ./module.jl:60
  [24] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})
     @ Base ./module.jl:101
  [25] top-level scope
     @ ~/.julia/packages/FASTX/KGKFv/src/FASTX.jl:4
  [26] include(mod::Module, _path::String)
     @ Base ./Base.jl:309
  [27] __require_prelocked(pkg::Base.PkgId, env::String)
     @ Base ./loading.jl:2817
  [28] _require_prelocked(uuidkey::Base.PkgId, env::String)
     @ Base ./loading.jl:2576
  [29] macro expansion
     @ ./loading.jl:2504 [inlined]
  [30] macro expansion
     @ ./lock.jl:376 [inlined]
  [31] __require(into::Module, mod::Symbol)
     @ Base ./loading.jl:2468
  [32] require
     @ ./loading.jl:2444 [inlined]
  [33] eval_import_path
     @ ./module.jl:36 [inlined]
  [34] eval_import_path_all(at::Module, path::Expr, keyword::String)
     @ Base ./module.jl:60
  [35] _eval_using(to::Module, path::Expr)
     @ Base ./module.jl:137
  [36] top-level scope
     @ ~/.julia/packages/BioSequenceMappings/Yj4fV/src/BioSequenceMappings.jl:4
  [37] include(mod::Module, _path::String)
     @ Base ./Base.jl:309
  [38] __require_prelocked(pkg::Base.PkgId, env::String)
     @ Base ./loading.jl:2817
  [39] _require_prelocked(uuidkey::Base.PkgId, env::String)
     @ Base ./loading.jl:2576
  [40] macro expansion
     @ ./loading.jl:2504 [inlined]
  [41] macro expansion
     @ ./lock.jl:376 [inlined]
  [42] __require(into::Module, mod::Symbol)
     @ Base ./loading.jl:2468
  [43] require
     @ ./loading.jl:2444 [inlined]
  [44] eval_import_path
     @ ./module.jl:36 [inlined]
  [45] eval_import_path_all(at::Module, path::Expr, keyword::String)
     @ Base ./module.jl:60
  [46] _eval_using(to::Module, path::Expr)
     @ Base ./module.jl:137
  [47] top-level scope
     @ ~/.julia/packages/BioSequenceMappings/Yj4fV/test/runtests.jl:1
  [48] include(mapexpr::Function, mod::Module, _path::String)
     @ Base ./Base.jl:310
  [49] top-level scope
     @ none:6
  [50] eval(m::Module, e::Any)
     @ Core ./boot.jl:489
  [51] exec_options(opts::Base.JLOptions)
     @ Base ./client.jl:310
  [52] _start()
     @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/SIMD/UiGbs/src/arrayops.jl:4
in expression starting at /home/pkgeval/.julia/packages/SIMD/UiGbs/src/SIMD.jl:1
in expression starting at /home/pkgeval/.julia/packages/Automa/EyNRt/src/Automa.jl:1
in expression starting at /home/pkgeval/.julia/packages/FASTX/KGKFv/src/FASTX.jl:1
in expression starting at /home/pkgeval/.julia/packages/BioSequenceMappings/Yj4fV/src/BioSequenceMappings.jl:1
in expression starting at /home/pkgeval/.julia/packages/BioSequenceMappings/Yj4fV/test/runtests.jl:1

Testing failed after 100.28s

ERROR: LoadError: Package BioSequenceMappings 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:2936
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2785 [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 201.86s: package tests unexpectedly errored