Package evaluation to load GFF3 on Julia 1.14.0-DEV.29 (7d6ae45e5a*) started at 2025-11-05T07:35:16.140


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


Set-up completed after 0.1s


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

Installing GFF3...
   Resolving package versions...
   Installed SIMD ─────────────── v3.7.2
   Installed Compat ───────────── v4.18.1
   Installed GFF3 ─────────────── v0.2.3
   Installed Indexes ──────────── v0.1.3
   Installed Preferences ──────── v1.5.0
   Installed DataStructures ───── v0.18.22
   Installed Automa ───────────── v0.8.4
   Installed PrecompileTools ──── v1.3.3
   Installed StringViews ──────── v1.3.5
   Installed URIParser ────────── v0.4.1
   Installed BGZFStreams ──────── v0.3.2
   Installed ScanByte ─────────── v0.4.0
   Installed TranscodingStreams ─ v0.9.13
   Installed BioGenerics ──────── v0.1.5
   Installed CodecZlib ────────── v0.7.8
   Installed GenomicFeatures ──── v2.1.0
   Installed IntervalTrees ────── v1.1.0
   Installed OrderedCollections ─ v1.8.1
   Installed FASTX ────────────── v2.1.2
    Updating `~/.julia/environments/v1.14/Project.toml`
  [af1dc308] + GFF3 v0.2.3
    Updating `~/.julia/environments/v1.14/Manifest.toml`
⌅ [67c07d97] + Automa v0.8.4
  [28d598bf] + BGZFStreams v0.3.2
  [47718e42] + BioGenerics v0.1.5
  [944b1d66] + CodecZlib v0.7.8
  [34da2185] + Compat v4.18.1
⌅ [864edb3b] + DataStructures v0.18.22
⌃ [c2308a5c] + FASTX v2.1.2
  [af1dc308] + GFF3 v0.2.3
⌅ [899a7d2d] + GenomicFeatures v2.1.0
⌅ [4ffb77ac] + Indexes v0.1.3
  [524e6230] + IntervalTrees v1.1.0
  [bac558e1] + OrderedCollections v1.8.1
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [fdea26ae] + SIMD v3.7.2
  [7b38b023] + ScanByte v0.4.0
  [354b36f9] + StringViews v1.3.5
⌅ [3bb67fe8] + TranscodingStreams v0.9.13
  [30578b45] + URIParser v0.4.1
  [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
  [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
  [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
  [83775a58] + Zlib_jll v1.3.1+2
        Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`

Installation completed after 6.66s


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

Precompiling PkgEval dependencies...
     Project No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml`
    Manifest No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml`

Precompiling package dependencies...
Precompiling packages...
   1090.7 ms  ✓ IntervalTrees
    978.9 ms  ✓ OrderedCollections
    795.7 ms  ✓ StringViews
    795.8 ms  ✓ URIParser
   1122.1 ms  ✓ Preferences
    820.2 ms  ✓ Compat
   1724.2 ms  ✓ TranscodingStreams
    905.6 ms  ✓ PrecompileTools
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("399d05d3-28fc-5cf5-932b-b3ee5b53232d"), "CompatLinearAlgebraExt") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0)
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] __require_prelocked(pkg::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2717
  [3] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2576
  [4] _require_prelocked
    @ ./loading.jl:2570 [inlined]
  [5] run_extension_callbacks(extid::Base.ExtensionId)
    @ Base ./loading.jl:1622
  [6] run_extension_callbacks(pkgid::Base.PkgId)
    @ Base ./loading.jl:1659
  [7] run_package_callbacks(modkey::Base.PkgId)
    @ Base ./loading.jl:1475
  [8] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2584
  [9] macro expansion
    @ ./loading.jl:2504 [inlined]
 [10] macro expansion
    @ ./lock.jl:376 [inlined]
 [11] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2468
 [12] require
    @ ./loading.jl:2444 [inlined]
 [13] eval_import_path
    @ ./module.jl:36 [inlined]
 [14] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base ./module.jl:60
 [15] _eval_using
    @ ./module.jl:137 [inlined]
 [16] _eval_using(to::Module, path::Expr)
    @ Base ./module.jl:137
 [17] top-level scope
    @ ~/.julia/packages/DataStructures/IrAJn/src/DataStructures.jl:9
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [19] 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:3148
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2994
 [23] include_string
    @ ./loading.jl:3004 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:342
 [25] _start()
    @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/DataStructures/IrAJn/src/DataStructures.jl:1
in expression starting at stdin:5

Precompilation completed after 17.14s


################################################################################
# Loading
#

Loading GFF3...
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("399d05d3-28fc-5cf5-932b-b3ee5b53232d"), "CompatLinearAlgebraExt") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0)
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] __require_prelocked(pkg::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2717
  [3] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2576
  [4] _require_prelocked
    @ ./loading.jl:2570 [inlined]
  [5] run_extension_callbacks(extid::Base.ExtensionId)
    @ Base ./loading.jl:1622
  [6] run_extension_callbacks(pkgid::Base.PkgId)
    @ Base ./loading.jl:1659
  [7] run_package_callbacks(modkey::Base.PkgId)
    @ Base ./loading.jl:1475
  [8] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2584
  [9] macro expansion
    @ ./loading.jl:2504 [inlined]
 [10] macro expansion
    @ ./lock.jl:376 [inlined]
 [11] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2468
 [12] require
    @ ./loading.jl:2444 [inlined]
 [13] eval_import_path
    @ ./module.jl:36 [inlined]
 [14] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base ./module.jl:60
 [15] _eval_using
    @ ./module.jl:137 [inlined]
 [16] _eval_using(to::Module, path::Expr)
    @ Base ./module.jl:137
 [17] top-level scope
    @ ~/.julia/packages/DataStructures/IrAJn/src/DataStructures.jl:9
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [19] 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:3148
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2994
 [23] include_string
    @ ./loading.jl:3004 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:342
 [25] _start()
    @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/DataStructures/IrAJn/src/DataStructures.jl:1
in expression starting at stdin:5
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("399d05d3-28fc-5cf5-932b-b3ee5b53232d"), "CompatLinearAlgebraExt") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0)
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] __require_prelocked(pkg::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2717
  [3] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2576
  [4] _require_prelocked
    @ ./loading.jl:2570 [inlined]
  [5] run_extension_callbacks(extid::Base.ExtensionId)
    @ Base ./loading.jl:1622
  [6] run_extension_callbacks(pkgid::Base.PkgId)
    @ Base ./loading.jl:1659
  [7] run_package_callbacks(modkey::Base.PkgId)
    @ Base ./loading.jl:1475
  [8] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2584
  [9] macro expansion
    @ ./loading.jl:2504 [inlined]
 [10] macro expansion
    @ ./lock.jl:376 [inlined]
 [11] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2468
 [12] require
    @ ./loading.jl:2444 [inlined]
 [13] eval_import_path
    @ ./module.jl:36 [inlined]
 [14] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base ./module.jl:60
 [15] _eval_using
    @ ./module.jl:137 [inlined]
 [16] _eval_using(to::Module, path::Expr)
    @ Base ./module.jl:137
 [17] top-level scope
    @ ~/.julia/packages/DataStructures/IrAJn/src/DataStructures.jl:9
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [19] 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:3148
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2994
 [23] include_string
    @ ./loading.jl:3004 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:342
 [25] _start()
    @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/DataStructures/IrAJn/src/DataStructures.jl:1
in expression starting at stdin:5
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("399d05d3-28fc-5cf5-932b-b3ee5b53232d"), "CompatLinearAlgebraExt") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0)
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] __require_prelocked(pkg::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2717
  [3] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2576
  [4] _require_prelocked
    @ ./loading.jl:2570 [inlined]
  [5] run_extension_callbacks(extid::Base.ExtensionId)
    @ Base ./loading.jl:1622
  [6] run_extension_callbacks(pkgid::Base.PkgId)
    @ Base ./loading.jl:1659
  [7] run_package_callbacks(modkey::Base.PkgId)
    @ Base ./loading.jl:1475
  [8] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2584
  [9] macro expansion
    @ ./loading.jl:2504 [inlined]
 [10] macro expansion
    @ ./lock.jl:376 [inlined]
 [11] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2468
 [12] require
    @ ./loading.jl:2444 [inlined]
 [13] eval_import_path
    @ ./module.jl:36 [inlined]
 [14] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base ./module.jl:60
 [15] _eval_using
    @ ./module.jl:137 [inlined]
 [16] _eval_using(to::Module, path::Expr)
    @ Base ./module.jl:137
 [17] top-level scope
    @ ~/.julia/packages/DataStructures/IrAJn/src/DataStructures.jl:9
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [19] 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:3148
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2994
 [23] include_string
    @ ./loading.jl:3004 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:342
 [25] _start()
    @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/DataStructures/IrAJn/src/DataStructures.jl:1
in expression starting at stdin:5
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("399d05d3-28fc-5cf5-932b-b3ee5b53232d"), "CompatLinearAlgebraExt") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0)
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] __require_prelocked(pkg::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2717
  [3] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2576
  [4] _require_prelocked
    @ ./loading.jl:2570 [inlined]
  [5] run_extension_callbacks(extid::Base.ExtensionId)
    @ Base ./loading.jl:1622
  [6] run_extension_callbacks(pkgid::Base.PkgId)
    @ Base ./loading.jl:1659
  [7] run_package_callbacks(modkey::Base.PkgId)
    @ Base ./loading.jl:1475
  [8] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2584
  [9] macro expansion
    @ ./loading.jl:2504 [inlined]
 [10] macro expansion
    @ ./lock.jl:376 [inlined]
 [11] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2468
 [12] require
    @ ./loading.jl:2444 [inlined]
 [13] eval_import_path
    @ ./module.jl:36 [inlined]
 [14] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base ./module.jl:60
 [15] _eval_using
    @ ./module.jl:137 [inlined]
 [16] _eval_using(to::Module, path::Expr)
    @ Base ./module.jl:137
 [17] top-level scope
    @ ~/.julia/packages/DataStructures/IrAJn/src/DataStructures.jl:9
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [19] 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:3148
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2994
 [23] include_string
    @ ./loading.jl:3004 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:342
 [25] _start()
    @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/DataStructures/IrAJn/src/DataStructures.jl:1
in expression starting at stdin:5

  1 dependency had output during precompilation:
┌ DataStructures
│  [Output was shown above]
└  
ERROR: LoadError: The following 1 package failed to precompile:

DataStructures 
Failed to precompile DataStructures [864edb3b-99cc-5e75-8d2d-829cb0a9cfe8] to "/home/pkgeval/.julia/compiled/v1.14/DataStructures/jl_CXpfdy" (ProcessExited(1)).

in expression starting at /home/pkgeval/.julia/packages/GenomicFeatures/Tgrmt/src/GenomicFeatures.jl:3
in expression starting at /home/pkgeval/.julia/packages/Indexes/GoZHL/src/Indexes.jl:9
in expression starting at /home/pkgeval/.julia/packages/GFF3/ocekA/src/GFF3.jl:4

Loading failed after 14.74s

ERROR: LoadError: failed process: Process(`/opt/julia/bin/julia -C native -J/opt/julia/lib/julia/sys.so -g1 --check-bounds=yes --inline=yes --pkgimages=existing -e 'using GFF3'`, ProcessExited(1)) [1]

Stacktrace:
 [1] pipeline_error
   @ ./process.jl:611 [inlined]
 [2] run(::Cmd; wait::Bool)
   @ Base ./process.jl:526
 [3] run(::Cmd)
   @ Base ./process.jl:523
 [4] top-level scope
   @ /PkgEval.jl/scripts/evaluate.jl:193
 [5] include(mod::Module, _path::String)
   @ Base ./Base.jl:309
 [6] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:344
 [7] _start()
   @ Base ./client.jl:577
in expression starting at /PkgEval.jl/scripts/evaluate.jl:184

PkgEval failed after 96.69s: package fails to precompile