Package evaluation to test CUBScout on Julia 1.14.0-DEV.14 (ec5cf08762*) started at 2025-11-02T18:05:57.769


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 9.77s


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

Installing CUBScout...
   Resolving package versions...
   Installed DelimitedFiles ────── v1.9.1
   Installed OpenSSH_jll ───────── v10.2.1+0
   Installed CodecZlib ─────────── v0.7.8
   Installed ExceptionUnwrapping ─ v0.1.11
   Installed StringViews ───────── v1.3.5
   Installed ConcurrentUtilities ─ v2.5.0
   Installed URIs ──────────────── v1.6.1
   Installed TranscodingStreams ── v0.11.3
   Installed SIMD ──────────────── v3.7.2
   Installed ProgressLogging ───── v0.1.5
   Installed Git_LFS_jll ───────── v3.7.0+0
   Installed OpenSSL ───────────── v1.6.0
   Installed Statistics ────────── v1.11.1
   Installed MbedTLS ───────────── v1.1.9
   Installed ArtifactUtils ─────── v0.2.4
   Installed PrecompileTools ───── v1.3.3
   Installed Expat_jll ─────────── v2.7.3+0
   Installed Git_jll ───────────── v2.51.3+0
   Installed BitFlags ──────────── v0.1.9
   Installed LoggingExtras ─────── v1.2.0
   Installed Twiddle ───────────── v1.1.2
   Installed BioGenerics ───────── v0.1.5
   Installed BioSymbols ────────── v5.2.0
   Installed HTTP ──────────────── v1.10.19
   Installed CUBScout ──────────── v1.0.0
   Installed Libiconv_jll ──────── v1.18.0+0
   Installed Git ───────────────── v1.5.0
   Installed Automa ────────────── v1.1.0
   Installed JLLWrappers ───────── v1.7.1
   Installed gh_cli_jll ────────── v2.63.2+0
   Installed SimpleBufferStream ── v1.2.0
   Installed FASTX ─────────────── v2.1.7
   Installed Preferences ───────── v1.5.0
   Installed MbedTLS_jll ───────── v2.28.10+0
   Installed BioSequences ──────── v3.5.0
  Installing 10 artifacts
   Installed artifact codon_dict_altstart 367 bytes
   Installed artifact codon_dict          359 bytes
   Installed artifact Libiconv            1.9 MiB
   Installed artifact example_genome      1.4 MiB
   Installed artifact OpenSSH             4.3 MiB
   Installed artifact MbedTLS             2.2 MiB
   Installed artifact Expat               283.3 KiB
   Installed artifact Git_LFS             9.6 MiB
   Installed artifact gh_cli              23.1 MiB
   Installed artifact Git                 48.9 MiB
    Updating `~/.julia/environments/v1.14/Project.toml`
  [5bb2324b] + CUBScout v1.0.0
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [8b73e784] + ArtifactUtils v0.2.4
  [67c07d97] + Automa v1.1.0
  [47718e42] + BioGenerics v0.1.5
  [7e6ae17a] + BioSequences v3.5.0
  [3c28c6f8] + BioSymbols v5.2.0
  [d1d4a3ce] + BitFlags v0.1.9
  [5bb2324b] + CUBScout v1.0.0
  [944b1d66] + CodecZlib v0.7.8
  [f0e56b4a] + ConcurrentUtilities v2.5.0
  [8bb1440f] + DelimitedFiles v1.9.1
  [460bff9d] + ExceptionUnwrapping v0.1.11
  [c2308a5c] + FASTX v2.1.7
  [d7ba0133] + Git v1.5.0
  [cd3eb016] + HTTP v1.10.19
  [692b3bcd] + JLLWrappers v1.7.1
  [e6f89c97] + LoggingExtras v1.2.0
  [739be429] + MbedTLS v1.1.9
  [4d8831e6] + OpenSSL v1.6.0
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [33c8b6b6] + ProgressLogging v0.1.5
  [fdea26ae] + SIMD v3.7.2
  [777ac1f9] + SimpleBufferStream v1.2.0
  [10745b16] + Statistics v1.11.1
  [354b36f9] + StringViews v1.3.5
  [3bb67fe8] + TranscodingStreams v0.11.3
  [7200193e] + Twiddle v1.1.2
  [5c2747f8] + URIs v1.6.1
  [2e619515] + Expat_jll v2.7.3+0
  [020c3dae] + Git_LFS_jll v3.7.0+0
  [f8c6e375] + Git_jll v2.51.3+0
  [94ce4f54] + Libiconv_jll v1.18.0+0
  [c8ffd9c3] + MbedTLS_jll v2.28.10+0
  [9bd350c2] + OpenSSH_jll v10.2.1+0
  [5d31d589] + gh_cli_jll v2.63.2+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
  [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
  [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 v8.16.0+0
  [e37daf67] + LibGit2_jll v1.9.1+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.9.9
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [458c3c95] + OpenSSL_jll v3.5.4+0
  [efcefdf7] + PCRE2_jll v10.47.0+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 v1.67.1+0
  [3f19e933] + p7zip_jll v17.6.0+0

Installation completed after 12.06s


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

Precompiling PkgEval dependencies...
Precompiling packages...
   4127.7 ms  ✓ TestEnv
  1 dependency successfully precompiled in 4 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...
   1163.9 ms  ✓ Statistics
   1122.5 ms  ✓ URIs
    666.8 ms  ✓ Twiddle
    690.4 ms  ✓ BitFlags
   1214.9 ms  ✓ ProgressLogging
   1805.0 ms  ✓ ConcurrentUtilities
   1073.9 ms  ✓ StringViews
   1258.7 ms  ✓ TranscodingStreams
    795.4 ms  ✓ SimpleBufferStream
    956.6 ms  ✓ DelimitedFiles
   1074.6 ms  ✓ LoggingExtras
   1118.2 ms  ✓ Preferences
   2485.0 ms  ✓ ExceptionUnwrapping
   3580.9 ms  ✓ OpenSSL
    897.3 ms  ✓ BioGenerics
    927.9 ms  ✓ CodecZlib
   1181.2 ms  ✓ JLLWrappers
    942.7 ms  ✓ PrecompileTools
   1402.3 ms  ✓ Libiconv_jll
   1061.1 ms  ✓ Git_LFS_jll
   1079.5 ms  ✓ MbedTLS_jll
   1434.3 ms  ✓ OpenSSH_jll
   1322.2 ms  ✓ gh_cli_jll
   1363.2 ms  ✓ Expat_jll
   2410.5 ms  ✓ BioSymbols


Precompilation completed after 61.94s


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

     Testing CUBScout
      Status `/tmp/jl_I6BpDo/Project.toml`
  [8b73e784] ArtifactUtils v0.2.4
  [7e6ae17a] BioSequences v3.5.0
  [5bb2324b] CUBScout v1.0.0
  [8bb1440f] DelimitedFiles v1.9.1
  [c2308a5c] FASTX v2.1.7
  [10745b16] Statistics v1.11.1
  [56f22d72] Artifacts v1.11.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_I6BpDo/Manifest.toml`
  [8b73e784] ArtifactUtils v0.2.4
  [67c07d97] Automa v1.1.0
  [47718e42] BioGenerics v0.1.5
  [7e6ae17a] BioSequences v3.5.0
  [3c28c6f8] BioSymbols v5.2.0
  [d1d4a3ce] BitFlags v0.1.9
  [5bb2324b] CUBScout v1.0.0
  [944b1d66] CodecZlib v0.7.8
  [f0e56b4a] ConcurrentUtilities v2.5.0
  [8bb1440f] DelimitedFiles v1.9.1
  [460bff9d] ExceptionUnwrapping v0.1.11
  [c2308a5c] FASTX v2.1.7
  [d7ba0133] Git v1.5.0
  [cd3eb016] HTTP v1.10.19
  [692b3bcd] JLLWrappers v1.7.1
  [e6f89c97] LoggingExtras v1.2.0
  [739be429] MbedTLS v1.1.9
  [4d8831e6] OpenSSL v1.6.0
  [aea7be01] PrecompileTools v1.3.3
  [21216c6a] Preferences v1.5.0
  [33c8b6b6] ProgressLogging v0.1.5
  [fdea26ae] SIMD v3.7.2
  [777ac1f9] SimpleBufferStream v1.2.0
  [10745b16] Statistics v1.11.1
  [354b36f9] StringViews v1.3.5
  [3bb67fe8] TranscodingStreams v0.11.3
  [7200193e] Twiddle v1.1.2
  [5c2747f8] URIs v1.6.1
  [2e619515] Expat_jll v2.7.3+0
  [020c3dae] Git_LFS_jll v3.7.0+0
  [f8c6e375] Git_jll v2.51.3+0
  [94ce4f54] Libiconv_jll v1.18.0+0
  [c8ffd9c3] MbedTLS_jll v2.28.10+0
  [9bd350c2] OpenSSH_jll v10.2.1+0
  [5d31d589] gh_cli_jll v2.63.2+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
  [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
  [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 v8.16.0+0
  [e37daf67] LibGit2_jll v1.9.1+0
  [29816b5a] LibSSH2_jll v1.11.3+1
  [14a3606d] MozillaCACerts_jll v2025.9.9
  [4536629a] OpenBLAS_jll v0.3.29+0
  [458c3c95] OpenSSL_jll v3.5.4+0
  [efcefdf7] PCRE2_jll v10.47.0+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 v1.67.1+0
  [3f19e933] p7zip_jll v17.6.0+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_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})
     @ Base ./module.jl:101
  [36] top-level scope
     @ ~/.julia/packages/CUBScout/X6ZXX/src/CUBScout.jl:3
  [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/CUBScout/X6ZXX/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/CUBScout/X6ZXX/src/CUBScout.jl:1
in expression starting at /home/pkgeval/.julia/packages/CUBScout/X6ZXX/test/runtests.jl:1

Testing failed after 95.64s

ERROR: LoadError: Package CUBScout 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 197.64s: package tests unexpectedly errored