Package evaluation to test PGENFiles on Julia 1.14.0-DEV.14 (ec5cf08762*) started at 2025-11-02T17:53:21.778


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 10.02s


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

Installing PGENFiles...
   Resolving package versions...
   Installed CodecZlib ─────────────────── v0.7.8
   Installed FilePathsBase ─────────────── v0.9.24
   Installed AliasTables ───────────────── v1.1.3
   Installed DataStructures ────────────── v0.19.1
   Installed InlineStrings ─────────────── v1.4.5
   Installed StatsBase ─────────────────── v0.34.7
   Installed TranscodingStreams ────────── v0.11.3
   Installed OrderedCollections ────────── v1.8.1
   Installed IteratorInterfaceExtensions ─ v1.0.0
   Installed Compat ────────────────────── v4.18.1
   Installed DataAPI ───────────────────── v1.16.0
   Installed InvertedIndices ───────────── v1.3.1
   Installed Statistics ────────────────── v1.11.1
   Installed DataValueInterfaces ───────── v1.0.0
   Installed StatsAPI ──────────────────── v1.7.1
   Installed SentinelArrays ────────────── v1.4.8
   Installed IrrationalConstants ───────── v0.2.6
   Installed StringManipulation ────────── v0.4.1
   Installed PrecompileTools ───────────── v1.3.3
   Installed BitIntegers ───────────────── v0.3.5
   Installed GeneticVariantBase ────────── v0.1.2
   Installed PGENFiles ─────────────────── v0.2.2
   Installed Parsers ───────────────────── v2.8.3
   Installed LogExpFunctions ───────────── v0.3.29
   Installed Tables ────────────────────── v1.12.1
   Installed PtrArrays ─────────────────── v1.3.0
   Installed Reexport ──────────────────── v1.2.2
   Installed Missings ──────────────────── v1.2.0
   Installed Preferences ───────────────── v1.5.0
   Installed PrettyTables ──────────────── v3.1.0
   Installed TableTraits ───────────────── v1.0.1
   Installed LaTeXStrings ──────────────── v1.4.0
   Installed WeakRefStrings ────────────── v1.4.2
   Installed PooledArrays ──────────────── v1.4.3
   Installed SortingAlgorithms ─────────── v1.2.2
   Installed Crayons ───────────────────── v4.1.1
   Installed DataFrames ────────────────── v1.8.1
   Installed DocStringExtensions ───────── v0.9.5
   Installed WorkerUtilities ───────────── v1.6.1
   Installed CSV ───────────────────────── v0.10.15
    Updating `~/.julia/environments/v1.14/Project.toml`
  [bbb59ef6] + PGENFiles v0.2.2
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [66dad0bd] + AliasTables v1.1.3
  [c3b6d118] + BitIntegers v0.3.5
  [336ed68f] + CSV v0.10.15
  [944b1d66] + CodecZlib v0.7.8
  [34da2185] + Compat v4.18.1
  [a8cc5b0e] + Crayons v4.1.1
  [9a962f9c] + DataAPI v1.16.0
  [a93c6f00] + DataFrames v1.8.1
  [864edb3b] + DataStructures v0.19.1
  [e2d170a0] + DataValueInterfaces v1.0.0
  [ffbed154] + DocStringExtensions v0.9.5
  [48062228] + FilePathsBase v0.9.24
  [2447270c] + GeneticVariantBase v0.1.2
  [842dd82b] + InlineStrings v1.4.5
  [41ab1584] + InvertedIndices v1.3.1
  [92d709cd] + IrrationalConstants v0.2.6
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [b964fa9f] + LaTeXStrings v1.4.0
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [e1d29d7a] + Missings v1.2.0
  [bac558e1] + OrderedCollections v1.8.1
  [bbb59ef6] + PGENFiles v0.2.2
  [69de0a69] + Parsers v2.8.3
  [2dfb63ee] + PooledArrays v1.4.3
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [08abe8d2] + PrettyTables v3.1.0
  [43287f4e] + PtrArrays v1.3.0
  [189a3867] + Reexport v1.2.2
  [91c51154] + SentinelArrays v1.4.8
  [a2af1166] + SortingAlgorithms v1.2.2
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.1
  [2913bbd2] + StatsBase v0.34.7
  [892a3eda] + StringManipulation v0.4.1
  [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
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [7b1f6079] + FileWatching v1.11.0
  [9fa8497b] + Future v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.13.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [de0858da] + Printf v1.11.0
  [3fa0cd96] + REPL 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
  [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
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850b90] + libblastrampoline_jll v5.15.0+0

Installation completed after 6.41s


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

Precompiling PkgEval dependencies...
Precompiling packages...
   4761.1 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...
   1684.9 ms  ✓ InlineStrings
    757.8 ms  ✓ Reexport
   1107.2 ms  ✓ Statistics
    841.4 ms  ✓ DataAPI
   2119.6 ms  ✓ IrrationalConstants
    752.9 ms  ✓ DataValueInterfaces
    805.5 ms  ✓ StatsAPI
   1229.4 ms  ✓ OrderedCollections
    898.8 ms  ✓ InvertedIndices
   1093.0 ms  ✓ DocStringExtensions
    967.6 ms  ✓ WorkerUtilities
    777.5 ms  ✓ PtrArrays
   1245.1 ms  ✓ TranscodingStreams
    734.3 ms  ✓ IteratorInterfaceExtensions
    832.6 ms  ✓ LaTeXStrings
   1293.7 ms  ✓ BitIntegers
   2048.6 ms  ✓ Crayons
   2812.8 ms  ✓ SentinelArrays
   1119.7 ms  ✓ Compat
   1155.1 ms  ✓ Preferences
   1508.2 ms  ✓ Statistics → SparseArraysExt
    950.9 ms  ✓ Missings
    999.2 ms  ✓ PooledArrays
   3520.7 ms  ✓ DataStructures
   1386.7 ms  ✓ LogExpFunctions
    953.4 ms  ✓ AliasTables
    917.1 ms  ✓ CodecZlib
    729.0 ms  ✓ TableTraits
    803.9 ms  ✓ Compat → CompatLinearAlgebraExt
    901.3 ms  ✓ PrecompileTools
   1095.1 ms  ✓ SortingAlgorithms
   1750.4 ms  ✓ Tables
   2105.0 ms  ✓ FilePathsBase
   3074.0 ms  ✓ StringManipulation
  16796.6 ms  ✓ Parsers
   4441.5 ms  ✓ StatsBase
    995.8 ms  ✓ FilePathsBase → FilePathsBaseMmapExt
  39628.5 ms  ✓ PrettyTables
    946.8 ms  ✓ InlineStrings → ParsersExt
   1836.0 ms  ✓ GeneticVariantBase
  92462.5 ms  ✓ DataFrames
   2557.5 ms  ✓ WeakRefStrings
  28697.9 ms  ✓ CSV
  12107.4 ms  ✓ PGENFiles
  44 dependencies successfully precompiled in 246 seconds. 17 already precompiled.
  1 dependency had output during precompilation:
┌ BitIntegers
│  WARNING: Imported binding GMP.ispos was undeclared at import time during import to BitIntegers.
└  

Precompilation completed after 262.15s


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

     Testing PGENFiles
      Status `/tmp/jl_nNojxL/Project.toml`
  [6db4b851] BGEN v0.2.2
  [2447270c] GeneticVariantBase v0.1.2
  [bbb59ef6] PGENFiles v0.2.2
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_nNojxL/Manifest.toml`
  [66dad0bd] AliasTables v1.1.3
  [6db4b851] BGEN v0.2.2
  [c3b6d118] BitIntegers v0.3.5
  [336ed68f] CSV v0.10.15
  [944b1d66] CodecZlib v0.7.8
  [6b39b394] CodecZstd v0.8.6
  [34da2185] Compat v4.18.1
  [a8cc5b0e] Crayons v4.1.1
  [a10d1c49] DBInterface v2.6.1
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.8.1
  [864edb3b] DataStructures v0.19.1
  [e2d170a0] DataValueInterfaces v1.0.0
  [ffbed154] DocStringExtensions v0.9.5
  [48062228] FilePathsBase v0.9.24
  [2447270c] GeneticVariantBase v0.1.2
  [842dd82b] InlineStrings v1.4.5
  [41ab1584] InvertedIndices v1.3.1
  [92d709cd] IrrationalConstants v0.2.6
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.7.1
  [b964fa9f] LaTeXStrings v1.4.0
  [2ab3a3ac] LogExpFunctions v0.3.29
  [e1d29d7a] Missings v1.2.0
  [bac558e1] OrderedCollections v1.8.1
  [bbb59ef6] PGENFiles v0.2.2
  [69de0a69] Parsers v2.8.3
  [2dfb63ee] PooledArrays v1.4.3
  [aea7be01] PrecompileTools v1.3.3
  [21216c6a] Preferences v1.5.0
  [08abe8d2] PrettyTables v3.1.0
  [43287f4e] PtrArrays v1.3.0
  [189a3867] Reexport v1.2.2
  [fdea26ae] SIMD v3.7.2
  [0aa819cd] SQLite v1.6.1
  [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 v0.34.7
  [892a3eda] StringManipulation v0.4.1
  [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
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [76ed43ae] SQLite_jll v3.48.0+0
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [7b1f6079] FileWatching v1.11.0
  [9fa8497b] Future 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
  [a63ad114] Mmap v1.11.0
  [de0858da] Printf v1.11.0
  [3fa0cd96] REPL 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
  [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
  [05823500] OpenLibm_jll v0.8.7+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
     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_using(to::Module, path::Expr)
    @ Base ./module.jl:137
 [14] top-level scope
    @ ~/.julia/packages/BGEN/KN7mm/src/BGEN.jl:21
 [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_using(to::Module, path::Expr)
    @ Base ./module.jl:137
 [25] top-level scope
    @ ~/.julia/packages/PGENFiles/N7YcR/test/runtests.jl:2
 [26] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
 [27] top-level scope
    @ none:6
 [28] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [29] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:310
 [30] _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/BGEN/KN7mm/src/BGEN.jl:1
in expression starting at /home/pkgeval/.julia/packages/PGENFiles/N7YcR/test/runtests.jl:2

Testing failed after 121.45s

ERROR: LoadError: Package PGENFiles 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 425.22s: package tests unexpectedly errored